From f8e15bf866d012cffd053f4f7e08405116904ce8 Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Thu, 23 Jan 2025 15:01:24 -0500 Subject: [PATCH 01/12] :recycle: Refactor legacy code to be in legacy package and start clean arch project structure --- README.md | 2 +- docker/web-and-data/Dockerfile | 2 +- docker/web-and-data/docker-entrypoint.sh | 2 +- .../{ => application}/AsyncConfig.java | 5 +- .../{ => application}/PortalApplication.java | 2 +- .../{ => application}/WebAppConfig.java | 6 +- .../documentation/ExternalPageController.java | 2 +- .../proxy/LegacyProxyController.java | 2 +- .../{ => application}/proxy/Monkifier.java | 2 +- .../proxy/ProxyController.java | 4 +- .../proxy/util/CheckDarwinAccessUtil.java | 2 +- .../CancerStudyPermissionEvaluator.java | 14 +- ...icRestfulAuthenticationSuccessHandler.java | 2 +- .../security/config/ApiSecurityConfig.java | 12 +- .../config/AutoconfigureExcludeConfig.java | 4 +- .../security/config/CorsConfig.java | 2 +- .../CustomOAuth2AuthorizationConfig.java | 8 +- .../security/config/MethodSecurityConfig.java | 6 +- .../security/config/NoSecurityConfig.java | 2 +- .../security/config/OAuth2SecurityConfig.java | 6 +- .../config/OptionalOAuth2SecurityConfig.java | 2 +- .../security/config/Saml2AndBasicConfig.java | 4 +- .../security/config/Saml2SecurityConfig.java | 4 +- .../token/RestAuthenticationEntryPoint.java | 2 +- .../token/TokenAuthenticationFilter.java | 4 +- .../TokenAuthenticationSuccessHandler.java | 2 +- .../token/config/DataAccessTokenConfig.java | 18 +-- .../token/oauth2/JwtTokenVerifierBuilder.java | 2 +- .../OAuth2BearerAuthenticationToken.java | 2 +- .../OAuth2DataAccessTokenServiceImpl.java | 6 +- .../OAuth2TokenAuthenticationProvider.java | 6 +- .../OAuth2TokenDataAccessConfiguration.java | 2 +- .../OAuth2TokenRefreshRestTemplate.java | 2 +- .../uuid/UuidTokenAuthenticationProvider.java | 6 +- .../security/util/ClaimRoleExtractorUtil.java | 2 +- .../security/util/GrantedAuthorityUtil.java | 2 +- .../model/AlleleSpecificCopyNumber.java | 2 +- .../{ => legacy}/model/Alteration.java | 2 +- .../model/AlterationCountBase.java | 2 +- .../model/AlterationCountByGene.java | 2 +- .../AlterationCountByStructuralVariant.java | 2 +- .../model/AlterationDriverAnnotation.java | 2 +- .../model/AlterationEnrichment.java | 2 +- .../{ => legacy}/model/AlterationFilter.java | 4 +- .../{ => legacy}/model/AlterationType.java | 2 +- .../model/BaseAlterationFilter.java | 4 +- .../{ => legacy}/model/Binnable.java | 2 +- .../cbioportal/{ => legacy}/model/CNA.java | 2 +- .../{ => legacy}/model/CancerStudy.java | 2 +- .../{ => legacy}/model/CancerStudyTags.java | 2 +- .../{ => legacy}/model/CaseListDataCount.java | 2 +- .../{ => legacy}/model/ClinicalAttribute.java | 2 +- .../model/ClinicalAttributeCount.java | 2 +- .../{ => legacy}/model/ClinicalData.java | 2 +- .../{ => legacy}/model/ClinicalDataBin.java | 2 +- .../{ => legacy}/model/ClinicalDataCount.java | 2 +- .../model/ClinicalDataCountItem.java | 2 +- .../model/ClinicalDataEnrichment.java | 2 +- .../{ => legacy}/model/ClinicalEvent.java | 2 +- .../{ => legacy}/model/ClinicalEventData.java | 2 +- .../model/ClinicalEventKeyCode.java | 2 +- .../model/ClinicalEventSample.java | 2 +- .../model/ClinicalEventTypeCount.java | 2 +- .../model/ClinicalViolinPlotBoxData.java | 2 +- .../model/ClinicalViolinPlotData.java | 2 +- .../ClinicalViolinPlotIndividualPoint.java | 2 +- .../model/ClinicalViolinPlotRowData.java | 2 +- .../{ => legacy}/model/CoExpression.java | 2 +- .../{ => legacy}/model/CopyNumberCount.java | 2 +- .../model/CopyNumberCountByGene.java | 2 +- .../{ => legacy}/model/CopyNumberSeg.java | 2 +- .../{ => legacy}/model/CosmicMutation.java | 2 +- .../{ => legacy}/model/CountSummary.java | 2 +- .../model/CustomDriverAnnotationReport.java | 2 +- .../{ => legacy}/model/DataAccessToken.java | 2 +- .../{ => legacy}/model/DataBin.java | 2 +- .../{ => legacy}/model/DensityPlotBin.java | 2 +- .../{ => legacy}/model/DensityPlotData.java | 2 +- .../model/DiscreteCopyNumberData.java | 2 +- .../{ => legacy}/model/EnrichmentType.java | 2 +- .../{ => legacy}/model/EntityType.java | 2 +- .../model/ExpressionEnrichment.java | 2 +- .../model/FractionGenomeAltered.java | 2 +- .../cbioportal/{ => legacy}/model/Gene.java | 2 +- .../{ => legacy}/model/GeneAlias.java | 2 +- .../{ => legacy}/model/GeneFilter.java | 2 +- .../{ => legacy}/model/GeneFilterQuery.java | 4 +- .../model/GeneMolecularAlteration.java | 2 +- .../{ => legacy}/model/GeneMolecularData.java | 2 +- .../{ => legacy}/model/GenePanel.java | 2 +- .../{ => legacy}/model/GenePanelData.java | 2 +- .../{ => legacy}/model/GenePanelToGene.java | 2 +- .../model/GenericAssayAdditionalProperty.java | 2 +- .../model/GenericAssayBinaryEnrichment.java | 2 +- .../GenericAssayCategoricalEnrichment.java | 2 +- .../model/GenericAssayCountSummary.java | 2 +- .../{ => legacy}/model/GenericAssayData.java | 2 +- .../model/GenericAssayDataBin.java | 2 +- .../model/GenericAssayDataCount.java | 2 +- .../model/GenericAssayDataCountItem.java | 2 +- .../model/GenericAssayEnrichment.java | 2 +- .../GenericAssayMolecularAlteration.java | 2 +- .../model/GenericEntityProperty.java | 2 +- .../{ => legacy}/model/Geneset.java | 2 +- .../model/GenesetCorrelation.java | 2 +- .../model/GenesetHierarchyInfo.java | 2 +- .../model/GenesetMolecularAlteration.java | 2 +- .../model/GenesetMolecularData.java | 2 +- .../{ => legacy}/model/GeneticEntity.java | 2 +- .../{ => legacy}/model/GenomicDataBin.java | 2 +- .../{ => legacy}/model/GenomicDataCount.java | 2 +- .../model/GenomicDataCountItem.java | 2 +- .../{ => legacy}/model/GenomicEnrichment.java | 2 +- .../cbioportal/{ => legacy}/model/Gistic.java | 2 +- .../{ => legacy}/model/GisticToGene.java | 2 +- .../{ => legacy}/model/GroupStatistics.java | 2 +- .../cbioportal/{ => legacy}/model/Info.java | 2 +- .../model/MolecularAlteration.java | 2 +- .../{ => legacy}/model/MolecularData.java | 2 +- .../{ => legacy}/model/MolecularProfile.java | 2 +- .../model/MolecularProfileCaseIdentifier.java | 2 +- .../model/MolecularProfileSamples.java | 2 +- .../{ => legacy}/model/MrnaPercentile.java | 2 +- .../cbioportal/{ => legacy}/model/MutSig.java | 2 +- .../{ => legacy}/model/Mutation.java | 2 +- .../model/MutationCountByGene.java | 2 +- .../model/MutationCountByPosition.java | 2 +- .../{ => legacy}/model/MutationEventType.java | 2 +- .../model/MutationFilterOption.java | 2 +- .../{ => legacy}/model/MutationSpectrum.java | 2 +- .../model/NumericGeneMolecularData.java | 2 +- .../{ => legacy}/model/Patient.java | 2 +- .../{ => legacy}/model/PatientTreatment.java | 2 +- .../model/PatientTreatmentReport.java | 2 +- .../model/PatientTreatmentRow.java | 2 +- .../{ => legacy}/model/QueryElement.java | 2 +- .../{ => legacy}/model/ReadPermission.java | 2 +- .../{ => legacy}/model/ReferenceGenome.java | 2 +- .../model/ReferenceGenomeGene.java | 2 +- .../{ => legacy}/model/ResourceData.java | 2 +- .../model/ResourceDefinition.java | 2 +- .../{ => legacy}/model/ResourceType.java | 2 +- .../cbioportal/{ => legacy}/model/Sample.java | 2 +- .../model/SampleClinicalDataCollection.java | 2 +- .../{ => legacy}/model/SampleList.java | 2 +- .../model/SampleListToSampleId.java | 2 +- .../{ => legacy}/model/SampleTreatment.java | 2 +- .../model/SampleTreatmentReport.java | 2 +- .../model/SampleTreatmentRow.java | 2 +- .../{ => legacy}/model/StructuralVariant.java | 4 +- .../model/StructuralVariantFilterQuery.java | 4 +- .../model/StructuralVariantGeneSubQuery.java | 2 +- .../model/StructuralVariantQuery.java | 2 +- .../model/StructuralVariantSpecialValue.java | 2 +- .../model/StudyViewFilterContext.java | 6 +- .../StudyViewStructuralVariantFilter.java | 2 +- .../model/TableTimestampPair.java | 2 +- .../{ => legacy}/model/TemporalRelation.java | 2 +- .../{ => legacy}/model/Treatment.java | 2 +- .../{ => legacy}/model/TreatmentRow.java | 2 +- .../{ => legacy}/model/TypeOfCancer.java | 2 +- .../{ => legacy}/model/UniqueKeyBase.java | 2 +- .../cbioportal/{ => legacy}/model/User.java | 2 +- .../{ => legacy}/model/UserAuthorities.java | 2 +- .../{ => legacy}/model/VariantCount.java | 2 +- .../{ => legacy}/model/meta/BaseMeta.java | 2 +- .../model/meta/GenericAssayMeta.java | 2 +- .../{ => legacy}/model/meta/MutationMeta.java | 2 +- .../{ => legacy}/model/util/QueryElement.java | 2 +- .../{ => legacy}/model/util/Select.java | 2 +- .../AlterationDriverAnnotationRepository.java | 4 +- .../persistence/AlterationRepository.java | 14 +- .../persistence/CacheEnabledConfig.java | 2 +- .../persistence/CancerTypeRepository.java | 6 +- .../ClinicalAttributeRepository.java | 8 +- .../persistence/ClinicalDataRepository.java | 8 +- .../persistence/ClinicalEventRepository.java | 8 +- .../CopyNumberSegmentRepository.java | 6 +- .../persistence/CosmicCountRepository.java | 4 +- .../DataAccessTokenRepository.java | 4 +- .../DiscreteCopyNumberRepository.java | 10 +- .../persistence/GenePanelRepository.java | 12 +- .../persistence/GeneRepository.java | 8 +- .../persistence/GenericAssayRepository.java | 6 +- .../GenesetHierarchyRepository.java | 6 +- .../persistence/GenesetRepository.java | 8 +- .../persistence/MolecularDataRepository.java | 10 +- .../MolecularProfileRepository.java | 6 +- .../persistence/MutationRepository.java | 12 +- .../persistence/PatientRepository.java | 6 +- .../persistence/PersistenceConstants.java | 2 +- .../ReferenceGenomeGeneRepository.java | 4 +- .../persistence/ResourceDataRepository.java | 4 +- .../ResourceDefinitionRepository.java | 4 +- .../persistence/SampleListRepository.java | 8 +- .../persistence/SampleRepository.java | 6 +- .../persistence/SecurityRepository.java | 6 +- ...SignificantCopyNumberRegionRepository.java | 8 +- .../SignificantlyMutatedGeneRepository.java | 6 +- .../StaticDataTimeStampRepository.java | 4 +- .../StructuralVariantRepository.java | 10 +- .../persistence/StudyRepository.java | 8 +- .../persistence/StudyViewRepository.java | 44 ++--- .../persistence/TreatmentRepository.java | 8 +- .../persistence/VariantCountRepository.java | 4 +- .../cachemaputil/CacheMapBuilder.java | 18 +-- .../cachemaputil/CacheMapUtil.java | 8 +- .../cachemaputil/InactiveCacheMapUtil.java | 8 +- .../SpringManagedCacheMapUtil.java | 8 +- .../cachemaputil/StaticRefCacheMapUtil.java | 8 +- .../persistence/config/EhCacheConfig.java | 8 +- .../persistence/config/RedisConfig.java | 8 +- .../enums/ClinicalAttributeDataType.java | 2 +- .../persistence/enums/DataSource.java | 2 +- .../helper/AlterationFilterHelper.java | 10 +- .../helper/StudyViewFilterHelper.java | 22 +-- .../model/SampleAcquisitionEventRecord.java | 2 +- .../persistence/model/TreatmentRecord.java | 2 +- .../mybatis/AlterationCountsMapper.java | 12 +- .../AlterationDriverAnnotationMapper.java | 4 +- ...tionDriverAnnotationMyBatisRepository.java | 6 +- .../mybatis/AlterationMyBatisRepository.java | 28 ++-- .../persistence/mybatis/CancerTypeMapper.java | 6 +- .../mybatis/CancerTypeMyBatisRepository.java | 12 +- .../mybatis/ClinicalAttributeMapper.java | 8 +- .../ClinicalAttributeMyBatisRepository.java | 16 +- .../mybatis/ClinicalDataMapper.java | 8 +- .../ClinicalDataMyBatisRepository.java | 24 +-- .../mybatis/ClinicalEventMapper.java | 8 +- .../ClinicalEventMyBatisRepository.java | 12 +- .../mybatis/CopyNumberSegmentMapper.java | 6 +- .../CopyNumberSegmentMyBatisRepository.java | 10 +- .../mybatis/CosmicCountMapper.java | 4 +- .../mybatis/CosmicCountMyBatisRepository.java | 6 +- .../mybatis/DataAccessTokenMapper.java | 4 +- .../DataAccessTokenMyBatisRepository.java | 6 +- .../mybatis/DiscreteCopyNumberMapper.java | 10 +- .../DiscreteCopyNumberMyBatisRepository.java | 12 +- .../persistence/mybatis/GeneMapper.java | 8 +- .../mybatis/GeneMyBatisRepository.java | 16 +- .../persistence/mybatis/GenePanelMapper.java | 12 +- .../mybatis/GenePanelMyBatisRepository.java | 18 +-- .../mybatis/GenericAssayMapper.java | 6 +- .../GenericAssayMyBatisRepository.java | 8 +- .../mybatis/GenesetHierarchyMapper.java | 6 +- .../GenesetHierarchyMyBatisRepository.java | 8 +- .../persistence/mybatis/GenesetMapper.java | 8 +- .../mybatis/GenesetMyBatisRepository.java | 14 +- .../mybatis/MolecularDataMapper.java | 10 +- .../MolecularDataMyBatisRepository.java | 13 +- .../mybatis/MolecularProfileMapper.java | 6 +- .../MolecularProfileMyBatisRepository.java | 12 +- .../persistence/mybatis/MutationMapper.java | 12 +- .../mybatis/MutationMyBatisRepository.java | 20 +-- .../persistence/mybatis/PatientMapper.java | 6 +- .../mybatis/PatientMyBatisRepository.java | 12 +- .../mybatis/ReferenceGenomeGeneMapper.java | 4 +- .../ReferenceGenomeGeneMyBatisRepository.java | 8 +- .../mybatis/ResourceDataMapper.java | 4 +- .../ResourceDataMyBatisRepository.java | 8 +- .../mybatis/ResourceDefinitionMapper.java | 4 +- .../ResourceDefinitionMyBatisRepository.java | 10 +- .../persistence/mybatis/SampleListMapper.java | 8 +- .../mybatis/SampleListMyBatisRepository.java | 14 +- .../persistence/mybatis/SampleMapper.java | 6 +- .../mybatis/SampleMyBatisRepository.java | 12 +- .../persistence/mybatis/SecurityMapper.java | 6 +- .../mybatis/SecurityMyBatisRepository.java | 8 +- .../SignificantCopyNumberRegionMapper.java | 8 +- ...cantCopyNumberRegionMyBatisRepository.java | 12 +- .../SignificantlyMutatedGeneMapper.java | 6 +- ...ificantlyMutatedGeneMyBatisRepository.java | 10 +- .../StaticDataTimeStampMyBatisRepository.java | 6 +- .../mybatis/StaticDataTimestampMapper.java | 4 +- .../mybatis/StructuralVariantMapper.java | 10 +- .../StructuralVariantMyBatisRepository.java | 14 +- .../persistence/mybatis/StudyMapper.java | 8 +- .../mybatis/StudyMyBatisRepository.java | 12 +- .../persistence/mybatis/TreatmentMapper.java | 6 +- .../mybatis/TreatmentMyBatisRepository.java | 8 +- .../mybatis/VariantCountMapper.java | 4 +- .../VariantCountMyBatisRepository.java | 6 +- .../mybatis/config/PersistenceConfig.java | 8 +- .../typehandler/SampleTypeTypeHandler.java | 4 +- .../util/CustomMyBatisObjectFactory.java | 2 +- .../util/LimitedPermissionArrayList.java | 2 +- .../MolecularProfileCaseIdentifierUtil.java | 2 +- .../mybatis/util/PaginationCalculator.java | 2 +- .../mybatisclickhouse/StudyViewMapper.java | 46 +++--- .../StudyViewMyBatisRepository.java | 58 +++---- .../config/PersistenceColumnarConfig.java | 6 +- .../persistence/util/CacheEventLogger.java | 2 +- .../persistence/util/CacheUtils.java | 2 +- .../util/CustomEhcachingProvider.java | 4 +- .../persistence/util/CustomKeyGenerator.java | 10 +- .../persistence/util/CustomRedisCache.java | 2 +- .../util/CustomRedisCacheManager.java | 2 +- .../util/CustomRedisCachingProvider.java | 2 +- .../persistence/util/EhCacheUtils.java | 4 +- .../persistence/util/EhcacheStatistics.java | 4 +- .../util/LoggingCacheErrorHandler.java | 2 +- .../persistence/util/RedisCacheUtils.java | 4 +- .../CustomDataSourceConfiguration.java | 4 +- .../properties/PortalProperties.java | 4 +- .../service/AlterationCountService.java | 15 +- .../AlterationDriverAnnotationService.java | 4 +- .../service/AlterationEnrichmentService.java | 12 +- .../service/AttributeByStudyService.java | 4 +- .../{ => legacy}/service/CacheService.java | 4 +- .../service/CacheStatisticsService.java | 4 +- .../service/CancerTypeService.java | 8 +- .../service/ClinicalAttributeService.java | 12 +- .../ClinicalDataDensityPlotService.java | 10 +- .../service/ClinicalDataService.java | 16 +- .../service/ClinicalEventService.java | 16 +- .../service/CoExpressionService.java | 14 +- .../service/CopyNumberSegmentService.java | 10 +- .../service/CosmicCountService.java | 4 +- .../service/CustomDataService.java | 4 +- .../service/DataAccessTokenService.java | 4 +- .../service/DiscreteCopyNumberService.java | 13 +- .../service/ExpressionEnrichmentService.java | 16 +- .../service/FrontendPropertiesService.java | 2 +- .../FrontendPropertiesServiceImpl.java | 2 +- .../service/GeneMemoizerService.java | 4 +- .../service/GenePanelService.java | 16 +- .../{ => legacy}/service/GeneService.java | 10 +- .../service/GenericAssayService.java | 8 +- .../service/GenesetCorrelationService.java | 10 +- .../service/GenesetDataService.java | 10 +- .../service/GenesetHierarchyService.java | 8 +- .../{ => legacy}/service/GenesetService.java | 10 +- .../service/MolecularDataService.java | 12 +- .../service/MolecularProfileService.java | 12 +- .../service/MrnaPercentileService.java | 6 +- .../{ => legacy}/service/MutationService.java | 16 +- .../service/MutationSpectrumService.java | 6 +- .../{ => legacy}/service/PatientService.java | 10 +- .../service/ReadPermissionService.java | 4 +- .../service/ReferenceGenomeGeneService.java | 4 +- .../service/ResourceDataService.java | 10 +- .../service/ResourceDefinitionService.java | 8 +- .../service/SampleListService.java | 10 +- .../{ => legacy}/service/SampleService.java | 12 +- .../legacy/service/ServerStatusService.java | 7 + .../SignificantCopyNumberRegionService.java | 8 +- .../SignificantlyMutatedGeneService.java | 8 +- .../service/StaticDataTimestampService.java | 4 +- .../service/StructuralVariantService.java | 10 +- .../{ => legacy}/service/StudyService.java | 12 +- .../service/StudyViewColumnarService.java | 42 ++--- .../service/StudyViewService.java | 18 +-- .../service/TreatmentService.java | 8 +- .../service/VariantCountService.java | 6 +- .../service/ViolinPlotService.java | 10 +- .../AlterationCountByGeneService.java | 10 +- .../AlterationCountByGeneServiceImpl.java | 30 ++-- .../exception/AccessForbiddenException.java | 2 +- .../exception/CacheNotFoundException.java | 2 +- .../exception/CacheOperationException.java | 2 +- .../CancerTypeNotFoundException.java | 2 +- .../ClinicalAttributeNotFoundException.java | 2 +- ...ataAccessTokenNoUserIdentityException.java | 2 +- ...ataAccessTokenProhibitedUserException.java | 2 +- .../exception/GeneNotFoundException.java | 2 +- .../exception/GenePanelNotFoundException.java | 2 +- .../GeneWithMultipleEntrezIdsException.java | 2 +- .../GenericAssayNotFoundException.java | 2 +- .../exception/GenesetNotFoundException.java | 2 +- .../InvalidDataAccessTokenException.java | 2 +- .../MolecularProfileNotFoundException.java | 2 +- .../exception/PatientNotFoundException.java | 2 +- .../ResourceDefinitionNotFoundException.java | 2 +- .../SampleListNotFoundException.java | 2 +- .../exception/SampleNotFoundException.java | 2 +- .../exception/StudyNotFoundException.java | 2 +- .../exception/TokenNotFoundException.java | 2 +- .../impl/AlterationCountServiceImpl.java | 34 ++-- ...AlterationDriverAnnotationServiceImpl.java | 10 +- .../impl/AlterationEnrichmentServiceImpl.java | 16 +- .../service/impl/CacheServiceImpl.java | 14 +- .../impl/CacheStatisticsServiceImpl.java | 10 +- .../service/impl/CancerTypeServiceImpl.java | 12 +- .../impl/ClinicalAttributeServiceImpl.java | 22 +-- .../ClinicalDataDensityPlotServiceImpl.java | 16 +- .../service/impl/ClinicalDataServiceImpl.java | 33 ++-- .../impl/ClinicalEventServiceImpl.java | 30 ++-- .../service/impl/CoExpressionServiceImpl.java | 31 ++-- .../impl/CopyNumberSegmentServiceImpl.java | 16 +- .../service/impl/CosmicCountServiceImpl.java | 8 +- .../service/impl/CustomDataServiceImpl.java | 10 +- .../impl/DiscreteCopyNumberServiceImpl.java | 30 ++-- .../impl/EhcacheStatisticsServiceImpl.java | 6 +- .../impl/ExpressionEnrichmentServiceImpl.java | 46 +++--- .../service/impl/GeneMemoizerServiceImpl.java | 8 +- .../service/impl/GenePanelServiceImpl.java | 29 ++-- .../service/impl/GeneServiceImpl.java | 16 +- .../service/impl/GenericAssayServiceImpl.java | 32 ++-- .../impl/GenesetCorrelationServiceImpl.java | 36 ++--- .../service/impl/GenesetDataServiceImpl.java | 26 +-- .../impl/GenesetHierarchyServiceImpl.java | 30 ++-- .../service/impl/GenesetServiceImpl.java | 14 +- .../impl/JwtDataAccessTokenServiceImpl.java | 12 +- .../impl/MolecularDataServiceImpl.java | 33 ++-- .../impl/MolecularProfileServiceImpl.java | 26 +-- .../impl/MrnaPercentileServiceImpl.java | 16 +- .../service/impl/MutationServiceImpl.java | 24 +-- .../impl/MutationSpectrumServiceImpl.java | 12 +- .../service/impl/PatientServiceImpl.java | 20 +-- .../impl/ReadPermissionServiceImpl.java | 10 +- .../impl/RedisCacheStatisticsServiceImpl.java | 12 +- .../impl/ReferenceGenomeGeneServiceImpl.java | 8 +- .../service/impl/ResourceDataServiceImpl.java | 20 +-- .../impl/ResourceDefinitionServiceImpl.java | 14 +- .../service/impl/SampleListServiceImpl.java | 22 +-- .../service/impl/SampleServiceImpl.java | 28 ++-- .../service/impl/ServerStatusServiceImpl.java | 8 +- ...ignificantCopyNumberRegionServiceImpl.java | 16 +- .../SignificantlyMutatedGeneServiceImpl.java | 16 +- .../impl/StaticDataTimestampServiceImpl.java | 8 +- .../impl/StructuralVariantServiceImpl.java | 18 +-- .../service/impl/StudyServiceImpl.java | 24 +-- .../impl/StudyViewColumnarServiceImpl.java | 66 ++++---- .../service/impl/StudyViewServiceImpl.java | 70 ++++---- .../service/impl/TreatmentServiceImpl.java | 13 +- .../UnauthDataAccessTokenServiceImpl.java | 8 +- .../impl/UuidDataAccessTokenServiceImpl.java | 12 +- .../service/impl/VariantCountServiceImpl.java | 20 +-- .../service/impl/ViolinPlotServiceImpl.java | 13 +- .../TreatmentCountReportService.java | 14 ++ .../TreatmentCountReportServiceImpl.java | 16 +- .../util/AlterationCountServiceUtil.java | 16 +- .../util/AlterationEnrichmentUtil.java | 28 ++-- .../service/util/BinnableCustomDataValue.java | 4 +- .../service/util/ChromosomeCalculator.java | 2 +- .../service/util/ClinicalAttributeUtil.java | 4 +- .../util/CoExpressionAsyncMethods.java | 4 +- .../service/util/CustomAttributeWithData.java | 2 +- .../service/util/CustomDataSession.java | 4 +- .../service/util/CustomDataValue.java | 2 +- .../util/ExpressionEnrichmentUtil.java | 34 ++-- .../util/FisherExactTestCalculator.java | 2 +- .../{ => legacy}/service/util/JwtUtils.java | 6 +- .../service/util/MolecularProfileUtil.java | 6 +- .../MskWholeSlideViewerTokenGenerator.java | 2 +- .../service/util/ProfiledCasesCounter.java | 16 +- .../service/util/SessionServiceConfig.java | 2 +- .../util/SessionServiceRequestHandler.java | 8 +- .../util/StudyViewColumnarServiceUtil.java | 18 +-- .../url_shortener/URLShortenerController.java | 2 +- .../url_shortener/URLShortenerResponse.java | 2 +- .../{ => legacy}/utils/Encoder.java | 2 +- .../utils/config/PropertyCondition.java | 4 +- .../annotation/ConditionalOnProperty.java | 4 +- .../{ => legacy}/utils/removeme/Session.java | 4 +- .../legacy/utils/security/AccessLevel.java | 5 + .../utils/security/PortalSecurityConfig.java | 2 +- .../utils/validation/AllowedValues.java | 2 +- .../AllowedValuesValidatorImpl.java | 2 +- .../AlterationDriverAnnotationController.java | 10 +- .../web/AlterationEnrichmentController.java | 22 +-- .../{ => legacy}/web/CacheController.java | 8 +- .../web/CacheStatsController.java | 8 +- .../web/CancerTypeController.java | 22 +-- .../web/ClinicalAttributeController.java | 30 ++-- .../web/ClinicalAttributeCountController.java | 16 +- .../web/ClinicalDataController.java | 46 +++--- .../web/ClinicalDataEnrichmentController.java | 24 +-- .../web/ClinicalEventController.java | 29 ++-- .../web/CoExpressionController.java | 14 +- .../web/CopyNumberSegmentController.java | 30 ++-- .../web/CosmicCountController.java | 8 +- .../web/DataAccessTokenController.java | 14 +- .../web/DiscreteCopyNumberController.java | 26 +-- .../DiscreteCopyNumberCountController.java | 16 +- .../web/DocRedirectController.java | 2 +- .../web/ExecuterTimeInterceptor.java | 2 +- .../web/ExpressionEnrichmentController.java | 26 +-- .../{ => legacy}/web/GeneController.java | 26 +-- .../{ => legacy}/web/GenePanelController.java | 22 +-- .../web/GenePanelDataController.java | 22 +-- .../web/GeneralControllerAdvice.java | 2 +- .../web/GenericAssayController.java | 16 +- .../web/GenericAssayDataController.java | 28 ++-- .../web/GenericAssayEnrichmentController.java | 22 +-- .../{ => legacy}/web/GenesetController.java | 16 +- .../web/GenesetCorrelationController.java | 16 +- .../web/GenesetDataController.java | 16 +- .../web/GenesetHierarchyController.java | 14 +- .../{ => legacy}/web/IndexPageController.java | 10 +- .../{ => legacy}/web/InfoController.java | 8 +- .../{ => legacy}/web/LegacyApiController.java | 2 +- .../{ => legacy}/web/LoginPageController.java | 6 +- .../web/MatchMinerController.java | 2 +- .../web/MolecularDataController.java | 30 ++-- .../web/MolecularProfileController.java | 34 ++-- .../web/MrnaPercentileController.java | 14 +- .../web/MskEntityTranslationController.java | 14 +- .../{ => legacy}/web/MutationController.java | 36 ++--- .../web/MutationCountController.java | 12 +- .../web/MutationSpectrumController.java | 14 +- .../web/OAuth2DataAccessTokenController.java | 14 +- .../{ => legacy}/web/PatientController.java | 36 ++--- .../web/PublicVirtualStudiesController.java | 14 +- .../web/ReferenceGenomeGeneController.java | 14 +- .../web/ResourceDataController.java | 32 ++-- .../web/ResourceDefinitionController.java | 28 ++-- .../web/SamlAndBasicLoginController.java | 6 +- .../{ => legacy}/web/SampleController.java | 54 +++---- .../web/SampleListController.java | 32 ++-- .../web/ServerStatusController.java | 8 +- .../web/SessionServiceController.java | 40 ++--- ...SignificantCopyNumberRegionController.java | 22 +-- .../SignificantlyMutatedGenesController.java | 22 +-- .../web/StaticDataTimestampController.java | 6 +- .../web/StructuralVariantController.java | 14 +- .../{ => legacy}/web/StudyController.java | 36 ++--- .../{ => legacy}/web/StudyViewController.java | 150 +++++++++--------- .../{ => legacy}/web/SurvivalController.java | 14 +- .../{ => legacy}/web/TestController.java | 2 +- .../{ => legacy}/web/TreatmentController.java | 30 ++-- .../web/VariantCountController.java | 14 +- .../web/columnar/BasicDataBinner.java | 40 +++-- .../web/columnar/ClinicalDataBinner.java | 32 ++-- .../StudyViewColumnStoreController.java | 128 +++++++-------- .../columnar/util/ClinicalDataXyPlotUtil.java | 6 +- .../columnar/util/CustomDataFilterUtil.java | 24 +-- .../columnar/util/NewClinicalDataBinUtil.java | 26 +-- .../columnar/util/NewStudyViewFilterUtil.java | 4 +- .../web/config/CustomObjectMapper.java | 134 ++++++++-------- .../web/config/DataAccessTokenConfig.java | 0 .../web/config/InternalApiTags.java | 2 +- .../web/config/JacksonConfig.java | 2 +- .../web/config/MethodValidationConfig.java | 2 +- .../web/config/PublicApiTags.java | 2 +- .../web/config/SwaggerConfig.java | 6 +- .../web/config/WebServletContextListener.java | 2 +- .../web/config/annotation/InternalApi.java | 2 +- .../web/config/annotation/PublicApi.java | 2 +- .../{ => legacy}/web/error/ErrorResponse.java | 2 +- .../web/error/GlobalExceptionHandler.java | 22 ++- .../web/interceptor/UniqueKeyInterceptor.java | 30 ++-- .../web/mixin/CancerStudyMixin.java | 4 +- .../mixin/ClinicalAttributeCountMixin.java | 2 +- .../web/mixin/ClinicalAttributeMixin.java | 2 +- .../web/mixin/ClinicalDataCountMixin.java | 2 +- .../web/mixin/ClinicalDataMixin.java | 2 +- .../web/mixin/ClinicalEventDataMixin.java | 2 +- .../web/mixin/ClinicalEventMixin.java | 2 +- .../web/mixin/CopyNumberSegMixin.java | 2 +- .../web/mixin/DataAccessTokenMixin.java | 2 +- .../mixin/DiscreteCopyNumberDataMixin.java | 2 +- .../legacy/web/mixin/GeneMixin.java | 5 + .../web/mixin/GenePanelMixin.java | 2 +- .../web/mixin/GenePanelToGeneMixin.java | 2 +- .../web/mixin/GenesetCorrelationMixin.java | 2 +- .../{ => legacy}/web/mixin/GenesetMixin.java | 2 +- .../web/mixin/GenesetMolecularDataMixin.java | 2 +- .../{ => legacy}/web/mixin/GisticMixin.java | 2 +- .../web/mixin/GisticToGeneMixin.java | 2 +- .../web/mixin/MolecularProfileMixin.java | 4 +- .../{ => legacy}/web/mixin/MutSigMixin.java | 2 +- .../{ => legacy}/web/mixin/MutationMixin.java | 2 +- .../web/mixin/MutationSpectrumMixin.java | 2 +- .../{ => legacy}/web/mixin/PatientMixin.java | 2 +- .../web/mixin/ReferenceGenomeGeneMixin.java | 2 +- .../web/mixin/ResourceDefinitionMixin.java | 2 +- .../web/mixin/SampleListMixin.java | 4 +- .../{ => legacy}/web/mixin/SampleMixin.java | 4 +- .../web/mixin/SessionDataMixin.java | 2 +- .../{ => legacy}/web/mixin/SessionMixin.java | 2 +- .../web/mixin/StructuralVariantMixin.java | 2 +- .../web/mixin/TypeOfCancerMixin.java | 2 +- .../web/parameter/BinsGeneratorConfig.java | 2 +- .../CategorizedClinicalDataCountFilter.java | 2 +- ...ategorizedGenericAssayDataCountFilter.java | 2 +- .../ClinicalAttributeCountFilter.java | 2 +- .../parameter/ClinicalDataBinCountFilter.java | 2 +- .../web/parameter/ClinicalDataBinFilter.java | 2 +- .../parameter/ClinicalDataCountFilter.java | 2 +- .../web/parameter/ClinicalDataFilter.java | 2 +- .../web/parameter/ClinicalDataIdentifier.java | 2 +- .../ClinicalDataMultiStudyFilter.java | 6 +- .../ClinicalDataSingleStudyFilter.java | 6 +- .../web/parameter/ClinicalDataType.java | 2 +- .../ClinicalEventAttributeRequest.java | 2 +- .../web/parameter/ClinicalEventRequest.java | 4 +- .../ClinicalEventRequestIdentifier.java | 2 +- .../web/parameter/ClinicalTrackConfig.java | 2 +- .../web/parameter/CoExpressionFilter.java | 2 +- .../parameter/CopyNumberCountIdentifier.java | 2 +- .../web/parameter/CustomGeneList.java | 4 +- .../web/parameter/CustomGeneListData.java | 2 +- .../web/parameter/CustomSampleIdentifier.java | 2 +- .../web/parameter/DataBinCountFilter.java | 2 +- .../web/parameter/DataBinFilter.java | 2 +- .../web/parameter/DataBinMethod.java | 2 +- .../web/parameter/DataFilter.java | 2 +- .../web/parameter/DataFilterValue.java | 2 +- .../{ => legacy}/web/parameter/Direction.java | 2 +- .../DiscreteCopyNumberEventType.java | 2 +- .../parameter/DiscreteCopyNumberFilter.java | 2 +- .../web/parameter/EnrichmentFilter.java | 2 +- .../web/parameter/GeneFilter.java | 4 +- .../web/parameter/GeneIdType.java | 2 +- .../web/parameter/GenePanelDataFilter.java | 2 +- .../GenePanelDataMultipleStudyFilter.java | 2 +- .../GenericAssayDataBinCountFilter.java | 2 +- .../parameter/GenericAssayDataBinFilter.java | 2 +- .../GenericAssayDataCountFilter.java | 2 +- .../web/parameter/GenericAssayDataFilter.java | 2 +- .../GenericAssayDataMultipleStudyFilter.java | 2 +- .../web/parameter/GenericAssayFilter.java | 2 +- .../web/parameter/GenericAssayMetaFilter.java | 2 +- .../parameter/GenesetDataFilterCriteria.java | 2 +- .../parameter/GenomicDataBinCountFilter.java | 2 +- .../web/parameter/GenomicDataBinFilter.java | 2 +- .../web/parameter/GenomicDataCountFilter.java | 2 +- .../web/parameter/GenomicDataFilter.java | 2 +- .../{ => legacy}/web/parameter/Group.java | 2 +- .../web/parameter/GroupFilter.java | 2 +- .../web/parameter/HeaderKeyConstants.java | 2 +- .../web/parameter/MolecularDataFilter.java | 2 +- .../MolecularDataMultipleStudyFilter.java | 2 +- ...fileCasesGroupAndAlterationTypeFilter.java | 4 +- .../MolecularProfileCasesGroupFilter.java | 4 +- .../web/parameter/MolecularProfileFilter.java | 2 +- .../web/parameter/MutationDataFilter.java | 2 +- .../web/parameter/MutationFilter.java | 2 +- .../MutationMultipleStudyFilter.java | 2 +- .../web/parameter/MutationOption.java | 2 +- .../parameter/MutationPositionIdentifier.java | 2 +- .../web/parameter/MutationSpectrumFilter.java | 2 +- .../web/parameter/OccurrencePosition.java | 2 +- .../web/parameter/PageSettings.java | 4 +- .../web/parameter/PageSettingsData.java | 2 +- .../web/parameter/PageSettingsIdentifier.java | 2 +- .../web/parameter/PagingConstants.java | 2 +- .../web/parameter/PatientFilter.java | 2 +- .../web/parameter/PatientIdentifier.java | 2 +- .../web/parameter/Projection.java | 2 +- .../web/parameter/ResultsPageSettings.java | 2 +- .../web/parameter/SampleFilter.java | 4 +- .../web/parameter/SampleIdentifier.java | 2 +- .../parameter/SampleMolecularIdentifier.java | 2 +- .../web/parameter/SessionPage.java | 2 +- .../parameter/StructuralVariantFilter.java | 4 +- .../web/parameter/StudyPageSettings.java | 2 +- .../web/parameter/StudyViewFilter.java | 11 +- .../web/parameter/SurvivalRequest.java | 2 +- .../web/parameter/VariantCountIdentifier.java | 2 +- .../web/parameter/VirtualStudy.java | 4 +- .../web/parameter/VirtualStudyData.java | 2 +- .../web/parameter/VirtualStudySamples.java | 2 +- .../filter/AndedPatientTreatmentFilters.java | 8 +- .../filter/AndedSampleTreatmentFilters.java | 8 +- .../filter/OredPatientTreatmentFilters.java | 8 +- .../filter/OredSampleTreatmentFilters.java | 6 +- .../filter/PatientTreatmentFilter.java | 4 +- .../filter/SampleTreatmentFilter.java | 8 +- .../web/parameter/sort/CancerTypeSortBy.java | 2 +- .../sort/ClinicalAttributeSortBy.java | 2 +- .../parameter/sort/ClinicalDataSortBy.java | 2 +- .../parameter/sort/ClinicalEventSortBy.java | 2 +- .../sort/CopyNumberSegmentSortBy.java | 2 +- .../sort/DiscreteCopyNumberSortBy.java | 2 +- .../web/parameter/sort/GenePanelSortBy.java | 2 +- .../web/parameter/sort/GeneSortBy.java | 2 +- .../sort/MolecularProfileSortBy.java | 2 +- .../web/parameter/sort/MutationSortBy.java | 2 +- .../web/parameter/sort/PatientSortBy.java | 2 +- .../parameter/sort/ResourceDataSortBy.java | 2 +- .../sort/ResourceDefinitionSortBy.java | 2 +- .../web/parameter/sort/SampleListSortBy.java | 2 +- .../web/parameter/sort/SampleSortBy.java | 2 +- .../SignificantCopyNumberRegionSortBy.java | 2 +- .../sort/SignificantlyMutatedGeneSortBy.java | 2 +- .../web/parameter/sort/StudySortBy.java | 2 +- .../web/studyview/CustomDataController.java | 28 ++-- .../{ => legacy}/web/util/BinningData.java | 6 +- .../{ => legacy}/web/util/BinningIds.java | 2 +- .../web/util/ClinicalDataBinUtil.java | 33 ++-- .../web/util/ClinicalDataEnrichmentUtil.java | 20 +-- .../ClinicalDataEqualityFilterApplier.java | 10 +- .../web/util/ClinicalDataFetcher.java | 10 +- .../web/util/ClinicalDataFilterApplier.java | 16 +- .../ClinicalDataIntervalFilterApplier.java | 12 +- .../web/util/CustomDataFilterApplier.java | 10 +- .../{ => legacy}/web/util/CustomDatatype.java | 2 +- .../{ => legacy}/web/util/DataBinHelper.java | 4 +- .../{ => legacy}/web/util/DataBinner.java | 14 +- .../web/util/DataFilterApplier.java | 6 +- .../web/util/DensityPlotParameters.java | 2 +- .../web/util/DiscreteDataBinner.java | 4 +- .../web/util/GoogleAnalyticsInterceptor.java | 2 +- .../GzippedInputStreamRequestWrapper.java | 2 +- .../web/util/HttpRequestUtils.java | 2 +- .../{ => legacy}/web/util/IdPopulator.java | 10 +- ...volvedCancerStudyExtractorInterceptor.java | 64 ++++---- .../web/util/LinearDataBinner.java | 4 +- .../web/util/LogScaleDataBinner.java | 4 +- .../web/util/RequestBodyGZipFilter.java | 2 +- .../ResettableHttpServletRequestFilter.java | 2 +- .../web/util/ScientificSmallDataBinner.java | 4 +- .../web/util/StudyViewFilterApplier.java | 114 ++++++------- .../web/util/StudyViewFilterUtil.java | 41 +++-- .../web/util/UniqueKeyExtractor.java | 4 +- .../AbstractPatientTreatmentFilter.java | 16 +- .../AbstractSampleTreatmentFilter.java | 16 +- .../appliers/ClinicalEventFilterApplier.java | 12 +- .../PatientTreatmentFilterApplier.java | 8 +- .../PatientTreatmentGroupFilterApplier.java | 8 +- .../PatientTreatmentTargetFilterApplier.java | 8 +- .../SampleTreatmentFilterApplier.java | 8 +- .../SampleTreatmentGroupFilterApplier.java | 8 +- .../SampleTreatmentTargetFilterApplier.java | 8 +- .../StructuralVariantSubFilterApplier.java | 20 +-- .../appliers/StudyViewSubFilterApplier.java | 6 +- .../util/appliers/TreatmentRowExtractor.java | 6 +- .../service/ServerStatusService.java | 7 - .../TreatmentCountReportService.java | 14 -- .../utils/security/AccessLevel.java | 5 - .../org/cbioportal/web/mixin/GeneMixin.java | 5 - .../mybatis/AlterationCountsMapper.xml | 16 +- .../AlterationDriverAnnotationMapper.xml | 4 +- .../persistence/mybatis/CancerTypeMapper.xml | 8 +- .../mybatis/ClinicalAttributeMapper.xml | 14 +- .../mybatis/ClinicalDataMapper.xml | 24 +-- .../mybatis/ClinicalEventMapper.xml | 22 +-- .../mybatis/CopyNumberSegmentMapper.xml | 8 +- .../persistence/mybatis/CosmicCountMapper.xml | 4 +- .../mybatis/DataAccessTokenMapper.xml | 8 +- .../mybatis/DiscreteCopyNumberMapper.xml | 18 +-- .../persistence/mybatis/GeneMapper.xml | 22 +-- .../persistence/mybatis/GenePanelMapper.xml | 22 +-- .../mybatis/GenericAssayMapper.xml | 6 +- .../mybatis/GenesetHierarchyMapper.xml | 10 +- .../persistence/mybatis/GenesetMapper.xml | 14 +- .../mybatis/MolecularDataMapper.xml | 24 +-- .../mybatis/MolecularProfileMapper.xml | 18 +-- .../persistence/mybatis/MutationMapper.xml | 26 +-- .../persistence/mybatis/PatientMapper.xml | 12 +- .../mybatis/ReferenceGenomeGeneMapper.xml | 12 +- .../mybatis/ResourceDataMapper.xml | 18 +-- .../mybatis/ResourceDefinitionMapper.xml | 6 +- .../persistence/mybatis/SampleListMapper.xml | 14 +- .../persistence/mybatis/SampleMapper.xml | 22 +-- .../persistence/mybatis/SecurityMapper.xml | 6 +- .../SignificantCopyNumberRegionMapper.xml | 8 +- .../SignificantlyMutatedGeneMapper.xml | 6 +- .../mybatis/StaticDataTimestampMapper.xml | 4 +- .../mybatis/StructuralVariantMapper.xml | 8 +- .../persistence/mybatis/StudyMapper.xml | 12 +- .../persistence/mybatis/TreatmentMapper.xml | 8 +- .../mybatis/VariantCountMapper.xml | 4 +- .../StudyViewAlterationFilterMapper.xml | 2 +- .../StudyViewFilterMapper.xml | 2 +- .../mybatisclickhouse/StudyViewMapper.xml | 52 +++--- .../helper/AlterationFilterHelperTest.java | 7 +- .../helper/StudyViewFilterHelperTest.java | 7 +- ...DriverAnnotationMyBatisRepositoryTest.java | 6 +- .../AlterationMyBatisRepositoryTest.java | 25 ++- .../CancerTypeMyBatisRepositoryTest.java | 8 +- ...linicalAttributeMyBatisRepositoryTest.java | 10 +- .../ClinicalDataMyBatisRepositoryTest.java | 15 +- .../ClinicalEventMyBatisRepositoryTest.java | 12 +- ...opyNumberSegmentMyBatisRepositoryTest.java | 8 +- .../CosmicCountMyBatisRepositoryTest.java | 6 +- .../DataAccessTokenMyBatisRepositoryTest.java | 6 +- ...screteCopyNumberMyBatisRepositoryTest.java | 20 +-- .../mybatis/GeneMyBatisRepositoryTest.java | 8 +- .../GenePanelMyBatisRepositoryTest.java | 14 +- .../GenericAssayMyBatisRepositoryTest.java | 8 +- ...GenesetHierarchyMyBatisRepositoryTest.java | 8 +- .../mybatis/GenesetMyBatisRepositoryTest.java | 12 +- .../MolecularDataMyBatisRepositoryTest.java | 10 +- ...MolecularProfileMyBatisRepositoryTest.java | 10 +- .../MutationMyBatisRepositoryTest.java | 24 +-- .../mybatis/PatientMyBatisRepositoryTest.java | 10 +- ...erenceGenomeGeneMyBatisRepositoryTest.java | 10 +- .../ResourceDataMyBatisRepositoryTest.java | 10 +- ...sourceDefinitionMyBatisRepositoryTest.java | 8 +- .../SampleListMyBatisRepositoryTest.java | 10 +- .../mybatis/SampleMyBatisRepositoryTest.java | 12 +- ...CopyNumberRegionMyBatisRepositoryTest.java | 10 +- ...antlyMutatedGeneMyBatisRepositoryTest.java | 8 +- ...tructuralVariantMyBatisRepositoryTest.java | 24 ++- .../mybatis/StudyMyBatisRepositoryTest.java | 12 +- .../TreatmentMyBatisRepositoryTest.java | 12 +- .../VariantCountMyBatisRepositoryTest.java | 6 +- .../mybatis/config/TestConfig.java | 4 +- ...olecularProfileCaseIdentifierUtilTest.java | 4 +- .../util/PaginationCalculatorTest.java | 5 +- .../AbstractTestcontainers.java | 2 +- .../mybatisclickhouse/CNAGenesTest.java | 14 +- .../ClinicalEventTypeCountsTest.java | 12 +- .../FilteredSamplesTest.java | 14 +- .../GenericAssayDataCountsTest.java | 14 +- .../GenomicDataCountsTest.java | 14 +- .../MolecularProfileCountTest.java | 8 +- .../mybatisclickhouse/MutatedGenesTest.java | 14 +- .../MutationDataCountsTest.java | 14 +- .../PatientTreatmentCountsTest.java | 16 +- .../mybatisclickhouse/ProfiledCountsTest.java | 8 +- .../ProteinExpressionCountsTest.java | 18 +-- .../SampleTreatmentCountsTest.java | 18 +-- .../StructuralVariantGenesTest.java | 10 +- .../StudyViewCaseListSamplesCountsTest.java | 10 +- .../StudyViewMapperClinicalDataCountTest.java | 16 +- .../config/MyBatisConfig.java | 2 +- .../util/CustomKeyGeneratorTest.java | 9 +- .../util/CustomRedisCacheIntegrationTest.java | 4 +- .../util/CustomRedisCacheManagerTest.java | 3 +- .../util/CustomRedisCacheTest.java | 4 +- .../persistence/util/EhCacheUtilsTest.java | 3 +- .../persistence/util/RedisCacheUtilsTest.java | 3 +- .../MockInMemoryRedissonClient.java | 2 +- .../util/fakeclient/MockRBucket.java | 2 +- .../util/fakeclient/MockRKeys.java | 2 +- .../{ => legacy}/proxy/MonkifierTest.java | 3 +- .../impl/AlterationCountServiceImplTest.java | 32 ++-- ...rationDriverAnnotationServiceImplTest.java | 9 +- .../AlterationEnrichmentServiceImplTest.java | 24 +-- .../service/impl/BaseServiceImplTest.java | 2 +- .../service/impl/CacheServiceImplTest.java | 13 +- .../impl/CancerTypeServiceImplTest.java | 10 +- .../ClinicalAttributeServiceImplTest.java | 18 +-- .../impl/ClinicalDataServiceImplTest.java | 26 ++- .../impl/ClinicalEventServiceImplTest.java | 30 ++-- .../impl/CoExpressionServiceImplTest.java | 32 ++-- .../CopyNumberSegmentServiceImplTest.java | 12 +- .../impl/CosmicCountServiceImplTest.java | 6 +- .../DiscreteCopyNumberServiceImplTest.java | 21 ++- .../ExpressionEnrichmentServiceImplTest.java | 34 ++-- .../service/impl/GeneMemoizerServiceTest.java | 7 +- .../impl/GenePanelServiceImplTest.java | 18 ++- .../service/impl/GeneServiceImplTest.java | 12 +- ...GenericAssayEnrichmentServiceImplTest.java | 44 ++--- .../impl/GenericAssayServiceImpTest.java | 30 ++-- .../GenesetCorrelationServiceImplTest.java | 22 +-- .../impl/GenesetDataServiceImplTest.java | 18 +-- .../impl/GenesetHierarchyServiceImplTest.java | 22 +-- .../service/impl/GenesetServiceImplTest.java | 16 +- .../impl/MolecularDataServiceImplTest.java | 28 ++-- .../impl/MolecularProfileServiceImplTest.java | 18 +-- .../impl/MrnaPercentileServiceImplTest.java | 12 +- .../service/impl/MutationServiceImplTest.java | 28 ++-- .../impl/MutationSpectrumServiceImplTest.java | 8 +- .../service/impl/PatientServiceImplTest.java | 16 +- .../impl/ReadPermissionServiceImplTest.java | 9 +- .../ReferenceGenomeGeneServiceImplTest.java | 15 +- .../impl/SampleListServiceImplTest.java | 18 +-- .../service/impl/SampleServiceImplTest.java | 28 ++-- .../impl/ServerStatusServiceImplTest.java | 7 +- ...ficantCopyNumberRegionServiceImplTest.java | 14 +- ...gnificantlyMutatedGeneServiceImplTest.java | 12 +- .../StaticDataTimestampServiceImplTest.java | 6 +- .../StructuralVariantServiceImplTest.java | 10 +- .../service/impl/StudyServiceImplTest.java | 18 +-- .../impl/StudyViewServiceImplTest.java | 54 +++---- .../impl/TreatmentServiceImplTest.java | 14 +- .../UuidDataAccessTokenServiceImplTest.java | 17 +- ...cessTokenServiceImplTestConfiguration.java | 7 +- ...essTokenServiceImplTestFiveTokenLimit.java | 17 +- .../impl/VariantCountServiceImplTest.java | 18 +-- .../impl/ViolinPlotServiceImplTest.java | 13 +- .../util/AlterationCountServiceUtilTest.java | 17 +- .../util/AlterationEnrichmentUtilTest.java | 12 +- .../util/CoExpressionAsyncMethodsTest.java | 5 +- .../service/util/JwtUtilsTest.java | 4 +- .../util/JwtUtilsTestConfiguration.java | 3 +- .../util/MolecularProfileUtilTest.java | 8 +- .../util/ProfiledCasesCounterTest.java | 15 +- .../StudyViewColumnarServiceUtilTest.java | 19 +-- .../utils/config/PropertyConditionTest.java | 3 +- ...erationDriverAnnotationControllerTest.java | 8 +- .../AlterationEnrichmentControllerTest.java | 24 +-- .../{ => legacy}/web/CacheControllerTest.java | 10 +- .../web/CacheStatsControllerTest.java | 8 +- .../web/CancerTypeControllerTest.java | 14 +- .../web/ClinicalAttributeControllerTest.java | 17 +- .../ClinicalAttributeCountControllerTest.java | 17 +- .../web/ClinicalDataControllerTest.java | 20 +-- .../ClinicalDataEnrichmentControllerTest.java | 22 +-- .../web/ClinicalEventControllerTest.java | 20 +-- .../web/CoExpressionControllerTest.java | 12 +- .../web/CopyNumberSegmentControllerTest.java | 14 +- .../web/CosmicCountControllerTest.java | 8 +- .../web/DataAccessTokenControllerTest.java | 14 +- .../web/DiscreteCopyNumberControllerTest.java | 21 ++- ...DiscreteCopyNumberCountControllerTest.java | 10 +- .../web/DocRedirectControllerTest.java | 10 +- .../ExpressionEnrichmentControllerTest.java | 14 +- .../{ => legacy}/web/GeneControllerTest.java | 15 +- .../web/GenePanelControllerTest.java | 22 +-- .../web/GenePanelDataControllerTest.java | 23 +-- .../web/GenericAssayControllerTest.java | 10 +- .../web/GenericAssayDataControllerTest.java | 19 +-- .../web/GenesetControllerTest.java | 8 +- .../web/GenesetCorrelationControllerTest.java | 8 +- .../web/GenesetDataControllerTest.java | 10 +- .../web/GenesetHierarchyControllerTest.java | 10 +- .../{ => legacy}/web/InfoControllerTest.java | 4 +- .../web/MolecularDataControllerTest.java | 14 +- .../web/MolecularProfileControllerTest.java | 18 +-- .../web/MrnaPercentileControllerTest.java | 8 +- .../web/MutationControllerTest.java | 26 +-- .../web/MutationCountControllerTest.java | 10 +- .../web/MutationSpectrumControllerTest.java | 10 +- .../web/PatientControllerTest.java | 20 +-- .../ReferenceGenomeGeneControllerTest.java | 10 +- .../web/ResourceDataControllerTest.java | 8 +- .../web/ResourceDefinitionControllerTest.java | 8 +- .../web/SampleControllerTest.java | 22 +-- .../web/SampleListControllerTest.java | 16 +- .../web/ServerStatusControllerTest.java | 4 +- .../web/SessionServiceControllerTest.java | 12 +- ...ificantCopyNumberRegionControllerTest.java | 14 +- ...gnificantlyMutatedGenesControllerTest.java | 12 +- .../StaticDataTimestampControllerTest.java | 6 +- .../web/StructuralVariantControllerTest.java | 19 +-- .../{ => legacy}/web/StudyControllerTest.java | 21 ++- .../web/StudyViewControllerTest.java | 116 +++++++------- .../web/SurvivalControllerTest.java | 18 +-- .../web/TreatmentControllerTest.java | 20 +-- .../web/VariantCountControllerTest.java | 10 +- .../web/config/CacheMapUtilConfig.java | 18 +-- .../DataAccessTokenControllerConfig.java | 6 +- .../DataAccessTokenControllerTestConfig.java | 2 +- .../config/RestAuthenticationEntryPoint.java | 2 +- .../{ => legacy}/web/config/TestConfig.java | 9 +- .../TokenAuthenticationSuccessHandler.java | 2 +- ...lterationFilterMockitoArgumentMatcher.java | 4 +- .../web/util/ClinicalDataBinUtilTest.java | 40 +++-- .../util/ClinicalDataEnrichmentUtilTest.java | 23 +-- .../web/util/DataBinHelperTest.java | 4 +- .../web/util/DataBinnerMocker.java | 2 +- .../{ => legacy}/web/util/DataBinnerTest.java | 20 +-- .../util/SelectMockitoArgumentMatcher.java | 4 +- .../web/util/StudyViewFilterApplierTest.java | 84 +++++----- .../PatientTreatmentFilterApplierTest.java | 20 +-- .../SampleTreatmentFilterApplierTest.java | 28 ++-- ...StructuralVariantSubFilterApplierTest.java | 25 +-- .../PublicVirtualStudiesIntegrationTest.java | 8 +- .../security/OAuth2AuthIntegrationTest.java | 2 +- 945 files changed, 4728 insertions(+), 4590 deletions(-) rename src/main/java/org/cbioportal/{ => application}/AsyncConfig.java (84%) rename src/main/java/org/cbioportal/{ => application}/PortalApplication.java (97%) rename src/main/java/org/cbioportal/{ => application}/WebAppConfig.java (94%) rename src/main/java/org/cbioportal/{ => application}/documentation/ExternalPageController.java (97%) rename src/main/java/org/cbioportal/{ => application}/proxy/LegacyProxyController.java (99%) rename src/main/java/org/cbioportal/{ => application}/proxy/Monkifier.java (97%) rename src/main/java/org/cbioportal/{ => application}/proxy/ProxyController.java (98%) rename src/main/java/org/cbioportal/{ => application}/proxy/util/CheckDarwinAccessUtil.java (99%) rename src/main/java/org/cbioportal/{ => application}/security/CancerStudyPermissionEvaluator.java (98%) rename src/main/java/org/cbioportal/{ => application}/security/basic/BasicRestfulAuthenticationSuccessHandler.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/config/ApiSecurityConfig.java (91%) rename src/main/java/org/cbioportal/{ => application}/security/config/AutoconfigureExcludeConfig.java (92%) rename src/main/java/org/cbioportal/{ => application}/security/config/CorsConfig.java (96%) rename src/main/java/org/cbioportal/{ => application}/security/config/CustomOAuth2AuthorizationConfig.java (94%) rename src/main/java/org/cbioportal/{ => application}/security/config/MethodSecurityConfig.java (90%) rename src/main/java/org/cbioportal/{ => application}/security/config/NoSecurityConfig.java (95%) rename src/main/java/org/cbioportal/{ => application}/security/config/OAuth2SecurityConfig.java (96%) rename src/main/java/org/cbioportal/{ => application}/security/config/OptionalOAuth2SecurityConfig.java (96%) rename src/main/java/org/cbioportal/{ => application}/security/config/Saml2AndBasicConfig.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/config/Saml2SecurityConfig.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/token/RestAuthenticationEntryPoint.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/token/TokenAuthenticationFilter.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/token/TokenAuthenticationSuccessHandler.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/token/config/DataAccessTokenConfig.java (69%) rename src/main/java/org/cbioportal/{ => application}/security/token/oauth2/JwtTokenVerifierBuilder.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/token/oauth2/OAuth2BearerAuthenticationToken.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/token/oauth2/OAuth2TokenAuthenticationProvider.java (95%) rename src/main/java/org/cbioportal/{ => application}/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java (97%) rename src/main/java/org/cbioportal/{ => application}/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java (98%) rename src/main/java/org/cbioportal/{ => application}/security/token/uuid/UuidTokenAuthenticationProvider.java (91%) rename src/main/java/org/cbioportal/{ => application}/security/util/ClaimRoleExtractorUtil.java (98%) rename src/main/java/org/cbioportal/{ => application}/security/util/GrantedAuthorityUtil.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/model/AlleleSpecificCopyNumber.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/Alteration.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/AlterationCountBase.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/AlterationCountByGene.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/AlterationCountByStructuralVariant.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/AlterationDriverAnnotation.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/AlterationEnrichment.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/AlterationFilter.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/AlterationType.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/model/BaseAlterationFilter.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/Binnable.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/model/CNA.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/CancerStudy.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/model/CancerStudyTags.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/CaseListDataCount.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalAttribute.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalAttributeCount.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalData.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalDataBin.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalDataCount.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalDataCountItem.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalDataEnrichment.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalEvent.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalEventData.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalEventKeyCode.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalEventSample.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalEventTypeCount.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalViolinPlotBoxData.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalViolinPlotData.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalViolinPlotIndividualPoint.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/ClinicalViolinPlotRowData.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/CoExpression.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/CopyNumberCount.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/CopyNumberCountByGene.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/CopyNumberSeg.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/CosmicMutation.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/CountSummary.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/CustomDriverAnnotationReport.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/DataAccessToken.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/DataBin.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/DensityPlotBin.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/DensityPlotData.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/DiscreteCopyNumberData.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/EnrichmentType.java (60%) rename src/main/java/org/cbioportal/{ => legacy}/model/EntityType.java (70%) rename src/main/java/org/cbioportal/{ => legacy}/model/ExpressionEnrichment.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/FractionGenomeAltered.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/Gene.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/GeneAlias.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/model/GeneFilter.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/GeneFilterQuery.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/GeneMolecularAlteration.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/GeneMolecularData.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenePanel.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenePanelData.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenePanelToGene.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayAdditionalProperty.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayBinaryEnrichment.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayCategoricalEnrichment.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayCountSummary.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayData.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayDataBin.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayDataCount.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayDataCountItem.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayEnrichment.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericAssayMolecularAlteration.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenericEntityProperty.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/Geneset.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenesetCorrelation.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenesetHierarchyInfo.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenesetMolecularAlteration.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenesetMolecularData.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/GeneticEntity.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenomicDataBin.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenomicDataCount.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenomicDataCountItem.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/GenomicEnrichment.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/Gistic.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/GisticToGene.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/GroupStatistics.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/Info.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/MolecularAlteration.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/MolecularData.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/MolecularProfile.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/model/MolecularProfileCaseIdentifier.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/MolecularProfileSamples.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/MrnaPercentile.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/MutSig.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/Mutation.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/model/MutationCountByGene.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/model/MutationCountByPosition.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/MutationEventType.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/MutationFilterOption.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/model/MutationSpectrum.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/NumericGeneMolecularData.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/Patient.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/PatientTreatment.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/model/PatientTreatmentReport.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/model/PatientTreatmentRow.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/QueryElement.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/model/ReadPermission.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/model/ReferenceGenome.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/model/ReferenceGenomeGene.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/ResourceData.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/ResourceDefinition.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/ResourceType.java (63%) rename src/main/java/org/cbioportal/{ => legacy}/model/Sample.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/SampleClinicalDataCollection.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/SampleList.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/SampleListToSampleId.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/SampleTreatment.java (71%) rename src/main/java/org/cbioportal/{ => legacy}/model/SampleTreatmentReport.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/model/SampleTreatmentRow.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/StructuralVariant.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/model/StructuralVariantFilterQuery.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/model/StructuralVariantGeneSubQuery.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/StructuralVariantQuery.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/StructuralVariantSpecialValue.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/model/StudyViewFilterContext.java (55%) rename src/main/java/org/cbioportal/{ => legacy}/model/StudyViewStructuralVariantFilter.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/TableTimestampPair.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/TemporalRelation.java (58%) rename src/main/java/org/cbioportal/{ => legacy}/model/Treatment.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/TreatmentRow.java (74%) rename src/main/java/org/cbioportal/{ => legacy}/model/TypeOfCancer.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/model/UniqueKeyBase.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/model/User.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/UserAuthorities.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/VariantCount.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/model/meta/BaseMeta.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/model/meta/GenericAssayMeta.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/model/meta/MutationMeta.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/model/util/QueryElement.java (57%) rename src/main/java/org/cbioportal/{ => legacy}/model/util/Select.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/AlterationDriverAnnotationRepository.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/AlterationRepository.java (82%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/CacheEnabledConfig.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/CancerTypeRepository.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/ClinicalAttributeRepository.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/ClinicalDataRepository.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/ClinicalEventRepository.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/CopyNumberSegmentRepository.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/CosmicCountRepository.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/DataAccessTokenRepository.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/DiscreteCopyNumberRepository.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/GenePanelRepository.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/GeneRepository.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/GenericAssayRepository.java (81%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/GenesetHierarchyRepository.java (82%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/GenesetRepository.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/MolecularDataRepository.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/MolecularProfileRepository.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/MutationRepository.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/PatientRepository.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/PersistenceConstants.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/ReferenceGenomeGeneRepository.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/ResourceDataRepository.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/ResourceDefinitionRepository.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/SampleListRepository.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/SampleRepository.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/SecurityRepository.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/SignificantCopyNumberRegionRepository.java (81%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/SignificantlyMutatedGeneRepository.java (82%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/StaticDataTimeStampRepository.java (62%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/StructuralVariantRepository.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/StudyRepository.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/StudyViewRepository.java (74%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/TreatmentRepository.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/VariantCountRepository.java (81%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/cachemaputil/CacheMapBuilder.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/cachemaputil/CacheMapUtil.java (55%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/cachemaputil/InactiveCacheMapUtil.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/cachemaputil/SpringManagedCacheMapUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/cachemaputil/StaticRefCacheMapUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/config/EhCacheConfig.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/config/RedisConfig.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/enums/ClinicalAttributeDataType.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/enums/DataSource.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/helper/AlterationFilterHelper.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/helper/StudyViewFilterHelper.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/model/SampleAcquisitionEventRecord.java (72%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/model/TreatmentRecord.java (68%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/AlterationCountsMapper.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/AlterationDriverAnnotationMapper.java (69%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/AlterationMyBatisRepository.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/CancerTypeMapper.java (69%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/CancerTypeMyBatisRepository.java (73%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalAttributeMapper.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalAttributeMyBatisRepository.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalDataMapper.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalDataMyBatisRepository.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalEventMapper.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalEventMyBatisRepository.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/CopyNumberSegmentMapper.java (82%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/CosmicCountMapper.java (57%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/CosmicCountMyBatisRepository.java (73%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/DataAccessTokenMapper.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/DataAccessTokenMyBatisRepository.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/DiscreteCopyNumberMapper.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GeneMapper.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GeneMyBatisRepository.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenePanelMapper.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenePanelMyBatisRepository.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenericAssayMapper.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenericAssayMyBatisRepository.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenesetHierarchyMapper.java (71%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenesetHierarchyMyBatisRepository.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenesetMapper.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenesetMyBatisRepository.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/MolecularDataMapper.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/MolecularDataMyBatisRepository.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/MolecularProfileMapper.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/MolecularProfileMyBatisRepository.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/MutationMapper.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/MutationMyBatisRepository.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/PatientMapper.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/PatientMyBatisRepository.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ReferenceGenomeGeneMapper.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ResourceDataMapper.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ResourceDataMyBatisRepository.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ResourceDefinitionMapper.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/ResourceDefinitionMyBatisRepository.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SampleListMapper.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SampleListMyBatisRepository.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SampleMapper.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SampleMyBatisRepository.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SecurityMapper.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SecurityMyBatisRepository.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SignificantCopyNumberRegionMapper.java (68%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SignificantlyMutatedGeneMapper.java (69%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/StaticDataTimestampMapper.java (59%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/StructuralVariantMapper.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/StructuralVariantMyBatisRepository.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/StudyMapper.java (70%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/StudyMyBatisRepository.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/TreatmentMapper.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/TreatmentMyBatisRepository.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/VariantCountMapper.java (70%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/VariantCountMyBatisRepository.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/config/PersistenceConfig.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/typehandler/SampleTypeTypeHandler.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/util/CustomMyBatisObjectFactory.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/util/LimitedPermissionArrayList.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatis/util/PaginationCalculator.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/StudyViewMapper.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/CacheEventLogger.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/CacheUtils.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/CustomEhcachingProvider.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/CustomKeyGenerator.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/CustomRedisCache.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/CustomRedisCacheManager.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/CustomRedisCachingProvider.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/EhCacheUtils.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/EhcacheStatistics.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/LoggingCacheErrorHandler.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/persistence/util/RedisCacheUtils.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/properties/CustomDataSourceConfiguration.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/properties/PortalProperties.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/service/AlterationCountService.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/service/AlterationDriverAnnotationService.java (63%) rename src/main/java/org/cbioportal/{ => legacy}/service/AlterationEnrichmentService.java (51%) rename src/main/java/org/cbioportal/{ => legacy}/service/AttributeByStudyService.java (67%) rename src/main/java/org/cbioportal/{ => legacy}/service/CacheService.java (68%) rename src/main/java/org/cbioportal/{ => legacy}/service/CacheStatisticsService.java (71%) rename src/main/java/org/cbioportal/{ => legacy}/service/CancerTypeService.java (67%) rename src/main/java/org/cbioportal/{ => legacy}/service/ClinicalAttributeService.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/service/ClinicalDataDensityPlotService.java (50%) rename src/main/java/org/cbioportal/{ => legacy}/service/ClinicalDataService.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/service/ClinicalEventService.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/service/CoExpressionService.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/service/CopyNumberSegmentService.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/service/CosmicCountService.java (61%) rename src/main/java/org/cbioportal/{ => legacy}/service/CustomDataService.java (62%) rename src/main/java/org/cbioportal/{ => legacy}/service/DataAccessTokenService.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/service/DiscreteCopyNumberService.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/service/ExpressionEnrichmentService.java (73%) rename src/main/java/org/cbioportal/{ => legacy}/service/FrontendPropertiesService.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/service/FrontendPropertiesServiceImpl.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/service/GeneMemoizerService.java (68%) rename src/main/java/org/cbioportal/{ => legacy}/service/GenePanelService.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/service/GeneService.java (72%) rename src/main/java/org/cbioportal/{ => legacy}/service/GenericAssayService.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/service/GenesetCorrelationService.java (69%) rename src/main/java/org/cbioportal/{ => legacy}/service/GenesetDataService.java (64%) rename src/main/java/org/cbioportal/{ => legacy}/service/GenesetHierarchyService.java (73%) rename src/main/java/org/cbioportal/{ => legacy}/service/GenesetService.java (64%) rename src/main/java/org/cbioportal/{ => legacy}/service/MolecularDataService.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/service/MolecularProfileService.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/service/MrnaPercentileService.java (58%) rename src/main/java/org/cbioportal/{ => legacy}/service/MutationService.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/service/MutationSpectrumService.java (68%) rename src/main/java/org/cbioportal/{ => legacy}/service/PatientService.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/service/ReadPermissionService.java (73%) rename src/main/java/org/cbioportal/{ => legacy}/service/ReferenceGenomeGeneService.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/service/ResourceDataService.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/service/ResourceDefinitionService.java (69%) rename src/main/java/org/cbioportal/{ => legacy}/service/SampleListService.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/service/SampleService.java (85%) create mode 100644 src/main/java/org/cbioportal/legacy/service/ServerStatusService.java rename src/main/java/org/cbioportal/{ => legacy}/service/SignificantCopyNumberRegionService.java (67%) rename src/main/java/org/cbioportal/{ => legacy}/service/SignificantlyMutatedGeneService.java (66%) rename src/main/java/org/cbioportal/{ => legacy}/service/StaticDataTimestampService.java (72%) rename src/main/java/org/cbioportal/{ => legacy}/service/StructuralVariantService.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/service/StudyService.java (70%) rename src/main/java/org/cbioportal/{ => legacy}/service/StudyViewColumnarService.java (67%) rename src/main/java/org/cbioportal/{ => legacy}/service/StudyViewService.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/service/TreatmentService.java (71%) rename src/main/java/org/cbioportal/{ => legacy}/service/VariantCountService.java (58%) rename src/main/java/org/cbioportal/{ => legacy}/service/ViolinPlotService.java (64%) rename src/main/java/org/cbioportal/{ => legacy}/service/alteration/AlterationCountByGeneService.java (60%) rename src/main/java/org/cbioportal/{ => legacy}/service/alteration/AlterationCountByGeneServiceImpl.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/AccessForbiddenException.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/CacheNotFoundException.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/CacheOperationException.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/CancerTypeNotFoundException.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/ClinicalAttributeNotFoundException.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/DataAccessTokenNoUserIdentityException.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/DataAccessTokenProhibitedUserException.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/GeneNotFoundException.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/GenePanelNotFoundException.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/GeneWithMultipleEntrezIdsException.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/GenericAssayNotFoundException.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/GenesetNotFoundException.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/InvalidDataAccessTokenException.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/MolecularProfileNotFoundException.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/PatientNotFoundException.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/ResourceDefinitionNotFoundException.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/SampleListNotFoundException.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/SampleNotFoundException.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/StudyNotFoundException.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/service/exception/TokenNotFoundException.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/AlterationCountServiceImpl.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/AlterationDriverAnnotationServiceImpl.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/AlterationEnrichmentServiceImpl.java (81%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/CacheServiceImpl.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/CacheStatisticsServiceImpl.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/CancerTypeServiceImpl.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ClinicalAttributeServiceImpl.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ClinicalDataDensityPlotServiceImpl.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ClinicalDataServiceImpl.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ClinicalEventServiceImpl.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/CoExpressionServiceImpl.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/CopyNumberSegmentServiceImpl.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/CosmicCountServiceImpl.java (68%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/CustomDataServiceImpl.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/DiscreteCopyNumberServiceImpl.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/EhcacheStatisticsServiceImpl.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ExpressionEnrichmentServiceImpl.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/GeneMemoizerServiceImpl.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/GenePanelServiceImpl.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/GeneServiceImpl.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/GenericAssayServiceImpl.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/GenesetCorrelationServiceImpl.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/GenesetDataServiceImpl.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/GenesetHierarchyServiceImpl.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/GenesetServiceImpl.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/JwtDataAccessTokenServiceImpl.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/MolecularDataServiceImpl.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/MolecularProfileServiceImpl.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/MrnaPercentileServiceImpl.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/MutationServiceImpl.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/MutationSpectrumServiceImpl.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/PatientServiceImpl.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ReadPermissionServiceImpl.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/RedisCacheStatisticsServiceImpl.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ReferenceGenomeGeneServiceImpl.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ResourceDataServiceImpl.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ResourceDefinitionServiceImpl.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/SampleListServiceImpl.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/SampleServiceImpl.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ServerStatusServiceImpl.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/SignificantCopyNumberRegionServiceImpl.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/SignificantlyMutatedGeneServiceImpl.java (73%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/StaticDataTimestampServiceImpl.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/StructuralVariantServiceImpl.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/StudyServiceImpl.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/StudyViewColumnarServiceImpl.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/StudyViewServiceImpl.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/TreatmentServiceImpl.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/UnauthDataAccessTokenServiceImpl.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/UuidDataAccessTokenServiceImpl.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/VariantCountServiceImpl.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/service/impl/ViolinPlotServiceImpl.java (95%) create mode 100644 src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportService.java rename src/main/java/org/cbioportal/{ => legacy}/service/treatment/TreatmentCountReportServiceImpl.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/AlterationCountServiceUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/AlterationEnrichmentUtil.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/BinnableCustomDataValue.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/ChromosomeCalculator.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/ClinicalAttributeUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/CoExpressionAsyncMethods.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/CustomAttributeWithData.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/CustomDataSession.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/CustomDataValue.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/ExpressionEnrichmentUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/FisherExactTestCalculator.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/JwtUtils.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/MolecularProfileUtil.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/MskWholeSlideViewerTokenGenerator.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/ProfiledCasesCounter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/SessionServiceConfig.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/SessionServiceRequestHandler.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/service/util/StudyViewColumnarServiceUtil.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/url_shortener/URLShortenerController.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/url_shortener/URLShortenerResponse.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/utils/Encoder.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/utils/config/PropertyCondition.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/utils/config/annotation/ConditionalOnProperty.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/utils/removeme/Session.java (95%) create mode 100644 src/main/java/org/cbioportal/legacy/utils/security/AccessLevel.java rename src/main/java/org/cbioportal/{ => legacy}/utils/security/PortalSecurityConfig.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/utils/validation/AllowedValues.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/utils/validation/AllowedValuesValidatorImpl.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/AlterationDriverAnnotationController.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/AlterationEnrichmentController.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/web/CacheController.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/CacheStatsController.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/CancerTypeController.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/ClinicalAttributeController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/ClinicalAttributeCountController.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/ClinicalDataController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/ClinicalDataEnrichmentController.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/ClinicalEventController.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/CoExpressionController.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/CopyNumberSegmentController.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/CosmicCountController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/DataAccessTokenController.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/DiscreteCopyNumberController.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/DiscreteCopyNumberCountController.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/web/DocRedirectController.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/ExecuterTimeInterceptor.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/ExpressionEnrichmentController.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/GeneController.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenePanelController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenePanelDataController.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/GeneralControllerAdvice.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenericAssayController.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenericAssayDataController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenericAssayEnrichmentController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenesetController.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenesetCorrelationController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenesetDataController.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/GenesetHierarchyController.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/IndexPageController.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/InfoController.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/LegacyApiController.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/LoginPageController.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/MatchMinerController.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/web/MolecularDataController.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/MolecularProfileController.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/MrnaPercentileController.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/web/MskEntityTranslationController.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/MutationController.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/MutationCountController.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/MutationSpectrumController.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/web/OAuth2DataAccessTokenController.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/PatientController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/PublicVirtualStudiesController.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/ReferenceGenomeGeneController.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/ResourceDataController.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/ResourceDefinitionController.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/web/SamlAndBasicLoginController.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/SampleController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/SampleListController.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/ServerStatusController.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/SessionServiceController.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/SignificantCopyNumberRegionController.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/web/SignificantlyMutatedGenesController.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/web/StaticDataTimestampController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/StructuralVariantController.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/StudyController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/StudyViewController.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/SurvivalController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/TestController.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/TreatmentController.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/VariantCountController.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/columnar/BasicDataBinner.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/columnar/ClinicalDataBinner.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/web/columnar/StudyViewColumnStoreController.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/columnar/util/ClinicalDataXyPlotUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/columnar/util/CustomDataFilterUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/columnar/util/NewClinicalDataBinUtil.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/columnar/util/NewStudyViewFilterUtil.java (73%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/CustomObjectMapper.java (56%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/DataAccessTokenConfig.java (100%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/InternalApiTags.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/JacksonConfig.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/MethodValidationConfig.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/PublicApiTags.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/SwaggerConfig.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/WebServletContextListener.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/annotation/InternalApi.java (74%) rename src/main/java/org/cbioportal/{ => legacy}/web/config/annotation/PublicApi.java (74%) rename src/main/java/org/cbioportal/{ => legacy}/web/error/ErrorResponse.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/error/GlobalExceptionHandler.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/interceptor/UniqueKeyInterceptor.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/CancerStudyMixin.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/ClinicalAttributeCountMixin.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/ClinicalAttributeMixin.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/ClinicalDataCountMixin.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/ClinicalDataMixin.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/ClinicalEventDataMixin.java (78%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/ClinicalEventMixin.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/CopyNumberSegMixin.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/DataAccessTokenMixin.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/DiscreteCopyNumberDataMixin.java (80%) create mode 100644 src/main/java/org/cbioportal/legacy/web/mixin/GeneMixin.java rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/GenePanelMixin.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/GenePanelToGeneMixin.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/GenesetCorrelationMixin.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/GenesetMixin.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/GenesetMolecularDataMixin.java (81%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/GisticMixin.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/GisticToGeneMixin.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/MolecularProfileMixin.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/MutSigMixin.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/MutationMixin.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/MutationSpectrumMixin.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/PatientMixin.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/ReferenceGenomeGeneMixin.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/ResourceDefinitionMixin.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/SampleListMixin.java (82%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/SampleMixin.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/SessionDataMixin.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/SessionMixin.java (83%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/StructuralVariantMixin.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/web/mixin/TypeOfCancerMixin.java (79%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/BinsGeneratorConfig.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/CategorizedClinicalDataCountFilter.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/CategorizedGenericAssayDataCountFilter.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalAttributeCountFilter.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalDataBinCountFilter.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalDataBinFilter.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalDataCountFilter.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalDataFilter.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalDataIdentifier.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalDataMultiStudyFilter.java (81%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalDataSingleStudyFilter.java (77%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalDataType.java (56%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalEventAttributeRequest.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalEventRequest.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalEventRequestIdentifier.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ClinicalTrackConfig.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/CoExpressionFilter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/CopyNumberCountIdentifier.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/CustomGeneList.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/CustomGeneListData.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/CustomSampleIdentifier.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/DataBinCountFilter.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/DataBinFilter.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/DataBinMethod.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/DataFilter.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/DataFilterValue.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/Direction.java (50%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/DiscreteCopyNumberEventType.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/DiscreteCopyNumberFilter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/EnrichmentFilter.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GeneFilter.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GeneIdType.java (60%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenePanelDataFilter.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenePanelDataMultipleStudyFilter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenericAssayDataBinCountFilter.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenericAssayDataBinFilter.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenericAssayDataCountFilter.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenericAssayDataFilter.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenericAssayDataMultipleStudyFilter.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenericAssayFilter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenericAssayMetaFilter.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenesetDataFilterCriteria.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenomicDataBinCountFilter.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenomicDataBinFilter.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenomicDataCountFilter.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GenomicDataFilter.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/Group.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/GroupFilter.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/HeaderKeyConstants.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MolecularDataFilter.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MolecularDataMultipleStudyFilter.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MolecularProfileCasesGroupFilter.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MolecularProfileFilter.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MutationDataFilter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MutationFilter.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MutationMultipleStudyFilter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MutationOption.java (81%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MutationPositionIdentifier.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/MutationSpectrumFilter.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/OccurrencePosition.java (55%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/PageSettings.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/PageSettingsData.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/PageSettingsIdentifier.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/PagingConstants.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/PatientFilter.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/PatientIdentifier.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/Projection.java (61%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/ResultsPageSettings.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/SampleFilter.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/SampleIdentifier.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/SampleMolecularIdentifier.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/SessionPage.java (58%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/StructuralVariantFilter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/StudyPageSettings.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/StudyViewFilter.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/SurvivalRequest.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/VariantCountIdentifier.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/VirtualStudy.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/VirtualStudyData.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/VirtualStudySamples.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/filter/AndedPatientTreatmentFilters.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/filter/AndedSampleTreatmentFilters.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/filter/OredPatientTreatmentFilters.java (75%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/filter/OredSampleTreatmentFilters.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/filter/PatientTreatmentFilter.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/filter/SampleTreatmentFilter.java (82%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/CancerTypeSortBy.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/ClinicalAttributeSortBy.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/ClinicalDataSortBy.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/ClinicalEventSortBy.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/CopyNumberSegmentSortBy.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/DiscreteCopyNumberSortBy.java (86%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/GenePanelSortBy.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/GeneSortBy.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/MolecularProfileSortBy.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/MutationSortBy.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/PatientSortBy.java (84%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/ResourceDataSortBy.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/ResourceDefinitionSortBy.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/SampleListSortBy.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/SampleSortBy.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/SignificantCopyNumberRegionSortBy.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/SignificantlyMutatedGeneSortBy.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/parameter/sort/StudySortBy.java (90%) rename src/main/java/org/cbioportal/{ => legacy}/web/studyview/CustomDataController.java (85%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/BinningData.java (88%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/BinningIds.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/ClinicalDataBinUtil.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/ClinicalDataEnrichmentUtil.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/ClinicalDataEqualityFilterApplier.java (87%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/ClinicalDataFetcher.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/ClinicalDataFilterApplier.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/ClinicalDataIntervalFilterApplier.java (93%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/CustomDataFilterApplier.java (94%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/CustomDatatype.java (76%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/DataBinHelper.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/DataBinner.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/DataFilterApplier.java (60%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/DensityPlotParameters.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/DiscreteDataBinner.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/GoogleAnalyticsInterceptor.java (99%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/GzippedInputStreamRequestWrapper.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/HttpRequestUtils.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/IdPopulator.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/InvolvedCancerStudyExtractorInterceptor.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/LinearDataBinner.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/LogScaleDataBinner.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/RequestBodyGZipFilter.java (98%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/ResettableHttpServletRequestFilter.java (96%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/ScientificSmallDataBinner.java (97%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/StudyViewFilterApplier.java (95%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/StudyViewFilterUtil.java (92%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/UniqueKeyExtractor.java (91%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/AbstractPatientTreatmentFilter.java (81%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/AbstractSampleTreatmentFilter.java (80%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/ClinicalEventFilterApplier.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/PatientTreatmentFilterApplier.java (62%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/PatientTreatmentGroupFilterApplier.java (63%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/PatientTreatmentTargetFilterApplier.java (63%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/SampleTreatmentFilterApplier.java (62%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/SampleTreatmentGroupFilterApplier.java (63%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/SampleTreatmentTargetFilterApplier.java (63%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/StructuralVariantSubFilterApplier.java (89%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/StudyViewSubFilterApplier.java (57%) rename src/main/java/org/cbioportal/{ => legacy}/web/util/appliers/TreatmentRowExtractor.java (69%) delete mode 100644 src/main/java/org/cbioportal/service/ServerStatusService.java delete mode 100644 src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java delete mode 100644 src/main/java/org/cbioportal/utils/security/AccessLevel.java delete mode 100644 src/main/java/org/cbioportal/web/mixin/GeneMixin.java rename src/test/java/org/cbioportal/{ => legacy}/persistence/helper/AlterationFilterHelperTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/helper/StudyViewFilterHelperTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/AlterationMyBatisRepositoryTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java (90%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/GeneMyBatisRepositoryTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenePanelMyBatisRepositoryTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java (89%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/GenesetMyBatisRepositoryTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/MutationMyBatisRepositoryTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/PatientMyBatisRepositoryTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/SampleListMyBatisRepositoryTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/SampleMyBatisRepositoryTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/StudyMyBatisRepositoryTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/TreatmentMyBatisRepositoryTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/VariantCountMyBatisRepositoryTest.java (92%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/config/TestConfig.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatis/util/PaginationCalculatorTest.java (90%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/AbstractTestcontainers.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/CNAGenesTest.java (87%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java (86%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/FilteredSamplesTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java (87%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/GenomicDataCountsTest.java (87%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/MolecularProfileCountTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/MutatedGenesTest.java (90%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/MutationDataCountsTest.java (87%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java (84%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/ProfiledCountsTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java (89%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java (83%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/StructuralVariantGenesTest.java (86%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/mybatisclickhouse/config/MyBatisConfig.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/CustomKeyGeneratorTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/CustomRedisCacheIntegrationTest.java (89%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/CustomRedisCacheManagerTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/CustomRedisCacheTest.java (99%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/EhCacheUtilsTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/RedisCacheUtilsTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/fakeclient/MockInMemoryRedissonClient.java (99%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/fakeclient/MockRBucket.java (99%) rename src/test/java/org/cbioportal/{ => legacy}/persistence/util/fakeclient/MockRKeys.java (99%) rename src/test/java/org/cbioportal/{ => legacy}/proxy/MonkifierTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/AlterationCountServiceImplTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/AlterationDriverAnnotationServiceImplTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/AlterationEnrichmentServiceImplTest.java (85%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/BaseServiceImplTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/CacheServiceImplTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/CancerTypeServiceImplTest.java (88%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/ClinicalAttributeServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/ClinicalDataServiceImplTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/ClinicalEventServiceImplTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/CoExpressionServiceImplTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/CopyNumberSegmentServiceImplTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/CosmicCountServiceImplTest.java (87%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/DiscreteCopyNumberServiceImplTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/ExpressionEnrichmentServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GeneMemoizerServiceTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GenePanelServiceImplTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GeneServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GenericAssayEnrichmentServiceImplTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GenericAssayServiceImpTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GenesetCorrelationServiceImplTest.java (92%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GenesetDataServiceImplTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GenesetHierarchyServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/GenesetServiceImplTest.java (89%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/MolecularDataServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/MolecularProfileServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/MrnaPercentileServiceImplTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/MutationServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/MutationSpectrumServiceImplTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/PatientServiceImplTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/ReadPermissionServiceImplTest.java (89%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/ReferenceGenomeGeneServiceImplTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/SampleListServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/SampleServiceImplTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/ServerStatusServiceImplTest.java (86%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/SignificantCopyNumberRegionServiceImplTest.java (89%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/SignificantlyMutatedGeneServiceImplTest.java (87%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/StaticDataTimestampServiceImplTest.java (86%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/StructuralVariantServiceImplTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/StudyServiceImplTest.java (88%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/StudyViewServiceImplTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/TreatmentServiceImplTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/UuidDataAccessTokenServiceImplTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/VariantCountServiceImplTest.java (82%) rename src/test/java/org/cbioportal/{ => legacy}/service/impl/ViolinPlotServiceImplTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/service/util/AlterationCountServiceUtilTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/service/util/AlterationEnrichmentUtilTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/service/util/CoExpressionAsyncMethodsTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/service/util/JwtUtilsTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/service/util/JwtUtilsTestConfiguration.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/service/util/MolecularProfileUtilTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/service/util/ProfiledCasesCounterTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/service/util/StudyViewColumnarServiceUtilTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/utils/config/PropertyConditionTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/AlterationDriverAnnotationControllerTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/web/AlterationEnrichmentControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/CacheControllerTest.java (92%) rename src/test/java/org/cbioportal/{ => legacy}/web/CacheStatsControllerTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/web/CancerTypeControllerTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/web/ClinicalAttributeControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/ClinicalAttributeCountControllerTest.java (92%) rename src/test/java/org/cbioportal/{ => legacy}/web/ClinicalDataControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/ClinicalDataEnrichmentControllerTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/ClinicalEventControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/CoExpressionControllerTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/web/CopyNumberSegmentControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/CosmicCountControllerTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/DataAccessTokenControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/DiscreteCopyNumberControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/DiscreteCopyNumberCountControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/DocRedirectControllerTest.java (85%) rename src/test/java/org/cbioportal/{ => legacy}/web/ExpressionEnrichmentControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/GeneControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/GenePanelControllerTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/web/GenePanelDataControllerTest.java (92%) rename src/test/java/org/cbioportal/{ => legacy}/web/GenericAssayControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/GenericAssayDataControllerTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/web/GenesetControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/GenesetCorrelationControllerTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/GenesetDataControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/GenesetHierarchyControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/InfoControllerTest.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/web/MolecularDataControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/MolecularProfileControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/MrnaPercentileControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/MutationControllerTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/web/MutationCountControllerTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/MutationSpectrumControllerTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/PatientControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/ReferenceGenomeGeneControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/ResourceDataControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/ResourceDefinitionControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/SampleControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/SampleListControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/ServerStatusControllerTest.java (93%) rename src/test/java/org/cbioportal/{ => legacy}/web/SessionServiceControllerTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/web/SignificantCopyNumberRegionControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/SignificantlyMutatedGenesControllerTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/StaticDataTimestampControllerTest.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/web/StructuralVariantControllerTest.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/web/StudyControllerTest.java (97%) rename src/test/java/org/cbioportal/{ => legacy}/web/StudyViewControllerTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/SurvivalControllerTest.java (92%) rename src/test/java/org/cbioportal/{ => legacy}/web/TreatmentControllerTest.java (92%) rename src/test/java/org/cbioportal/{ => legacy}/web/VariantCountControllerTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/config/CacheMapUtilConfig.java (78%) rename src/test/java/org/cbioportal/{ => legacy}/web/config/DataAccessTokenControllerConfig.java (91%) rename src/test/java/org/cbioportal/{ => legacy}/web/config/DataAccessTokenControllerTestConfig.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/web/config/RestAuthenticationEntryPoint.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/web/config/TestConfig.java (83%) rename src/test/java/org/cbioportal/{ => legacy}/web/config/TokenAuthenticationSuccessHandler.java (98%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/AlterationFilterMockitoArgumentMatcher.java (94%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/ClinicalDataBinUtilTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/ClinicalDataEnrichmentUtilTest.java (96%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/DataBinHelperTest.java (99%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/DataBinnerMocker.java (99%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/DataBinnerTest.java (99%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/SelectMockitoArgumentMatcher.java (87%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/StudyViewFilterApplierTest.java (95%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/appliers/PatientTreatmentFilterApplierTest.java (88%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/appliers/SampleTreatmentFilterApplierTest.java (87%) rename src/test/java/org/cbioportal/{ => legacy}/web/util/appliers/StructuralVariantSubFilterApplierTest.java (87%) diff --git a/README.md b/README.md index 8b164e38dd1..a2558fc31ce 100644 --- a/README.md +++ b/README.md @@ -67,7 +67,7 @@ java -Xms2g -Xmx4g \ -Dapp.name='my-portal' \ -Ddbconnector=dbcp \ -cp "$PWD:$PWD/BOOT-INF/lib/*" \ - org.cbioportal.PortalApplication + org.cbioportal.application.PortalApplication ``` The app should now show up at http://localhost:8080. diff --git a/docker/web-and-data/Dockerfile b/docker/web-and-data/Dockerfile index c8658f23fac..dcabf787a54 100644 --- a/docker/web-and-data/Dockerfile +++ b/docker/web-and-data/Dockerfile @@ -73,4 +73,4 @@ COPY --from=build ${DEPENDENCY}/BOOT-INF/classes $PORTAL_WEB_HOME/ # add entrypoint COPY --from=build /cbioportal/docker/web-and-data/docker-entrypoint.sh /usr/local/bin/ ENTRYPOINT ["docker-entrypoint.sh"] -CMD ["sh", "-c", "java $(echo $JAVA_OPTS) -cp /cbioportal-webapp:/cbioportal-webapp/lib/* org.cbioportal.PortalApplication $(echo $WEBAPP_OPTS)"] +CMD ["sh", "-c", "java $(echo $JAVA_OPTS) -cp /cbioportal-webapp:/cbioportal-webapp/lib/* org.cbioportal.application.PortalApplication $(echo $WEBAPP_OPTS)"] diff --git a/docker/web-and-data/docker-entrypoint.sh b/docker/web-and-data/docker-entrypoint.sh index a0cd507d5b7..675bdc2c977 100755 --- a/docker/web-and-data/docker-entrypoint.sh +++ b/docker/web-and-data/docker-entrypoint.sh @@ -135,7 +135,7 @@ _main() { # Check if the application is found in the arguments if [ "$found" = true ]; then echo "Running Migrate DB Script" - # Custom logic to handle the case when "org.cbioportal.PortalApplication" is present + # Custom logic to handle the case when "org.cbioportal.application.PortalApplication" is present # Parse database config. Use command line parameters (e.g. -Ddb.host) if # available, otherwise use application.properties if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then diff --git a/src/main/java/org/cbioportal/AsyncConfig.java b/src/main/java/org/cbioportal/application/AsyncConfig.java similarity index 84% rename from src/main/java/org/cbioportal/AsyncConfig.java rename to src/main/java/org/cbioportal/application/AsyncConfig.java index a1e5b3041a4..7a9d543ab91 100644 --- a/src/main/java/org/cbioportal/AsyncConfig.java +++ b/src/main/java/org/cbioportal/application/AsyncConfig.java @@ -1,14 +1,11 @@ -package org.cbioportal; +package org.cbioportal.application; import org.springframework.beans.factory.annotation.Value; -import org.springframework.core.env.Environment; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Configuration; import org.springframework.scheduling.annotation.EnableAsync; import org.springframework.scheduling.annotation.AsyncConfigurer; import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor; -import java.lang.Runtime; import java.util.concurrent.Executor; @Configuration diff --git a/src/main/java/org/cbioportal/PortalApplication.java b/src/main/java/org/cbioportal/application/PortalApplication.java similarity index 97% rename from src/main/java/org/cbioportal/PortalApplication.java rename to src/main/java/org/cbioportal/application/PortalApplication.java index bfe458a121b..1292fe2de16 100644 --- a/src/main/java/org/cbioportal/PortalApplication.java +++ b/src/main/java/org/cbioportal/application/PortalApplication.java @@ -1,4 +1,4 @@ -package org.cbioportal; +package org.cbioportal.application; import org.springframework.boot.SpringApplication; import org.springframework.boot.autoconfigure.SpringBootApplication; diff --git a/src/main/java/org/cbioportal/WebAppConfig.java b/src/main/java/org/cbioportal/application/WebAppConfig.java similarity index 94% rename from src/main/java/org/cbioportal/WebAppConfig.java rename to src/main/java/org/cbioportal/application/WebAppConfig.java index 2f951690c33..dd04ee7c5e0 100644 --- a/src/main/java/org/cbioportal/WebAppConfig.java +++ b/src/main/java/org/cbioportal/application/WebAppConfig.java @@ -1,9 +1,9 @@ -package org.cbioportal; +package org.cbioportal.application; import java.util.List; -import org.cbioportal.web.ExecuterTimeInterceptor; -import org.cbioportal.web.util.InvolvedCancerStudyExtractorInterceptor; +import org.cbioportal.legacy.web.ExecuterTimeInterceptor; +import org.cbioportal.legacy.web.util.InvolvedCancerStudyExtractorInterceptor; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; diff --git a/src/main/java/org/cbioportal/documentation/ExternalPageController.java b/src/main/java/org/cbioportal/application/documentation/ExternalPageController.java similarity index 97% rename from src/main/java/org/cbioportal/documentation/ExternalPageController.java rename to src/main/java/org/cbioportal/application/documentation/ExternalPageController.java index c8a246d38ed..a6a2d1f21f1 100644 --- a/src/main/java/org/cbioportal/documentation/ExternalPageController.java +++ b/src/main/java/org/cbioportal/application/documentation/ExternalPageController.java @@ -1,4 +1,4 @@ -package org.cbioportal.documentation; +package org.cbioportal.application.documentation; import org.springframework.stereotype.Controller; import org.springframework.transaction.annotation.Transactional; diff --git a/src/main/java/org/cbioportal/proxy/LegacyProxyController.java b/src/main/java/org/cbioportal/application/proxy/LegacyProxyController.java similarity index 99% rename from src/main/java/org/cbioportal/proxy/LegacyProxyController.java rename to src/main/java/org/cbioportal/application/proxy/LegacyProxyController.java index a2403f22f86..636a205df2f 100644 --- a/src/main/java/org/cbioportal/proxy/LegacyProxyController.java +++ b/src/main/java/org/cbioportal/application/proxy/LegacyProxyController.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.proxy; +package org.cbioportal.application.proxy; import java.io.IOException; import java.net.URI; diff --git a/src/main/java/org/cbioportal/proxy/Monkifier.java b/src/main/java/org/cbioportal/application/proxy/Monkifier.java similarity index 97% rename from src/main/java/org/cbioportal/proxy/Monkifier.java rename to src/main/java/org/cbioportal/application/proxy/Monkifier.java index b50d6da4dfb..ac368ab3f9c 100644 --- a/src/main/java/org/cbioportal/proxy/Monkifier.java +++ b/src/main/java/org/cbioportal/application/proxy/Monkifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.proxy; +package org.cbioportal.application.proxy; import jakarta.servlet.http.HttpServletRequest; import org.apache.commons.codec.binary.Base64; diff --git a/src/main/java/org/cbioportal/proxy/ProxyController.java b/src/main/java/org/cbioportal/application/proxy/ProxyController.java similarity index 98% rename from src/main/java/org/cbioportal/proxy/ProxyController.java rename to src/main/java/org/cbioportal/application/proxy/ProxyController.java index 0296aec3390..1158e427adc 100644 --- a/src/main/java/org/cbioportal/proxy/ProxyController.java +++ b/src/main/java/org/cbioportal/application/proxy/ProxyController.java @@ -1,8 +1,8 @@ -package org.cbioportal.proxy; +package org.cbioportal.application.proxy; import jakarta.servlet.http.HttpServletRequest; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.proxy.util.CheckDarwinAccessUtil; +import org.cbioportal.application.proxy.util.CheckDarwinAccessUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpEntity; diff --git a/src/main/java/org/cbioportal/proxy/util/CheckDarwinAccessUtil.java b/src/main/java/org/cbioportal/application/proxy/util/CheckDarwinAccessUtil.java similarity index 99% rename from src/main/java/org/cbioportal/proxy/util/CheckDarwinAccessUtil.java rename to src/main/java/org/cbioportal/application/proxy/util/CheckDarwinAccessUtil.java index be9dc2b1152..39e6ba1e7bf 100644 --- a/src/main/java/org/cbioportal/proxy/util/CheckDarwinAccessUtil.java +++ b/src/main/java/org/cbioportal/application/proxy/util/CheckDarwinAccessUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.proxy.util; +package org.cbioportal.application.proxy.util; import com.fasterxml.jackson.annotation.JsonAnyGetter; import com.fasterxml.jackson.annotation.JsonAnySetter; diff --git a/src/main/java/org/cbioportal/security/CancerStudyPermissionEvaluator.java b/src/main/java/org/cbioportal/application/security/CancerStudyPermissionEvaluator.java similarity index 98% rename from src/main/java/org/cbioportal/security/CancerStudyPermissionEvaluator.java rename to src/main/java/org/cbioportal/application/security/CancerStudyPermissionEvaluator.java index 3cd7c732b7c..d92ecd70a5d 100644 --- a/src/main/java/org/cbioportal/security/CancerStudyPermissionEvaluator.java +++ b/src/main/java/org/cbioportal/application/security/CancerStudyPermissionEvaluator.java @@ -30,18 +30,18 @@ * along with this program. If not, see . */ -package org.cbioportal.security; +package org.cbioportal.application.security; import java.io.Serializable; import java.util.*; import java.util.stream.Collectors; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Patient; -import org.cbioportal.model.SampleList; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.utils.security.AccessLevel; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.security.access.PermissionEvaluator; diff --git a/src/main/java/org/cbioportal/security/basic/BasicRestfulAuthenticationSuccessHandler.java b/src/main/java/org/cbioportal/application/security/basic/BasicRestfulAuthenticationSuccessHandler.java similarity index 97% rename from src/main/java/org/cbioportal/security/basic/BasicRestfulAuthenticationSuccessHandler.java rename to src/main/java/org/cbioportal/application/security/basic/BasicRestfulAuthenticationSuccessHandler.java index 9291f27abcd..e0620f0f6f6 100644 --- a/src/main/java/org/cbioportal/security/basic/BasicRestfulAuthenticationSuccessHandler.java +++ b/src/main/java/org/cbioportal/application/security/basic/BasicRestfulAuthenticationSuccessHandler.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.basic; +package org.cbioportal.application.security.basic; import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; diff --git a/src/main/java/org/cbioportal/security/config/ApiSecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/ApiSecurityConfig.java similarity index 91% rename from src/main/java/org/cbioportal/security/config/ApiSecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/ApiSecurityConfig.java index b83524d0869..902af9a9440 100644 --- a/src/main/java/org/cbioportal/security/config/ApiSecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/ApiSecurityConfig.java @@ -1,10 +1,10 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.security.token.RestAuthenticationEntryPoint; -import org.cbioportal.security.token.TokenAuthenticationFilter; -import org.cbioportal.security.token.TokenAuthenticationSuccessHandler; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.application.security.token.RestAuthenticationEntryPoint; +import org.cbioportal.application.security.token.TokenAuthenticationFilter; +import org.cbioportal.application.security.token.TokenAuthenticationSuccessHandler; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; diff --git a/src/main/java/org/cbioportal/security/config/AutoconfigureExcludeConfig.java b/src/main/java/org/cbioportal/application/security/config/AutoconfigureExcludeConfig.java similarity index 92% rename from src/main/java/org/cbioportal/security/config/AutoconfigureExcludeConfig.java rename to src/main/java/org/cbioportal/application/security/config/AutoconfigureExcludeConfig.java index 5c14beb51e6..5c4c8ee61bc 100644 --- a/src/main/java/org/cbioportal/security/config/AutoconfigureExcludeConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/AutoconfigureExcludeConfig.java @@ -1,6 +1,6 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.boot.autoconfigure.EnableAutoConfiguration; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.boot.autoconfigure.data.redis.RedisAutoConfiguration; diff --git a/src/main/java/org/cbioportal/security/config/CorsConfig.java b/src/main/java/org/cbioportal/application/security/config/CorsConfig.java similarity index 96% rename from src/main/java/org/cbioportal/security/config/CorsConfig.java rename to src/main/java/org/cbioportal/application/security/config/CorsConfig.java index d96050013cc..830e52c18b6 100644 --- a/src/main/java/org/cbioportal/security/config/CorsConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/CorsConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/security/config/CustomOAuth2AuthorizationConfig.java b/src/main/java/org/cbioportal/application/security/config/CustomOAuth2AuthorizationConfig.java similarity index 94% rename from src/main/java/org/cbioportal/security/config/CustomOAuth2AuthorizationConfig.java rename to src/main/java/org/cbioportal/application/security/config/CustomOAuth2AuthorizationConfig.java index 7929fdce39f..4561c996079 100644 --- a/src/main/java/org/cbioportal/security/config/CustomOAuth2AuthorizationConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/CustomOAuth2AuthorizationConfig.java @@ -1,8 +1,8 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.model.User; -import org.cbioportal.model.UserAuthorities; -import org.cbioportal.persistence.SecurityRepository; +import org.cbioportal.legacy.model.User; +import org.cbioportal.legacy.model.UserAuthorities; +import org.cbioportal.legacy.persistence.SecurityRepository; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/security/config/MethodSecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/MethodSecurityConfig.java similarity index 90% rename from src/main/java/org/cbioportal/security/config/MethodSecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/MethodSecurityConfig.java index c6bd8d04645..c48c8532ed6 100644 --- a/src/main/java/org/cbioportal/security/config/MethodSecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/MethodSecurityConfig.java @@ -1,7 +1,7 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.security.CancerStudyPermissionEvaluator; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.application.security.CancerStudyPermissionEvaluator; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/security/config/NoSecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/NoSecurityConfig.java similarity index 95% rename from src/main/java/org/cbioportal/security/config/NoSecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/NoSecurityConfig.java index 42f49c96cd3..9c8d7e068e8 100644 --- a/src/main/java/org/cbioportal/security/config/NoSecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/NoSecurityConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/security/config/OAuth2SecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/OAuth2SecurityConfig.java similarity index 96% rename from src/main/java/org/cbioportal/security/config/OAuth2SecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/OAuth2SecurityConfig.java index fd3b8b48b3f..ee82bc1adba 100644 --- a/src/main/java/org/cbioportal/security/config/OAuth2SecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/OAuth2SecurityConfig.java @@ -1,7 +1,7 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.security.util.ClaimRoleExtractorUtil; -import org.cbioportal.security.util.GrantedAuthorityUtil; +import org.cbioportal.application.security.util.ClaimRoleExtractorUtil; +import org.cbioportal.application.security.util.GrantedAuthorityUtil; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Value; diff --git a/src/main/java/org/cbioportal/security/config/OptionalOAuth2SecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/OptionalOAuth2SecurityConfig.java similarity index 96% rename from src/main/java/org/cbioportal/security/config/OptionalOAuth2SecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/OptionalOAuth2SecurityConfig.java index 248921b2235..8d8649b4b9d 100644 --- a/src/main/java/org/cbioportal/security/config/OptionalOAuth2SecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/OptionalOAuth2SecurityConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.boot.autoconfigure.security.SecurityProperties; diff --git a/src/main/java/org/cbioportal/security/config/Saml2AndBasicConfig.java b/src/main/java/org/cbioportal/application/security/config/Saml2AndBasicConfig.java similarity index 97% rename from src/main/java/org/cbioportal/security/config/Saml2AndBasicConfig.java rename to src/main/java/org/cbioportal/application/security/config/Saml2AndBasicConfig.java index 691979c0072..e4117b8ba2a 100644 --- a/src/main/java/org/cbioportal/security/config/Saml2AndBasicConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/Saml2AndBasicConfig.java @@ -1,6 +1,6 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.security.basic.BasicRestfulAuthenticationSuccessHandler; +import org.cbioportal.application.security.basic.BasicRestfulAuthenticationSuccessHandler; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/security/config/Saml2SecurityConfig.java b/src/main/java/org/cbioportal/application/security/config/Saml2SecurityConfig.java similarity index 97% rename from src/main/java/org/cbioportal/security/config/Saml2SecurityConfig.java rename to src/main/java/org/cbioportal/application/security/config/Saml2SecurityConfig.java index 527df01140b..5e71912965e 100644 --- a/src/main/java/org/cbioportal/security/config/Saml2SecurityConfig.java +++ b/src/main/java/org/cbioportal/application/security/config/Saml2SecurityConfig.java @@ -1,6 +1,6 @@ -package org.cbioportal.security.config; +package org.cbioportal.application.security.config; -import org.cbioportal.security.util.GrantedAuthorityUtil; +import org.cbioportal.application.security.util.GrantedAuthorityUtil; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; diff --git a/src/main/java/org/cbioportal/security/token/RestAuthenticationEntryPoint.java b/src/main/java/org/cbioportal/application/security/token/RestAuthenticationEntryPoint.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/RestAuthenticationEntryPoint.java rename to src/main/java/org/cbioportal/application/security/token/RestAuthenticationEntryPoint.java index 8b5136520b2..3f91aec7a19 100644 --- a/src/main/java/org/cbioportal/security/token/RestAuthenticationEntryPoint.java +++ b/src/main/java/org/cbioportal/application/security/token/RestAuthenticationEntryPoint.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token; +package org.cbioportal.application.security.token; import java.io.IOException; diff --git a/src/main/java/org/cbioportal/security/token/TokenAuthenticationFilter.java b/src/main/java/org/cbioportal/application/security/token/TokenAuthenticationFilter.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/TokenAuthenticationFilter.java rename to src/main/java/org/cbioportal/application/security/token/TokenAuthenticationFilter.java index 42988160137..e1cef698518 100644 --- a/src/main/java/org/cbioportal/security/token/TokenAuthenticationFilter.java +++ b/src/main/java/org/cbioportal/application/security/token/TokenAuthenticationFilter.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token; +package org.cbioportal.application.security.token; import jakarta.servlet.ServletException; import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; -import org.cbioportal.service.DataAccessTokenService; +import org.cbioportal.legacy.service.DataAccessTokenService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.security.authentication.AuthenticationManager; diff --git a/src/main/java/org/cbioportal/security/token/TokenAuthenticationSuccessHandler.java b/src/main/java/org/cbioportal/application/security/token/TokenAuthenticationSuccessHandler.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/TokenAuthenticationSuccessHandler.java rename to src/main/java/org/cbioportal/application/security/token/TokenAuthenticationSuccessHandler.java index b2db8dddabf..9eefe2a66cc 100644 --- a/src/main/java/org/cbioportal/security/token/TokenAuthenticationSuccessHandler.java +++ b/src/main/java/org/cbioportal/application/security/token/TokenAuthenticationSuccessHandler.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token; +package org.cbioportal.application.security.token; import jakarta.servlet.ServletException; import jakarta.servlet.http.HttpServletRequest; diff --git a/src/main/java/org/cbioportal/security/token/config/DataAccessTokenConfig.java b/src/main/java/org/cbioportal/application/security/token/config/DataAccessTokenConfig.java similarity index 69% rename from src/main/java/org/cbioportal/security/token/config/DataAccessTokenConfig.java rename to src/main/java/org/cbioportal/application/security/token/config/DataAccessTokenConfig.java index a800772cfa7..58126b1143f 100644 --- a/src/main/java/org/cbioportal/security/token/config/DataAccessTokenConfig.java +++ b/src/main/java/org/cbioportal/application/security/token/config/DataAccessTokenConfig.java @@ -1,13 +1,13 @@ -package org.cbioportal.security.token.config; +package org.cbioportal.application.security.token.config; -import org.cbioportal.persistence.SecurityRepository; -import org.cbioportal.security.token.oauth2.JwtTokenVerifierBuilder; -import org.cbioportal.security.token.oauth2.OAuth2DataAccessTokenServiceImpl; -import org.cbioportal.security.token.oauth2.OAuth2TokenAuthenticationProvider; -import org.cbioportal.security.token.oauth2.OAuth2TokenRefreshRestTemplate; -import org.cbioportal.security.token.uuid.UuidTokenAuthenticationProvider; -import org.cbioportal.service.impl.UnauthDataAccessTokenServiceImpl; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.SecurityRepository; +import org.cbioportal.application.security.token.oauth2.JwtTokenVerifierBuilder; +import org.cbioportal.application.security.token.oauth2.OAuth2DataAccessTokenServiceImpl; +import org.cbioportal.application.security.token.oauth2.OAuth2TokenAuthenticationProvider; +import org.cbioportal.application.security.token.oauth2.OAuth2TokenRefreshRestTemplate; +import org.cbioportal.application.security.token.uuid.UuidTokenAuthenticationProvider; +import org.cbioportal.legacy.service.impl.UnauthDataAccessTokenServiceImpl; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; import org.springframework.web.client.RestTemplate; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/JwtTokenVerifierBuilder.java b/src/main/java/org/cbioportal/application/security/token/oauth2/JwtTokenVerifierBuilder.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/oauth2/JwtTokenVerifierBuilder.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/JwtTokenVerifierBuilder.java index a14fba88b1e..5f82071f317 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/JwtTokenVerifierBuilder.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/JwtTokenVerifierBuilder.java @@ -29,7 +29,7 @@ * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import java.net.MalformedURLException; import java.net.URL; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2BearerAuthenticationToken.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2BearerAuthenticationToken.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2BearerAuthenticationToken.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2BearerAuthenticationToken.java index 1e60681df90..833488780d7 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2BearerAuthenticationToken.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2BearerAuthenticationToken.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import java.util.Collection; import java.util.HashSet; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java index 9e546ce10bf..d2e5a548f78 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2DataAccessTokenServiceImpl.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpEntity; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenAuthenticationProvider.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenAuthenticationProvider.java similarity index 95% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenAuthenticationProvider.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenAuthenticationProvider.java index d8dfafa7b66..903f069df23 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenAuthenticationProvider.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenAuthenticationProvider.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.security.util.ClaimRoleExtractorUtil; -import org.cbioportal.security.util.GrantedAuthorityUtil; +import org.cbioportal.application.security.util.ClaimRoleExtractorUtil; +import org.cbioportal.application.security.util.GrantedAuthorityUtil; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.authentication.AuthenticationProvider; import org.springframework.security.authentication.BadCredentialsException; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java similarity index 97% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java index f9dc65c0889..c3453f8a89e 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenDataAccessConfiguration.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; diff --git a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java similarity index 98% rename from src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java rename to src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java index fefe7ccb2d8..47b81bf7b3c 100644 --- a/src/main/java/org/cbioportal/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java +++ b/src/main/java/org/cbioportal/application/security/token/oauth2/OAuth2TokenRefreshRestTemplate.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.security.token.oauth2; +package org.cbioportal.application.security.token.oauth2; import com.fasterxml.jackson.databind.ObjectMapper; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/security/token/uuid/UuidTokenAuthenticationProvider.java b/src/main/java/org/cbioportal/application/security/token/uuid/UuidTokenAuthenticationProvider.java similarity index 91% rename from src/main/java/org/cbioportal/security/token/uuid/UuidTokenAuthenticationProvider.java rename to src/main/java/org/cbioportal/application/security/token/uuid/UuidTokenAuthenticationProvider.java index 85268a3df22..9dcebe548f6 100644 --- a/src/main/java/org/cbioportal/security/token/uuid/UuidTokenAuthenticationProvider.java +++ b/src/main/java/org/cbioportal/application/security/token/uuid/UuidTokenAuthenticationProvider.java @@ -1,7 +1,7 @@ -package org.cbioportal.security.token.uuid; +package org.cbioportal.application.security.token.uuid; -import org.cbioportal.model.UserAuthorities; -import org.cbioportal.persistence.SecurityRepository; +import org.cbioportal.legacy.model.UserAuthorities; +import org.cbioportal.legacy.persistence.SecurityRepository; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.security.authentication.AuthenticationProvider; diff --git a/src/main/java/org/cbioportal/security/util/ClaimRoleExtractorUtil.java b/src/main/java/org/cbioportal/application/security/util/ClaimRoleExtractorUtil.java similarity index 98% rename from src/main/java/org/cbioportal/security/util/ClaimRoleExtractorUtil.java rename to src/main/java/org/cbioportal/application/security/util/ClaimRoleExtractorUtil.java index 1f3e094529a..5f36f077cb3 100644 --- a/src/main/java/org/cbioportal/security/util/ClaimRoleExtractorUtil.java +++ b/src/main/java/org/cbioportal/application/security/util/ClaimRoleExtractorUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.util; +package org.cbioportal.application.security.util; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/src/main/java/org/cbioportal/security/util/GrantedAuthorityUtil.java b/src/main/java/org/cbioportal/application/security/util/GrantedAuthorityUtil.java similarity index 91% rename from src/main/java/org/cbioportal/security/util/GrantedAuthorityUtil.java rename to src/main/java/org/cbioportal/application/security/util/GrantedAuthorityUtil.java index 68645faf456..456b03385b4 100644 --- a/src/main/java/org/cbioportal/security/util/GrantedAuthorityUtil.java +++ b/src/main/java/org/cbioportal/application/security/util/GrantedAuthorityUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.security.util; +package org.cbioportal.application.security.util; import org.springframework.security.core.GrantedAuthority; import org.springframework.security.core.authority.SimpleGrantedAuthority; diff --git a/src/main/java/org/cbioportal/model/AlleleSpecificCopyNumber.java b/src/main/java/org/cbioportal/legacy/model/AlleleSpecificCopyNumber.java similarity index 98% rename from src/main/java/org/cbioportal/model/AlleleSpecificCopyNumber.java rename to src/main/java/org/cbioportal/legacy/model/AlleleSpecificCopyNumber.java index 4ac94988d19..81f1bac9086 100644 --- a/src/main/java/org/cbioportal/model/AlleleSpecificCopyNumber.java +++ b/src/main/java/org/cbioportal/legacy/model/AlleleSpecificCopyNumber.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/Alteration.java b/src/main/java/org/cbioportal/legacy/model/Alteration.java similarity index 98% rename from src/main/java/org/cbioportal/model/Alteration.java rename to src/main/java/org/cbioportal/legacy/model/Alteration.java index 1e7e6e96cde..3df1a3992a0 100644 --- a/src/main/java/org/cbioportal/model/Alteration.java +++ b/src/main/java/org/cbioportal/legacy/model/Alteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/AlterationCountBase.java b/src/main/java/org/cbioportal/legacy/model/AlterationCountBase.java similarity index 97% rename from src/main/java/org/cbioportal/model/AlterationCountBase.java rename to src/main/java/org/cbioportal/legacy/model/AlterationCountBase.java index cbe79790563..a57c487e6a9 100644 --- a/src/main/java/org/cbioportal/model/AlterationCountBase.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationCountBase.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Set; diff --git a/src/main/java/org/cbioportal/model/AlterationCountByGene.java b/src/main/java/org/cbioportal/legacy/model/AlterationCountByGene.java similarity index 97% rename from src/main/java/org/cbioportal/model/AlterationCountByGene.java rename to src/main/java/org/cbioportal/legacy/model/AlterationCountByGene.java index 0c09a79351f..92e0558e3e0 100644 --- a/src/main/java/org/cbioportal/model/AlterationCountByGene.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationCountByGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/model/AlterationCountByStructuralVariant.java b/src/main/java/org/cbioportal/legacy/model/AlterationCountByStructuralVariant.java similarity index 97% rename from src/main/java/org/cbioportal/model/AlterationCountByStructuralVariant.java rename to src/main/java/org/cbioportal/legacy/model/AlterationCountByStructuralVariant.java index 88800d1f84f..1e629c61b40 100644 --- a/src/main/java/org/cbioportal/model/AlterationCountByStructuralVariant.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationCountByStructuralVariant.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public class AlterationCountByStructuralVariant extends AlterationCountBase { diff --git a/src/main/java/org/cbioportal/model/AlterationDriverAnnotation.java b/src/main/java/org/cbioportal/legacy/model/AlterationDriverAnnotation.java similarity index 98% rename from src/main/java/org/cbioportal/model/AlterationDriverAnnotation.java rename to src/main/java/org/cbioportal/legacy/model/AlterationDriverAnnotation.java index 02f0f909db9..4297e967b1e 100644 --- a/src/main/java/org/cbioportal/model/AlterationDriverAnnotation.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationDriverAnnotation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/AlterationEnrichment.java b/src/main/java/org/cbioportal/legacy/model/AlterationEnrichment.java similarity index 97% rename from src/main/java/org/cbioportal/model/AlterationEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/AlterationEnrichment.java index d1fdbc4ba34..95fe0f5e25f 100644 --- a/src/main/java/org/cbioportal/model/AlterationEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/AlterationFilter.java b/src/main/java/org/cbioportal/legacy/model/AlterationFilter.java similarity index 98% rename from src/main/java/org/cbioportal/model/AlterationFilter.java rename to src/main/java/org/cbioportal/legacy/model/AlterationFilter.java index c10f8d697e7..d59bd52fa18 100644 --- a/src/main/java/org/cbioportal/model/AlterationFilter.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Arrays; @@ -10,7 +10,7 @@ import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/model/AlterationType.java b/src/main/java/org/cbioportal/legacy/model/AlterationType.java similarity index 77% rename from src/main/java/org/cbioportal/model/AlterationType.java rename to src/main/java/org/cbioportal/legacy/model/AlterationType.java index b20a642669d..c143b182b73 100644 --- a/src/main/java/org/cbioportal/model/AlterationType.java +++ b/src/main/java/org/cbioportal/legacy/model/AlterationType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum AlterationType { MUTATION_EXTENDED, diff --git a/src/main/java/org/cbioportal/model/BaseAlterationFilter.java b/src/main/java/org/cbioportal/legacy/model/BaseAlterationFilter.java similarity index 98% rename from src/main/java/org/cbioportal/model/BaseAlterationFilter.java rename to src/main/java/org/cbioportal/legacy/model/BaseAlterationFilter.java index df2d2f72a63..e4957b8339f 100644 --- a/src/main/java/org/cbioportal/model/BaseAlterationFilter.java +++ b/src/main/java/org/cbioportal/legacy/model/BaseAlterationFilter.java @@ -1,10 +1,10 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.annotation.JsonInclude.Include; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import java.io.Serializable; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/model/Binnable.java b/src/main/java/org/cbioportal/legacy/model/Binnable.java similarity index 87% rename from src/main/java/org/cbioportal/model/Binnable.java rename to src/main/java/org/cbioportal/legacy/model/Binnable.java index 358cafc1685..ee2d3aff1be 100644 --- a/src/main/java/org/cbioportal/model/Binnable.java +++ b/src/main/java/org/cbioportal/legacy/model/Binnable.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; /** * Data that can be binned, clinical or custom diff --git a/src/main/java/org/cbioportal/model/CNA.java b/src/main/java/org/cbioportal/legacy/model/CNA.java similarity index 95% rename from src/main/java/org/cbioportal/model/CNA.java rename to src/main/java/org/cbioportal/legacy/model/CNA.java index 1840eb7e6f5..3513cec79c5 100644 --- a/src/main/java/org/cbioportal/model/CNA.java +++ b/src/main/java/org/cbioportal/legacy/model/CNA.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.HashMap; import java.util.Map; diff --git a/src/main/java/org/cbioportal/model/CancerStudy.java b/src/main/java/org/cbioportal/legacy/model/CancerStudy.java similarity index 99% rename from src/main/java/org/cbioportal/model/CancerStudy.java rename to src/main/java/org/cbioportal/legacy/model/CancerStudy.java index 8504a8bd55a..8d12850c09f 100644 --- a/src/main/java/org/cbioportal/model/CancerStudy.java +++ b/src/main/java/org/cbioportal/legacy/model/CancerStudy.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Date; diff --git a/src/main/java/org/cbioportal/model/CancerStudyTags.java b/src/main/java/org/cbioportal/legacy/model/CancerStudyTags.java similarity index 94% rename from src/main/java/org/cbioportal/model/CancerStudyTags.java rename to src/main/java/org/cbioportal/legacy/model/CancerStudyTags.java index 48f987036c0..ffe0354c932 100644 --- a/src/main/java/org/cbioportal/model/CancerStudyTags.java +++ b/src/main/java/org/cbioportal/legacy/model/CancerStudyTags.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/CaseListDataCount.java b/src/main/java/org/cbioportal/legacy/model/CaseListDataCount.java similarity index 94% rename from src/main/java/org/cbioportal/model/CaseListDataCount.java rename to src/main/java/org/cbioportal/legacy/model/CaseListDataCount.java index 218a83ffd3c..68842379d4c 100644 --- a/src/main/java/org/cbioportal/model/CaseListDataCount.java +++ b/src/main/java/org/cbioportal/legacy/model/CaseListDataCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalAttribute.java b/src/main/java/org/cbioportal/legacy/model/ClinicalAttribute.java similarity index 98% rename from src/main/java/org/cbioportal/model/ClinicalAttribute.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalAttribute.java index ef1d10e9026..db97f3dca48 100644 --- a/src/main/java/org/cbioportal/model/ClinicalAttribute.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalAttribute.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ClinicalAttributeCount.java b/src/main/java/org/cbioportal/legacy/model/ClinicalAttributeCount.java similarity index 91% rename from src/main/java/org/cbioportal/model/ClinicalAttributeCount.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalAttributeCount.java index 440654eb68f..8828273a0de 100644 --- a/src/main/java/org/cbioportal/model/ClinicalAttributeCount.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalAttributeCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalData.java similarity index 97% rename from src/main/java/org/cbioportal/model/ClinicalData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalData.java index 3943de6044f..1a2be4a7e68 100644 --- a/src/main/java/org/cbioportal/model/ClinicalData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ClinicalDataBin.java b/src/main/java/org/cbioportal/legacy/model/ClinicalDataBin.java similarity index 89% rename from src/main/java/org/cbioportal/model/ClinicalDataBin.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalDataBin.java index 86be0ae127c..7ed24fff9df 100644 --- a/src/main/java/org/cbioportal/model/ClinicalDataBin.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalDataBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalDataCount.java b/src/main/java/org/cbioportal/legacy/model/ClinicalDataCount.java similarity index 93% rename from src/main/java/org/cbioportal/model/ClinicalDataCount.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalDataCount.java index c16e98ba08c..594b59a6fbd 100644 --- a/src/main/java/org/cbioportal/model/ClinicalDataCount.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalDataCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalDataCountItem.java b/src/main/java/org/cbioportal/legacy/model/ClinicalDataCountItem.java similarity index 93% rename from src/main/java/org/cbioportal/model/ClinicalDataCountItem.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalDataCountItem.java index aaf56ec10ba..cfb068b976d 100644 --- a/src/main/java/org/cbioportal/model/ClinicalDataCountItem.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalDataCountItem.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/ClinicalDataEnrichment.java b/src/main/java/org/cbioportal/legacy/model/ClinicalDataEnrichment.java similarity index 96% rename from src/main/java/org/cbioportal/model/ClinicalDataEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalDataEnrichment.java index 10c13ac2242..9cd83c65e9b 100644 --- a/src/main/java/org/cbioportal/model/ClinicalDataEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalDataEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/ClinicalEvent.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEvent.java similarity index 98% rename from src/main/java/org/cbioportal/model/ClinicalEvent.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEvent.java index c98a7ea95f0..91ec86ff4c4 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEvent.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEvent.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ClinicalEventData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEventData.java similarity index 95% rename from src/main/java/org/cbioportal/model/ClinicalEventData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEventData.java index 6430954af39..01408270785 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEventData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEventData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ClinicalEventKeyCode.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEventKeyCode.java similarity index 95% rename from src/main/java/org/cbioportal/model/ClinicalEventKeyCode.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEventKeyCode.java index 3808f8aed10..bc57dc416ce 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEventKeyCode.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEventKeyCode.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; /** * Clinical event data objects are key value pairs. diff --git a/src/main/java/org/cbioportal/model/ClinicalEventSample.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEventSample.java similarity index 97% rename from src/main/java/org/cbioportal/model/ClinicalEventSample.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEventSample.java index 75d53fc84f7..10e62881b07 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEventSample.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEventSample.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Objects; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalEventTypeCount.java b/src/main/java/org/cbioportal/legacy/model/ClinicalEventTypeCount.java similarity index 94% rename from src/main/java/org/cbioportal/model/ClinicalEventTypeCount.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalEventTypeCount.java index 95d1e129fb5..00eba0a728b 100644 --- a/src/main/java/org/cbioportal/model/ClinicalEventTypeCount.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalEventTypeCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotBoxData.java similarity index 97% rename from src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotBoxData.java index c2e24d4d4e2..dabe4eeec5a 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotBoxData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotData.java similarity index 96% rename from src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotData.java index 452cabf0bcd..21371353f2d 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotIndividualPoint.java similarity index 95% rename from src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotIndividualPoint.java index 7cff49930b0..3bfd0dd91ff 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotIndividualPoint.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotRowData.java similarity index 97% rename from src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java rename to src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotRowData.java index 3a2ef647e35..5675e10d598 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java +++ b/src/main/java/org/cbioportal/legacy/model/ClinicalViolinPlotRowData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/CoExpression.java b/src/main/java/org/cbioportal/legacy/model/CoExpression.java similarity index 97% rename from src/main/java/org/cbioportal/model/CoExpression.java rename to src/main/java/org/cbioportal/legacy/model/CoExpression.java index 22fdec80784..88ab187e1f8 100644 --- a/src/main/java/org/cbioportal/model/CoExpression.java +++ b/src/main/java/org/cbioportal/legacy/model/CoExpression.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/CopyNumberCount.java b/src/main/java/org/cbioportal/legacy/model/CopyNumberCount.java similarity index 97% rename from src/main/java/org/cbioportal/model/CopyNumberCount.java rename to src/main/java/org/cbioportal/legacy/model/CopyNumberCount.java index 3748da9228c..2d2f8a89159 100644 --- a/src/main/java/org/cbioportal/model/CopyNumberCount.java +++ b/src/main/java/org/cbioportal/legacy/model/CopyNumberCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/CopyNumberCountByGene.java b/src/main/java/org/cbioportal/legacy/model/CopyNumberCountByGene.java similarity index 94% rename from src/main/java/org/cbioportal/model/CopyNumberCountByGene.java rename to src/main/java/org/cbioportal/legacy/model/CopyNumberCountByGene.java index ef1143066e7..f60447d6740 100644 --- a/src/main/java/org/cbioportal/model/CopyNumberCountByGene.java +++ b/src/main/java/org/cbioportal/legacy/model/CopyNumberCountByGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/CopyNumberSeg.java b/src/main/java/org/cbioportal/legacy/model/CopyNumberSeg.java similarity index 98% rename from src/main/java/org/cbioportal/model/CopyNumberSeg.java rename to src/main/java/org/cbioportal/legacy/model/CopyNumberSeg.java index ea304052666..aca3ff34415 100644 --- a/src/main/java/org/cbioportal/model/CopyNumberSeg.java +++ b/src/main/java/org/cbioportal/legacy/model/CopyNumberSeg.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.math.BigDecimal; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/CosmicMutation.java b/src/main/java/org/cbioportal/legacy/model/CosmicMutation.java similarity index 96% rename from src/main/java/org/cbioportal/model/CosmicMutation.java rename to src/main/java/org/cbioportal/legacy/model/CosmicMutation.java index 2656205c146..4ba6bafd089 100644 --- a/src/main/java/org/cbioportal/model/CosmicMutation.java +++ b/src/main/java/org/cbioportal/legacy/model/CosmicMutation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/CountSummary.java b/src/main/java/org/cbioportal/legacy/model/CountSummary.java similarity index 95% rename from src/main/java/org/cbioportal/model/CountSummary.java rename to src/main/java/org/cbioportal/legacy/model/CountSummary.java index 3466117a2ba..119d36694c0 100644 --- a/src/main/java/org/cbioportal/model/CountSummary.java +++ b/src/main/java/org/cbioportal/legacy/model/CountSummary.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/CustomDriverAnnotationReport.java b/src/main/java/org/cbioportal/legacy/model/CustomDriverAnnotationReport.java similarity index 93% rename from src/main/java/org/cbioportal/model/CustomDriverAnnotationReport.java rename to src/main/java/org/cbioportal/legacy/model/CustomDriverAnnotationReport.java index e86668f82e3..507a19ba410 100644 --- a/src/main/java/org/cbioportal/model/CustomDriverAnnotationReport.java +++ b/src/main/java/org/cbioportal/legacy/model/CustomDriverAnnotationReport.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Set; diff --git a/src/main/java/org/cbioportal/model/DataAccessToken.java b/src/main/java/org/cbioportal/legacy/model/DataAccessToken.java similarity index 98% rename from src/main/java/org/cbioportal/model/DataAccessToken.java rename to src/main/java/org/cbioportal/legacy/model/DataAccessToken.java index 0895475428d..e0223d4a573 100644 --- a/src/main/java/org/cbioportal/model/DataAccessToken.java +++ b/src/main/java/org/cbioportal/legacy/model/DataAccessToken.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Date; diff --git a/src/main/java/org/cbioportal/model/DataBin.java b/src/main/java/org/cbioportal/legacy/model/DataBin.java similarity index 95% rename from src/main/java/org/cbioportal/model/DataBin.java rename to src/main/java/org/cbioportal/legacy/model/DataBin.java index f39c57704da..7158d4d6079 100644 --- a/src/main/java/org/cbioportal/model/DataBin.java +++ b/src/main/java/org/cbioportal/legacy/model/DataBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/DensityPlotBin.java b/src/main/java/org/cbioportal/legacy/model/DensityPlotBin.java similarity index 97% rename from src/main/java/org/cbioportal/model/DensityPlotBin.java rename to src/main/java/org/cbioportal/legacy/model/DensityPlotBin.java index 6bff6384fbe..4cfebeefd43 100644 --- a/src/main/java/org/cbioportal/model/DensityPlotBin.java +++ b/src/main/java/org/cbioportal/legacy/model/DensityPlotBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/DensityPlotData.java b/src/main/java/org/cbioportal/legacy/model/DensityPlotData.java similarity index 95% rename from src/main/java/org/cbioportal/model/DensityPlotData.java rename to src/main/java/org/cbioportal/legacy/model/DensityPlotData.java index 06adc10bca5..ba24806ce15 100644 --- a/src/main/java/org/cbioportal/model/DensityPlotData.java +++ b/src/main/java/org/cbioportal/legacy/model/DensityPlotData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java b/src/main/java/org/cbioportal/legacy/model/DiscreteCopyNumberData.java similarity index 95% rename from src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java rename to src/main/java/org/cbioportal/legacy/model/DiscreteCopyNumberData.java index 11c20fe6068..419a59cd4c8 100644 --- a/src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java +++ b/src/main/java/org/cbioportal/legacy/model/DiscreteCopyNumberData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonRawValue; diff --git a/src/main/java/org/cbioportal/model/EnrichmentType.java b/src/main/java/org/cbioportal/legacy/model/EnrichmentType.java similarity index 60% rename from src/main/java/org/cbioportal/model/EnrichmentType.java rename to src/main/java/org/cbioportal/legacy/model/EnrichmentType.java index af13ab2020e..833d881c30b 100644 --- a/src/main/java/org/cbioportal/model/EnrichmentType.java +++ b/src/main/java/org/cbioportal/legacy/model/EnrichmentType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum EnrichmentType { SAMPLE, diff --git a/src/main/java/org/cbioportal/model/EntityType.java b/src/main/java/org/cbioportal/legacy/model/EntityType.java similarity index 70% rename from src/main/java/org/cbioportal/model/EntityType.java rename to src/main/java/org/cbioportal/legacy/model/EntityType.java index 507b9b6d090..94070bfe1ba 100644 --- a/src/main/java/org/cbioportal/model/EntityType.java +++ b/src/main/java/org/cbioportal/legacy/model/EntityType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum EntityType { GENE, diff --git a/src/main/java/org/cbioportal/model/ExpressionEnrichment.java b/src/main/java/org/cbioportal/legacy/model/ExpressionEnrichment.java similarity index 95% rename from src/main/java/org/cbioportal/model/ExpressionEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/ExpressionEnrichment.java index c6c562c4b64..fd1b5e35162 100644 --- a/src/main/java/org/cbioportal/model/ExpressionEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/ExpressionEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/FractionGenomeAltered.java b/src/main/java/org/cbioportal/legacy/model/FractionGenomeAltered.java similarity index 96% rename from src/main/java/org/cbioportal/model/FractionGenomeAltered.java rename to src/main/java/org/cbioportal/legacy/model/FractionGenomeAltered.java index f9e3d67fcdb..2020536cfd8 100644 --- a/src/main/java/org/cbioportal/model/FractionGenomeAltered.java +++ b/src/main/java/org/cbioportal/legacy/model/FractionGenomeAltered.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.math.BigDecimal; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/Gene.java b/src/main/java/org/cbioportal/legacy/model/Gene.java similarity index 96% rename from src/main/java/org/cbioportal/model/Gene.java rename to src/main/java/org/cbioportal/legacy/model/Gene.java index a2325da6856..ef58277d17b 100644 --- a/src/main/java/org/cbioportal/model/Gene.java +++ b/src/main/java/org/cbioportal/legacy/model/Gene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GeneAlias.java b/src/main/java/org/cbioportal/legacy/model/GeneAlias.java similarity index 92% rename from src/main/java/org/cbioportal/model/GeneAlias.java rename to src/main/java/org/cbioportal/legacy/model/GeneAlias.java index 664a73cb831..15f7e00ef43 100644 --- a/src/main/java/org/cbioportal/model/GeneAlias.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneAlias.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GeneFilter.java b/src/main/java/org/cbioportal/legacy/model/GeneFilter.java similarity index 94% rename from src/main/java/org/cbioportal/model/GeneFilter.java rename to src/main/java/org/cbioportal/legacy/model/GeneFilter.java index ae6f62890dc..9f1d2105440 100644 --- a/src/main/java/org/cbioportal/model/GeneFilter.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GeneFilterQuery.java b/src/main/java/org/cbioportal/legacy/model/GeneFilterQuery.java similarity index 95% rename from src/main/java/org/cbioportal/model/GeneFilterQuery.java rename to src/main/java/org/cbioportal/legacy/model/GeneFilterQuery.java index e8280b4ce27..1035c91cbca 100644 --- a/src/main/java/org/cbioportal/model/GeneFilterQuery.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneFilterQuery.java @@ -1,6 +1,6 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GeneMolecularAlteration.java b/src/main/java/org/cbioportal/legacy/model/GeneMolecularAlteration.java similarity index 95% rename from src/main/java/org/cbioportal/model/GeneMolecularAlteration.java rename to src/main/java/org/cbioportal/legacy/model/GeneMolecularAlteration.java index 05938ed539c..427f382ffce 100644 --- a/src/main/java/org/cbioportal/model/GeneMolecularAlteration.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneMolecularAlteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GeneMolecularData.java b/src/main/java/org/cbioportal/legacy/model/GeneMolecularData.java similarity index 94% rename from src/main/java/org/cbioportal/model/GeneMolecularData.java rename to src/main/java/org/cbioportal/legacy/model/GeneMolecularData.java index 6ce9e1cef68..a634b7aa69c 100644 --- a/src/main/java/org/cbioportal/model/GeneMolecularData.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneMolecularData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenePanel.java b/src/main/java/org/cbioportal/legacy/model/GenePanel.java similarity index 96% rename from src/main/java/org/cbioportal/model/GenePanel.java rename to src/main/java/org/cbioportal/legacy/model/GenePanel.java index 6c47f89016d..ec8e62d93e5 100644 --- a/src/main/java/org/cbioportal/model/GenePanel.java +++ b/src/main/java/org/cbioportal/legacy/model/GenePanel.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GenePanelData.java b/src/main/java/org/cbioportal/legacy/model/GenePanelData.java similarity index 97% rename from src/main/java/org/cbioportal/model/GenePanelData.java rename to src/main/java/org/cbioportal/legacy/model/GenePanelData.java index ac1bfbf78b4..30892b83e79 100644 --- a/src/main/java/org/cbioportal/model/GenePanelData.java +++ b/src/main/java/org/cbioportal/legacy/model/GenePanelData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenePanelToGene.java b/src/main/java/org/cbioportal/legacy/model/GenePanelToGene.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenePanelToGene.java rename to src/main/java/org/cbioportal/legacy/model/GenePanelToGene.java index b09698966f3..b4a787f8931 100644 --- a/src/main/java/org/cbioportal/model/GenePanelToGene.java +++ b/src/main/java/org/cbioportal/legacy/model/GenePanelToGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenericAssayAdditionalProperty.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayAdditionalProperty.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenericAssayAdditionalProperty.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayAdditionalProperty.java index 8fab77071aa..ab4e6277c8b 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayAdditionalProperty.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayAdditionalProperty.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericAssayBinaryEnrichment.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayBinaryEnrichment.java similarity index 92% rename from src/main/java/org/cbioportal/model/GenericAssayBinaryEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayBinaryEnrichment.java index 24e84145227..9bf443593cf 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayBinaryEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayBinaryEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/GenericAssayCategoricalEnrichment.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayCategoricalEnrichment.java similarity index 92% rename from src/main/java/org/cbioportal/model/GenericAssayCategoricalEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayCategoricalEnrichment.java index afc72993136..0159bed7927 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayCategoricalEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayCategoricalEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonProperty; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenericAssayCountSummary.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayCountSummary.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenericAssayCountSummary.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayCountSummary.java index 49edb224e4a..2356b38cd6a 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayCountSummary.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayCountSummary.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericAssayData.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayData.java similarity index 94% rename from src/main/java/org/cbioportal/model/GenericAssayData.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayData.java index 3fd08f55e77..150e1d00644 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayData.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GenericAssayDataBin.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataBin.java similarity index 93% rename from src/main/java/org/cbioportal/model/GenericAssayDataBin.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayDataBin.java index 62b44070388..22fc03d4717 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayDataBin.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericAssayDataCount.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataCount.java similarity index 94% rename from src/main/java/org/cbioportal/model/GenericAssayDataCount.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayDataCount.java index 62c14562fca..fb3d15640ce 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayDataCount.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataCountItem.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayDataCountItem.java index c272b617f87..da6c4a2260b 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayDataCountItem.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GenericAssayEnrichment.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayEnrichment.java similarity index 97% rename from src/main/java/org/cbioportal/model/GenericAssayEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayEnrichment.java index 9116783494a..79256bde774 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/GenericAssayMolecularAlteration.java b/src/main/java/org/cbioportal/legacy/model/GenericAssayMolecularAlteration.java similarity index 96% rename from src/main/java/org/cbioportal/model/GenericAssayMolecularAlteration.java rename to src/main/java/org/cbioportal/legacy/model/GenericAssayMolecularAlteration.java index 24ddbcd09bb..1c06f7961ff 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayMolecularAlteration.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericAssayMolecularAlteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenericEntityProperty.java b/src/main/java/org/cbioportal/legacy/model/GenericEntityProperty.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenericEntityProperty.java rename to src/main/java/org/cbioportal/legacy/model/GenericEntityProperty.java index da2fbac1631..3d10afa784d 100644 --- a/src/main/java/org/cbioportal/model/GenericEntityProperty.java +++ b/src/main/java/org/cbioportal/legacy/model/GenericEntityProperty.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/Geneset.java b/src/main/java/org/cbioportal/legacy/model/Geneset.java similarity index 97% rename from src/main/java/org/cbioportal/model/Geneset.java rename to src/main/java/org/cbioportal/legacy/model/Geneset.java index 5fc022ae804..1a564ba88a0 100644 --- a/src/main/java/org/cbioportal/model/Geneset.java +++ b/src/main/java/org/cbioportal/legacy/model/Geneset.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenesetCorrelation.java b/src/main/java/org/cbioportal/legacy/model/GenesetCorrelation.java similarity index 97% rename from src/main/java/org/cbioportal/model/GenesetCorrelation.java rename to src/main/java/org/cbioportal/legacy/model/GenesetCorrelation.java index 6bfe13ba346..8bb672d7ed7 100644 --- a/src/main/java/org/cbioportal/model/GenesetCorrelation.java +++ b/src/main/java/org/cbioportal/legacy/model/GenesetCorrelation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenesetHierarchyInfo.java b/src/main/java/org/cbioportal/legacy/model/GenesetHierarchyInfo.java similarity index 96% rename from src/main/java/org/cbioportal/model/GenesetHierarchyInfo.java rename to src/main/java/org/cbioportal/legacy/model/GenesetHierarchyInfo.java index dac02f3d454..1567d55378a 100644 --- a/src/main/java/org/cbioportal/model/GenesetHierarchyInfo.java +++ b/src/main/java/org/cbioportal/legacy/model/GenesetHierarchyInfo.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GenesetMolecularAlteration.java b/src/main/java/org/cbioportal/legacy/model/GenesetMolecularAlteration.java similarity index 94% rename from src/main/java/org/cbioportal/model/GenesetMolecularAlteration.java rename to src/main/java/org/cbioportal/legacy/model/GenesetMolecularAlteration.java index e4720949596..938f84dfd6f 100644 --- a/src/main/java/org/cbioportal/model/GenesetMolecularAlteration.java +++ b/src/main/java/org/cbioportal/legacy/model/GenesetMolecularAlteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenesetMolecularData.java b/src/main/java/org/cbioportal/legacy/model/GenesetMolecularData.java similarity index 93% rename from src/main/java/org/cbioportal/model/GenesetMolecularData.java rename to src/main/java/org/cbioportal/legacy/model/GenesetMolecularData.java index 16fb8b7161a..25e28a3dd87 100644 --- a/src/main/java/org/cbioportal/model/GenesetMolecularData.java +++ b/src/main/java/org/cbioportal/legacy/model/GenesetMolecularData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GeneticEntity.java b/src/main/java/org/cbioportal/legacy/model/GeneticEntity.java similarity index 97% rename from src/main/java/org/cbioportal/model/GeneticEntity.java rename to src/main/java/org/cbioportal/legacy/model/GeneticEntity.java index f6bf9335db7..97c25b8d990 100644 --- a/src/main/java/org/cbioportal/model/GeneticEntity.java +++ b/src/main/java/org/cbioportal/legacy/model/GeneticEntity.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenomicDataBin.java b/src/main/java/org/cbioportal/legacy/model/GenomicDataBin.java similarity index 93% rename from src/main/java/org/cbioportal/model/GenomicDataBin.java rename to src/main/java/org/cbioportal/legacy/model/GenomicDataBin.java index f177bd8c35c..6df471cc2f9 100644 --- a/src/main/java/org/cbioportal/model/GenomicDataBin.java +++ b/src/main/java/org/cbioportal/legacy/model/GenomicDataBin.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/GenomicDataCount.java b/src/main/java/org/cbioportal/legacy/model/GenomicDataCount.java similarity index 97% rename from src/main/java/org/cbioportal/model/GenomicDataCount.java rename to src/main/java/org/cbioportal/legacy/model/GenomicDataCount.java index f86fda5bc8f..b8f10bb056c 100644 --- a/src/main/java/org/cbioportal/model/GenomicDataCount.java +++ b/src/main/java/org/cbioportal/legacy/model/GenomicDataCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/GenomicDataCountItem.java b/src/main/java/org/cbioportal/legacy/model/GenomicDataCountItem.java similarity index 96% rename from src/main/java/org/cbioportal/model/GenomicDataCountItem.java rename to src/main/java/org/cbioportal/legacy/model/GenomicDataCountItem.java index a2123a9386c..dd546a6f7b4 100644 --- a/src/main/java/org/cbioportal/model/GenomicDataCountItem.java +++ b/src/main/java/org/cbioportal/legacy/model/GenomicDataCountItem.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/GenomicEnrichment.java b/src/main/java/org/cbioportal/legacy/model/GenomicEnrichment.java similarity index 95% rename from src/main/java/org/cbioportal/model/GenomicEnrichment.java rename to src/main/java/org/cbioportal/legacy/model/GenomicEnrichment.java index a4442cf1cf1..a7c8f999b60 100644 --- a/src/main/java/org/cbioportal/model/GenomicEnrichment.java +++ b/src/main/java/org/cbioportal/legacy/model/GenomicEnrichment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/Gistic.java b/src/main/java/org/cbioportal/legacy/model/Gistic.java similarity index 98% rename from src/main/java/org/cbioportal/model/Gistic.java rename to src/main/java/org/cbioportal/legacy/model/Gistic.java index 66a8646e2d3..0acc1368137 100644 --- a/src/main/java/org/cbioportal/model/Gistic.java +++ b/src/main/java/org/cbioportal/legacy/model/Gistic.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/GisticToGene.java b/src/main/java/org/cbioportal/legacy/model/GisticToGene.java similarity index 95% rename from src/main/java/org/cbioportal/model/GisticToGene.java rename to src/main/java/org/cbioportal/legacy/model/GisticToGene.java index 49593eedaf9..2ade673dd21 100644 --- a/src/main/java/org/cbioportal/model/GisticToGene.java +++ b/src/main/java/org/cbioportal/legacy/model/GisticToGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/GroupStatistics.java b/src/main/java/org/cbioportal/legacy/model/GroupStatistics.java similarity index 95% rename from src/main/java/org/cbioportal/model/GroupStatistics.java rename to src/main/java/org/cbioportal/legacy/model/GroupStatistics.java index df0950caf02..98b862d3dba 100644 --- a/src/main/java/org/cbioportal/model/GroupStatistics.java +++ b/src/main/java/org/cbioportal/legacy/model/GroupStatistics.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/Info.java b/src/main/java/org/cbioportal/legacy/model/Info.java similarity index 98% rename from src/main/java/org/cbioportal/model/Info.java rename to src/main/java/org/cbioportal/legacy/model/Info.java index beee09b26d7..443ead4e5db 100644 --- a/src/main/java/org/cbioportal/model/Info.java +++ b/src/main/java/org/cbioportal/legacy/model/Info.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/MolecularAlteration.java b/src/main/java/org/cbioportal/legacy/model/MolecularAlteration.java similarity index 96% rename from src/main/java/org/cbioportal/model/MolecularAlteration.java rename to src/main/java/org/cbioportal/legacy/model/MolecularAlteration.java index 0728d8aebbf..a8096d96639 100644 --- a/src/main/java/org/cbioportal/model/MolecularAlteration.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularAlteration.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/MolecularData.java b/src/main/java/org/cbioportal/legacy/model/MolecularData.java similarity index 96% rename from src/main/java/org/cbioportal/model/MolecularData.java rename to src/main/java/org/cbioportal/legacy/model/MolecularData.java index 260f20d9e34..c9906b84983 100644 --- a/src/main/java/org/cbioportal/model/MolecularData.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/MolecularProfile.java b/src/main/java/org/cbioportal/legacy/model/MolecularProfile.java similarity index 99% rename from src/main/java/org/cbioportal/model/MolecularProfile.java rename to src/main/java/org/cbioportal/legacy/model/MolecularProfile.java index da172984a56..ace865909d9 100644 --- a/src/main/java/org/cbioportal/model/MolecularProfile.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularProfile.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/MolecularProfileCaseIdentifier.java b/src/main/java/org/cbioportal/legacy/model/MolecularProfileCaseIdentifier.java similarity index 98% rename from src/main/java/org/cbioportal/model/MolecularProfileCaseIdentifier.java rename to src/main/java/org/cbioportal/legacy/model/MolecularProfileCaseIdentifier.java index 743fee3cb0d..ebced8cc65d 100644 --- a/src/main/java/org/cbioportal/model/MolecularProfileCaseIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularProfileCaseIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/MolecularProfileSamples.java b/src/main/java/org/cbioportal/legacy/model/MolecularProfileSamples.java similarity index 97% rename from src/main/java/org/cbioportal/model/MolecularProfileSamples.java rename to src/main/java/org/cbioportal/legacy/model/MolecularProfileSamples.java index ee3b23b5c3c..1c020eb0d0f 100644 --- a/src/main/java/org/cbioportal/model/MolecularProfileSamples.java +++ b/src/main/java/org/cbioportal/legacy/model/MolecularProfileSamples.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/MrnaPercentile.java b/src/main/java/org/cbioportal/legacy/model/MrnaPercentile.java similarity index 97% rename from src/main/java/org/cbioportal/model/MrnaPercentile.java rename to src/main/java/org/cbioportal/legacy/model/MrnaPercentile.java index 278e65eb61b..9b100b308e2 100644 --- a/src/main/java/org/cbioportal/model/MrnaPercentile.java +++ b/src/main/java/org/cbioportal/legacy/model/MrnaPercentile.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/MutSig.java b/src/main/java/org/cbioportal/legacy/model/MutSig.java similarity index 98% rename from src/main/java/org/cbioportal/model/MutSig.java rename to src/main/java/org/cbioportal/legacy/model/MutSig.java index 1d60c06e801..cd52a34aaa1 100644 --- a/src/main/java/org/cbioportal/model/MutSig.java +++ b/src/main/java/org/cbioportal/legacy/model/MutSig.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/Mutation.java b/src/main/java/org/cbioportal/legacy/model/Mutation.java similarity index 99% rename from src/main/java/org/cbioportal/model/Mutation.java rename to src/main/java/org/cbioportal/legacy/model/Mutation.java index 3ddae915587..c0026638504 100644 --- a/src/main/java/org/cbioportal/model/Mutation.java +++ b/src/main/java/org/cbioportal/legacy/model/Mutation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonRawValue; import io.swagger.v3.oas.annotations.media.Schema; diff --git a/src/main/java/org/cbioportal/model/MutationCountByGene.java b/src/main/java/org/cbioportal/legacy/model/MutationCountByGene.java similarity index 77% rename from src/main/java/org/cbioportal/model/MutationCountByGene.java rename to src/main/java/org/cbioportal/legacy/model/MutationCountByGene.java index 0f949838fc1..d9ae4ee30e1 100644 --- a/src/main/java/org/cbioportal/model/MutationCountByGene.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationCountByGene.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/MutationCountByPosition.java b/src/main/java/org/cbioportal/legacy/model/MutationCountByPosition.java similarity index 96% rename from src/main/java/org/cbioportal/model/MutationCountByPosition.java rename to src/main/java/org/cbioportal/legacy/model/MutationCountByPosition.java index f92b2fb1d17..dae52601468 100644 --- a/src/main/java/org/cbioportal/model/MutationCountByPosition.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationCountByPosition.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/MutationEventType.java b/src/main/java/org/cbioportal/legacy/model/MutationEventType.java similarity index 98% rename from src/main/java/org/cbioportal/model/MutationEventType.java rename to src/main/java/org/cbioportal/legacy/model/MutationEventType.java index e1957f20e71..507d2bba2ba 100644 --- a/src/main/java/org/cbioportal/model/MutationEventType.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationEventType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum MutationEventType { diff --git a/src/main/java/org/cbioportal/model/MutationFilterOption.java b/src/main/java/org/cbioportal/legacy/model/MutationFilterOption.java similarity index 92% rename from src/main/java/org/cbioportal/model/MutationFilterOption.java rename to src/main/java/org/cbioportal/legacy/model/MutationFilterOption.java index fd83da4f051..c846da87fd8 100644 --- a/src/main/java/org/cbioportal/model/MutationFilterOption.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationFilterOption.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum MutationFilterOption { MUTATED("Mutated"), // Samples that have mutations diff --git a/src/main/java/org/cbioportal/model/MutationSpectrum.java b/src/main/java/org/cbioportal/legacy/model/MutationSpectrum.java similarity index 98% rename from src/main/java/org/cbioportal/model/MutationSpectrum.java rename to src/main/java/org/cbioportal/legacy/model/MutationSpectrum.java index f130728b86d..277f9c61e9f 100644 --- a/src/main/java/org/cbioportal/model/MutationSpectrum.java +++ b/src/main/java/org/cbioportal/legacy/model/MutationSpectrum.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/NumericGeneMolecularData.java b/src/main/java/org/cbioportal/legacy/model/NumericGeneMolecularData.java similarity index 97% rename from src/main/java/org/cbioportal/model/NumericGeneMolecularData.java rename to src/main/java/org/cbioportal/legacy/model/NumericGeneMolecularData.java index 3e519807477..71e08c4a6a6 100644 --- a/src/main/java/org/cbioportal/model/NumericGeneMolecularData.java +++ b/src/main/java/org/cbioportal/legacy/model/NumericGeneMolecularData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/model/Patient.java b/src/main/java/org/cbioportal/legacy/model/Patient.java similarity index 97% rename from src/main/java/org/cbioportal/model/Patient.java rename to src/main/java/org/cbioportal/legacy/model/Patient.java index 4d2a2f1d9a6..18f906fd275 100644 --- a/src/main/java/org/cbioportal/model/Patient.java +++ b/src/main/java/org/cbioportal/legacy/model/Patient.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/PatientTreatment.java b/src/main/java/org/cbioportal/legacy/model/PatientTreatment.java similarity index 77% rename from src/main/java/org/cbioportal/model/PatientTreatment.java rename to src/main/java/org/cbioportal/legacy/model/PatientTreatment.java index c838d23777e..73393494319 100644 --- a/src/main/java/org/cbioportal/model/PatientTreatment.java +++ b/src/main/java/org/cbioportal/legacy/model/PatientTreatment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/PatientTreatmentReport.java b/src/main/java/org/cbioportal/legacy/model/PatientTreatmentReport.java similarity index 91% rename from src/main/java/org/cbioportal/model/PatientTreatmentReport.java rename to src/main/java/org/cbioportal/legacy/model/PatientTreatmentReport.java index d09a2276f06..240f0b44189 100644 --- a/src/main/java/org/cbioportal/model/PatientTreatmentReport.java +++ b/src/main/java/org/cbioportal/legacy/model/PatientTreatmentReport.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Collections; diff --git a/src/main/java/org/cbioportal/model/PatientTreatmentRow.java b/src/main/java/org/cbioportal/legacy/model/PatientTreatmentRow.java similarity index 97% rename from src/main/java/org/cbioportal/model/PatientTreatmentRow.java rename to src/main/java/org/cbioportal/legacy/model/PatientTreatmentRow.java index 6fc5f75395e..0e0f28dd8ea 100644 --- a/src/main/java/org/cbioportal/model/PatientTreatmentRow.java +++ b/src/main/java/org/cbioportal/legacy/model/PatientTreatmentRow.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/QueryElement.java b/src/main/java/org/cbioportal/legacy/model/QueryElement.java similarity index 91% rename from src/main/java/org/cbioportal/model/QueryElement.java rename to src/main/java/org/cbioportal/legacy/model/QueryElement.java index 0112edbdc44..7132d8db007 100644 --- a/src/main/java/org/cbioportal/model/QueryElement.java +++ b/src/main/java/org/cbioportal/legacy/model/QueryElement.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; /* QueryElement represents three types of behavior for a SQL statement in MyBatis mappers diff --git a/src/main/java/org/cbioportal/model/ReadPermission.java b/src/main/java/org/cbioportal/legacy/model/ReadPermission.java similarity index 78% rename from src/main/java/org/cbioportal/model/ReadPermission.java rename to src/main/java/org/cbioportal/legacy/model/ReadPermission.java index c215b4aa648..9721a17245d 100644 --- a/src/main/java/org/cbioportal/model/ReadPermission.java +++ b/src/main/java/org/cbioportal/legacy/model/ReadPermission.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public interface ReadPermission { public void setReadPermission(Boolean permission); diff --git a/src/main/java/org/cbioportal/model/ReferenceGenome.java b/src/main/java/org/cbioportal/legacy/model/ReferenceGenome.java similarity index 99% rename from src/main/java/org/cbioportal/model/ReferenceGenome.java rename to src/main/java/org/cbioportal/legacy/model/ReferenceGenome.java index 287b17272ef..95f640228a1 100644 --- a/src/main/java/org/cbioportal/model/ReferenceGenome.java +++ b/src/main/java/org/cbioportal/legacy/model/ReferenceGenome.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Date; diff --git a/src/main/java/org/cbioportal/model/ReferenceGenomeGene.java b/src/main/java/org/cbioportal/legacy/model/ReferenceGenomeGene.java similarity index 98% rename from src/main/java/org/cbioportal/model/ReferenceGenomeGene.java rename to src/main/java/org/cbioportal/legacy/model/ReferenceGenomeGene.java index 34ff3d82c9f..f76cb6fb26b 100644 --- a/src/main/java/org/cbioportal/model/ReferenceGenomeGene.java +++ b/src/main/java/org/cbioportal/legacy/model/ReferenceGenomeGene.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.net.Inet4Address; diff --git a/src/main/java/org/cbioportal/model/ResourceData.java b/src/main/java/org/cbioportal/legacy/model/ResourceData.java similarity index 97% rename from src/main/java/org/cbioportal/model/ResourceData.java rename to src/main/java/org/cbioportal/legacy/model/ResourceData.java index 243b86af47c..fdfb09812b7 100644 --- a/src/main/java/org/cbioportal/model/ResourceData.java +++ b/src/main/java/org/cbioportal/legacy/model/ResourceData.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/ResourceDefinition.java b/src/main/java/org/cbioportal/legacy/model/ResourceDefinition.java similarity index 97% rename from src/main/java/org/cbioportal/model/ResourceDefinition.java rename to src/main/java/org/cbioportal/legacy/model/ResourceDefinition.java index 73eacd6f287..1bffe659837 100644 --- a/src/main/java/org/cbioportal/model/ResourceDefinition.java +++ b/src/main/java/org/cbioportal/legacy/model/ResourceDefinition.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/ResourceType.java b/src/main/java/org/cbioportal/legacy/model/ResourceType.java similarity index 63% rename from src/main/java/org/cbioportal/model/ResourceType.java rename to src/main/java/org/cbioportal/legacy/model/ResourceType.java index 17a9a09df40..a2eb1d649e4 100644 --- a/src/main/java/org/cbioportal/model/ResourceType.java +++ b/src/main/java/org/cbioportal/legacy/model/ResourceType.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum ResourceType { STUDY, diff --git a/src/main/java/org/cbioportal/model/Sample.java b/src/main/java/org/cbioportal/legacy/model/Sample.java similarity index 98% rename from src/main/java/org/cbioportal/model/Sample.java rename to src/main/java/org/cbioportal/legacy/model/Sample.java index a3d72e955ce..ac8e2ba79d5 100644 --- a/src/main/java/org/cbioportal/model/Sample.java +++ b/src/main/java/org/cbioportal/legacy/model/Sample.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/SampleClinicalDataCollection.java b/src/main/java/org/cbioportal/legacy/model/SampleClinicalDataCollection.java similarity index 96% rename from src/main/java/org/cbioportal/model/SampleClinicalDataCollection.java rename to src/main/java/org/cbioportal/legacy/model/SampleClinicalDataCollection.java index c67d5277e8b..00b1c4e4df9 100644 --- a/src/main/java/org/cbioportal/model/SampleClinicalDataCollection.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleClinicalDataCollection.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Collections; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/model/SampleList.java b/src/main/java/org/cbioportal/legacy/model/SampleList.java similarity index 98% rename from src/main/java/org/cbioportal/model/SampleList.java rename to src/main/java/org/cbioportal/legacy/model/SampleList.java index bda4d2fc681..a9de3585687 100644 --- a/src/main/java/org/cbioportal/model/SampleList.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleList.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/SampleListToSampleId.java b/src/main/java/org/cbioportal/legacy/model/SampleListToSampleId.java similarity index 93% rename from src/main/java/org/cbioportal/model/SampleListToSampleId.java rename to src/main/java/org/cbioportal/legacy/model/SampleListToSampleId.java index bfbdb9f548b..a4110199bcd 100644 --- a/src/main/java/org/cbioportal/model/SampleListToSampleId.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleListToSampleId.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/SampleTreatment.java b/src/main/java/org/cbioportal/legacy/model/SampleTreatment.java similarity index 71% rename from src/main/java/org/cbioportal/model/SampleTreatment.java rename to src/main/java/org/cbioportal/legacy/model/SampleTreatment.java index edf9ef7541a..5dfacd6075f 100644 --- a/src/main/java/org/cbioportal/model/SampleTreatment.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleTreatment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public record SampleTreatment(String treatment, int preSampleCount, int postSampleCount) { } diff --git a/src/main/java/org/cbioportal/model/SampleTreatmentReport.java b/src/main/java/org/cbioportal/legacy/model/SampleTreatmentReport.java similarity index 78% rename from src/main/java/org/cbioportal/model/SampleTreatmentReport.java rename to src/main/java/org/cbioportal/legacy/model/SampleTreatmentReport.java index 12cf93f4fa6..60ac34247d3 100644 --- a/src/main/java/org/cbioportal/model/SampleTreatmentReport.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleTreatmentReport.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Collection; diff --git a/src/main/java/org/cbioportal/model/SampleTreatmentRow.java b/src/main/java/org/cbioportal/legacy/model/SampleTreatmentRow.java similarity index 98% rename from src/main/java/org/cbioportal/model/SampleTreatmentRow.java rename to src/main/java/org/cbioportal/legacy/model/SampleTreatmentRow.java index ff3c56693c9..0feef887361 100644 --- a/src/main/java/org/cbioportal/model/SampleTreatmentRow.java +++ b/src/main/java/org/cbioportal/legacy/model/SampleTreatmentRow.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/StructuralVariant.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariant.java similarity index 99% rename from src/main/java/org/cbioportal/model/StructuralVariant.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariant.java index 3c803a1b337..9c8a4151ffc 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariant.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariant.java @@ -21,11 +21,11 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.*; import io.swagger.v3.oas.annotations.media.Schema; -import org.cbioportal.model.UniqueKeyBase; +import org.cbioportal.legacy.model.UniqueKeyBase; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/StructuralVariantFilterQuery.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariantFilterQuery.java similarity index 95% rename from src/main/java/org/cbioportal/model/StructuralVariantFilterQuery.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariantFilterQuery.java index 0b857f2367a..cddf930357f 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariantFilterQuery.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariantFilterQuery.java @@ -1,6 +1,6 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import org.springframework.lang.Nullable; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/StructuralVariantGeneSubQuery.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariantGeneSubQuery.java similarity index 98% rename from src/main/java/org/cbioportal/model/StructuralVariantGeneSubQuery.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariantGeneSubQuery.java index 224ba6bec2a..a0454de9033 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariantGeneSubQuery.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariantGeneSubQuery.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import com.fasterxml.jackson.annotation.JsonIgnore; import org.springframework.lang.Nullable; diff --git a/src/main/java/org/cbioportal/model/StructuralVariantQuery.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariantQuery.java similarity index 96% rename from src/main/java/org/cbioportal/model/StructuralVariantQuery.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariantQuery.java index 6dc8856869e..fe34e3dd0ef 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariantQuery.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariantQuery.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.Valid; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/StructuralVariantSpecialValue.java b/src/main/java/org/cbioportal/legacy/model/StructuralVariantSpecialValue.java similarity index 80% rename from src/main/java/org/cbioportal/model/StructuralVariantSpecialValue.java rename to src/main/java/org/cbioportal/legacy/model/StructuralVariantSpecialValue.java index 8af29b9fd75..8a165e03928 100644 --- a/src/main/java/org/cbioportal/model/StructuralVariantSpecialValue.java +++ b/src/main/java/org/cbioportal/legacy/model/StructuralVariantSpecialValue.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum StructuralVariantSpecialValue { diff --git a/src/main/java/org/cbioportal/model/StudyViewFilterContext.java b/src/main/java/org/cbioportal/legacy/model/StudyViewFilterContext.java similarity index 55% rename from src/main/java/org/cbioportal/model/StudyViewFilterContext.java rename to src/main/java/org/cbioportal/legacy/model/StudyViewFilterContext.java index e23e5f7d9d4..22406ecd128 100644 --- a/src/main/java/org/cbioportal/model/StudyViewFilterContext.java +++ b/src/main/java/org/cbioportal/legacy/model/StudyViewFilterContext.java @@ -1,7 +1,7 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import java.util.List; diff --git a/src/main/java/org/cbioportal/model/StudyViewStructuralVariantFilter.java b/src/main/java/org/cbioportal/legacy/model/StudyViewStructuralVariantFilter.java similarity index 98% rename from src/main/java/org/cbioportal/model/StudyViewStructuralVariantFilter.java rename to src/main/java/org/cbioportal/legacy/model/StudyViewStructuralVariantFilter.java index d4ae0879873..41300c91961 100644 --- a/src/main/java/org/cbioportal/model/StudyViewStructuralVariantFilter.java +++ b/src/main/java/org/cbioportal/legacy/model/StudyViewStructuralVariantFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.AssertTrue; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/TableTimestampPair.java b/src/main/java/org/cbioportal/legacy/model/TableTimestampPair.java similarity index 93% rename from src/main/java/org/cbioportal/model/TableTimestampPair.java rename to src/main/java/org/cbioportal/legacy/model/TableTimestampPair.java index 1587bfc8e85..6bc8e3c1c5e 100644 --- a/src/main/java/org/cbioportal/model/TableTimestampPair.java +++ b/src/main/java/org/cbioportal/legacy/model/TableTimestampPair.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import jakarta.validation.constraints.NotNull; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/TemporalRelation.java b/src/main/java/org/cbioportal/legacy/model/TemporalRelation.java similarity index 58% rename from src/main/java/org/cbioportal/model/TemporalRelation.java rename to src/main/java/org/cbioportal/legacy/model/TemporalRelation.java index 8c204c46208..66448ed3ab0 100644 --- a/src/main/java/org/cbioportal/model/TemporalRelation.java +++ b/src/main/java/org/cbioportal/legacy/model/TemporalRelation.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; public enum TemporalRelation { Pre, diff --git a/src/main/java/org/cbioportal/model/Treatment.java b/src/main/java/org/cbioportal/legacy/model/Treatment.java similarity index 97% rename from src/main/java/org/cbioportal/model/Treatment.java rename to src/main/java/org/cbioportal/legacy/model/Treatment.java index 746d88dcebe..c40c8377efb 100644 --- a/src/main/java/org/cbioportal/model/Treatment.java +++ b/src/main/java/org/cbioportal/legacy/model/Treatment.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/model/TreatmentRow.java b/src/main/java/org/cbioportal/legacy/model/TreatmentRow.java similarity index 74% rename from src/main/java/org/cbioportal/model/TreatmentRow.java rename to src/main/java/org/cbioportal/legacy/model/TreatmentRow.java index 32662b7222c..f19152585ac 100644 --- a/src/main/java/org/cbioportal/model/TreatmentRow.java +++ b/src/main/java/org/cbioportal/legacy/model/TreatmentRow.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.util.Set; diff --git a/src/main/java/org/cbioportal/model/TypeOfCancer.java b/src/main/java/org/cbioportal/legacy/model/TypeOfCancer.java similarity index 96% rename from src/main/java/org/cbioportal/model/TypeOfCancer.java rename to src/main/java/org/cbioportal/legacy/model/TypeOfCancer.java index 6c564c3e37a..3f706f5e367 100644 --- a/src/main/java/org/cbioportal/model/TypeOfCancer.java +++ b/src/main/java/org/cbioportal/legacy/model/TypeOfCancer.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/UniqueKeyBase.java b/src/main/java/org/cbioportal/legacy/model/UniqueKeyBase.java similarity index 93% rename from src/main/java/org/cbioportal/model/UniqueKeyBase.java rename to src/main/java/org/cbioportal/legacy/model/UniqueKeyBase.java index 33198b81f3b..7b079b4f3db 100644 --- a/src/main/java/org/cbioportal/model/UniqueKeyBase.java +++ b/src/main/java/org/cbioportal/legacy/model/UniqueKeyBase.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/User.java b/src/main/java/org/cbioportal/legacy/model/User.java similarity index 98% rename from src/main/java/org/cbioportal/model/User.java rename to src/main/java/org/cbioportal/legacy/model/User.java index 646e8cac647..481b41cd851 100644 --- a/src/main/java/org/cbioportal/model/User.java +++ b/src/main/java/org/cbioportal/legacy/model/User.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/UserAuthorities.java b/src/main/java/org/cbioportal/legacy/model/UserAuthorities.java similarity index 98% rename from src/main/java/org/cbioportal/model/UserAuthorities.java rename to src/main/java/org/cbioportal/legacy/model/UserAuthorities.java index d8d4e641f6c..2bc42b84c88 100644 --- a/src/main/java/org/cbioportal/model/UserAuthorities.java +++ b/src/main/java/org/cbioportal/legacy/model/UserAuthorities.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.model; +package org.cbioportal.legacy.model; // imports import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/VariantCount.java b/src/main/java/org/cbioportal/legacy/model/VariantCount.java similarity index 97% rename from src/main/java/org/cbioportal/model/VariantCount.java rename to src/main/java/org/cbioportal/legacy/model/VariantCount.java index fdc43b721cb..f6e8b5dcbe0 100644 --- a/src/main/java/org/cbioportal/model/VariantCount.java +++ b/src/main/java/org/cbioportal/legacy/model/VariantCount.java @@ -1,4 +1,4 @@ -package org.cbioportal.model; +package org.cbioportal.legacy.model; import java.io.Serializable; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/model/meta/BaseMeta.java b/src/main/java/org/cbioportal/legacy/model/meta/BaseMeta.java similarity index 87% rename from src/main/java/org/cbioportal/model/meta/BaseMeta.java rename to src/main/java/org/cbioportal/legacy/model/meta/BaseMeta.java index dac0a7caba4..81102101bc4 100644 --- a/src/main/java/org/cbioportal/model/meta/BaseMeta.java +++ b/src/main/java/org/cbioportal/legacy/model/meta/BaseMeta.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.meta; +package org.cbioportal.legacy.model.meta; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/model/meta/GenericAssayMeta.java b/src/main/java/org/cbioportal/legacy/model/meta/GenericAssayMeta.java similarity index 98% rename from src/main/java/org/cbioportal/model/meta/GenericAssayMeta.java rename to src/main/java/org/cbioportal/legacy/model/meta/GenericAssayMeta.java index 2f22fd9b5e0..2a94c66498b 100644 --- a/src/main/java/org/cbioportal/model/meta/GenericAssayMeta.java +++ b/src/main/java/org/cbioportal/legacy/model/meta/GenericAssayMeta.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.meta; +package org.cbioportal.legacy.model.meta; import java.io.Serializable; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/model/meta/MutationMeta.java b/src/main/java/org/cbioportal/legacy/model/meta/MutationMeta.java similarity index 86% rename from src/main/java/org/cbioportal/model/meta/MutationMeta.java rename to src/main/java/org/cbioportal/legacy/model/meta/MutationMeta.java index bb9f82a83a0..49a5226f950 100644 --- a/src/main/java/org/cbioportal/model/meta/MutationMeta.java +++ b/src/main/java/org/cbioportal/legacy/model/meta/MutationMeta.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.meta; +package org.cbioportal.legacy.model.meta; public class MutationMeta extends BaseMeta { diff --git a/src/main/java/org/cbioportal/model/util/QueryElement.java b/src/main/java/org/cbioportal/legacy/model/util/QueryElement.java similarity index 57% rename from src/main/java/org/cbioportal/model/util/QueryElement.java rename to src/main/java/org/cbioportal/legacy/model/util/QueryElement.java index d7b78a96de2..2948f6b81e1 100644 --- a/src/main/java/org/cbioportal/model/util/QueryElement.java +++ b/src/main/java/org/cbioportal/legacy/model/util/QueryElement.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.util; +package org.cbioportal.legacy.model.util; public enum QueryElement { INACTIVE, ACTIVE, PASS diff --git a/src/main/java/org/cbioportal/model/util/Select.java b/src/main/java/org/cbioportal/legacy/model/util/Select.java similarity index 98% rename from src/main/java/org/cbioportal/model/util/Select.java rename to src/main/java/org/cbioportal/legacy/model/util/Select.java index e10f2c0ebda..bc0e320afd2 100644 --- a/src/main/java/org/cbioportal/model/util/Select.java +++ b/src/main/java/org/cbioportal/legacy/model/util/Select.java @@ -1,4 +1,4 @@ -package org.cbioportal.model.util; +package org.cbioportal.legacy.model.util; import java.util.*; import java.util.function.Function; diff --git a/src/main/java/org/cbioportal/persistence/AlterationDriverAnnotationRepository.java b/src/main/java/org/cbioportal/legacy/persistence/AlterationDriverAnnotationRepository.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/AlterationDriverAnnotationRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/AlterationDriverAnnotationRepository.java index d89b33ed9b6..2a2d55c8f0e 100644 --- a/src/main/java/org/cbioportal/persistence/AlterationDriverAnnotationRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/AlterationDriverAnnotationRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/AlterationRepository.java b/src/main/java/org/cbioportal/legacy/persistence/AlterationRepository.java similarity index 82% rename from src/main/java/org/cbioportal/persistence/AlterationRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/AlterationRepository.java index b8f436eea09..00e83d942d4 100644 --- a/src/main/java/org/cbioportal/persistence/AlterationRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/AlterationRepository.java @@ -1,7 +1,11 @@ -package org.cbioportal.persistence; - -import org.cbioportal.model.*; -import org.cbioportal.model.util.Select; +package org.cbioportal.legacy.persistence; + +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; import org.springframework.cache.annotation.Cacheable; import java.util.List; @@ -31,7 +35,7 @@ List getPatientCnaGeneCounts(Set getSampleStructuralVariantCounts(Set molecularProfileCaseIdentifiers, - AlterationFilter alterationFilter); + AlterationFilter alterationFilter); @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()") List getPatientStructuralVariantCounts(Set molecularProfileCaseIdentifiers, diff --git a/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java b/src/main/java/org/cbioportal/legacy/persistence/CacheEnabledConfig.java similarity index 97% rename from src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/CacheEnabledConfig.java index 45b22f5bbf4..056810fb731 100644 --- a/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/CacheEnabledConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import jakarta.annotation.PostConstruct; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/persistence/CancerTypeRepository.java b/src/main/java/org/cbioportal/legacy/persistence/CancerTypeRepository.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/CancerTypeRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/CancerTypeRepository.java index a670d074007..667bdd9beaa 100644 --- a/src/main/java/org/cbioportal/persistence/CancerTypeRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/CancerTypeRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/ClinicalAttributeRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ClinicalAttributeRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/ClinicalAttributeRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ClinicalAttributeRepository.java index aa7c8ede12f..4828ad541e7 100644 --- a/src/main/java/org/cbioportal/persistence/ClinicalAttributeRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ClinicalAttributeRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/ClinicalDataRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ClinicalDataRepository.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/ClinicalDataRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ClinicalDataRepository.java index ed320908d2e..305455aec13 100644 --- a/src/main/java/org/cbioportal/persistence/ClinicalDataRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ClinicalDataRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/ClinicalEventRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ClinicalEventRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/ClinicalEventRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ClinicalEventRepository.java index bf6d31470c9..bbdd597a142 100644 --- a/src/main/java/org/cbioportal/persistence/ClinicalEventRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ClinicalEventRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/CopyNumberSegmentRepository.java b/src/main/java/org/cbioportal/legacy/persistence/CopyNumberSegmentRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/CopyNumberSegmentRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/CopyNumberSegmentRepository.java index 3618de022df..03a92ef60f4 100644 --- a/src/main/java/org/cbioportal/persistence/CopyNumberSegmentRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/CopyNumberSegmentRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/CosmicCountRepository.java b/src/main/java/org/cbioportal/legacy/persistence/CosmicCountRepository.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/CosmicCountRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/CosmicCountRepository.java index c45133c25e8..4f3a7ec7e30 100644 --- a/src/main/java/org/cbioportal/persistence/CosmicCountRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/CosmicCountRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.CosmicMutation; +import org.cbioportal.legacy.model.CosmicMutation; import org.springframework.cache.annotation.Cacheable; public interface CosmicCountRepository { diff --git a/src/main/java/org/cbioportal/persistence/DataAccessTokenRepository.java b/src/main/java/org/cbioportal/legacy/persistence/DataAccessTokenRepository.java similarity index 79% rename from src/main/java/org/cbioportal/persistence/DataAccessTokenRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/DataAccessTokenRepository.java index ddd46236a9e..47d4dd92a06 100644 --- a/src/main/java/org/cbioportal/persistence/DataAccessTokenRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/DataAccessTokenRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.DataAccessToken; +import org.cbioportal.legacy.model.DataAccessToken; import java.util.List; public interface DataAccessTokenRepository { diff --git a/src/main/java/org/cbioportal/persistence/DiscreteCopyNumberRepository.java b/src/main/java/org/cbioportal/legacy/persistence/DiscreteCopyNumberRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/DiscreteCopyNumberRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/DiscreteCopyNumberRepository.java index ae07f0e3f2f..c2ef1a85434 100644 --- a/src/main/java/org/cbioportal/persistence/DiscreteCopyNumberRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/DiscreteCopyNumberRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/GenePanelRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GenePanelRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/GenePanelRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GenePanelRepository.java index 49817ff86be..d8fdd05d52a 100644 --- a/src/main/java/org/cbioportal/persistence/GenePanelRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GenePanelRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/GeneRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GeneRepository.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/GeneRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GeneRepository.java index a0bdd4b5715..4a5a14cc62f 100644 --- a/src/main/java/org/cbioportal/persistence/GeneRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GeneRepository.java @@ -29,11 +29,11 @@ * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . */ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneAlias; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneAlias; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/GenericAssayRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GenericAssayRepository.java similarity index 81% rename from src/main/java/org/cbioportal/persistence/GenericAssayRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GenericAssayRepository.java index 27f8f1f8964..3c8c10e724a 100644 --- a/src/main/java/org/cbioportal/persistence/GenericAssayRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GenericAssayRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; import org.springframework.cache.annotation.Cacheable; public interface GenericAssayRepository { diff --git a/src/main/java/org/cbioportal/persistence/GenesetHierarchyRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GenesetHierarchyRepository.java similarity index 82% rename from src/main/java/org/cbioportal/persistence/GenesetHierarchyRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GenesetHierarchyRepository.java index 5db19320acf..c8157388660 100644 --- a/src/main/java/org/cbioportal/persistence/GenesetHierarchyRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GenesetHierarchyRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/GenesetRepository.java b/src/main/java/org/cbioportal/legacy/persistence/GenesetRepository.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/GenesetRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/GenesetRepository.java index dcd73779403..6de723c09cb 100644 --- a/src/main/java/org/cbioportal/persistence/GenesetRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/GenesetRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/MolecularDataRepository.java b/src/main/java/org/cbioportal/legacy/persistence/MolecularDataRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/MolecularDataRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/MolecularDataRepository.java index 5c2f8a9600a..28bdc404e44 100644 --- a/src/main/java/org/cbioportal/persistence/MolecularDataRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/MolecularDataRepository.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; import java.util.Map; import java.util.Set; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; import org.springframework.cache.annotation.Cacheable; -import org.cbioportal.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.MolecularProfileSamples; public interface MolecularDataRepository { diff --git a/src/main/java/org/cbioportal/persistence/MolecularProfileRepository.java b/src/main/java/org/cbioportal/legacy/persistence/MolecularProfileRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/MolecularProfileRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/MolecularProfileRepository.java index 41cb01bc8ec..bffe6f952d7 100644 --- a/src/main/java/org/cbioportal/persistence/MolecularProfileRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/MolecularProfileRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/MutationRepository.java b/src/main/java/org/cbioportal/legacy/persistence/MutationRepository.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/MutationRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/MutationRepository.java index ffcef1b6f0c..78867ccfefc 100644 --- a/src/main/java/org/cbioportal/persistence/MutationRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/MutationRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/PatientRepository.java b/src/main/java/org/cbioportal/legacy/persistence/PatientRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/PatientRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/PatientRepository.java index 54c92024b79..5a881416792 100644 --- a/src/main/java/org/cbioportal/persistence/PatientRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/PatientRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/PersistenceConstants.java b/src/main/java/org/cbioportal/legacy/persistence/PersistenceConstants.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/PersistenceConstants.java rename to src/main/java/org/cbioportal/legacy/persistence/PersistenceConstants.java index c5b3124a7ef..c141621346f 100644 --- a/src/main/java/org/cbioportal/persistence/PersistenceConstants.java +++ b/src/main/java/org/cbioportal/legacy/persistence/PersistenceConstants.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; public class PersistenceConstants { diff --git a/src/main/java/org/cbioportal/persistence/ReferenceGenomeGeneRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ReferenceGenomeGeneRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/ReferenceGenomeGeneRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ReferenceGenomeGeneRepository.java index 7b906fed60a..a4aa1d7e66b 100644 --- a/src/main/java/org/cbioportal/persistence/ReferenceGenomeGeneRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ReferenceGenomeGeneRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.ReferenceGenomeGene; import java.util.List; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/ResourceDataRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ResourceDataRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/ResourceDataRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ResourceDataRepository.java index c93898dd2ce..29b84fe7eca 100644 --- a/src/main/java/org/cbioportal/persistence/ResourceDataRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ResourceDataRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.ResourceData; +import org.cbioportal.legacy.model.ResourceData; import org.springframework.cache.annotation.Cacheable; public interface ResourceDataRepository { diff --git a/src/main/java/org/cbioportal/persistence/ResourceDefinitionRepository.java b/src/main/java/org/cbioportal/legacy/persistence/ResourceDefinitionRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/ResourceDefinitionRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/ResourceDefinitionRepository.java index 1f248d5775c..248689c8a25 100644 --- a/src/main/java/org/cbioportal/persistence/ResourceDefinitionRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/ResourceDefinitionRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.ResourceDefinition; +import org.cbioportal.legacy.model.ResourceDefinition; import org.springframework.cache.annotation.Cacheable; public interface ResourceDefinitionRepository { diff --git a/src/main/java/org/cbioportal/persistence/SampleListRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SampleListRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/SampleListRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SampleListRepository.java index 0c0e7745d8a..5faae73b52d 100644 --- a/src/main/java/org/cbioportal/persistence/SampleListRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SampleListRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/SampleRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SampleRepository.java similarity index 96% rename from src/main/java/org/cbioportal/persistence/SampleRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SampleRepository.java index 8ce831fe951..97834540aa2 100644 --- a/src/main/java/org/cbioportal/persistence/SampleRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SampleRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/SecurityRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SecurityRepository.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/SecurityRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SecurityRepository.java index 68ff9f1a3a5..111cadd2fe4 100644 --- a/src/main/java/org/cbioportal/persistence/SecurityRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SecurityRepository.java @@ -30,13 +30,13 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; // imports import java.util.Set; -import org.cbioportal.model.User; -import org.cbioportal.model.UserAuthorities; +import org.cbioportal.legacy.model.User; +import org.cbioportal.legacy.model.UserAuthorities; /** * Interface to use to retrieve diff --git a/src/main/java/org/cbioportal/persistence/SignificantCopyNumberRegionRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SignificantCopyNumberRegionRepository.java similarity index 81% rename from src/main/java/org/cbioportal/persistence/SignificantCopyNumberRegionRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SignificantCopyNumberRegionRepository.java index 4e5fa225ce0..92c753b1487 100644 --- a/src/main/java/org/cbioportal/persistence/SignificantCopyNumberRegionRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SignificantCopyNumberRegionRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/SignificantlyMutatedGeneRepository.java b/src/main/java/org/cbioportal/legacy/persistence/SignificantlyMutatedGeneRepository.java similarity index 82% rename from src/main/java/org/cbioportal/persistence/SignificantlyMutatedGeneRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/SignificantlyMutatedGeneRepository.java index 4c20a80e31d..c220b92f9b8 100644 --- a/src/main/java/org/cbioportal/persistence/SignificantlyMutatedGeneRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/SignificantlyMutatedGeneRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/StaticDataTimeStampRepository.java b/src/main/java/org/cbioportal/legacy/persistence/StaticDataTimeStampRepository.java similarity index 62% rename from src/main/java/org/cbioportal/persistence/StaticDataTimeStampRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/StaticDataTimeStampRepository.java index 616d5e158d5..aae13dd31e9 100644 --- a/src/main/java/org/cbioportal/persistence/StaticDataTimeStampRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/StaticDataTimeStampRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.TableTimestampPair; +import org.cbioportal.legacy.model.TableTimestampPair; import java.util.Date; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/StructuralVariantRepository.java b/src/main/java/org/cbioportal/legacy/persistence/StructuralVariantRepository.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/StructuralVariantRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/StructuralVariantRepository.java index 8818779e193..f3ac9db08dc 100644 --- a/src/main/java/org/cbioportal/persistence/StructuralVariantRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/StructuralVariantRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; import java.util.List; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; import org.springframework.cache.annotation.Cacheable; public interface StructuralVariantRepository { diff --git a/src/main/java/org/cbioportal/persistence/StudyRepository.java b/src/main/java/org/cbioportal/legacy/persistence/StudyRepository.java similarity index 88% rename from src/main/java/org/cbioportal/persistence/StudyRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/StudyRepository.java index 875250b5b23..4efa5d6a8eb 100644 --- a/src/main/java/org/cbioportal/persistence/StudyRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/StudyRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/legacy/persistence/StudyViewRepository.java similarity index 74% rename from src/main/java/org/cbioportal/persistence/StudyViewRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/StudyViewRepository.java index c39158ad433..dbda846e43e 100644 --- a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/StudyViewRepository.java @@ -1,26 +1,26 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.PatientTreatment; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatment; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.PatientTreatment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatment; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/persistence/TreatmentRepository.java b/src/main/java/org/cbioportal/legacy/persistence/TreatmentRepository.java similarity index 88% rename from src/main/java/org/cbioportal/persistence/TreatmentRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/TreatmentRepository.java index bc2e0705b16..60e1257a447 100644 --- a/src/main/java/org/cbioportal/persistence/TreatmentRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/TreatmentRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.Treatment; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.Treatment; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/VariantCountRepository.java b/src/main/java/org/cbioportal/legacy/persistence/VariantCountRepository.java similarity index 81% rename from src/main/java/org/cbioportal/persistence/VariantCountRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/VariantCountRepository.java index b3f6e078cbd..bd8b953a4a5 100644 --- a/src/main/java/org/cbioportal/persistence/VariantCountRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/VariantCountRepository.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence; +package org.cbioportal.legacy.persistence; -import org.cbioportal.model.VariantCount; +import org.cbioportal.legacy.model.VariantCount; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapBuilder.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapBuilder.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapBuilder.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapBuilder.java index ed189f01c7d..e1ea290ede9 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapBuilder.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapBuilder.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; import java.util.function.Function; import java.util.stream.Collectors; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.EntityType; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; -import org.cbioportal.persistence.GenericAssayRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.StudyRepository; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.persistence.GenericAssayRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.StudyRepository; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapUtil.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapUtil.java similarity index 55% rename from src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapUtil.java index f476c301186..89237b721e9 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/CacheMapUtil.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; import java.util.Map; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/InactiveCacheMapUtil.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/InactiveCacheMapUtil.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/cachemaputil/InactiveCacheMapUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/InactiveCacheMapUtil.java index 8213ede2aaf..b7b57c6c717 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/InactiveCacheMapUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/InactiveCacheMapUtil.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/SpringManagedCacheMapUtil.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/SpringManagedCacheMapUtil.java index c492b2400b0..0325dd78f74 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/SpringManagedCacheMapUtil.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; import jakarta.annotation.PostConstruct; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/StaticRefCacheMapUtil.java b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/StaticRefCacheMapUtil.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/cachemaputil/StaticRefCacheMapUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/cachemaputil/StaticRefCacheMapUtil.java index 48d07e0bff1..c9af82f0b31 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/StaticRefCacheMapUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/cachemaputil/StaticRefCacheMapUtil.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.cachemaputil; +package org.cbioportal.legacy.persistence.cachemaputil; import jakarta.annotation.PostConstruct; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/persistence/config/EhCacheConfig.java b/src/main/java/org/cbioportal/legacy/persistence/config/EhCacheConfig.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/config/EhCacheConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/config/EhCacheConfig.java index 15c7d10f76b..2b64da7e2ca 100644 --- a/src/main/java/org/cbioportal/persistence/config/EhCacheConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/config/EhCacheConfig.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.config; +package org.cbioportal.legacy.persistence.config; -import org.cbioportal.persistence.util.CustomEhcachingProvider; -import org.cbioportal.persistence.util.CustomKeyGenerator; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.util.CustomEhcachingProvider; +import org.cbioportal.legacy.persistence.util.CustomKeyGenerator; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.cache.CacheManager; import org.springframework.cache.annotation.CachingConfigurerSupport; import org.springframework.cache.annotation.EnableCaching; diff --git a/src/main/java/org/cbioportal/persistence/config/RedisConfig.java b/src/main/java/org/cbioportal/legacy/persistence/config/RedisConfig.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/config/RedisConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/config/RedisConfig.java index 99c225a33bd..4333b8661d5 100644 --- a/src/main/java/org/cbioportal/persistence/config/RedisConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/config/RedisConfig.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.config; +package org.cbioportal.legacy.persistence.config; -import org.cbioportal.persistence.util.CustomKeyGenerator; -import org.cbioportal.persistence.util.CustomRedisCachingProvider; -import org.cbioportal.persistence.util.LoggingCacheErrorHandler; +import org.cbioportal.legacy.persistence.util.CustomKeyGenerator; +import org.cbioportal.legacy.persistence.util.CustomRedisCachingProvider; +import org.cbioportal.legacy.persistence.util.LoggingCacheErrorHandler; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.cache.CacheManager; diff --git a/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java b/src/main/java/org/cbioportal/legacy/persistence/enums/ClinicalAttributeDataType.java similarity index 85% rename from src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java rename to src/main/java/org/cbioportal/legacy/persistence/enums/ClinicalAttributeDataType.java index 591f67e117d..f91798a828a 100644 --- a/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java +++ b/src/main/java/org/cbioportal/legacy/persistence/enums/ClinicalAttributeDataType.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.enums; +package org.cbioportal.legacy.persistence.enums; public enum ClinicalAttributeDataType { CATEGORICAL("CATEGORICAL"), diff --git a/src/main/java/org/cbioportal/persistence/enums/DataSource.java b/src/main/java/org/cbioportal/legacy/persistence/enums/DataSource.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/enums/DataSource.java rename to src/main/java/org/cbioportal/legacy/persistence/enums/DataSource.java index 09b81b79edb..4a9eecb1fdd 100644 --- a/src/main/java/org/cbioportal/persistence/enums/DataSource.java +++ b/src/main/java/org/cbioportal/legacy/persistence/enums/DataSource.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.enums; +package org.cbioportal.legacy.persistence.enums; public enum DataSource { PATIENT("PATIENT"),SAMPLE("SAMPLE"); diff --git a/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java b/src/main/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelper.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java rename to src/main/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelper.java index 1d8f63a55f2..420bf4de630 100644 --- a/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelper.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.helper; +package org.cbioportal.legacy.persistence.helper; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; import org.springframework.lang.NonNull; import org.springframework.lang.Nullable; diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelper.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java rename to src/main/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelper.java index d88956864af..cd9c75ba4e4 100644 --- a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelper.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.helper; +package org.cbioportal.legacy.persistence.helper; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.persistence.enums.DataSource; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.CategorizedGenericAssayDataCountFilter; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.persistence.enums.DataSource; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.CategorizedGenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.lang.NonNull; import org.springframework.lang.Nullable; diff --git a/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java b/src/main/java/org/cbioportal/legacy/persistence/model/SampleAcquisitionEventRecord.java similarity index 72% rename from src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java rename to src/main/java/org/cbioportal/legacy/persistence/model/SampleAcquisitionEventRecord.java index b02c24c7100..a0eddeb4eb9 100644 --- a/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java +++ b/src/main/java/org/cbioportal/legacy/persistence/model/SampleAcquisitionEventRecord.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.model; +package org.cbioportal.legacy.persistence.model; public record SampleAcquisitionEventRecord(String sampleId, String patientUniqueId, String cancerStudyId, int timeTaken) { } diff --git a/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java b/src/main/java/org/cbioportal/legacy/persistence/model/TreatmentRecord.java similarity index 68% rename from src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java rename to src/main/java/org/cbioportal/legacy/persistence/model/TreatmentRecord.java index aeeac35723b..54bad64fe84 100644 --- a/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java +++ b/src/main/java/org/cbioportal/legacy/persistence/model/TreatmentRecord.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.model; +package org.cbioportal.legacy.persistence.model; public record TreatmentRecord(String patientUniqueId, String treatment, int startTime, int stopTime) { } diff --git a/src/main/java/org/cbioportal/persistence/mybatis/AlterationCountsMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.java similarity index 96% rename from src/main/java/org/cbioportal/persistence/mybatis/AlterationCountsMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.java index 4b1461cdbb8..585efd73e58 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/AlterationCountsMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationCountsMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.java similarity index 69% rename from src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.java index 34b5a02eb05..8bfd91c9615 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import org.apache.ibatis.annotations.Param; -import org.cbioportal.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java similarity index 79% rename from src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java index 222336aac14..ffb087d8228 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.*; -import org.cbioportal.persistence.AlterationDriverAnnotationRepository; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.persistence.AlterationDriverAnnotationRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepository.java index a48b6476b59..4344b8da3ca 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepository.java @@ -1,17 +1,17 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.AlterationRepository; -import org.cbioportal.persistence.MolecularProfileRepository; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.AlterationRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.java similarity index 69% rename from src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.java index 4fbe328f514..7957f368b6f 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepository.java similarity index 73% rename from src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepository.java index 64cc83d3af3..70d62797edd 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.java index cfee6ac5933..4cdaf28d418 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepository.java index 58fbbba59a2..31d55612d22 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalAttributeRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.java index 50bb0c4e197..2e95cfa2409 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepository.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepository.java index 19cdde259fa..40be60a5a8c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepository.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalDataRepository; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalDataRepository; +import org.cbioportal.legacy.persistence.ClinicalAttributeRepository; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import org.springframework.util.Assert; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.java similarity index 85% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.java index d87b0e8467d..c983210b3fa 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepository.java index ef65f4fa879..0f09e58c567 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalEventRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalEventRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.java similarity index 82% rename from src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.java index 1a0878bd654..24d2df192c0 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java index 4e586ddb8c6..85da2187e46 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.java similarity index 57% rename from src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.java index bfa7dec8af9..e9c8787eb4e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CosmicMutation; +import org.cbioportal.legacy.model.CosmicMutation; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepository.java similarity index 73% rename from src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepository.java index 9c2612f6576..417ccbf0c8b 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import java.util.List; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.persistence.CosmicCountRepository; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.persistence.CosmicCountRepository; @Repository public class CosmicCountMyBatisRepository implements CosmicCountRepository { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.java index bdadadf7e83..9c7dd88f201 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.DataAccessToken; +import org.cbioportal.legacy.model.DataAccessToken; import java.util.List; public interface DataAccessTokenMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepository.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepository.java index e0e15bcd751..8689df346e6 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.DataAccessTokenRepository; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.java index ab2934e6496..e5ba6252215 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMapper.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java index fdde1d8d0c6..43e76412dff 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GeneMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMapper.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatis/GeneMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMapper.java index 79cc63318df..15330c13435 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GeneMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneAlias; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneAlias; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepository.java index abf41874294..e9fc0275e5e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneAlias; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GeneRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneAlias; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GeneRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenePanelMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/mybatis/GenePanelMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.java index 5d5d8371754..741fafa3b45 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenePanelMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepository.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepository.java index cd984b312f1..0c7c7002f9d 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepository.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenePanelRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenePanelRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.java index 08a2f175fdd..9321118fbee 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.HashMap; import java.util.List; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; public interface GenericAssayMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepository.java similarity index 90% rename from src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepository.java index 4ee5a68de22..aeb9a3e2084 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepository.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.GenericAssayAdditionalProperty; -import org.cbioportal.persistence.GenericAssayRepository; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.persistence.GenericAssayRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import org.springframework.cache.annotation.Cacheable; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.java similarity index 71% rename from src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.java index aa612490fe0..eb5088ce6f4 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; import org.apache.ibatis.annotations.Param; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; public interface GenesetHierarchyMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepository.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepository.java index a5ab47711a7..001d8d2daff 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.persistence.GenesetHierarchyRepository; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.persistence.GenesetHierarchyRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenesetMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.java similarity index 80% rename from src/main/java/org/cbioportal/persistence/mybatis/GenesetMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.java index b6484cb55ff..07cd96d5f82 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenesetMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; public interface GenesetMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepository.java similarity index 75% rename from src/main/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepository.java index 0cba9bef284..cf0658621d9 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepository.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenesetRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenesetRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.java similarity index 85% rename from src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.java index 9191f75494c..89dd3911c4c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfileSamples; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepository.java similarity index 89% rename from src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepository.java index b724350c86f..b93f08e519b 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepository.java @@ -1,7 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.*; -import org.cbioportal.persistence.MolecularDataRepository; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.persistence.MolecularDataRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; @@ -34,7 +37,7 @@ public Map commaSeparatedSampleIdsOfMolecularPr } @Override - public List getGeneMolecularAlterations(String molecularProfileId, + public List getGeneMolecularAlterations(String molecularProfileId, List entrezGeneIds, String projection) { return molecularDataMapper.getGeneMolecularAlterations(molecularProfileId, entrezGeneIds, projection); @@ -66,7 +69,7 @@ public List getGeneMolecularAlterationsInMultipleMolecu } @Override - public List getGenesetMolecularAlterations(String molecularProfileId, + public List getGenesetMolecularAlterations(String molecularProfileId, List genesetIds, String projection) { return molecularDataMapper.getGenesetMolecularAlterations(molecularProfileId, genesetIds, projection); diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.java index 64bf0a5936d..ea972aca916 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepository.java similarity index 89% rename from src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepository.java index bf0e656f401..fdae0ff7eba 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import java.util.Arrays; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMapper.java similarity index 89% rename from src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMapper.java index 26a26ddfad9..aa854e74422 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMapper.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepository.java index d5e5ae0d3f6..24325692773 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepository.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.persistence.MutationRepository; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.persistence.MutationRepository; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/PatientMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMapper.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/mybatis/PatientMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMapper.java index 70864aa54ec..0a9ec0f173e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/PatientMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepository.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepository.java index af4f1593030..2f8415fa730 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.java similarity index 85% rename from src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.java index 39e7bdb5d50..0bf6f0250c6 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.ReferenceGenomeGene; import java.util.List; public interface ReferenceGenomeGeneMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java index dc4091a2ec7..882f8e66806 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.persistence.ReferenceGenomeGeneRepository; -import org.cbioportal.persistence.PersistenceConstants; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.persistence.ReferenceGenomeGeneRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.java similarity index 91% rename from src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.java index ec3ea25ab9d..9e76d96b45a 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ResourceData; +import org.cbioportal.legacy.model.ResourceData; public interface ResourceDataMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepository.java similarity index 91% rename from src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepository.java index 79a66956f5c..252ec7da68a 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ResourceData; -import org.cbioportal.persistence.ResourceDataRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.persistence.ResourceDataRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.java index e15c5218bb0..e41c5c09dcf 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ResourceDefinition; +import org.cbioportal.legacy.model.ResourceDefinition; public interface ResourceDefinitionMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepository.java similarity index 75% rename from src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepository.java index 4a07420fb73..54e4f8a62f6 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepository.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.ResourceDefinitionRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.ResourceDefinitionRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SampleListMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.java similarity index 75% rename from src/main/java/org/cbioportal/persistence/mybatis/SampleListMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.java index af777db0597..8130882d0f2 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SampleListMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepository.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepository.java index f7141eef555..a27b268a33c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepository.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; import org.springframework.cache.annotation.Cacheable; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SampleMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMapper.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/mybatis/SampleMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMapper.java index 8d77020b1fc..6d67151dd04 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SampleMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepository.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepository.java index 0fc72b39234..29e9347938c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SampleRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SampleRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SecurityMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/mybatis/SecurityMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.java index 3f47af78354..c37ce170225 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SecurityMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMapper.java @@ -30,13 +30,13 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; // imports import org.apache.ibatis.annotations.Param; -import org.cbioportal.model.User; -import org.cbioportal.model.UserAuthorities; +import org.cbioportal.legacy.model.User; +import org.cbioportal.legacy.model.UserAuthorities; /** * Interface to use to retrieve diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SecurityMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMyBatisRepository.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/mybatis/SecurityMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMyBatisRepository.java index 3172948d2a5..edc29b31f6c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SecurityMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SecurityMyBatisRepository.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; // imports import java.util.Arrays; @@ -41,9 +41,9 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.cbioportal.model.User; -import org.cbioportal.model.UserAuthorities; -import org.cbioportal.persistence.SecurityRepository; +import org.cbioportal.legacy.model.User; +import org.cbioportal.legacy.model.UserAuthorities; +import org.cbioportal.legacy.persistence.SecurityRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.java similarity index 68% rename from src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.java index dbcc1f2b852..61ea2bb38a7 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java index 7cadd7e8cd1..29a273c297e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantCopyNumberRegionRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantCopyNumberRegionRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.java similarity index 69% rename from src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.java index 0cb1eccefe6..61a86f9ff06 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java index 69225317885..b31f209ad2d 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepository.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantlyMutatedGeneRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantlyMutatedGeneRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java similarity index 77% rename from src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java index bdcf5eb308a..66bdd7fd252 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimeStampMyBatisRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.TableTimestampPair; -import org.cbioportal.persistence.StaticDataTimeStampRepository; +import org.cbioportal.legacy.model.TableTimestampPair; +import org.cbioportal.legacy.persistence.StaticDataTimeStampRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.java similarity index 59% rename from src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.java index 573d0d8be6c..667f659d4f0 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StaticDataTimestampMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.TableTimestampPair; +import org.cbioportal.legacy.model.TableTimestampPair; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.java similarity index 87% rename from src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.java index 2a24f753b0d..27c88835e1e 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMapper.java @@ -21,14 +21,14 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; public interface StructuralVariantMapper { diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepository.java similarity index 89% rename from src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepository.java index f03d42130da..0affdf9fada 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepository.java @@ -21,14 +21,14 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.persistence.StructuralVariantRepository; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.persistence.StructuralVariantRepository; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StudyMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMapper.java similarity index 70% rename from src/main/java/org/cbioportal/persistence/mybatis/StudyMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMapper.java index 04290b77c80..2394f2128ff 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StudyMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMapper.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.meta.BaseMeta; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.meta.BaseMeta; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepository.java similarity index 83% rename from src/main/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepository.java index 813c6ff5ab6..22f59350cd0 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepository.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/TreatmentMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/TreatmentMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.java index 44e4f856079..344cdb0b9b8 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/TreatmentMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMapper.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.Treatment; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.Treatment; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepository.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepository.java index d44bdfc808a..cc4ec1c42f3 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepository.java @@ -1,7 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.*; -import org.cbioportal.persistence.TreatmentRepository; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.Treatment; +import org.cbioportal.legacy.persistence.TreatmentRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/VariantCountMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.java similarity index 70% rename from src/main/java/org/cbioportal/persistence/mybatis/VariantCountMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.java index 2d67d112897..3ec11587d6a 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/VariantCountMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMapper.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.VariantCount; +import org.cbioportal.legacy.model.VariantCount; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepository.java similarity index 78% rename from src/main/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepository.java index 723c2bafa30..6b726f882a1 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepository.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.VariantCount; -import org.cbioportal.persistence.VariantCountRepository; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.persistence.VariantCountRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/config/PersistenceConfig.java similarity index 91% rename from src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/config/PersistenceConfig.java index b8dba141ae4..81da76847ea 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/config/PersistenceConfig.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis.config; +package org.cbioportal.legacy.persistence.mybatis.config; -import org.cbioportal.model.Sample; -import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.persistence.mybatis.typehandler.SampleTypeTypeHandler; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; import org.mybatis.spring.boot.autoconfigure.ConfigurationCustomizer; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/typehandler/SampleTypeTypeHandler.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/typehandler/SampleTypeTypeHandler.java similarity index 91% rename from src/main/java/org/cbioportal/persistence/mybatis/typehandler/SampleTypeTypeHandler.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/typehandler/SampleTypeTypeHandler.java index 1b3d7b9986b..676ae17f8fb 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/typehandler/SampleTypeTypeHandler.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/typehandler/SampleTypeTypeHandler.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis.typehandler; +package org.cbioportal.legacy.persistence.mybatis.typehandler; import org.apache.ibatis.type.JdbcType; import org.apache.ibatis.type.MappedTypes; import org.apache.ibatis.type.TypeHandler; -import org.cbioportal.model.Sample; +import org.cbioportal.legacy.model.Sample; import java.sql.CallableStatement; import java.sql.PreparedStatement; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/util/CustomMyBatisObjectFactory.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/CustomMyBatisObjectFactory.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/mybatis/util/CustomMyBatisObjectFactory.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/util/CustomMyBatisObjectFactory.java index 4899efbed12..43000f0e6db 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/util/CustomMyBatisObjectFactory.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/CustomMyBatisObjectFactory.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; import org.apache.ibatis.reflection.factory.DefaultObjectFactory; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/util/LimitedPermissionArrayList.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/LimitedPermissionArrayList.java similarity index 97% rename from src/main/java/org/cbioportal/persistence/mybatis/util/LimitedPermissionArrayList.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/util/LimitedPermissionArrayList.java index 3c864c42d72..fb194add891 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/util/LimitedPermissionArrayList.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/LimitedPermissionArrayList.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; import java.util.*; import java.util.function.*; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java similarity index 95% rename from src/main/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java index 699f3f239b5..1c2785e1732 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; import org.apache.commons.math3.util.Pair; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/persistence/mybatis/util/PaginationCalculator.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculator.java similarity index 93% rename from src/main/java/org/cbioportal/persistence/mybatis/util/PaginationCalculator.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculator.java index ab2b4588052..d2f123ce39c 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/util/PaginationCalculator.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculator.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; public class PaginationCalculator { diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapper.java similarity index 75% rename from src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapper.java index dca5ad64125..3a2eea2f9b2 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapper.java @@ -1,28 +1,28 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; import org.apache.ibatis.annotations.Param; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.PatientTreatment; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatment; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.PatientTreatment; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatment; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java similarity index 86% rename from src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java index d3f594d61be..ef76a7926ca 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java @@ -1,32 +1,32 @@ -package org.cbioportal.persistence.mybatisclickhouse; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.PatientTreatment; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatment; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.persistence.enums.DataSource; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.service.util.StudyViewColumnarServiceUtil; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.PatientTreatment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatment; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.persistence.enums.DataSource; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java similarity index 84% rename from src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java rename to src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java index 7acea62ecec..5719b894cbb 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java +++ b/src/main/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java @@ -1,7 +1,7 @@ -package org.cbioportal.persistence.mybatisclickhouse.config; +package org.cbioportal.legacy.persistence.mybatisclickhouse.config; -import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.mybatis.typehandler.SampleTypeTypeHandler; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; import org.springframework.beans.factory.annotation.Qualifier; diff --git a/src/main/java/org/cbioportal/persistence/util/CacheEventLogger.java b/src/main/java/org/cbioportal/legacy/persistence/util/CacheEventLogger.java similarity index 98% rename from src/main/java/org/cbioportal/persistence/util/CacheEventLogger.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CacheEventLogger.java index d7dd14d1374..f3c6a813086 100644 --- a/src/main/java/org/cbioportal/persistence/util/CacheEventLogger.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CacheEventLogger.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import org.ehcache.event.*; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/persistence/util/CacheUtils.java b/src/main/java/org/cbioportal/legacy/persistence/util/CacheUtils.java similarity index 76% rename from src/main/java/org/cbioportal/persistence/util/CacheUtils.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CacheUtils.java index 46b33334ab7..b6ebdc6411b 100644 --- a/src/main/java/org/cbioportal/persistence/util/CacheUtils.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CacheUtils.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import java.util.List; diff --git a/src/main/java/org/cbioportal/persistence/util/CustomEhcachingProvider.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomEhcachingProvider.java similarity index 99% rename from src/main/java/org/cbioportal/persistence/util/CustomEhcachingProvider.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomEhcachingProvider.java index b4591cc3600..10cf9b5631f 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomEhcachingProvider.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomEhcachingProvider.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import java.io.*; import java.net.URL; @@ -49,7 +49,7 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.ehcache.impl.config.persistence.DefaultPersistenceConfiguration; -import org.cbioportal.persistence.CacheEnabledConfig; +import org.cbioportal.legacy.persistence.CacheEnabledConfig; public class CustomEhcachingProvider extends EhcacheCachingProvider { diff --git a/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomKeyGenerator.java similarity index 94% rename from src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomKeyGenerator.java index 948d5d344c5..91146f40e4e 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomKeyGenerator.java @@ -30,14 +30,14 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.CacheEnabledConfig; -import org.cbioportal.persistence.StudyRepository; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.CacheEnabledConfig; +import org.cbioportal.legacy.persistence.StudyRepository; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/persistence/util/CustomRedisCache.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCache.java similarity index 99% rename from src/main/java/org/cbioportal/persistence/util/CustomRedisCache.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCache.java index 5036bdd6e9a..a05f201cc89 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomRedisCache.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCache.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import org.redisson.api.RedissonClient; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/persistence/util/CustomRedisCacheManager.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManager.java similarity index 97% rename from src/main/java/org/cbioportal/persistence/util/CustomRedisCacheManager.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManager.java index 0c5cdb93dcd..4f7a941fb9b 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomRedisCacheManager.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManager.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import jakarta.validation.constraints.NotNull; import org.redisson.api.RedissonClient; diff --git a/src/main/java/org/cbioportal/persistence/util/CustomRedisCachingProvider.java b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCachingProvider.java similarity index 98% rename from src/main/java/org/cbioportal/persistence/util/CustomRedisCachingProvider.java rename to src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCachingProvider.java index 88b6aaa79c3..d2449d5509d 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomRedisCachingProvider.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/CustomRedisCachingProvider.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import org.redisson.Redisson; import org.redisson.api.RedissonClient; diff --git a/src/main/java/org/cbioportal/persistence/util/EhCacheUtils.java b/src/main/java/org/cbioportal/legacy/persistence/util/EhCacheUtils.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/util/EhCacheUtils.java rename to src/main/java/org/cbioportal/legacy/persistence/util/EhCacheUtils.java index b8226ec0f80..7c219f7824d 100644 --- a/src/main/java/org/cbioportal/persistence/util/EhCacheUtils.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/EhCacheUtils.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import jakarta.annotation.PostConstruct; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/persistence/util/EhcacheStatistics.java b/src/main/java/org/cbioportal/legacy/persistence/util/EhcacheStatistics.java similarity index 98% rename from src/main/java/org/cbioportal/persistence/util/EhcacheStatistics.java rename to src/main/java/org/cbioportal/legacy/persistence/util/EhcacheStatistics.java index bbf5d273ed9..ae6244bb2cc 100644 --- a/src/main/java/org/cbioportal/persistence/util/EhcacheStatistics.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/EhcacheStatistics.java @@ -30,10 +30,10 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import jakarta.annotation.PostConstruct; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.ehcache.core.statistics.*; import org.ehcache.config.ResourceType; import org.ehcache.impl.internal.statistics.DefaultStatisticsService; diff --git a/src/main/java/org/cbioportal/persistence/util/LoggingCacheErrorHandler.java b/src/main/java/org/cbioportal/legacy/persistence/util/LoggingCacheErrorHandler.java similarity index 97% rename from src/main/java/org/cbioportal/persistence/util/LoggingCacheErrorHandler.java rename to src/main/java/org/cbioportal/legacy/persistence/util/LoggingCacheErrorHandler.java index a682c568dca..74893052276 100644 --- a/src/main/java/org/cbioportal/persistence/util/LoggingCacheErrorHandler.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/LoggingCacheErrorHandler.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java b/src/main/java/org/cbioportal/legacy/persistence/util/RedisCacheUtils.java similarity index 92% rename from src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java rename to src/main/java/org/cbioportal/legacy/persistence/util/RedisCacheUtils.java index ec5579c544d..121339bb96b 100644 --- a/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java +++ b/src/main/java/org/cbioportal/legacy/persistence/util/RedisCacheUtils.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; -import static org.cbioportal.persistence.util.CustomRedisCache.DELIMITER; +import static org.cbioportal.legacy.persistence.util.CustomRedisCache.DELIMITER; import org.redisson.api.RedissonClient; diff --git a/src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java b/src/main/java/org/cbioportal/legacy/properties/CustomDataSourceConfiguration.java similarity index 90% rename from src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java rename to src/main/java/org/cbioportal/legacy/properties/CustomDataSourceConfiguration.java index f71d07b1393..d2b78d4e4e9 100644 --- a/src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java +++ b/src/main/java/org/cbioportal/legacy/properties/CustomDataSourceConfiguration.java @@ -1,6 +1,6 @@ -package org.cbioportal.properties; +package org.cbioportal.legacy.properties; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties; import org.springframework.boot.context.properties.ConfigurationProperties; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/properties/PortalProperties.java b/src/main/java/org/cbioportal/legacy/properties/PortalProperties.java similarity index 85% rename from src/main/java/org/cbioportal/properties/PortalProperties.java rename to src/main/java/org/cbioportal/legacy/properties/PortalProperties.java index 298c343a7be..5d315c9c960 100644 --- a/src/main/java/org/cbioportal/properties/PortalProperties.java +++ b/src/main/java/org/cbioportal/legacy/properties/PortalProperties.java @@ -1,6 +1,6 @@ -package org.cbioportal.properties; +package org.cbioportal.legacy.properties; -import org.cbioportal.utils.validation.AllowedValues; +import org.cbioportal.legacy.utils.validation.AllowedValues; import org.springframework.boot.context.properties.ConfigurationProperties; import org.springframework.context.annotation.Configuration; import org.springframework.validation.annotation.Validated; diff --git a/src/main/java/org/cbioportal/service/AlterationCountService.java b/src/main/java/org/cbioportal/legacy/service/AlterationCountService.java similarity index 94% rename from src/main/java/org/cbioportal/service/AlterationCountService.java rename to src/main/java/org/cbioportal/legacy/service/AlterationCountService.java index 639c1daab7d..5210c59e9d6 100644 --- a/src/main/java/org/cbioportal/service/AlterationCountService.java +++ b/src/main/java/org/cbioportal/legacy/service/AlterationCountService.java @@ -1,13 +1,12 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.*; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/AlterationDriverAnnotationService.java b/src/main/java/org/cbioportal/legacy/service/AlterationDriverAnnotationService.java similarity index 63% rename from src/main/java/org/cbioportal/service/AlterationDriverAnnotationService.java rename to src/main/java/org/cbioportal/legacy/service/AlterationDriverAnnotationService.java index 6f13a93f0f0..0cc2dda4fca 100644 --- a/src/main/java/org/cbioportal/service/AlterationDriverAnnotationService.java +++ b/src/main/java/org/cbioportal/legacy/service/AlterationDriverAnnotationService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/AlterationEnrichmentService.java b/src/main/java/org/cbioportal/legacy/service/AlterationEnrichmentService.java similarity index 51% rename from src/main/java/org/cbioportal/service/AlterationEnrichmentService.java rename to src/main/java/org/cbioportal/legacy/service/AlterationEnrichmentService.java index 98d01347e38..fe094702477 100644 --- a/src/main/java/org/cbioportal/service/AlterationEnrichmentService.java +++ b/src/main/java/org/cbioportal/legacy/service/AlterationEnrichmentService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/AttributeByStudyService.java b/src/main/java/org/cbioportal/legacy/service/AttributeByStudyService.java similarity index 67% rename from src/main/java/org/cbioportal/service/AttributeByStudyService.java rename to src/main/java/org/cbioportal/legacy/service/AttributeByStudyService.java index a1f198d1e15..1dd37130aaa 100644 --- a/src/main/java/org/cbioportal/service/AttributeByStudyService.java +++ b/src/main/java/org/cbioportal/legacy/service/AttributeByStudyService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttribute; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/CacheService.java b/src/main/java/org/cbioportal/legacy/service/CacheService.java similarity index 68% rename from src/main/java/org/cbioportal/service/CacheService.java rename to src/main/java/org/cbioportal/legacy/service/CacheService.java index ca0831f361e..75e8cecceac 100644 --- a/src/main/java/org/cbioportal/service/CacheService.java +++ b/src/main/java/org/cbioportal/legacy/service/CacheService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.service.exception.CacheOperationException; +import org.cbioportal.legacy.service.exception.CacheOperationException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/CacheStatisticsService.java b/src/main/java/org/cbioportal/legacy/service/CacheStatisticsService.java similarity index 71% rename from src/main/java/org/cbioportal/service/CacheStatisticsService.java rename to src/main/java/org/cbioportal/legacy/service/CacheStatisticsService.java index 94453f84c6f..6fe7d878920 100644 --- a/src/main/java/org/cbioportal/service/CacheStatisticsService.java +++ b/src/main/java/org/cbioportal/legacy/service/CacheStatisticsService.java @@ -1,7 +1,7 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.*; -import org.cbioportal.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; public interface CacheStatisticsService { diff --git a/src/main/java/org/cbioportal/service/CancerTypeService.java b/src/main/java/org/cbioportal/legacy/service/CancerTypeService.java similarity index 67% rename from src/main/java/org/cbioportal/service/CancerTypeService.java rename to src/main/java/org/cbioportal/legacy/service/CancerTypeService.java index fad6e41b1d3..97919472a89 100644 --- a/src/main/java/org/cbioportal/service/CancerTypeService.java +++ b/src/main/java/org/cbioportal/legacy/service/CancerTypeService.java @@ -1,8 +1,8 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/ClinicalAttributeService.java b/src/main/java/org/cbioportal/legacy/service/ClinicalAttributeService.java similarity index 77% rename from src/main/java/org/cbioportal/service/ClinicalAttributeService.java rename to src/main/java/org/cbioportal/legacy/service/ClinicalAttributeService.java index 3b648824419..6d7a3120744 100644 --- a/src/main/java/org/cbioportal/service/ClinicalAttributeService.java +++ b/src/main/java/org/cbioportal/legacy/service/ClinicalAttributeService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java b/src/main/java/org/cbioportal/legacy/service/ClinicalDataDensityPlotService.java similarity index 50% rename from src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java rename to src/main/java/org/cbioportal/legacy/service/ClinicalDataDensityPlotService.java index 211963e11b8..280b7a991d1 100644 --- a/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java +++ b/src/main/java/org/cbioportal/legacy/service/ClinicalDataDensityPlotService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.DensityPlotData; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DensityPlotParameters; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.DensityPlotData; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DensityPlotParameters; import java.math.BigDecimal; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ClinicalDataService.java b/src/main/java/org/cbioportal/legacy/service/ClinicalDataService.java similarity index 86% rename from src/main/java/org/cbioportal/service/ClinicalDataService.java rename to src/main/java/org/cbioportal/legacy/service/ClinicalDataService.java index b57474d1c4f..1b96099ee97 100644 --- a/src/main/java/org/cbioportal/service/ClinicalDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/ClinicalDataService.java @@ -1,13 +1,13 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.SampleClinicalDataCollection; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; public interface ClinicalDataService { diff --git a/src/main/java/org/cbioportal/service/ClinicalEventService.java b/src/main/java/org/cbioportal/legacy/service/ClinicalEventService.java similarity index 77% rename from src/main/java/org/cbioportal/service/ClinicalEventService.java rename to src/main/java/org/cbioportal/legacy/service/ClinicalEventService.java index ad0009ac0b6..8610e0af939 100644 --- a/src/main/java/org/cbioportal/service/ClinicalEventService.java +++ b/src/main/java/org/cbioportal/legacy/service/ClinicalEventService.java @@ -1,12 +1,12 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/CoExpressionService.java b/src/main/java/org/cbioportal/legacy/service/CoExpressionService.java similarity index 77% rename from src/main/java/org/cbioportal/service/CoExpressionService.java rename to src/main/java/org/cbioportal/legacy/service/CoExpressionService.java index fe9137f806f..1068413d3ab 100644 --- a/src/main/java/org/cbioportal/service/CoExpressionService.java +++ b/src/main/java/org/cbioportal/legacy/service/CoExpressionService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.CoExpression; -import org.cbioportal.model.EntityType; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/CopyNumberSegmentService.java b/src/main/java/org/cbioportal/legacy/service/CopyNumberSegmentService.java similarity index 78% rename from src/main/java/org/cbioportal/service/CopyNumberSegmentService.java rename to src/main/java/org/cbioportal/legacy/service/CopyNumberSegmentService.java index f251e710474..6656a397262 100644 --- a/src/main/java/org/cbioportal/service/CopyNumberSegmentService.java +++ b/src/main/java/org/cbioportal/legacy/service/CopyNumberSegmentService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/CosmicCountService.java b/src/main/java/org/cbioportal/legacy/service/CosmicCountService.java similarity index 61% rename from src/main/java/org/cbioportal/service/CosmicCountService.java rename to src/main/java/org/cbioportal/legacy/service/CosmicCountService.java index 4ba451f6008..b9614760fdd 100644 --- a/src/main/java/org/cbioportal/service/CosmicCountService.java +++ b/src/main/java/org/cbioportal/legacy/service/CosmicCountService.java @@ -1,8 +1,8 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.CosmicMutation; +import org.cbioportal.legacy.model.CosmicMutation; public interface CosmicCountService { diff --git a/src/main/java/org/cbioportal/service/CustomDataService.java b/src/main/java/org/cbioportal/legacy/service/CustomDataService.java similarity index 62% rename from src/main/java/org/cbioportal/service/CustomDataService.java rename to src/main/java/org/cbioportal/legacy/service/CustomDataService.java index 6f1b96f8c65..9cadacb327c 100644 --- a/src/main/java/org/cbioportal/service/CustomDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/CustomDataService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.CustomDataSession; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/DataAccessTokenService.java b/src/main/java/org/cbioportal/legacy/service/DataAccessTokenService.java similarity index 96% rename from src/main/java/org/cbioportal/service/DataAccessTokenService.java rename to src/main/java/org/cbioportal/legacy/service/DataAccessTokenService.java index 77447dab63e..2679b8b0f64 100644 --- a/src/main/java/org/cbioportal/service/DataAccessTokenService.java +++ b/src/main/java/org/cbioportal/legacy/service/DataAccessTokenService.java @@ -30,12 +30,12 @@ * along with this program. If not, see . */ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.Date; import java.util.List; -import org.cbioportal.model.DataAccessToken; +import org.cbioportal.legacy.model.DataAccessToken; import org.springframework.security.core.Authentication; public interface DataAccessTokenService { diff --git a/src/main/java/org/cbioportal/service/DiscreteCopyNumberService.java b/src/main/java/org/cbioportal/legacy/service/DiscreteCopyNumberService.java similarity index 90% rename from src/main/java/org/cbioportal/service/DiscreteCopyNumberService.java rename to src/main/java/org/cbioportal/legacy/service/DiscreteCopyNumberService.java index 7dbd1e8a5a9..a6de88b9752 100644 --- a/src/main/java/org/cbioportal/service/DiscreteCopyNumberService.java +++ b/src/main/java/org/cbioportal/legacy/service/DiscreteCopyNumberService.java @@ -1,8 +1,11 @@ -package org.cbioportal.service; - -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.model.CopyNumberCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java b/src/main/java/org/cbioportal/legacy/service/ExpressionEnrichmentService.java similarity index 73% rename from src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java rename to src/main/java/org/cbioportal/legacy/service/ExpressionEnrichmentService.java index d3c2a444bd8..03bd46668fa 100644 --- a/src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java +++ b/src/main/java/org/cbioportal/legacy/service/ExpressionEnrichmentService.java @@ -1,15 +1,15 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; import java.util.Map; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; public interface ExpressionEnrichmentService { diff --git a/src/main/java/org/cbioportal/service/FrontendPropertiesService.java b/src/main/java/org/cbioportal/legacy/service/FrontendPropertiesService.java similarity index 84% rename from src/main/java/org/cbioportal/service/FrontendPropertiesService.java rename to src/main/java/org/cbioportal/legacy/service/FrontendPropertiesService.java index a965eaf40d1..647cdce704e 100644 --- a/src/main/java/org/cbioportal/service/FrontendPropertiesService.java +++ b/src/main/java/org/cbioportal/legacy/service/FrontendPropertiesService.java @@ -1,4 +1,4 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/FrontendPropertiesServiceImpl.java similarity index 99% rename from src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/FrontendPropertiesServiceImpl.java index abe7f299226..e760e3fd985 100644 --- a/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/FrontendPropertiesServiceImpl.java @@ -1,4 +1,4 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import jakarta.annotation.PostConstruct; import org.slf4j.Logger; diff --git a/src/main/java/org/cbioportal/service/GeneMemoizerService.java b/src/main/java/org/cbioportal/legacy/service/GeneMemoizerService.java similarity index 68% rename from src/main/java/org/cbioportal/service/GeneMemoizerService.java rename to src/main/java/org/cbioportal/legacy/service/GeneMemoizerService.java index 995afc60a27..67dc7bfcba5 100644 --- a/src/main/java/org/cbioportal/service/GeneMemoizerService.java +++ b/src/main/java/org/cbioportal/legacy/service/GeneMemoizerService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.ReferenceGenomeGene; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/GenePanelService.java b/src/main/java/org/cbioportal/legacy/service/GenePanelService.java similarity index 79% rename from src/main/java/org/cbioportal/service/GenePanelService.java rename to src/main/java/org/cbioportal/legacy/service/GenePanelService.java index 9c0b2c6c8e6..d6205b28544 100644 --- a/src/main/java/org/cbioportal/service/GenePanelService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenePanelService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; - -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.cache.annotation.Cacheable; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/GeneService.java b/src/main/java/org/cbioportal/legacy/service/GeneService.java similarity index 72% rename from src/main/java/org/cbioportal/service/GeneService.java rename to src/main/java/org/cbioportal/legacy/service/GeneService.java index ce60d3a4c79..6544f52485a 100644 --- a/src/main/java/org/cbioportal/service/GeneService.java +++ b/src/main/java/org/cbioportal/legacy/service/GeneService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.exception.GeneWithMultipleEntrezIdsException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GeneWithMultipleEntrezIdsException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/GenericAssayService.java b/src/main/java/org/cbioportal/legacy/service/GenericAssayService.java similarity index 80% rename from src/main/java/org/cbioportal/service/GenericAssayService.java rename to src/main/java/org/cbioportal/legacy/service/GenericAssayService.java index 8f85a4fd179..3051d564ba8 100644 --- a/src/main/java/org/cbioportal/service/GenericAssayService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenericAssayService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; public interface GenericAssayService { diff --git a/src/main/java/org/cbioportal/service/GenesetCorrelationService.java b/src/main/java/org/cbioportal/legacy/service/GenesetCorrelationService.java similarity index 69% rename from src/main/java/org/cbioportal/service/GenesetCorrelationService.java rename to src/main/java/org/cbioportal/legacy/service/GenesetCorrelationService.java index 8136290b344..f27e8b18dfb 100644 --- a/src/main/java/org/cbioportal/service/GenesetCorrelationService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenesetCorrelationService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; public interface GenesetCorrelationService { diff --git a/src/main/java/org/cbioportal/service/GenesetDataService.java b/src/main/java/org/cbioportal/legacy/service/GenesetDataService.java similarity index 64% rename from src/main/java/org/cbioportal/service/GenesetDataService.java rename to src/main/java/org/cbioportal/legacy/service/GenesetDataService.java index 9ad80bf9f08..87936bccdf7 100644 --- a/src/main/java/org/cbioportal/service/GenesetDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenesetDataService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; public interface GenesetDataService { diff --git a/src/main/java/org/cbioportal/service/GenesetHierarchyService.java b/src/main/java/org/cbioportal/legacy/service/GenesetHierarchyService.java similarity index 73% rename from src/main/java/org/cbioportal/service/GenesetHierarchyService.java rename to src/main/java/org/cbioportal/legacy/service/GenesetHierarchyService.java index 4aea20dab8e..84b82a74e97 100644 --- a/src/main/java/org/cbioportal/service/GenesetHierarchyService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenesetHierarchyService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; public interface GenesetHierarchyService { diff --git a/src/main/java/org/cbioportal/service/GenesetService.java b/src/main/java/org/cbioportal/legacy/service/GenesetService.java similarity index 64% rename from src/main/java/org/cbioportal/service/GenesetService.java rename to src/main/java/org/cbioportal/legacy/service/GenesetService.java index 29a3630f5c3..92a511d5872 100644 --- a/src/main/java/org/cbioportal/service/GenesetService.java +++ b/src/main/java/org/cbioportal/legacy/service/GenesetService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; public interface GenesetService { diff --git a/src/main/java/org/cbioportal/service/MolecularDataService.java b/src/main/java/org/cbioportal/legacy/service/MolecularDataService.java similarity index 86% rename from src/main/java/org/cbioportal/service/MolecularDataService.java rename to src/main/java/org/cbioportal/legacy/service/MolecularDataService.java index b1ac3fa3eaa..9e2da76bec4 100644 --- a/src/main/java/org/cbioportal/service/MolecularDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/MolecularDataService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/MolecularProfileService.java b/src/main/java/org/cbioportal/legacy/service/MolecularProfileService.java similarity index 85% rename from src/main/java/org/cbioportal/service/MolecularProfileService.java rename to src/main/java/org/cbioportal/legacy/service/MolecularProfileService.java index e3724261798..47e0f31351d 100644 --- a/src/main/java/org/cbioportal/service/MolecularProfileService.java +++ b/src/main/java/org/cbioportal/legacy/service/MolecularProfileService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; import java.util.Set; diff --git a/src/main/java/org/cbioportal/service/MrnaPercentileService.java b/src/main/java/org/cbioportal/legacy/service/MrnaPercentileService.java similarity index 58% rename from src/main/java/org/cbioportal/service/MrnaPercentileService.java rename to src/main/java/org/cbioportal/legacy/service/MrnaPercentileService.java index 98e0ed5a0f5..b9c276a5ac2 100644 --- a/src/main/java/org/cbioportal/service/MrnaPercentileService.java +++ b/src/main/java/org/cbioportal/legacy/service/MrnaPercentileService.java @@ -1,7 +1,7 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/MutationService.java b/src/main/java/org/cbioportal/legacy/service/MutationService.java similarity index 88% rename from src/main/java/org/cbioportal/service/MutationService.java rename to src/main/java/org/cbioportal/legacy/service/MutationService.java index c51153d1111..662664a83a0 100644 --- a/src/main/java/org/cbioportal/service/MutationService.java +++ b/src/main/java/org/cbioportal/legacy/service/MutationService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; - -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/MutationSpectrumService.java b/src/main/java/org/cbioportal/legacy/service/MutationSpectrumService.java similarity index 68% rename from src/main/java/org/cbioportal/service/MutationSpectrumService.java rename to src/main/java/org/cbioportal/legacy/service/MutationSpectrumService.java index 63c0a050991..4002bc200d5 100644 --- a/src/main/java/org/cbioportal/service/MutationSpectrumService.java +++ b/src/main/java/org/cbioportal/legacy/service/MutationSpectrumService.java @@ -1,7 +1,7 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/PatientService.java b/src/main/java/org/cbioportal/legacy/service/PatientService.java similarity index 77% rename from src/main/java/org/cbioportal/service/PatientService.java rename to src/main/java/org/cbioportal/legacy/service/PatientService.java index 7ee3b93db76..04e62f18f3f 100644 --- a/src/main/java/org/cbioportal/service/PatientService.java +++ b/src/main/java/org/cbioportal/legacy/service/PatientService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ReadPermissionService.java b/src/main/java/org/cbioportal/legacy/service/ReadPermissionService.java similarity index 73% rename from src/main/java/org/cbioportal/service/ReadPermissionService.java rename to src/main/java/org/cbioportal/legacy/service/ReadPermissionService.java index 7c3bc23c8d4..fdd9c3cab64 100644 --- a/src/main/java/org/cbioportal/service/ReadPermissionService.java +++ b/src/main/java/org/cbioportal/legacy/service/ReadPermissionService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ReadPermission; +import org.cbioportal.legacy.model.ReadPermission; import org.springframework.security.core.Authentication; import java.util.Collection; diff --git a/src/main/java/org/cbioportal/service/ReferenceGenomeGeneService.java b/src/main/java/org/cbioportal/legacy/service/ReferenceGenomeGeneService.java similarity index 85% rename from src/main/java/org/cbioportal/service/ReferenceGenomeGeneService.java rename to src/main/java/org/cbioportal/legacy/service/ReferenceGenomeGeneService.java index 1fb09b586c9..604207db053 100644 --- a/src/main/java/org/cbioportal/service/ReferenceGenomeGeneService.java +++ b/src/main/java/org/cbioportal/legacy/service/ReferenceGenomeGeneService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.ReferenceGenomeGene; import java.util.List; public interface ReferenceGenomeGeneService { diff --git a/src/main/java/org/cbioportal/service/ResourceDataService.java b/src/main/java/org/cbioportal/legacy/service/ResourceDataService.java similarity index 78% rename from src/main/java/org/cbioportal/service/ResourceDataService.java rename to src/main/java/org/cbioportal/legacy/service/ResourceDataService.java index 5727906394c..d04336283cc 100644 --- a/src/main/java/org/cbioportal/service/ResourceDataService.java +++ b/src/main/java/org/cbioportal/legacy/service/ResourceDataService.java @@ -1,11 +1,11 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.ResourceData; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; public interface ResourceDataService { diff --git a/src/main/java/org/cbioportal/service/ResourceDefinitionService.java b/src/main/java/org/cbioportal/legacy/service/ResourceDefinitionService.java similarity index 69% rename from src/main/java/org/cbioportal/service/ResourceDefinitionService.java rename to src/main/java/org/cbioportal/legacy/service/ResourceDefinitionService.java index 9c413cf64b5..4c4754678a3 100644 --- a/src/main/java/org/cbioportal/service/ResourceDefinitionService.java +++ b/src/main/java/org/cbioportal/legacy/service/ResourceDefinitionService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.service.exception.ResourceDefinitionNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.service.exception.ResourceDefinitionNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; public interface ResourceDefinitionService { diff --git a/src/main/java/org/cbioportal/service/SampleListService.java b/src/main/java/org/cbioportal/legacy/service/SampleListService.java similarity index 75% rename from src/main/java/org/cbioportal/service/SampleListService.java rename to src/main/java/org/cbioportal/legacy/service/SampleListService.java index bae2e8205e5..0a921258022 100644 --- a/src/main/java/org/cbioportal/service/SampleListService.java +++ b/src/main/java/org/cbioportal/legacy/service/SampleListService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/SampleService.java b/src/main/java/org/cbioportal/legacy/service/SampleService.java similarity index 85% rename from src/main/java/org/cbioportal/service/SampleService.java rename to src/main/java/org/cbioportal/legacy/service/SampleService.java index 4d1c6d9c9e1..7ee43f334e9 100644 --- a/src/main/java/org/cbioportal/service/SampleService.java +++ b/src/main/java/org/cbioportal/legacy/service/SampleService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/legacy/service/ServerStatusService.java b/src/main/java/org/cbioportal/legacy/service/ServerStatusService.java new file mode 100644 index 00000000000..5bde6e3ed55 --- /dev/null +++ b/src/main/java/org/cbioportal/legacy/service/ServerStatusService.java @@ -0,0 +1,7 @@ +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.service.impl.ServerStatusServiceImpl.ServerStatusMessage; + +public interface ServerStatusService { + ServerStatusMessage getServerStatus(); +} diff --git a/src/main/java/org/cbioportal/service/SignificantCopyNumberRegionService.java b/src/main/java/org/cbioportal/legacy/service/SignificantCopyNumberRegionService.java similarity index 67% rename from src/main/java/org/cbioportal/service/SignificantCopyNumberRegionService.java rename to src/main/java/org/cbioportal/legacy/service/SignificantCopyNumberRegionService.java index 712e980a99b..7b10c8ee5f3 100644 --- a/src/main/java/org/cbioportal/service/SignificantCopyNumberRegionService.java +++ b/src/main/java/org/cbioportal/legacy/service/SignificantCopyNumberRegionService.java @@ -1,8 +1,8 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/SignificantlyMutatedGeneService.java b/src/main/java/org/cbioportal/legacy/service/SignificantlyMutatedGeneService.java similarity index 66% rename from src/main/java/org/cbioportal/service/SignificantlyMutatedGeneService.java rename to src/main/java/org/cbioportal/legacy/service/SignificantlyMutatedGeneService.java index dc60a5b485b..820cf8d8936 100644 --- a/src/main/java/org/cbioportal/service/SignificantlyMutatedGeneService.java +++ b/src/main/java/org/cbioportal/legacy/service/SignificantlyMutatedGeneService.java @@ -1,8 +1,8 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/StaticDataTimestampService.java b/src/main/java/org/cbioportal/legacy/service/StaticDataTimestampService.java similarity index 72% rename from src/main/java/org/cbioportal/service/StaticDataTimestampService.java rename to src/main/java/org/cbioportal/legacy/service/StaticDataTimestampService.java index 07c6abb0221..6831ec0a400 100644 --- a/src/main/java/org/cbioportal/service/StaticDataTimestampService.java +++ b/src/main/java/org/cbioportal/legacy/service/StaticDataTimestampService.java @@ -1,6 +1,6 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.TableTimestampPair; +import org.cbioportal.legacy.model.TableTimestampPair; import java.util.Date; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/StructuralVariantService.java b/src/main/java/org/cbioportal/legacy/service/StructuralVariantService.java similarity index 86% rename from src/main/java/org/cbioportal/service/StructuralVariantService.java rename to src/main/java/org/cbioportal/legacy/service/StructuralVariantService.java index 6fe7dc5d34d..ca7228411a8 100644 --- a/src/main/java/org/cbioportal/service/StructuralVariantService.java +++ b/src/main/java/org/cbioportal/legacy/service/StructuralVariantService.java @@ -21,14 +21,14 @@ * along with this program. If not, see . */ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; public interface StructuralVariantService { diff --git a/src/main/java/org/cbioportal/service/StudyService.java b/src/main/java/org/cbioportal/legacy/service/StudyService.java similarity index 70% rename from src/main/java/org/cbioportal/service/StudyService.java rename to src/main/java/org/cbioportal/legacy/service/StudyService.java index 4d80c394d65..96082714a3d 100644 --- a/src/main/java/org/cbioportal/service/StudyService.java +++ b/src/main/java/org/cbioportal/legacy/service/StudyService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.springframework.security.core.Authentication; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/legacy/service/StudyViewColumnarService.java similarity index 67% rename from src/main/java/org/cbioportal/service/StudyViewColumnarService.java rename to src/main/java/org/cbioportal/legacy/service/StudyViewColumnarService.java index 67ee1f9efe4..5643abc01b7 100644 --- a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java +++ b/src/main/java/org/cbioportal/legacy/service/StudyViewColumnarService.java @@ -1,24 +1,24 @@ -package org.cbioportal.service; - -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +package org.cbioportal.legacy.service; + +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import java.util.List; import java.util.Map; diff --git a/src/main/java/org/cbioportal/service/StudyViewService.java b/src/main/java/org/cbioportal/legacy/service/StudyViewService.java similarity index 75% rename from src/main/java/org/cbioportal/service/StudyViewService.java rename to src/main/java/org/cbioportal/legacy/service/StudyViewService.java index c4cb00151e5..d1f2604476d 100644 --- a/src/main/java/org/cbioportal/service/StudyViewService.java +++ b/src/main/java/org/cbioportal/legacy/service/StudyViewService.java @@ -1,14 +1,14 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/TreatmentService.java b/src/main/java/org/cbioportal/legacy/service/TreatmentService.java similarity index 71% rename from src/main/java/org/cbioportal/service/TreatmentService.java rename to src/main/java/org/cbioportal/legacy/service/TreatmentService.java index 0c7ff536b49..b518eac149b 100644 --- a/src/main/java/org/cbioportal/service/TreatmentService.java +++ b/src/main/java/org/cbioportal/legacy/service/TreatmentService.java @@ -1,10 +1,10 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; import java.util.List; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; public interface TreatmentService { public List getAllSampleTreatmentRows(List samples, List studies, ClinicalEventKeyCode key); diff --git a/src/main/java/org/cbioportal/service/VariantCountService.java b/src/main/java/org/cbioportal/legacy/service/VariantCountService.java similarity index 58% rename from src/main/java/org/cbioportal/service/VariantCountService.java rename to src/main/java/org/cbioportal/legacy/service/VariantCountService.java index 74dc9758461..e5631b272b0 100644 --- a/src/main/java/org/cbioportal/service/VariantCountService.java +++ b/src/main/java/org/cbioportal/legacy/service/VariantCountService.java @@ -1,7 +1,7 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.VariantCount; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/ViolinPlotService.java b/src/main/java/org/cbioportal/legacy/service/ViolinPlotService.java similarity index 64% rename from src/main/java/org/cbioportal/service/ViolinPlotService.java rename to src/main/java/org/cbioportal/legacy/service/ViolinPlotService.java index 37eade2f739..e3177b33b72 100644 --- a/src/main/java/org/cbioportal/service/ViolinPlotService.java +++ b/src/main/java/org/cbioportal/legacy/service/ViolinPlotService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service; +package org.cbioportal.legacy.service; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalViolinPlotData; -import org.cbioportal.model.Sample; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import java.math.BigDecimal; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneService.java b/src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneService.java similarity index 60% rename from src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneService.java rename to src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneService.java index 79d29dc8ff3..bd43d19924b 100644 --- a/src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneService.java +++ b/src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneService.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.alteration; +package org.cbioportal.legacy.service.alteration; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import java.util.List; diff --git a/src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneServiceImpl.java similarity index 92% rename from src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneServiceImpl.java index 9aea4ade562..18cdc722dff 100644 --- a/src/main/java/org/cbioportal/service/alteration/AlterationCountByGeneServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/alteration/AlterationCountByGeneServiceImpl.java @@ -1,20 +1,20 @@ -package org.cbioportal.service.alteration; +package org.cbioportal.legacy.service.alteration; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationType; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.AlterationCountServiceUtil; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationType; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.AlterationCountServiceUtil; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.lang.NonNull; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/exception/AccessForbiddenException.java b/src/main/java/org/cbioportal/legacy/service/exception/AccessForbiddenException.java similarity index 75% rename from src/main/java/org/cbioportal/service/exception/AccessForbiddenException.java rename to src/main/java/org/cbioportal/legacy/service/exception/AccessForbiddenException.java index d9dd8b64bd5..200830035ef 100644 --- a/src/main/java/org/cbioportal/service/exception/AccessForbiddenException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/AccessForbiddenException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class AccessForbiddenException extends RuntimeException { public AccessForbiddenException(String message) { diff --git a/src/main/java/org/cbioportal/service/exception/CacheNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/CacheNotFoundException.java similarity index 89% rename from src/main/java/org/cbioportal/service/exception/CacheNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/CacheNotFoundException.java index 457db60daa2..7585d074973 100644 --- a/src/main/java/org/cbioportal/service/exception/CacheNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/CacheNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class CacheNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/CacheOperationException.java b/src/main/java/org/cbioportal/legacy/service/exception/CacheOperationException.java similarity index 77% rename from src/main/java/org/cbioportal/service/exception/CacheOperationException.java rename to src/main/java/org/cbioportal/legacy/service/exception/CacheOperationException.java index 1580a77c476..5a7b45a5d18 100644 --- a/src/main/java/org/cbioportal/service/exception/CacheOperationException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/CacheOperationException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class CacheOperationException extends Exception { public CacheOperationException(String message, Throwable cause) { diff --git a/src/main/java/org/cbioportal/service/exception/CancerTypeNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/CancerTypeNotFoundException.java similarity index 89% rename from src/main/java/org/cbioportal/service/exception/CancerTypeNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/CancerTypeNotFoundException.java index e8f0ef923d6..3dbb4e7784d 100644 --- a/src/main/java/org/cbioportal/service/exception/CancerTypeNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/CancerTypeNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class CancerTypeNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/ClinicalAttributeNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/ClinicalAttributeNotFoundException.java similarity index 93% rename from src/main/java/org/cbioportal/service/exception/ClinicalAttributeNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/ClinicalAttributeNotFoundException.java index beca71b82e9..12c41d224fa 100644 --- a/src/main/java/org/cbioportal/service/exception/ClinicalAttributeNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/ClinicalAttributeNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class ClinicalAttributeNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/DataAccessTokenNoUserIdentityException.java b/src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenNoUserIdentityException.java similarity index 97% rename from src/main/java/org/cbioportal/service/exception/DataAccessTokenNoUserIdentityException.java rename to src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenNoUserIdentityException.java index e698c562792..83b09e3e33c 100644 --- a/src/main/java/org/cbioportal/service/exception/DataAccessTokenNoUserIdentityException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenNoUserIdentityException.java @@ -46,7 +46,7 @@ * along with this program. If not, see . */ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class DataAccessTokenNoUserIdentityException extends RuntimeException { diff --git a/src/main/java/org/cbioportal/service/exception/DataAccessTokenProhibitedUserException.java b/src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenProhibitedUserException.java similarity index 97% rename from src/main/java/org/cbioportal/service/exception/DataAccessTokenProhibitedUserException.java rename to src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenProhibitedUserException.java index 6ed9a7ac6dc..c6277dda5c5 100644 --- a/src/main/java/org/cbioportal/service/exception/DataAccessTokenProhibitedUserException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/DataAccessTokenProhibitedUserException.java @@ -46,7 +46,7 @@ * along with this program. If not, see . */ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class DataAccessTokenProhibitedUserException extends RuntimeException { diff --git a/src/main/java/org/cbioportal/service/exception/GeneNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/GeneNotFoundException.java similarity index 87% rename from src/main/java/org/cbioportal/service/exception/GeneNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GeneNotFoundException.java index 4f69921765e..d4b814d4332 100644 --- a/src/main/java/org/cbioportal/service/exception/GeneNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GeneNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class GeneNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/GenePanelNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/GenePanelNotFoundException.java similarity index 88% rename from src/main/java/org/cbioportal/service/exception/GenePanelNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GenePanelNotFoundException.java index 0511561f851..424543e925a 100644 --- a/src/main/java/org/cbioportal/service/exception/GenePanelNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GenePanelNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class GenePanelNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/GeneWithMultipleEntrezIdsException.java b/src/main/java/org/cbioportal/legacy/service/exception/GeneWithMultipleEntrezIdsException.java similarity index 89% rename from src/main/java/org/cbioportal/service/exception/GeneWithMultipleEntrezIdsException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GeneWithMultipleEntrezIdsException.java index e475eb07546..fdeecf15f46 100644 --- a/src/main/java/org/cbioportal/service/exception/GeneWithMultipleEntrezIdsException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GeneWithMultipleEntrezIdsException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; //TODO: this class should be removed once the issue is resolved database public class GeneWithMultipleEntrezIdsException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/GenericAssayNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/GenericAssayNotFoundException.java similarity index 90% rename from src/main/java/org/cbioportal/service/exception/GenericAssayNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GenericAssayNotFoundException.java index ec19640c509..1761e39d3a4 100644 --- a/src/main/java/org/cbioportal/service/exception/GenericAssayNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GenericAssayNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class GenericAssayNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/GenesetNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/GenesetNotFoundException.java similarity index 88% rename from src/main/java/org/cbioportal/service/exception/GenesetNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/GenesetNotFoundException.java index 6019759bf58..eaae23c36db 100644 --- a/src/main/java/org/cbioportal/service/exception/GenesetNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/GenesetNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class GenesetNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/InvalidDataAccessTokenException.java b/src/main/java/org/cbioportal/legacy/service/exception/InvalidDataAccessTokenException.java similarity index 98% rename from src/main/java/org/cbioportal/service/exception/InvalidDataAccessTokenException.java rename to src/main/java/org/cbioportal/legacy/service/exception/InvalidDataAccessTokenException.java index d158d258a7c..7fda71ec58f 100644 --- a/src/main/java/org/cbioportal/service/exception/InvalidDataAccessTokenException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/InvalidDataAccessTokenException.java @@ -47,7 +47,7 @@ */ // TODO move back package org.cbioportal.security.exception; -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class InvalidDataAccessTokenException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/MolecularProfileNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/MolecularProfileNotFoundException.java similarity index 90% rename from src/main/java/org/cbioportal/service/exception/MolecularProfileNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/MolecularProfileNotFoundException.java index 574356a8e18..83ec3bb9fcd 100644 --- a/src/main/java/org/cbioportal/service/exception/MolecularProfileNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/MolecularProfileNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class MolecularProfileNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/PatientNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/PatientNotFoundException.java similarity index 92% rename from src/main/java/org/cbioportal/service/exception/PatientNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/PatientNotFoundException.java index 7f19e4d9e0c..007eb7fecc1 100644 --- a/src/main/java/org/cbioportal/service/exception/PatientNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/PatientNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class PatientNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/ResourceDefinitionNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/ResourceDefinitionNotFoundException.java similarity index 92% rename from src/main/java/org/cbioportal/service/exception/ResourceDefinitionNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/ResourceDefinitionNotFoundException.java index 45451464f5e..e6aa86889e2 100644 --- a/src/main/java/org/cbioportal/service/exception/ResourceDefinitionNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/ResourceDefinitionNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class ResourceDefinitionNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/SampleListNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/SampleListNotFoundException.java similarity index 89% rename from src/main/java/org/cbioportal/service/exception/SampleListNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/SampleListNotFoundException.java index fcda0ca5ba0..6f67343565a 100644 --- a/src/main/java/org/cbioportal/service/exception/SampleListNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/SampleListNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class SampleListNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/SampleNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/SampleNotFoundException.java similarity index 92% rename from src/main/java/org/cbioportal/service/exception/SampleNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/SampleNotFoundException.java index d95f89d0712..76db484c137 100644 --- a/src/main/java/org/cbioportal/service/exception/SampleNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/SampleNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class SampleNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/StudyNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/StudyNotFoundException.java similarity index 87% rename from src/main/java/org/cbioportal/service/exception/StudyNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/StudyNotFoundException.java index 119acd4a898..70f79a70c0b 100644 --- a/src/main/java/org/cbioportal/service/exception/StudyNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/StudyNotFoundException.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class StudyNotFoundException extends Exception { diff --git a/src/main/java/org/cbioportal/service/exception/TokenNotFoundException.java b/src/main/java/org/cbioportal/legacy/service/exception/TokenNotFoundException.java similarity index 97% rename from src/main/java/org/cbioportal/service/exception/TokenNotFoundException.java rename to src/main/java/org/cbioportal/legacy/service/exception/TokenNotFoundException.java index 7a964e7aa98..2150e39af8c 100644 --- a/src/main/java/org/cbioportal/service/exception/TokenNotFoundException.java +++ b/src/main/java/org/cbioportal/legacy/service/exception/TokenNotFoundException.java @@ -48,7 +48,7 @@ */ // TODO move back package org.cbioportal.security.exception; -package org.cbioportal.service.exception; +package org.cbioportal.legacy.service.exception; public class TokenNotFoundException extends RuntimeException { diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImpl.java index 8c5ebc5c1fa..9bf3db30278 100644 --- a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImpl.java @@ -1,22 +1,22 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountBase; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.AlterationRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.util.AlterationCountServiceUtil; -import org.cbioportal.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.model.AlterationCountBase; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.AlterationRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.util.AlterationCountServiceUtil; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImpl.java similarity index 79% rename from src/main/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImpl.java index d5846ca02c1..0010c723bdb 100644 --- a/src/main/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImpl.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.AlterationDriverAnnotation; -import org.cbioportal.model.CustomDriverAnnotationReport; -import org.cbioportal.persistence.AlterationDriverAnnotationRepository; -import org.cbioportal.service.AlterationDriverAnnotationService; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.persistence.AlterationDriverAnnotationRepository; +import org.cbioportal.legacy.service.AlterationDriverAnnotationService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImpl.java similarity index 81% rename from src/main/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImpl.java index cbe49e76429..9cb2d091760 100644 --- a/src/main/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImpl.java @@ -1,11 +1,15 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.*; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.AlterationEnrichmentService; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.service.AlterationEnrichmentService; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/CacheServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CacheServiceImpl.java similarity index 90% rename from src/main/java/org/cbioportal/service/impl/CacheServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CacheServiceImpl.java index 41896b98d9b..4c7364adb69 100644 --- a/src/main/java/org/cbioportal/service/impl/CacheServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CacheServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.persistence.cachemaputil.StaticRefCacheMapUtil; -import org.cbioportal.persistence.util.CacheUtils; -import org.cbioportal.service.CacheService; -import org.cbioportal.service.exception.CacheOperationException; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.persistence.cachemaputil.StaticRefCacheMapUtil; +import org.cbioportal.legacy.persistence.util.CacheUtils; +import org.cbioportal.legacy.service.CacheService; +import org.cbioportal.legacy.service.exception.CacheOperationException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.CacheManager; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/impl/CacheStatisticsServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CacheStatisticsServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/CacheStatisticsServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CacheStatisticsServiceImpl.java index f5f74f15e23..8404198ee73 100644 --- a/src/main/java/org/cbioportal/service/impl/CacheStatisticsServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CacheStatisticsServiceImpl.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import jakarta.annotation.PostConstruct; -import org.cbioportal.persistence.util.CustomEhcachingProvider; -import org.cbioportal.service.CacheStatisticsService; -import org.cbioportal.service.exception.CacheNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.util.CustomEhcachingProvider; +import org.cbioportal.legacy.service.CacheStatisticsService; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImpl.java similarity index 87% rename from src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImpl.java index e039b58eaab..515421eccb6 100644 --- a/src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImpl.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import jakarta.annotation.PostConstruct; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalAttributeServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImpl.java similarity index 86% rename from src/main/java/org/cbioportal/service/impl/ClinicalAttributeServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImpl.java index bb245846cc9..423faf0d256 100644 --- a/src/main/java/org/cbioportal/service/impl/ClinicalAttributeServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalAttributeRepository; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.access.prepost.PostFilter; @@ -27,7 +27,7 @@ public class ClinicalAttributeServiceImpl implements ClinicalAttributeService { private String AUTHENTICATE; @Override - @PostFilter("hasPermission(filterObject.cancerStudyIdentifier, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostFilter("hasPermission(filterObject.cancerStudyIdentifier, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public List getAllClinicalAttributes(String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataDensityPlotServiceImpl.java similarity index 94% rename from src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataDensityPlotServiceImpl.java index cb4d8d780e9..f153b2ef134 100644 --- a/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataDensityPlotServiceImpl.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.correlation.PearsonsCorrelation; import org.apache.commons.math3.stat.correlation.SpearmansCorrelation; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.DensityPlotBin; -import org.cbioportal.model.DensityPlotData; -import org.cbioportal.service.ClinicalDataDensityPlotService; -import org.cbioportal.web.columnar.StudyViewColumnStoreController; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DensityPlotParameters; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.DensityPlotBin; +import org.cbioportal.legacy.model.DensityPlotData; +import org.cbioportal.legacy.service.ClinicalDataDensityPlotService; +import org.cbioportal.legacy.web.columnar.StudyViewColumnStoreController; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DensityPlotParameters; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImpl.java similarity index 90% rename from src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImpl.java index 7258f8e313e..beb3e8af12f 100644 --- a/src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImpl.java @@ -1,13 +1,24 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalDataRepository; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; -import org.cbioportal.service.*; -import org.cbioportal.service.exception.*; -import org.cbioportal.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalDataRepository; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; @@ -16,7 +27,7 @@ import java.util.stream.Collectors; import java.util.stream.Stream; -import static org.cbioportal.utils.Encoder.calculateBase64; +import static org.cbioportal.legacy.utils.Encoder.calculateBase64; @Service public class ClinicalDataServiceImpl implements ClinicalDataService { @@ -35,7 +46,7 @@ public class ClinicalDataServiceImpl implements ClinicalDataService { private ClinicalAttributeUtil clinicalAttributeUtil; @Override - public List getAllClinicalDataOfSampleInStudy(String studyId, String sampleId, String attributeId, + public List getAllClinicalDataOfSampleInStudy(String studyId, String sampleId, String attributeId, String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) throws SampleNotFoundException, StudyNotFoundException { @@ -134,7 +145,7 @@ public BaseMeta fetchMetaClinicalData(List studyIds, List ids, L @Override public List fetchClinicalDataCounts(List studyIds, List sampleIds, - List attributeIds) { + List attributeIds) { if (attributeIds.isEmpty()) { return new ArrayList<>(); diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalEventServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/ClinicalEventServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImpl.java index 187bec33ef1..dfb89a38bc8 100644 --- a/src/main/java/org/cbioportal/service/impl/ClinicalEventServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImpl.java @@ -1,20 +1,20 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalEventRepository; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.parameter.ClinicalEventRequestIdentifier; -import org.cbioportal.web.parameter.OccurrencePosition; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalEventRepository; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequestIdentifier; +import org.cbioportal.legacy.web.parameter.OccurrencePosition; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/CoExpressionServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/CoExpressionServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImpl.java index ced09b17dc5..256a897555d 100644 --- a/src/main/java/org/cbioportal/service/impl/CoExpressionServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImpl.java @@ -1,11 +1,24 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.*; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.*; -import org.cbioportal.service.exception.*; -import org.cbioportal.service.util.CoExpressionAsyncMethods; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.model.MolecularAlteration; +import org.cbioportal.legacy.model.MolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.CoExpressionService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.util.CoExpressionAsyncMethods; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.transaction.annotation.Transactional; import org.springframework.stereotype.Service; @@ -38,7 +51,7 @@ public class CoExpressionServiceImpl implements CoExpressionService { // transaction needs to be setup here in order to return Iterable from molecularDataService in fetchCoExpressions @Transactional(readOnly=true) public List getCoExpressions(String geneticEntityId, EntityType geneticEntityType, - String sampleListId, String molecularProfileIdA, String molecularProfileIdB, Double threshold) + String sampleListId, String molecularProfileIdA, String molecularProfileIdB, Double threshold) throws MolecularProfileNotFoundException, SampleListNotFoundException, GenesetNotFoundException, GeneNotFoundException { diff --git a/src/main/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImpl.java similarity index 85% rename from src/main/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImpl.java index efa3a34c482..1665f3ba54f 100644 --- a/src/main/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.service.CopyNumberSegmentService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.service.CopyNumberSegmentService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/CosmicCountServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImpl.java similarity index 68% rename from src/main/java/org/cbioportal/service/impl/CosmicCountServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImpl.java index 218201c21db..cef62e6b65b 100644 --- a/src/main/java/org/cbioportal/service/impl/CosmicCountServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import java.util.List; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.service.CosmicCountService; -import org.cbioportal.persistence.CosmicCountRepository; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.service.CosmicCountService; +import org.cbioportal.legacy.persistence.CosmicCountRepository; @Service public class CosmicCountServiceImpl implements CosmicCountService { diff --git a/src/main/java/org/cbioportal/service/impl/CustomDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/CustomDataServiceImpl.java similarity index 88% rename from src/main/java/org/cbioportal/service/impl/CustomDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/CustomDataServiceImpl.java index 3d339efb176..58178eebb31 100644 --- a/src/main/java/org/cbioportal/service/impl/CustomDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/CustomDataServiceImpl.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.utils.removeme.Session; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImpl.java index c862e7924ce..9975b249462 100644 --- a/src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImpl.java @@ -1,18 +1,18 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/EhcacheStatisticsServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/EhcacheStatisticsServiceImpl.java similarity index 79% rename from src/main/java/org/cbioportal/service/impl/EhcacheStatisticsServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/EhcacheStatisticsServiceImpl.java index dfa1019e51f..76f5ed21fa4 100644 --- a/src/main/java/org/cbioportal/service/impl/EhcacheStatisticsServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/EhcacheStatisticsServiceImpl.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.persistence.util.EhcacheStatistics; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.util.EhcacheStatistics; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Primary; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImpl.java similarity index 92% rename from src/main/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImpl.java index 849983cbd3c..967fe1f9064 100644 --- a/src/main/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImpl.java @@ -1,32 +1,32 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.math.BigDecimal; import java.util.*; import java.util.function.Function; import java.util.stream.Collectors; import org.apache.commons.lang3.BooleanUtils; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.ExpressionEnrichmentService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.ExpressionEnrichmentUtil; -import org.cbioportal.service.util.FisherExactTestCalculator; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.ExpressionEnrichmentService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.ExpressionEnrichmentUtil; +import org.cbioportal.legacy.service.util.FisherExactTestCalculator; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/main/java/org/cbioportal/service/impl/GeneMemoizerServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceImpl.java similarity index 87% rename from src/main/java/org/cbioportal/service/impl/GeneMemoizerServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceImpl.java index 2c0a097f16a..f6bf7752ab9 100644 --- a/src/main/java/org/cbioportal/service/impl/GeneMemoizerServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceImpl.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.service.GeneMemoizerService; -import org.cbioportal.service.StaticDataTimestampService; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.service.GeneMemoizerService; +import org.cbioportal.legacy.service.StaticDataTimestampService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenePanelServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenePanelServiceImpl.java similarity index 89% rename from src/main/java/org/cbioportal/service/impl/GenePanelServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenePanelServiceImpl.java index cde04fc14d6..94d2840a340 100644 --- a/src/main/java/org/cbioportal/service/impl/GenePanelServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenePanelServiceImpl.java @@ -1,16 +1,21 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenePanelRepository; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenePanelRepository; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; @@ -37,7 +42,7 @@ public class GenePanelServiceImpl implements GenePanelService { private final Function PATIENT_IDENTIFIER_GENERATOR = d -> d.getMolecularProfileId() + d.getPatientId(); @Override - public List getAllGenePanels(String projection, Integer pageSize, Integer pageNumber, String sortBy, + public List getAllGenePanels(String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { List genePanels = genePanelRepository.getAllGenePanels(projection, pageSize, pageNumber, sortBy, diff --git a/src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GeneServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GeneServiceImpl.java index a8ae132a090..4f8156dc231 100644 --- a/src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GeneServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import jakarta.annotation.PostConstruct; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneAlias; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GeneRepository; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.exception.GeneWithMultipleEntrezIdsException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneAlias; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GeneRepository; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GeneWithMultipleEntrezIdsException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenericAssayServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/GenericAssayServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpl.java index 9b8ddd1ba9b..2d3f214d666 100644 --- a/src/main/java/org/cbioportal/service/impl/GenericAssayServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpl.java @@ -1,24 +1,24 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.*; import java.util.function.Function; import java.util.stream.Collectors; -import org.cbioportal.model.GenericAssayAdditionalProperty; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.persistence.GenericAssayRepository; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.persistence.GenericAssayRepository; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenesetCorrelationServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/GenesetCorrelationServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImpl.java index ccf39027515..24d61d2aac6 100644 --- a/src/main/java/org/cbioportal/service/impl/GenesetCorrelationServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImpl.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; @@ -32,23 +32,23 @@ import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.correlation.SpearmansCorrelation; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.GenesetCorrelationService; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.GenesetCorrelationService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenesetDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImpl.java similarity index 85% rename from src/main/java/org/cbioportal/service/impl/GenesetDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImpl.java index 0b0a762fd61..6b8646bff14 100644 --- a/src/main/java/org/cbioportal/service/impl/GenesetDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImpl.java @@ -21,25 +21,25 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenesetHierarchyServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImpl.java similarity index 94% rename from src/main/java/org/cbioportal/service/impl/GenesetHierarchyServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImpl.java index 0c831bf19e3..85826f072d4 100644 --- a/src/main/java/org/cbioportal/service/impl/GenesetHierarchyServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImpl.java @@ -20,7 +20,7 @@ * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; @@ -31,20 +31,20 @@ import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.persistence.GenesetHierarchyRepository; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.GenesetHierarchyService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.persistence.GenesetHierarchyRepository; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.GenesetHierarchyService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/GenesetServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/GenesetServiceImpl.java similarity index 80% rename from src/main/java/org/cbioportal/service/impl/GenesetServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/GenesetServiceImpl.java index d0184582870..e2c58f7c653 100644 --- a/src/main/java/org/cbioportal/service/impl/GenesetServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/GenesetServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenesetRepository; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenesetRepository; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/JwtDataAccessTokenServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/JwtDataAccessTokenServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/JwtDataAccessTokenServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/JwtDataAccessTokenServiceImpl.java index f3fbbe3b21f..f67a20132c5 100644 --- a/src/main/java/org/cbioportal/service/impl/JwtDataAccessTokenServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/JwtDataAccessTokenServiceImpl.java @@ -30,15 +30,15 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; -import org.cbioportal.service.util.JwtUtils; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.InvalidDataAccessTokenException; +import org.cbioportal.legacy.service.util.JwtUtils; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.security.authentication.BadCredentialsException; import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; diff --git a/src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImpl.java similarity index 93% rename from src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImpl.java index 40f60c0dbff..def0c45cdd9 100644 --- a/src/main/java/org/cbioportal/service/impl/MolecularDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImpl.java @@ -1,16 +1,21 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.*; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.security.access.prepost.PreAuthorize; import org.springframework.stereotype.Service; @@ -261,7 +266,7 @@ public List getMolecularDataInMultipleMolecularProfilesByGene } @Override - @PreAuthorize("hasPermission(#molecularProfileIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public BaseMeta getMetaMolecularDataInMultipleMolecularProfiles(List molecularProfileIds, List sampleIds, List entrezGeneIds) { diff --git a/src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImpl.java similarity index 89% rename from src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImpl.java index 3a4d6c8a1d7..3c91568e123 100644 --- a/src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImpl.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.Projection; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.access.prepost.PostFilter; @@ -34,7 +34,7 @@ public class MolecularProfileServiceImpl implements MolecularProfileService { private String AUTHENTICATE; @Override - @PostFilter("hasPermission(filterObject, T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostFilter("hasPermission(filterObject, T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public List getAllMolecularProfiles(String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { diff --git a/src/main/java/org/cbioportal/service/impl/MrnaPercentileServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImpl.java similarity index 88% rename from src/main/java/org/cbioportal/service/impl/MrnaPercentileServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImpl.java index af97c101c09..102073de20e 100644 --- a/src/main/java/org/cbioportal/service/impl/MrnaPercentileServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImpl.java @@ -1,16 +1,16 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.ranking.NaNStrategy; import org.apache.commons.math3.stat.ranking.NaturalRanking; import org.apache.commons.math3.stat.ranking.TiesStrategy; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MrnaPercentileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MrnaPercentileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/MutationServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MutationServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/MutationServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MutationServiceImpl.java index 44602217b68..01df4b19132 100644 --- a/src/main/java/org/cbioportal/service/impl/MutationServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MutationServiceImpl.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.persistence.MutationRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.persistence.MutationRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/MutationSpectrumServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImpl.java similarity index 91% rename from src/main/java/org/cbioportal/service/impl/MutationSpectrumServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImpl.java index 36c685b14f4..ac4b62f060b 100644 --- a/src/main/java/org/cbioportal/service/impl/MutationSpectrumServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImpl.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.MutationSpectrumService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.MutationSpectrumService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/PatientServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/PatientServiceImpl.java similarity index 84% rename from src/main/java/org/cbioportal/service/impl/PatientServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/PatientServiceImpl.java index a317dce672f..26dba601205 100644 --- a/src/main/java/org/cbioportal/service/impl/PatientServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/PatientServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.access.prepost.PostFilter; @@ -26,7 +26,7 @@ public class PatientServiceImpl implements PatientService { private String AUTHENTICATE; @Override - @PostFilter("hasPermission(filterObject, T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostFilter("hasPermission(filterObject, T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public List getAllPatients(String keyword, String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { diff --git a/src/main/java/org/cbioportal/service/impl/ReadPermissionServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImpl.java similarity index 79% rename from src/main/java/org/cbioportal/service/impl/ReadPermissionServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImpl.java index 0662008422b..d48cdc3f7e3 100644 --- a/src/main/java/org/cbioportal/service/impl/ReadPermissionServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImpl.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.service.ReadPermissionService; -import org.cbioportal.model.ReadPermission; -import org.cbioportal.security.CancerStudyPermissionEvaluator; -import org.cbioportal.utils.security.AccessLevel; +import org.cbioportal.legacy.service.ReadPermissionService; +import org.cbioportal.legacy.model.ReadPermission; +import org.cbioportal.application.security.CancerStudyPermissionEvaluator; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.security.core.Authentication; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/RedisCacheStatisticsServiceImpl.java similarity index 90% rename from src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/RedisCacheStatisticsServiceImpl.java index ef8e447355a..1114e92dece 100644 --- a/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/RedisCacheStatisticsServiceImpl.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.persistence.util.CustomKeyGenerator; -import org.cbioportal.persistence.util.CustomRedisCache; -import org.cbioportal.service.CacheStatisticsService; -import org.cbioportal.service.exception.CacheNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.persistence.util.CustomKeyGenerator; +import org.cbioportal.legacy.persistence.util.CustomRedisCache; +import org.cbioportal.legacy.service.CacheStatisticsService; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; diff --git a/src/main/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImpl.java similarity index 85% rename from src/main/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImpl.java index d371743f716..287ac235530 100644 --- a/src/main/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImpl.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.persistence.ReferenceGenomeGeneRepository; -import org.cbioportal.service.ReferenceGenomeGeneService; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.persistence.ReferenceGenomeGeneRepository; +import org.cbioportal.legacy.service.ReferenceGenomeGeneService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ResourceDataServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ResourceDataServiceImpl.java similarity index 83% rename from src/main/java/org/cbioportal/service/impl/ResourceDataServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ResourceDataServiceImpl.java index 6e1d94ebe77..b57b21b4655 100644 --- a/src/main/java/org/cbioportal/service/impl/ResourceDataServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ResourceDataServiceImpl.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.List; import java.util.ArrayList; -import org.cbioportal.model.ResourceData; -import org.cbioportal.persistence.ResourceDataRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.ResourceDataService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.persistence.ResourceDataRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.ResourceDataService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ResourceDefinitionServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ResourceDefinitionServiceImpl.java similarity index 78% rename from src/main/java/org/cbioportal/service/impl/ResourceDefinitionServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ResourceDefinitionServiceImpl.java index 4fa493d1294..11b1d13e304 100644 --- a/src/main/java/org/cbioportal/service/impl/ResourceDefinitionServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ResourceDefinitionServiceImpl.java @@ -1,14 +1,14 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.Collections; import java.util.List; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.persistence.ResourceDefinitionRepository; -import org.cbioportal.service.ResourceDefinitionService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.ResourceDefinitionNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.persistence.ResourceDefinitionRepository; +import org.cbioportal.legacy.service.ResourceDefinitionService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.ResourceDefinitionNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/SampleListServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/SampleListServiceImpl.java similarity index 88% rename from src/main/java/org/cbioportal/service/impl/SampleListServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/SampleListServiceImpl.java index 583a4a29fb9..6dd175ce6a7 100644 --- a/src/main/java/org/cbioportal/service/impl/SampleListServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/SampleListServiceImpl.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.access.prepost.PostFilter; @@ -29,7 +29,7 @@ public class SampleListServiceImpl implements SampleListService { private String AUTHENTICATE; @Override - @PostFilter("hasPermission(filterObject, T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostFilter("hasPermission(filterObject, T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") public List getAllSampleLists(String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction) { diff --git a/src/main/java/org/cbioportal/service/impl/SampleServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/SampleServiceImpl.java similarity index 90% rename from src/main/java/org/cbioportal/service/impl/SampleServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/SampleServiceImpl.java index 5d3bd389517..bf308a59481 100644 --- a/src/main/java/org/cbioportal/service/impl/SampleServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/SampleServiceImpl.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.SampleRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.SampleRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ServerStatusServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImpl.java similarity index 85% rename from src/main/java/org/cbioportal/service/impl/ServerStatusServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImpl.java index 4a60a65ea58..8ae8d850d35 100644 --- a/src/main/java/org/cbioportal/service/impl/ServerStatusServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImpl.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.io.Serializable; import java.util.List; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.service.ServerStatusService; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.service.ServerStatusService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImpl.java similarity index 79% rename from src/main/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImpl.java index c1616ac8473..64e81dfa85c 100644 --- a/src/main/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantCopyNumberRegionRepository; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantCopyNumberRegionRepository; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImpl.java similarity index 73% rename from src/main/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImpl.java index e48c8c259fe..294027699db 100644 --- a/src/main/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImpl.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantlyMutatedGeneRepository; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantlyMutatedGeneRepository; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/StaticDataTimestampServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImpl.java similarity index 86% rename from src/main/java/org/cbioportal/service/impl/StaticDataTimestampServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImpl.java index 47ad5e78220..40674d934f5 100644 --- a/src/main/java/org/cbioportal/service/impl/StaticDataTimestampServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImpl.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.TableTimestampPair; -import org.cbioportal.service.StaticDataTimestampService; -import org.cbioportal.persistence.StaticDataTimeStampRepository; +import org.cbioportal.legacy.model.TableTimestampPair; +import org.cbioportal.legacy.service.StaticDataTimestampService; +import org.cbioportal.legacy.persistence.StaticDataTimeStampRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/StructuralVariantServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImpl.java similarity index 83% rename from src/main/java/org/cbioportal/service/impl/StructuralVariantServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImpl.java index 07222ad3ee6..0d80f405fa6 100644 --- a/src/main/java/org/cbioportal/service/impl/StructuralVariantServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImpl.java @@ -21,22 +21,22 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.persistence.StructuralVariantRepository; -import org.cbioportal.service.StructuralVariantService; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.persistence.StructuralVariantRepository; +import org.cbioportal.legacy.service.StructuralVariantService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import java.util.List; import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; import org.springframework.util.CollectionUtils; @Service diff --git a/src/main/java/org/cbioportal/service/impl/StudyServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StudyServiceImpl.java similarity index 89% rename from src/main/java/org/cbioportal/service/impl/StudyServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StudyServiceImpl.java index a2209fe38d9..cd0e79b429f 100644 --- a/src/main/java/org/cbioportal/service/impl/StudyServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StudyServiceImpl.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.ReadPermissionService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.ReadPermissionService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.security.access.prepost.PostFilter; import org.springframework.security.access.prepost.PreAuthorize; diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StudyViewColumnarServiceImpl.java similarity index 87% rename from src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StudyViewColumnarServiceImpl.java index f827a33411f..4e24dcf881d 100644 --- a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StudyViewColumnarServiceImpl.java @@ -1,40 +1,40 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.service.StudyViewColumnarService; -import org.cbioportal.service.alteration.AlterationCountByGeneService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.treatment.TreatmentCountReportService; -import org.cbioportal.service.util.StudyViewColumnarServiceUtil; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.columnar.util.CustomDataFilterUtil; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.service.StudyViewColumnarService; +import org.cbioportal.legacy.service.alteration.AlterationCountByGeneService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.treatment.TreatmentCountReportService; +import org.cbioportal.legacy.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.columnar.util.CustomDataFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; -import static org.cbioportal.web.columnar.util.ClinicalDataXyPlotUtil.combineClinicalDataForXyPlot; +import static org.cbioportal.legacy.web.columnar.util.ClinicalDataXyPlotUtil.combineClinicalDataForXyPlot; import java.util.ArrayList; import java.util.Collections; diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/StudyViewServiceImpl.java similarity index 92% rename from src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/StudyViewServiceImpl.java index 67276a42b38..98dee029793 100644 --- a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/StudyViewServiceImpl.java @@ -1,42 +1,42 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.collections4.map.MultiKeyMap; import org.apache.commons.lang3.StringUtils; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.GenericAssayDataCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.MutationFilterOption; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.StudyViewService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.GeneIdType; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.GenericAssayDataCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.MutationFilterOption; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.StudyViewService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.web.parameter.GeneIdType; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/TreatmentServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/TreatmentServiceImpl.java similarity index 94% rename from src/main/java/org/cbioportal/service/impl/TreatmentServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/TreatmentServiceImpl.java index 75784a01c15..380ad8897d0 100644 --- a/src/main/java/org/cbioportal/service/impl/TreatmentServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/TreatmentServiceImpl.java @@ -1,10 +1,15 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; -import org.cbioportal.model.*; -import org.cbioportal.persistence.TreatmentRepository; -import org.cbioportal.service.TreatmentService; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.model.Treatment; +import org.cbioportal.legacy.persistence.TreatmentRepository; +import org.cbioportal.legacy.service.TreatmentService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/UnauthDataAccessTokenServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/UnauthDataAccessTokenServiceImpl.java similarity index 94% rename from src/main/java/org/cbioportal/service/impl/UnauthDataAccessTokenServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/UnauthDataAccessTokenServiceImpl.java index 11cb8749223..fbca7235531 100644 --- a/src/main/java/org/cbioportal/service/impl/UnauthDataAccessTokenServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/UnauthDataAccessTokenServiceImpl.java @@ -30,11 +30,11 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.security.access.AccessDeniedException; import org.springframework.security.core.Authentication; diff --git a/src/main/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImpl.java similarity index 95% rename from src/main/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImpl.java index b1c977edb75..9020ddaf6ad 100644 --- a/src/main/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImpl.java @@ -30,15 +30,15 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.DataAccessTokenRepository; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.TokenNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.TokenNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.authentication.BadCredentialsException; diff --git a/src/main/java/org/cbioportal/service/impl/VariantCountServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/VariantCountServiceImpl.java similarity index 80% rename from src/main/java/org/cbioportal/service/impl/VariantCountServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/VariantCountServiceImpl.java index 0c1bdfd2fbe..d41be62a5d8 100644 --- a/src/main/java/org/cbioportal/service/impl/VariantCountServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/VariantCountServiceImpl.java @@ -1,14 +1,14 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.VariantCount; -import org.cbioportal.persistence.VariantCountRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.VariantCountService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.persistence.VariantCountRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.VariantCountService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImpl.java similarity index 95% rename from src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImpl.java index 92c0ef233a9..545edd70595 100644 --- a/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImpl.java @@ -1,11 +1,16 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.analysis.function.Gaussian; import org.apache.commons.math3.stat.descriptive.rank.Percentile; -import org.cbioportal.model.*; -import org.cbioportal.service.ViolinPlotService; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalViolinPlotBoxData; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.ClinicalViolinPlotIndividualPoint; +import org.cbioportal.legacy.model.ClinicalViolinPlotRowData; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ViolinPlotService; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportService.java b/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportService.java new file mode 100644 index 00000000000..82ca2829d96 --- /dev/null +++ b/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportService.java @@ -0,0 +1,14 @@ +package org.cbioportal.legacy.service.treatment; + +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; + +import java.util.List; + +public interface TreatmentCountReportService { + PatientTreatmentReport getPatientTreatmentReport(StudyViewFilterContext studyViewFilterContext); + SampleTreatmentReport getSampleTreatmentReport(StudyViewFilterContext studyViewFilterContext); +} diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java b/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportServiceImpl.java similarity index 80% rename from src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java rename to src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportServiceImpl.java index 4a96bcdaf85..1cbdc366a29 100644 --- a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java +++ b/src/main/java/org/cbioportal/legacy/service/treatment/TreatmentCountReportServiceImpl.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.treatment; +package org.cbioportal.legacy.service.treatment; -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.model.TemporalRelation; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.StudyViewFilterContext; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.persistence.StudyViewRepository; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; diff --git a/src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java b/src/main/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtil.java similarity index 95% rename from src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtil.java index 9f565e216fc..926cb03ff73 100644 --- a/src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtil.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountBase; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MutSig; +import org.cbioportal.legacy.model.AlterationCountBase; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MutSig; import org.springframework.lang.NonNull; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/service/util/AlterationEnrichmentUtil.java b/src/main/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtil.java similarity index 93% rename from src/main/java/org/cbioportal/service/util/AlterationEnrichmentUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtil.java index 8113cc63f73..a234f7928fd 100644 --- a/src/main/java/org/cbioportal/service/util/AlterationEnrichmentUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtil.java @@ -1,20 +1,20 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.apache.commons.math3.stat.inference.ChiSquareTest; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountBase; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.CountSummary; -import org.cbioportal.model.Gene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.model.AlterationCountBase; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.CountSummary; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/BinnableCustomDataValue.java b/src/main/java/org/cbioportal/legacy/service/util/BinnableCustomDataValue.java similarity index 92% rename from src/main/java/org/cbioportal/service/util/BinnableCustomDataValue.java rename to src/main/java/org/cbioportal/legacy/service/util/BinnableCustomDataValue.java index a8b07f0dd4a..c88c14f5cb2 100644 --- a/src/main/java/org/cbioportal/service/util/BinnableCustomDataValue.java +++ b/src/main/java/org/cbioportal/legacy/service/util/BinnableCustomDataValue.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; -import org.cbioportal.model.Binnable; +import org.cbioportal.legacy.model.Binnable; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/service/util/ChromosomeCalculator.java b/src/main/java/org/cbioportal/legacy/service/util/ChromosomeCalculator.java similarity index 93% rename from src/main/java/org/cbioportal/service/util/ChromosomeCalculator.java rename to src/main/java/org/cbioportal/legacy/service/util/ChromosomeCalculator.java index 21b81cdd73f..f5e26b904fc 100644 --- a/src/main/java/org/cbioportal/service/util/ChromosomeCalculator.java +++ b/src/main/java/org/cbioportal/legacy/service/util/ChromosomeCalculator.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/ClinicalAttributeUtil.java b/src/main/java/org/cbioportal/legacy/service/util/ClinicalAttributeUtil.java similarity index 95% rename from src/main/java/org/cbioportal/service/util/ClinicalAttributeUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/ClinicalAttributeUtil.java index fc64d5b8d58..aaca33921a3 100644 --- a/src/main/java/org/cbioportal/service/util/ClinicalAttributeUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/ClinicalAttributeUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.util.HashSet; import java.util.List; @@ -6,7 +6,7 @@ import java.util.Set; import java.util.stream.Collectors; -import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttribute; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/service/util/CoExpressionAsyncMethods.java b/src/main/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethods.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/CoExpressionAsyncMethods.java rename to src/main/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethods.java index 6e07ab2c1a9..88d172e20ae 100644 --- a/src/main/java/org/cbioportal/service/util/CoExpressionAsyncMethods.java +++ b/src/main/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethods.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.springframework.stereotype.Component; import org.springframework.scheduling.annotation.Async; -import org.cbioportal.model.CoExpression; +import org.cbioportal.legacy.model.CoExpression; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.linear.Array2DRowRealMatrix; import org.apache.commons.math3.linear.RealMatrix; diff --git a/src/main/java/org/cbioportal/service/util/CustomAttributeWithData.java b/src/main/java/org/cbioportal/legacy/service/util/CustomAttributeWithData.java similarity index 98% rename from src/main/java/org/cbioportal/service/util/CustomAttributeWithData.java rename to src/main/java/org/cbioportal/legacy/service/util/CustomAttributeWithData.java index ce7e5bcd159..fd4f766d30c 100644 --- a/src/main/java/org/cbioportal/service/util/CustomAttributeWithData.java +++ b/src/main/java/org/cbioportal/legacy/service/util/CustomAttributeWithData.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.io.Serializable; import java.util.Arrays; diff --git a/src/main/java/org/cbioportal/service/util/CustomDataSession.java b/src/main/java/org/cbioportal/legacy/service/util/CustomDataSession.java similarity index 91% rename from src/main/java/org/cbioportal/service/util/CustomDataSession.java rename to src/main/java/org/cbioportal/legacy/service/util/CustomDataSession.java index 151af9b4227..0061488acc2 100644 --- a/src/main/java/org/cbioportal/service/util/CustomDataSession.java +++ b/src/main/java/org/cbioportal/legacy/service/util/CustomDataSession.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.io.IOException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.utils.removeme.Session; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/src/main/java/org/cbioportal/service/util/CustomDataValue.java b/src/main/java/org/cbioportal/legacy/service/util/CustomDataValue.java similarity index 95% rename from src/main/java/org/cbioportal/service/util/CustomDataValue.java rename to src/main/java/org/cbioportal/legacy/service/util/CustomDataValue.java index 9e9343a7e2a..96ccb8bda4a 100644 --- a/src/main/java/org/cbioportal/service/util/CustomDataValue.java +++ b/src/main/java/org/cbioportal/legacy/service/util/CustomDataValue.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java b/src/main/java/org/cbioportal/legacy/service/util/ExpressionEnrichmentUtil.java similarity index 95% rename from src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/ExpressionEnrichmentUtil.java index 2fedb6eb5dd..1706bbca0cd 100644 --- a/src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/ExpressionEnrichmentUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.math.BigDecimal; import java.util.ArrayList; @@ -12,20 +12,20 @@ import java.util.stream.Collectors; import java.util.stream.IntStream; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.ExpressionEnrichment; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.GroupStatistics; -import org.cbioportal.model.GenericAssayCountSummary; -import org.cbioportal.model.MolecularAlteration; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.ExpressionEnrichment; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.GroupStatistics; +import org.cbioportal.legacy.model.GenericAssayCountSummary; +import org.cbioportal.legacy.model.MolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.StatUtils; @@ -33,8 +33,8 @@ import org.apache.commons.math3.stat.inference.ChiSquareTest; import org.apache.commons.math3.stat.inference.OneWayAnova; import org.apache.commons.math3.stat.inference.TestUtils; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.SampleService; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.SampleService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/FisherExactTestCalculator.java b/src/main/java/org/cbioportal/legacy/service/util/FisherExactTestCalculator.java similarity index 98% rename from src/main/java/org/cbioportal/service/util/FisherExactTestCalculator.java rename to src/main/java/org/cbioportal/legacy/service/util/FisherExactTestCalculator.java index 150fb370178..e0ebbf1c173 100644 --- a/src/main/java/org/cbioportal/service/util/FisherExactTestCalculator.java +++ b/src/main/java/org/cbioportal/legacy/service/util/FisherExactTestCalculator.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/JwtUtils.java b/src/main/java/org/cbioportal/legacy/service/util/JwtUtils.java similarity index 97% rename from src/main/java/org/cbioportal/service/util/JwtUtils.java rename to src/main/java/org/cbioportal/legacy/service/util/JwtUtils.java index e7022de31a7..8b67b1f8af2 100644 --- a/src/main/java/org/cbioportal/service/util/JwtUtils.java +++ b/src/main/java/org/cbioportal/legacy/service/util/JwtUtils.java @@ -46,10 +46,10 @@ * along with this program. If not, see . */ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.exception.InvalidDataAccessTokenException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/cbioportal/service/util/MolecularProfileUtil.java b/src/main/java/org/cbioportal/legacy/service/util/MolecularProfileUtil.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/MolecularProfileUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/MolecularProfileUtil.java index a9cbfa3839e..d9b62752a0b 100644 --- a/src/main/java/org/cbioportal/service/util/MolecularProfileUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/MolecularProfileUtil.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; import org.springframework.stereotype.Component; import java.util.ArrayList; diff --git a/src/main/java/org/cbioportal/service/util/MskWholeSlideViewerTokenGenerator.java b/src/main/java/org/cbioportal/legacy/service/util/MskWholeSlideViewerTokenGenerator.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/MskWholeSlideViewerTokenGenerator.java rename to src/main/java/org/cbioportal/legacy/service/util/MskWholeSlideViewerTokenGenerator.java index 22ac7e776ae..be192127af0 100644 --- a/src/main/java/org/cbioportal/service/util/MskWholeSlideViewerTokenGenerator.java +++ b/src/main/java/org/cbioportal/legacy/service/util/MskWholeSlideViewerTokenGenerator.java @@ -1,5 +1,5 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.util.Base64; import javax.crypto.Mac; diff --git a/src/main/java/org/cbioportal/service/util/ProfiledCasesCounter.java b/src/main/java/org/cbioportal/legacy/service/util/ProfiledCasesCounter.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/ProfiledCasesCounter.java rename to src/main/java/org/cbioportal/legacy/service/util/ProfiledCasesCounter.java index 874a2cd0652..a9b1b8d272e 100644 --- a/src/main/java/org/cbioportal/service/util/ProfiledCasesCounter.java +++ b/src/main/java/org/cbioportal/legacy/service/util/ProfiledCasesCounter.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountBase; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.service.GenePanelService; +import org.cbioportal.legacy.model.AlterationCountBase; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.service.GenePanelService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/service/util/SessionServiceConfig.java b/src/main/java/org/cbioportal/legacy/service/util/SessionServiceConfig.java similarity index 91% rename from src/main/java/org/cbioportal/service/util/SessionServiceConfig.java rename to src/main/java/org/cbioportal/legacy/service/util/SessionServiceConfig.java index ff0adc546ef..d19ef4a7025 100644 --- a/src/main/java/org/cbioportal/service/util/SessionServiceConfig.java +++ b/src/main/java/org/cbioportal/legacy/service/util/SessionServiceConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/src/main/java/org/cbioportal/service/util/SessionServiceRequestHandler.java b/src/main/java/org/cbioportal/legacy/service/util/SessionServiceRequestHandler.java similarity index 96% rename from src/main/java/org/cbioportal/service/util/SessionServiceRequestHandler.java rename to src/main/java/org/cbioportal/legacy/service/util/SessionServiceRequestHandler.java index af9749ee052..f02dc93bb52 100644 --- a/src/main/java/org/cbioportal/service/util/SessionServiceRequestHandler.java +++ b/src/main/java/org/cbioportal/legacy/service/util/SessionServiceRequestHandler.java @@ -1,6 +1,6 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import static org.cbioportal.utils.removeme.Session.*; +import static org.cbioportal.legacy.utils.removeme.Session.*; import java.nio.charset.Charset; @@ -10,8 +10,8 @@ import com.mongodb.BasicDBObject; import org.apache.commons.codec.binary.Base64; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; +import org.cbioportal.legacy.web.parameter.VirtualStudy; +import org.cbioportal.legacy.web.parameter.VirtualStudyData; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Value; diff --git a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java b/src/main/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtil.java similarity index 94% rename from src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java rename to src/main/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtil.java index 981dbb80cf2..7af71652243 100644 --- a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java +++ b/src/main/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtil.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.util; - -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.web.parameter.GenomicDataFilter; +package org.cbioportal.legacy.service.util; + +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import java.util.ArrayList; import java.util.Collection; diff --git a/src/main/java/org/cbioportal/url_shortener/URLShortenerController.java b/src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerController.java similarity index 97% rename from src/main/java/org/cbioportal/url_shortener/URLShortenerController.java rename to src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerController.java index 00804ca9769..5816d264812 100644 --- a/src/main/java/org/cbioportal/url_shortener/URLShortenerController.java +++ b/src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerController.java @@ -1,4 +1,4 @@ -package org.cbioportal.url_shortener; +package org.cbioportal.legacy.url_shortener; import fr.plaisance.bitly.Bit; import fr.plaisance.bitly.Bitly; diff --git a/src/main/java/org/cbioportal/url_shortener/URLShortenerResponse.java b/src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerResponse.java similarity index 92% rename from src/main/java/org/cbioportal/url_shortener/URLShortenerResponse.java rename to src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerResponse.java index bf822857b05..a023fdb2c83 100644 --- a/src/main/java/org/cbioportal/url_shortener/URLShortenerResponse.java +++ b/src/main/java/org/cbioportal/legacy/url_shortener/URLShortenerResponse.java @@ -1,4 +1,4 @@ -package org.cbioportal.url_shortener; +package org.cbioportal.legacy.url_shortener; public class URLShortenerResponse { diff --git a/src/main/java/org/cbioportal/utils/Encoder.java b/src/main/java/org/cbioportal/legacy/utils/Encoder.java similarity index 94% rename from src/main/java/org/cbioportal/utils/Encoder.java rename to src/main/java/org/cbioportal/legacy/utils/Encoder.java index 4cbe5f3f8dc..d9cd7207541 100644 --- a/src/main/java/org/cbioportal/utils/Encoder.java +++ b/src/main/java/org/cbioportal/legacy/utils/Encoder.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils; +package org.cbioportal.legacy.utils; import java.util.Base64; diff --git a/src/main/java/org/cbioportal/utils/config/PropertyCondition.java b/src/main/java/org/cbioportal/legacy/utils/config/PropertyCondition.java similarity index 96% rename from src/main/java/org/cbioportal/utils/config/PropertyCondition.java rename to src/main/java/org/cbioportal/legacy/utils/config/PropertyCondition.java index 42a61f22f9b..04b35373619 100644 --- a/src/main/java/org/cbioportal/utils/config/PropertyCondition.java +++ b/src/main/java/org/cbioportal/legacy/utils/config/PropertyCondition.java @@ -29,9 +29,9 @@ * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . */ -package org.cbioportal.utils.config; +package org.cbioportal.legacy.utils.config; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.context.annotation.Condition; import org.springframework.context.annotation.ConditionContext; import org.springframework.context.annotation.PropertySource; diff --git a/src/main/java/org/cbioportal/utils/config/annotation/ConditionalOnProperty.java b/src/main/java/org/cbioportal/legacy/utils/config/annotation/ConditionalOnProperty.java similarity index 94% rename from src/main/java/org/cbioportal/utils/config/annotation/ConditionalOnProperty.java rename to src/main/java/org/cbioportal/legacy/utils/config/annotation/ConditionalOnProperty.java index 57257cb4908..764db0c06e8 100644 --- a/src/main/java/org/cbioportal/utils/config/annotation/ConditionalOnProperty.java +++ b/src/main/java/org/cbioportal/legacy/utils/config/annotation/ConditionalOnProperty.java @@ -1,6 +1,6 @@ -package org.cbioportal.utils.config.annotation; +package org.cbioportal.legacy.utils.config.annotation; -import org.cbioportal.utils.config.PropertyCondition; +import org.cbioportal.legacy.utils.config.PropertyCondition; import org.springframework.context.annotation.Conditional; import java.lang.annotation.ElementType; diff --git a/src/main/java/org/cbioportal/utils/removeme/Session.java b/src/main/java/org/cbioportal/legacy/utils/removeme/Session.java similarity index 95% rename from src/main/java/org/cbioportal/utils/removeme/Session.java rename to src/main/java/org/cbioportal/legacy/utils/removeme/Session.java index 6d12df58d79..ceeaab8d960 100644 --- a/src/main/java/org/cbioportal/utils/removeme/Session.java +++ b/src/main/java/org/cbioportal/legacy/utils/removeme/Session.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils.removeme; +package org.cbioportal.legacy.utils.removeme; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.annotation.JsonView; @@ -66,7 +66,7 @@ public void setType(SessionType type) { this.type = type; } - @JsonView(org.cbioportal.utils.removeme.Session.Views.Full.class) + @JsonView(Session.Views.Full.class) public SessionType getType() { return type; } diff --git a/src/main/java/org/cbioportal/legacy/utils/security/AccessLevel.java b/src/main/java/org/cbioportal/legacy/utils/security/AccessLevel.java new file mode 100644 index 00000000000..c98448c1407 --- /dev/null +++ b/src/main/java/org/cbioportal/legacy/utils/security/AccessLevel.java @@ -0,0 +1,5 @@ +package org.cbioportal.legacy.utils.security; + +public enum AccessLevel { + READ, LIST +} diff --git a/src/main/java/org/cbioportal/utils/security/PortalSecurityConfig.java b/src/main/java/org/cbioportal/legacy/utils/security/PortalSecurityConfig.java similarity index 89% rename from src/main/java/org/cbioportal/utils/security/PortalSecurityConfig.java rename to src/main/java/org/cbioportal/legacy/utils/security/PortalSecurityConfig.java index 068a1641d68..383ea699093 100644 --- a/src/main/java/org/cbioportal/utils/security/PortalSecurityConfig.java +++ b/src/main/java/org/cbioportal/legacy/utils/security/PortalSecurityConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils.security; +package org.cbioportal.legacy.utils.security; public class PortalSecurityConfig { diff --git a/src/main/java/org/cbioportal/utils/validation/AllowedValues.java b/src/main/java/org/cbioportal/legacy/utils/validation/AllowedValues.java similarity index 94% rename from src/main/java/org/cbioportal/utils/validation/AllowedValues.java rename to src/main/java/org/cbioportal/legacy/utils/validation/AllowedValues.java index b42d3b0679b..a4ea42cd2a6 100644 --- a/src/main/java/org/cbioportal/utils/validation/AllowedValues.java +++ b/src/main/java/org/cbioportal/legacy/utils/validation/AllowedValues.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils.validation; +package org.cbioportal.legacy.utils.validation; import jakarta.validation.Constraint; import jakarta.validation.Payload; diff --git a/src/main/java/org/cbioportal/utils/validation/AllowedValuesValidatorImpl.java b/src/main/java/org/cbioportal/legacy/utils/validation/AllowedValuesValidatorImpl.java similarity index 95% rename from src/main/java/org/cbioportal/utils/validation/AllowedValuesValidatorImpl.java rename to src/main/java/org/cbioportal/legacy/utils/validation/AllowedValuesValidatorImpl.java index 08eb9800b5c..b018f09df33 100644 --- a/src/main/java/org/cbioportal/utils/validation/AllowedValuesValidatorImpl.java +++ b/src/main/java/org/cbioportal/legacy/utils/validation/AllowedValuesValidatorImpl.java @@ -1,4 +1,4 @@ -package org.cbioportal.utils.validation; +package org.cbioportal.legacy.utils.validation; import jakarta.validation.ConstraintValidator; import jakarta.validation.ConstraintValidatorContext; diff --git a/src/main/java/org/cbioportal/web/AlterationDriverAnnotationController.java b/src/main/java/org/cbioportal/legacy/web/AlterationDriverAnnotationController.java similarity index 87% rename from src/main/java/org/cbioportal/web/AlterationDriverAnnotationController.java rename to src/main/java/org/cbioportal/legacy/web/AlterationDriverAnnotationController.java index 35880303b77..4c730566343 100644 --- a/src/main/java/org/cbioportal/web/AlterationDriverAnnotationController.java +++ b/src/main/java/org/cbioportal/legacy/web/AlterationDriverAnnotationController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -6,9 +6,9 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.model.CustomDriverAnnotationReport; -import org.cbioportal.service.AlterationDriverAnnotationService; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.service.AlterationDriverAnnotationService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -33,7 +33,7 @@ public class AlterationDriverAnnotationController { @Autowired private AlterationDriverAnnotationService alterationDriverAnnotationService; - @PreAuthorize("hasPermission(#molecularProfileIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/custom-driver-annotation-report/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(summary = "Return availability of custom driver annotations for molecular profiles") diff --git a/src/main/java/org/cbioportal/web/AlterationEnrichmentController.java b/src/main/java/org/cbioportal/legacy/web/AlterationEnrichmentController.java similarity index 84% rename from src/main/java/org/cbioportal/web/AlterationEnrichmentController.java rename to src/main/java/org/cbioportal/legacy/web/AlterationEnrichmentController.java index 2d635e1e3e9..6c752b67780 100644 --- a/src/main/java/org/cbioportal/web/AlterationEnrichmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/AlterationEnrichmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,15 +8,15 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.AlterationEnrichmentService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.AlterationEnrichmentService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -46,7 +46,7 @@ public class AlterationEnrichmentController { @Autowired private AlterationEnrichmentService alterationEnrichmentService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/alteration-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(summary ="Fetch alteration enrichments in molecular profiles") diff --git a/src/main/java/org/cbioportal/web/CacheController.java b/src/main/java/org/cbioportal/legacy/web/CacheController.java similarity index 94% rename from src/main/java/org/cbioportal/web/CacheController.java rename to src/main/java/org/cbioportal/legacy/web/CacheController.java index c86982c2b6f..694cef77c96 100644 --- a/src/main/java/org/cbioportal/web/CacheController.java +++ b/src/main/java/org/cbioportal/legacy/web/CacheController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -6,9 +6,9 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.service.CacheService; -import org.cbioportal.service.exception.CacheOperationException; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.service.CacheService; +import org.cbioportal.legacy.service.exception.CacheOperationException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/CacheStatsController.java b/src/main/java/org/cbioportal/legacy/web/CacheStatsController.java similarity index 92% rename from src/main/java/org/cbioportal/web/CacheStatsController.java rename to src/main/java/org/cbioportal/legacy/web/CacheStatsController.java index abcdff97a9d..1363cc406e3 100644 --- a/src/main/java/org/cbioportal/web/CacheStatsController.java +++ b/src/main/java/org/cbioportal/legacy/web/CacheStatsController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Hidden; import io.swagger.v3.oas.annotations.Operation; @@ -8,9 +8,9 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.service.CacheStatisticsService; -import org.cbioportal.service.exception.CacheNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.service.CacheStatisticsService; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/CancerTypeController.java b/src/main/java/org/cbioportal/legacy/web/CancerTypeController.java similarity index 85% rename from src/main/java/org/cbioportal/web/CancerTypeController.java rename to src/main/java/org/cbioportal/legacy/web/CancerTypeController.java index 3ea034f775a..29aed4ad834 100644 --- a/src/main/java/org/cbioportal/web/CancerTypeController.java +++ b/src/main/java/org/cbioportal/legacy/web/CancerTypeController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,16 +9,16 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.exception.CancerTypeNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.CancerTypeSortBy; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.CancerTypeSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/ClinicalAttributeController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalAttributeController.java similarity index 90% rename from src/main/java/org/cbioportal/web/ClinicalAttributeController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalAttributeController.java index 730b8925810..b65e7debef7 100644 --- a/src/main/java/org/cbioportal/web/ClinicalAttributeController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalAttributeController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,17 +10,17 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.ClinicalAttributeSortBy; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ClinicalAttributeSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -79,7 +79,7 @@ public ResponseEntity> getAllClinicalAttributes( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-attributes", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical attributes in the specified study") @@ -115,7 +115,7 @@ public ResponseEntity> getAllClinicalAttributesInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-attributes/{clinicalAttributeId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get specified clinical attribute") @@ -132,7 +132,7 @@ public ResponseEntity getClinicalAttributeInStudy( HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-attributes/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical attributes") diff --git a/src/main/java/org/cbioportal/web/ClinicalAttributeCountController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalAttributeCountController.java similarity index 88% rename from src/main/java/org/cbioportal/web/ClinicalAttributeCountController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalAttributeCountController.java index 7bf96005675..8456ca07850 100644 --- a/src/main/java/org/cbioportal/web/ClinicalAttributeCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalAttributeCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,12 +8,12 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.ClinicalAttributeCountFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalAttributeCountFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -40,7 +40,7 @@ public class ClinicalAttributeCountController { @Autowired private ClinicalAttributeService clinicalAttributeService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-attributes/counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get counts for clinical attributes according to their data availability for selected samples/patients") diff --git a/src/main/java/org/cbioportal/web/ClinicalDataController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalDataController.java similarity index 90% rename from src/main/java/org/cbioportal/web/ClinicalDataController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalDataController.java index 1831c3b5689..f7df97657dd 100644 --- a/src/main/java/org/cbioportal/web/ClinicalDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,23 +10,23 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.ClinicalDataIdentifier; -import org.cbioportal.web.parameter.ClinicalDataMultiStudyFilter; -import org.cbioportal.web.parameter.ClinicalDataSingleStudyFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.ClinicalDataSortBy; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.ClinicalDataIdentifier; +import org.cbioportal.legacy.web.parameter.ClinicalDataMultiStudyFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataSingleStudyFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ClinicalDataSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -59,7 +59,7 @@ public class ClinicalDataController { @Autowired private ClinicalDataService clinicalDataService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}/clinical-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical data of a sample in a study") @@ -100,7 +100,7 @@ public ResponseEntity> getAllClinicalDataOfSampleInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}/clinical-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical data of a patient in a study") @@ -141,7 +141,7 @@ public ResponseEntity> getAllClinicalDataOfPatientInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical data in a study") @@ -181,7 +181,7 @@ public ResponseEntity> getAllClinicalDataInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data by patient IDs or sample IDs (specific study)") @@ -211,7 +211,7 @@ public ResponseEntity> fetchAllClinicalDataInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data by patient IDs or sample IDs (all studies)") diff --git a/src/main/java/org/cbioportal/web/ClinicalDataEnrichmentController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentController.java similarity index 89% rename from src/main/java/org/cbioportal/web/ClinicalDataEnrichmentController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentController.java index 7e880875916..2e5f488ceed 100644 --- a/src/main/java/org/cbioportal/web/ClinicalDataEnrichmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,16 +9,16 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalDataEnrichment; -import org.cbioportal.model.Sample; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.SampleService; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.GroupFilter; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.util.ClinicalDataEnrichmentUtil; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalDataEnrichment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.GroupFilter; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.util.ClinicalDataEnrichmentUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -54,7 +54,7 @@ public class ClinicalDataEnrichmentController { @Autowired private SampleService sampleService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data enrichments for the sample groups") @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/ClinicalEventController.java b/src/main/java/org/cbioportal/legacy/web/ClinicalEventController.java similarity index 89% rename from src/main/java/org/cbioportal/web/ClinicalEventController.java rename to src/main/java/org/cbioportal/legacy/web/ClinicalEventController.java index 487adbd479d..cfbd8f1db42 100644 --- a/src/main/java/org/cbioportal/web/ClinicalEventController.java +++ b/src/main/java/org/cbioportal/legacy/web/ClinicalEventController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,14 +10,19 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.*; -import org.cbioportal.web.parameter.sort.ClinicalEventSortBy; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalEventAttributeRequest; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ClinicalEventSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.http.HttpHeaders; @@ -48,7 +53,7 @@ public class ClinicalEventController { @Autowired private ClinicalEventService clinicalEventService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}/clinical-events", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical events of a patient in a study") @@ -87,7 +92,7 @@ public ResponseEntity> getAllClinicalEventsOfPatientInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/clinical-events", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all clinical events in a study") @@ -124,7 +129,7 @@ public ResponseEntity> getAllClinicalEventsInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-events-meta/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, diff --git a/src/main/java/org/cbioportal/web/CoExpressionController.java b/src/main/java/org/cbioportal/legacy/web/CoExpressionController.java similarity index 88% rename from src/main/java/org/cbioportal/web/CoExpressionController.java rename to src/main/java/org/cbioportal/legacy/web/CoExpressionController.java index fd71a7fabc7..7b6b20f0f42 100644 --- a/src/main/java/org/cbioportal/web/CoExpressionController.java +++ b/src/main/java/org/cbioportal/legacy/web/CoExpressionController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.CoExpression; -import org.cbioportal.model.EntityType; -import org.cbioportal.service.CoExpressionService; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.CoExpressionFilter; +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.service.CoExpressionService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.CoExpressionFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -38,7 +38,7 @@ public class CoExpressionController { private CoExpressionService coExpressionService; // requires permission to access both molecularProfileIdA and molecularProfileIdB because service layer does not enforce requirement that both profiles are in the same study - @PreAuthorize("hasPermission(#molecularProfileIdA, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ) and hasPermission(#molecularProfileIdB, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileIdA, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ) and hasPermission(#molecularProfileIdB, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/co-expressions/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/CopyNumberSegmentController.java b/src/main/java/org/cbioportal/legacy/web/CopyNumberSegmentController.java similarity index 88% rename from src/main/java/org/cbioportal/web/CopyNumberSegmentController.java rename to src/main/java/org/cbioportal/legacy/web/CopyNumberSegmentController.java index c16406066f1..93cc5cdb919 100644 --- a/src/main/java/org/cbioportal/web/CopyNumberSegmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/CopyNumberSegmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,18 +10,18 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.service.CopyNumberSegmentService; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.sort.CopyNumberSegmentSortBy; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.service.CopyNumberSegmentService; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.sort.CopyNumberSegmentSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -54,7 +54,7 @@ public class CopyNumberSegmentController { @Autowired private CopyNumberSegmentService copyNumberSegmentService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}/copy-number-segments", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get copy number segments in a sample in a study") @@ -95,7 +95,7 @@ public ResponseEntity> getCopyNumberSegmentsInSampleInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/copy-number-segments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch copy number segments by sample ID") diff --git a/src/main/java/org/cbioportal/web/CosmicCountController.java b/src/main/java/org/cbioportal/legacy/web/CosmicCountController.java similarity index 90% rename from src/main/java/org/cbioportal/web/CosmicCountController.java rename to src/main/java/org/cbioportal/legacy/web/CosmicCountController.java index b696179554a..dae701ddd79 100644 --- a/src/main/java/org/cbioportal/web/CosmicCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/CosmicCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,9 +8,9 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.service.CosmicCountService; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.service.CosmicCountService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/DataAccessTokenController.java b/src/main/java/org/cbioportal/legacy/web/DataAccessTokenController.java similarity index 94% rename from src/main/java/org/cbioportal/web/DataAccessTokenController.java rename to src/main/java/org/cbioportal/legacy/web/DataAccessTokenController.java index ca3681d1aec..61e7b798940 100644 --- a/src/main/java/org/cbioportal/web/DataAccessTokenController.java +++ b/src/main/java/org/cbioportal/legacy/web/DataAccessTokenController.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -27,12 +27,12 @@ import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.DataAccessTokenNoUserIdentityException; -import org.cbioportal.service.exception.DataAccessTokenProhibitedUserException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.DataAccessTokenNoUserIdentityException; +import org.cbioportal.legacy.service.exception.DataAccessTokenProhibitedUserException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/DiscreteCopyNumberController.java b/src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberController.java similarity index 89% rename from src/main/java/org/cbioportal/web/DiscreteCopyNumberController.java rename to src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberController.java index 5a865c054a0..604474d218b 100644 --- a/src/main/java/org/cbioportal/web/DiscreteCopyNumberController.java +++ b/src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,16 +8,16 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.DiscreteCopyNumberEventType; -import org.cbioportal.web.parameter.DiscreteCopyNumberFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberEventType; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -44,7 +44,7 @@ public class DiscreteCopyNumberController { @Autowired private DiscreteCopyNumberService discreteCopyNumberService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/discrete-copy-number", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get discrete copy number alterations in a molecular profile") @@ -74,7 +74,7 @@ public ResponseEntity> getDiscreteCopyNumbersInMole } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/discrete-copy-number/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/DiscreteCopyNumberCountController.java b/src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountController.java similarity index 86% rename from src/main/java/org/cbioportal/web/DiscreteCopyNumberCountController.java rename to src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountController.java index da8952d57ee..5ef9e5237b3 100644 --- a/src/main/java/org/cbioportal/web/DiscreteCopyNumberCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,12 +8,12 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.CopyNumberCount; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.CopyNumberCountIdentifier; +import org.cbioportal.legacy.model.CopyNumberCount; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.CopyNumberCountIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -41,7 +41,7 @@ public class DiscreteCopyNumberCountController { @Autowired private DiscreteCopyNumberService discreteCopyNumberService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/discrete-copy-number-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/DocRedirectController.java b/src/main/java/org/cbioportal/legacy/web/DocRedirectController.java similarity index 98% rename from src/main/java/org/cbioportal/web/DocRedirectController.java rename to src/main/java/org/cbioportal/legacy/web/DocRedirectController.java index e04443556f0..d4cb77317fc 100644 --- a/src/main/java/org/cbioportal/web/DocRedirectController.java +++ b/src/main/java/org/cbioportal/legacy/web/DocRedirectController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import jakarta.servlet.http.HttpServletRequest; import org.springframework.web.bind.annotation.GetMapping; diff --git a/src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java b/src/main/java/org/cbioportal/legacy/web/ExecuterTimeInterceptor.java similarity index 95% rename from src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java rename to src/main/java/org/cbioportal/legacy/web/ExecuterTimeInterceptor.java index cd53de8c347..d4a6e8548a0 100644 --- a/src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/ExecuterTimeInterceptor.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import org.springframework.ui.ModelMap; import org.springframework.web.context.request.WebRequest; diff --git a/src/main/java/org/cbioportal/web/ExpressionEnrichmentController.java b/src/main/java/org/cbioportal/legacy/web/ExpressionEnrichmentController.java similarity index 88% rename from src/main/java/org/cbioportal/web/ExpressionEnrichmentController.java rename to src/main/java/org/cbioportal/legacy/web/ExpressionEnrichmentController.java index a32ffd37a1d..11cb7be6fad 100644 --- a/src/main/java/org/cbioportal/web/ExpressionEnrichmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/ExpressionEnrichmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,16 +8,16 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.ExpressionEnrichment; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.ExpressionEnrichmentService; -import org.cbioportal.service.exception.GenericAssayNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.ExpressionEnrichment; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.ExpressionEnrichmentService; +import org.cbioportal.legacy.service.exception.GenericAssayNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -46,7 +46,7 @@ public class ExpressionEnrichmentController { @Autowired private ExpressionEnrichmentService expressionEnrichmentService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/expression-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -68,7 +68,7 @@ public ResponseEntity> fetchGenomicEnrichments( HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic-assay-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/GeneController.java b/src/main/java/org/cbioportal/legacy/web/GeneController.java similarity index 89% rename from src/main/java/org/cbioportal/web/GeneController.java rename to src/main/java/org/cbioportal/legacy/web/GeneController.java index 51774d20bfa..f3d25ad4689 100644 --- a/src/main/java/org/cbioportal/web/GeneController.java +++ b/src/main/java/org/cbioportal/legacy/web/GeneController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,18 +10,18 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.Gene; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.exception.GeneWithMultipleEntrezIdsException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.GeneIdType; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.GeneSortBy; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GeneWithMultipleEntrezIdsException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.GeneIdType; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.GeneSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/GenePanelController.java b/src/main/java/org/cbioportal/legacy/web/GenePanelController.java similarity index 90% rename from src/main/java/org/cbioportal/web/GenePanelController.java rename to src/main/java/org/cbioportal/legacy/web/GenePanelController.java index 9bd73ff27bd..8949849d41b 100644 --- a/src/main/java/org/cbioportal/web/GenePanelController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenePanelController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Hidden; import io.swagger.v3.oas.annotations.Operation; @@ -13,16 +13,16 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.GenePanel; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.GenePanelSortBy; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.GenePanelSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/GenePanelDataController.java b/src/main/java/org/cbioportal/legacy/web/GenePanelDataController.java similarity index 88% rename from src/main/java/org/cbioportal/web/GenePanelDataController.java rename to src/main/java/org/cbioportal/legacy/web/GenePanelDataController.java index 6864a6c5db3..9b9741fdc30 100644 --- a/src/main/java/org/cbioportal/web/GenePanelDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenePanelDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,14 +8,14 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.GenePanelDataFilter; -import org.cbioportal.web.parameter.GenePanelDataMultipleStudyFilter; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.GenePanelDataFilter; +import org.cbioportal.legacy.web.parameter.GenePanelDataMultipleStudyFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -45,7 +45,7 @@ public class GenePanelDataController { @Autowired private GenePanelService genePanelService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get gene panel data") @@ -69,7 +69,7 @@ public ResponseEntity> getGenePanelData( return new ResponseEntity<>(genePanelDataList, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/gene-panel-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch gene panel data") diff --git a/src/main/java/org/cbioportal/web/GeneralControllerAdvice.java b/src/main/java/org/cbioportal/legacy/web/GeneralControllerAdvice.java similarity index 97% rename from src/main/java/org/cbioportal/web/GeneralControllerAdvice.java rename to src/main/java/org/cbioportal/legacy/web/GeneralControllerAdvice.java index dbf2fc9d867..d916b0aeedd 100644 --- a/src/main/java/org/cbioportal/web/GeneralControllerAdvice.java +++ b/src/main/java/org/cbioportal/legacy/web/GeneralControllerAdvice.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import org.springframework.core.MethodParameter; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/GenericAssayController.java b/src/main/java/org/cbioportal/legacy/web/GenericAssayController.java similarity index 91% rename from src/main/java/org/cbioportal/web/GenericAssayController.java rename to src/main/java/org/cbioportal/legacy/web/GenericAssayController.java index ae10b64c88b..9bbafc1f703 100644 --- a/src/main/java/org/cbioportal/web/GenericAssayController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenericAssayController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,13 +8,13 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.exception.GenericAssayNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.GenericAssayMetaFilter; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.exception.GenericAssayNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.GenericAssayMetaFilter; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/GenericAssayDataController.java b/src/main/java/org/cbioportal/legacy/web/GenericAssayDataController.java similarity index 90% rename from src/main/java/org/cbioportal/web/GenericAssayDataController.java rename to src/main/java/org/cbioportal/legacy/web/GenericAssayDataController.java index 8cfc55bdb7a..9ecc0709fe7 100644 --- a/src/main/java/org/cbioportal/web/GenericAssayDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenericAssayDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,16 +9,16 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.GenericAssayDataMultipleStudyFilter; -import org.cbioportal.web.parameter.GenericAssayFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.GenericAssayDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -50,7 +50,7 @@ public class GenericAssayDataController { @Autowired private GenericAssayService genericAssayService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic-assay-data/{molecularProfileId}/generic-assay/{genericAssayStableId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get generic_assay_data in a molecular profile") @@ -77,7 +77,7 @@ public ResponseEntity> getGenericAssayDataInMolecularProf } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic_assay_data/{molecularProfileId}/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -110,7 +110,7 @@ public ResponseEntity> fetchGenericAssayDataInMolecularPr } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic_assay_data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch generic_assay_data") diff --git a/src/main/java/org/cbioportal/web/GenericAssayEnrichmentController.java b/src/main/java/org/cbioportal/legacy/web/GenericAssayEnrichmentController.java similarity index 90% rename from src/main/java/org/cbioportal/web/GenericAssayEnrichmentController.java rename to src/main/java/org/cbioportal/legacy/web/GenericAssayEnrichmentController.java index 8959681e09b..f37bbacb7b0 100644 --- a/src/main/java/org/cbioportal/web/GenericAssayEnrichmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenericAssayEnrichmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,14 +8,14 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.ExpressionEnrichmentService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.ExpressionEnrichmentService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -43,7 +43,7 @@ public class GenericAssayEnrichmentController { @Autowired private ExpressionEnrichmentService expressionEnrichmentService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/api/generic-assay-categorical-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -65,7 +65,7 @@ public ResponseEntity> fetchGenericAssay HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/api/generic-assay-binary-enrichments/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/GenesetController.java b/src/main/java/org/cbioportal/legacy/web/GenesetController.java similarity index 91% rename from src/main/java/org/cbioportal/web/GenesetController.java rename to src/main/java/org/cbioportal/legacy/web/GenesetController.java index 0e4eeb56bcc..4761de8af9d 100644 --- a/src/main/java/org/cbioportal/web/GenesetController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenesetController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,13 +10,13 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.Geneset; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; diff --git a/src/main/java/org/cbioportal/web/GenesetCorrelationController.java b/src/main/java/org/cbioportal/legacy/web/GenesetCorrelationController.java similarity index 90% rename from src/main/java/org/cbioportal/web/GenesetCorrelationController.java rename to src/main/java/org/cbioportal/legacy/web/GenesetCorrelationController.java index 1859079bbbe..09b9c7b7086 100644 --- a/src/main/java/org/cbioportal/web/GenesetCorrelationController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenesetCorrelationController.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -32,12 +32,12 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.service.GenesetCorrelationService; -import org.cbioportal.service.exception.GenesetNotFoundException; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.service.GenesetCorrelationService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -63,7 +63,7 @@ public class GenesetCorrelationController { @Autowired private GenesetCorrelationService genesetCorrelationService; - @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/genesets/{genesetId}/expression-correlation/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get the genes in a gene set that have expression correlated to the gene set scores (calculated using Spearman's correlation)") diff --git a/src/main/java/org/cbioportal/web/GenesetDataController.java b/src/main/java/org/cbioportal/legacy/web/GenesetDataController.java similarity index 87% rename from src/main/java/org/cbioportal/web/GenesetDataController.java rename to src/main/java/org/cbioportal/legacy/web/GenesetDataController.java index 9c911d8d18e..f95e4309a7b 100644 --- a/src/main/java/org/cbioportal/web/GenesetDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenesetDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -7,12 +7,12 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.GenesetDataFilterCriteria; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.GenesetDataFilterCriteria; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -38,7 +38,7 @@ public class GenesetDataController { @Autowired private GenesetDataService genesetDataService; - @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/genetic-profiles/{geneticProfileId}/geneset-genetic-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch gene set \"genetic data\" items (gene set scores) by profile Id, gene set ids and sample ids") diff --git a/src/main/java/org/cbioportal/web/GenesetHierarchyController.java b/src/main/java/org/cbioportal/legacy/web/GenesetHierarchyController.java similarity index 92% rename from src/main/java/org/cbioportal/web/GenesetHierarchyController.java rename to src/main/java/org/cbioportal/legacy/web/GenesetHierarchyController.java index 1efd7019138..85dd248ed34 100644 --- a/src/main/java/org/cbioportal/web/GenesetHierarchyController.java +++ b/src/main/java/org/cbioportal/legacy/web/GenesetHierarchyController.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -32,11 +32,11 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.service.GenesetHierarchyService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.service.GenesetHierarchyService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -61,7 +61,7 @@ public class GenesetHierarchyController { @Autowired private GenesetHierarchyService genesetHierarchyService; - @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/geneset-hierarchy/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get gene set hierarchical organization information. I.e. how different gene sets relate to other gene sets, in a hierarchy") diff --git a/src/main/java/org/cbioportal/web/IndexPageController.java b/src/main/java/org/cbioportal/legacy/web/IndexPageController.java similarity index 94% rename from src/main/java/org/cbioportal/web/IndexPageController.java rename to src/main/java/org/cbioportal/legacy/web/IndexPageController.java index 2bd3b95b66f..a00cec65b04 100644 --- a/src/main/java/org/cbioportal/web/IndexPageController.java +++ b/src/main/java/org/cbioportal/legacy/web/IndexPageController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.core.JsonGenerator; import com.fasterxml.jackson.core.JsonProcessingException; @@ -7,9 +7,9 @@ import com.fasterxml.jackson.databind.SerializerProvider; import com.fasterxml.jackson.databind.module.SimpleModule; import jakarta.servlet.http.HttpServletRequest; -import org.cbioportal.service.FrontendPropertiesService; -import org.cbioportal.service.util.MskWholeSlideViewerTokenGenerator; -import org.cbioportal.web.util.HttpRequestUtils; +import org.cbioportal.legacy.service.FrontendPropertiesService; +import org.cbioportal.legacy.service.util.MskWholeSlideViewerTokenGenerator; +import org.cbioportal.legacy.web.util.HttpRequestUtils; import org.json.simple.JSONObject; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -26,7 +26,7 @@ import java.util.HashMap; import java.util.Map; -import static org.cbioportal.service.FrontendPropertiesServiceImpl.FrontendProperty; +import static org.cbioportal.legacy.service.FrontendPropertiesServiceImpl.FrontendProperty; @Controller public class IndexPageController { diff --git a/src/main/java/org/cbioportal/web/InfoController.java b/src/main/java/org/cbioportal/legacy/web/InfoController.java similarity index 93% rename from src/main/java/org/cbioportal/web/InfoController.java rename to src/main/java/org/cbioportal/legacy/web/InfoController.java index 59e9352ca5b..2f899d2712a 100644 --- a/src/main/java/org/cbioportal/web/InfoController.java +++ b/src/main/java/org/cbioportal/legacy/web/InfoController.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.model.Info; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; +import org.cbioportal.legacy.model.Info; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/LegacyApiController.java b/src/main/java/org/cbioportal/legacy/web/LegacyApiController.java similarity index 98% rename from src/main/java/org/cbioportal/web/LegacyApiController.java rename to src/main/java/org/cbioportal/legacy/web/LegacyApiController.java index 6e696460b59..14055451944 100644 --- a/src/main/java/org/cbioportal/web/LegacyApiController.java +++ b/src/main/java/org/cbioportal/legacy/web/LegacyApiController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.JsonNode; diff --git a/src/main/java/org/cbioportal/web/LoginPageController.java b/src/main/java/org/cbioportal/legacy/web/LoginPageController.java similarity index 96% rename from src/main/java/org/cbioportal/web/LoginPageController.java rename to src/main/java/org/cbioportal/legacy/web/LoginPageController.java index cadcdb10838..ee31b83ed79 100644 --- a/src/main/java/org/cbioportal/web/LoginPageController.java +++ b/src/main/java/org/cbioportal/legacy/web/LoginPageController.java @@ -1,8 +1,8 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import jakarta.servlet.http.HttpServletRequest; -import org.cbioportal.service.FrontendPropertiesService; -import org.cbioportal.service.FrontendPropertiesServiceImpl; +import org.cbioportal.legacy.service.FrontendPropertiesService; +import org.cbioportal.legacy.service.FrontendPropertiesServiceImpl; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/web/MatchMinerController.java b/src/main/java/org/cbioportal/legacy/web/MatchMinerController.java similarity index 99% rename from src/main/java/org/cbioportal/web/MatchMinerController.java rename to src/main/java/org/cbioportal/legacy/web/MatchMinerController.java index 3b1ad15f694..7a870f5df3a 100644 --- a/src/main/java/org/cbioportal/web/MatchMinerController.java +++ b/src/main/java/org/cbioportal/legacy/web/MatchMinerController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; diff --git a/src/main/java/org/cbioportal/web/MolecularDataController.java b/src/main/java/org/cbioportal/legacy/web/MolecularDataController.java similarity index 91% rename from src/main/java/org/cbioportal/web/MolecularDataController.java rename to src/main/java/org/cbioportal/legacy/web/MolecularDataController.java index 69ed27f83bf..ac8c03494e9 100644 --- a/src/main/java/org/cbioportal/web/MolecularDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/MolecularDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,17 +9,17 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; import org.apache.commons.lang3.math.NumberUtils; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.NumericGeneMolecularData; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MolecularDataFilter; -import org.cbioportal.web.parameter.MolecularDataMultipleStudyFilter; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.NumericGeneMolecularData; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MolecularDataFilter; +import org.cbioportal.legacy.web.parameter.MolecularDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -51,7 +51,7 @@ public class MolecularDataController { @Autowired private MolecularDataService molecularDataService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/molecular-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all molecular data in a molecular profile") @@ -79,7 +79,7 @@ public ResponseEntity> getAllMolecularDataInMolec } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/molecular-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -112,7 +112,7 @@ public ResponseEntity> fetchAllMolecularDataInMol } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch molecular data") diff --git a/src/main/java/org/cbioportal/web/MolecularProfileController.java b/src/main/java/org/cbioportal/legacy/web/MolecularProfileController.java similarity index 89% rename from src/main/java/org/cbioportal/web/MolecularProfileController.java rename to src/main/java/org/cbioportal/legacy/web/MolecularProfileController.java index ee887e13eff..3a342f59bc6 100644 --- a/src/main/java/org/cbioportal/web/MolecularProfileController.java +++ b/src/main/java/org/cbioportal/legacy/web/MolecularProfileController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,19 +10,19 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MolecularProfileFilter; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.MolecularProfileSortBy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MolecularProfileFilter; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.MolecularProfileSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -83,7 +83,7 @@ public ResponseEntity> getAllMolecularProfiles( } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get molecular profile") @@ -96,7 +96,7 @@ public ResponseEntity getMolecularProfile( return new ResponseEntity<>(molecularProfileService.getMolecularProfile(molecularProfileId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/molecular-profiles", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all molecular profiles in a study") @@ -131,7 +131,7 @@ public ResponseEntity> getAllMolecularProfilesInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch molecular profiles") diff --git a/src/main/java/org/cbioportal/web/MrnaPercentileController.java b/src/main/java/org/cbioportal/legacy/web/MrnaPercentileController.java similarity index 86% rename from src/main/java/org/cbioportal/web/MrnaPercentileController.java rename to src/main/java/org/cbioportal/legacy/web/MrnaPercentileController.java index 816da438e08..c5624aaf905 100644 --- a/src/main/java/org/cbioportal/web/MrnaPercentileController.java +++ b/src/main/java/org/cbioportal/legacy/web/MrnaPercentileController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.MrnaPercentileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.PagingConstants; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.MrnaPercentileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.PagingConstants; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -38,7 +38,7 @@ public class MrnaPercentileController { @Autowired private MrnaPercentileService mrnaPercentileService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/mrna-percentile/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/MskEntityTranslationController.java b/src/main/java/org/cbioportal/legacy/web/MskEntityTranslationController.java similarity index 96% rename from src/main/java/org/cbioportal/web/MskEntityTranslationController.java rename to src/main/java/org/cbioportal/legacy/web/MskEntityTranslationController.java index a9152a02716..42fff4851aa 100644 --- a/src/main/java/org/cbioportal/web/MskEntityTranslationController.java +++ b/src/main/java/org/cbioportal/legacy/web/MskEntityTranslationController.java @@ -30,14 +30,14 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.PropertySource; diff --git a/src/main/java/org/cbioportal/web/MutationController.java b/src/main/java/org/cbioportal/legacy/web/MutationController.java similarity index 92% rename from src/main/java/org/cbioportal/web/MutationController.java rename to src/main/java/org/cbioportal/legacy/web/MutationController.java index 7c72d36db41..a98e793ab36 100644 --- a/src/main/java/org/cbioportal/web/MutationController.java +++ b/src/main/java/org/cbioportal/legacy/web/MutationController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,20 +10,20 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MutationFilter; -import org.cbioportal.web.parameter.MutationMultipleStudyFilter; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; -import org.cbioportal.web.parameter.sort.MutationSortBy; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MutationFilter; +import org.cbioportal.legacy.web.parameter.MutationMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.web.parameter.sort.MutationSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -54,7 +54,7 @@ public class MutationController { @Autowired private MutationService mutationService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/mutations", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get mutations in a molecular profile by Sample List ID") @@ -96,7 +96,7 @@ public ResponseEntity> getMutationsInMolecularProfileBySampleList } } - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/mutations/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch mutations in a molecular profile") @@ -151,7 +151,7 @@ public ResponseEntity> fetchMutationsInMolecularProfile( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/mutations/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch mutations in multiple molecular profiles by sample IDs") diff --git a/src/main/java/org/cbioportal/web/MutationCountController.java b/src/main/java/org/cbioportal/legacy/web/MutationCountController.java similarity index 88% rename from src/main/java/org/cbioportal/web/MutationCountController.java rename to src/main/java/org/cbioportal/legacy/web/MutationCountController.java index 7450c7fe131..d89f2701025 100644 --- a/src/main/java/org/cbioportal/web/MutationCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/MutationCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.service.MutationService; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MutationPositionIdentifier; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MutationPositionIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/MutationSpectrumController.java b/src/main/java/org/cbioportal/legacy/web/MutationSpectrumController.java similarity index 86% rename from src/main/java/org/cbioportal/web/MutationSpectrumController.java rename to src/main/java/org/cbioportal/legacy/web/MutationSpectrumController.java index c6c8a28b718..ecb8bb168a0 100644 --- a/src/main/java/org/cbioportal/web/MutationSpectrumController.java +++ b/src/main/java/org/cbioportal/legacy/web/MutationSpectrumController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.MutationSpectrumService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.MutationSpectrumFilter; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.MutationSpectrumService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.MutationSpectrumFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -37,7 +37,7 @@ public class MutationSpectrumController { @Autowired private MutationSpectrumService mutationSpectrumService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/mutation-spectrums/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/OAuth2DataAccessTokenController.java b/src/main/java/org/cbioportal/legacy/web/OAuth2DataAccessTokenController.java similarity index 95% rename from src/main/java/org/cbioportal/web/OAuth2DataAccessTokenController.java rename to src/main/java/org/cbioportal/legacy/web/OAuth2DataAccessTokenController.java index 94df3e2f7da..be563f0462c 100644 --- a/src/main/java/org/cbioportal/web/OAuth2DataAccessTokenController.java +++ b/src/main/java/org/cbioportal/legacy/web/OAuth2DataAccessTokenController.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -43,12 +43,12 @@ import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.DataAccessTokenNoUserIdentityException; -import org.cbioportal.service.exception.DataAccessTokenProhibitedUserException; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.DataAccessTokenNoUserIdentityException; +import org.cbioportal.legacy.service.exception.DataAccessTokenProhibitedUserException; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpHeaders; diff --git a/src/main/java/org/cbioportal/web/PatientController.java b/src/main/java/org/cbioportal/legacy/web/PatientController.java similarity index 90% rename from src/main/java/org/cbioportal/web/PatientController.java rename to src/main/java/org/cbioportal/legacy/web/PatientController.java index 7c082509bc9..1623b6ab028 100644 --- a/src/main/java/org/cbioportal/web/PatientController.java +++ b/src/main/java/org/cbioportal/legacy/web/PatientController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,20 +10,20 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.Patient; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.PatientFilter; -import org.cbioportal.web.parameter.PatientIdentifier; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.PatientSortBy; -import org.cbioportal.web.util.UniqueKeyExtractor; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.PatientFilter; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.PatientSortBy; +import org.cbioportal.legacy.web.util.UniqueKeyExtractor; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -87,7 +87,7 @@ public ResponseEntity> getAllPatients( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all patients in a study") @@ -122,7 +122,7 @@ public ResponseEntity> getAllPatientsInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get a patient in a study") @@ -137,7 +137,7 @@ public ResponseEntity getPatientInStudy( return new ResponseEntity<>(patientService.getPatientInStudy(studyId, patientId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/patients/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java b/src/main/java/org/cbioportal/legacy/web/PublicVirtualStudiesController.java similarity index 93% rename from src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java rename to src/main/java/org/cbioportal/legacy/web/PublicVirtualStudiesController.java index c48ac446041..30f615f001b 100644 --- a/src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java +++ b/src/main/java/org/cbioportal/legacy/web/PublicVirtualStudiesController.java @@ -1,14 +1,14 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.exception.AccessForbiddenException; -import org.cbioportal.service.exception.CancerTypeNotFoundException; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.exception.AccessForbiddenException; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.web.parameter.VirtualStudy; +import org.cbioportal.legacy.web.parameter.VirtualStudyData; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Value; diff --git a/src/main/java/org/cbioportal/web/ReferenceGenomeGeneController.java b/src/main/java/org/cbioportal/legacy/web/ReferenceGenomeGeneController.java similarity index 92% rename from src/main/java/org/cbioportal/web/ReferenceGenomeGeneController.java rename to src/main/java/org/cbioportal/legacy/web/ReferenceGenomeGeneController.java index 5273ba1a165..8558b9f81c8 100644 --- a/src/main/java/org/cbioportal/web/ReferenceGenomeGeneController.java +++ b/src/main/java/org/cbioportal/legacy/web/ReferenceGenomeGeneController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,12 +8,12 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.service.GeneMemoizerService; -import org.cbioportal.service.ReferenceGenomeGeneService; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.service.GeneMemoizerService; +import org.cbioportal.legacy.service.ReferenceGenomeGeneService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/ResourceDataController.java b/src/main/java/org/cbioportal/legacy/web/ResourceDataController.java similarity index 92% rename from src/main/java/org/cbioportal/web/ResourceDataController.java rename to src/main/java/org/cbioportal/legacy/web/ResourceDataController.java index 4920791285a..012d307df39 100644 --- a/src/main/java/org/cbioportal/web/ResourceDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/ResourceDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,17 +10,17 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.ResourceData; -import org.cbioportal.service.ResourceDataService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.ResourceDataSortBy; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.service.ResourceDataService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ResourceDataSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.ApplicationContext; import org.springframework.cache.annotation.Cacheable; @@ -62,7 +62,7 @@ private ResourceDataController getInstance() { return instance; } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}/resource-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource data of a sample in a study") @@ -100,7 +100,7 @@ public ResponseEntity> getAllResourceDataOfSampleInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}/resource-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource data of a patient in a study") @@ -138,7 +138,7 @@ public ResponseEntity> getAllResourceDataOfPatientInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/resource-data", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource data for a study") @@ -172,7 +172,7 @@ public ResponseEntity> getAllStudyResourceDataInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/resource-data-all", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource data for for all patients and all samples within a study") diff --git a/src/main/java/org/cbioportal/web/ResourceDefinitionController.java b/src/main/java/org/cbioportal/legacy/web/ResourceDefinitionController.java similarity index 86% rename from src/main/java/org/cbioportal/web/ResourceDefinitionController.java rename to src/main/java/org/cbioportal/legacy/web/ResourceDefinitionController.java index 4f4658166c8..13d1737dd14 100644 --- a/src/main/java/org/cbioportal/web/ResourceDefinitionController.java +++ b/src/main/java/org/cbioportal/legacy/web/ResourceDefinitionController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,16 +10,16 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.service.ResourceDefinitionService; -import org.cbioportal.service.exception.ResourceDefinitionNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.ResourceDefinitionSortBy; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.service.ResourceDefinitionService; +import org.cbioportal.legacy.service.exception.ResourceDefinitionNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.ResourceDefinitionSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -45,7 +45,7 @@ public class ResourceDefinitionController { @Autowired private ResourceDefinitionService resourceDefinitionService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/resource-definitions", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource definitions in the specified study") @@ -78,7 +78,7 @@ public ResponseEntity> getAllResourceDefinitionsInStudy } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/resource-definitions/{resourceId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get specified resource definition") @@ -95,7 +95,7 @@ public ResponseEntity getResourceDefinitionInStudy( HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/resource-definitions/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all resource definitions for specified studies") diff --git a/src/main/java/org/cbioportal/web/SamlAndBasicLoginController.java b/src/main/java/org/cbioportal/legacy/web/SamlAndBasicLoginController.java similarity index 87% rename from src/main/java/org/cbioportal/web/SamlAndBasicLoginController.java rename to src/main/java/org/cbioportal/legacy/web/SamlAndBasicLoginController.java index 0364e0d981f..6e0b60969df 100644 --- a/src/main/java/org/cbioportal/web/SamlAndBasicLoginController.java +++ b/src/main/java/org/cbioportal/legacy/web/SamlAndBasicLoginController.java @@ -1,8 +1,8 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import jakarta.servlet.http.HttpServletRequest; -import org.cbioportal.service.FrontendPropertiesService; -import org.cbioportal.service.FrontendPropertiesServiceImpl; +import org.cbioportal.legacy.service.FrontendPropertiesService; +import org.cbioportal.legacy.service.FrontendPropertiesServiceImpl; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/SampleController.java b/src/main/java/org/cbioportal/legacy/web/SampleController.java similarity index 90% rename from src/main/java/org/cbioportal/web/SampleController.java rename to src/main/java/org/cbioportal/legacy/web/SampleController.java index 83cd4df45b5..d9a3dd69106 100644 --- a/src/main/java/org/cbioportal/web/SampleController.java +++ b/src/main/java/org/cbioportal/legacy/web/SampleController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,28 +10,28 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; -import org.cbioportal.utils.security.PortalSecurityConfig; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.sort.SampleSortBy; -import org.cbioportal.web.util.UniqueKeyExtractor; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; +import org.cbioportal.legacy.utils.security.PortalSecurityConfig; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.sort.SampleSortBy; +import org.cbioportal.legacy.web.util.UniqueKeyExtractor; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpHeaders; @@ -145,7 +145,7 @@ public ResponseEntity> getSamplesByKeyword( ); } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all samples in a study") @@ -180,7 +180,7 @@ public ResponseEntity> getAllSamplesInStudy( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get a sample in a study") @@ -195,7 +195,7 @@ public ResponseEntity getSampleInStudy( return new ResponseEntity<>(sampleService.getSampleInStudy(studyId, sampleId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/patients/{patientId}/samples", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all samples of a patient in a study") @@ -233,7 +233,7 @@ public ResponseEntity> getAllSamplesOfPatientInStudy( } } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/samples/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch samples by ID") diff --git a/src/main/java/org/cbioportal/web/SampleListController.java b/src/main/java/org/cbioportal/legacy/web/SampleListController.java similarity index 89% rename from src/main/java/org/cbioportal/web/SampleListController.java rename to src/main/java/org/cbioportal/legacy/web/SampleListController.java index ce1e82eff1c..2ef821925dc 100644 --- a/src/main/java/org/cbioportal/web/SampleListController.java +++ b/src/main/java/org/cbioportal/legacy/web/SampleListController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -10,17 +10,17 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.SampleList; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.SampleListSortBy; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.SampleListSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -79,7 +79,7 @@ public ResponseEntity> getAllSampleLists( } } - @PreAuthorize("hasPermission(#sampleListId, 'SampleListId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#sampleListId, 'SampleListId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/sample-lists/{sampleListId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get sample list") @@ -92,7 +92,7 @@ public ResponseEntity getSampleList( return new ResponseEntity<>(sampleListService.getSampleList(sampleListId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/sample-lists", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all sample lists in a study") @@ -127,7 +127,7 @@ public ResponseEntity> getAllSampleListsInStudy( } } - @PreAuthorize("hasPermission(#sampleListId, 'SampleListId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#sampleListId, 'SampleListId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/sample-lists/{sampleListId}/sample-ids", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all sample IDs in a sample list") @@ -140,7 +140,7 @@ public ResponseEntity> getAllSampleIdsInSampleList( return new ResponseEntity<>(sampleListService.getAllSampleIdsInSampleList(sampleListId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#sampleListIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#sampleListIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/sample-lists/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch sample lists by ID") diff --git a/src/main/java/org/cbioportal/web/ServerStatusController.java b/src/main/java/org/cbioportal/legacy/web/ServerStatusController.java similarity index 85% rename from src/main/java/org/cbioportal/web/ServerStatusController.java rename to src/main/java/org/cbioportal/legacy/web/ServerStatusController.java index 4aa7963a63b..62dbb170e97 100644 --- a/src/main/java/org/cbioportal/web/ServerStatusController.java +++ b/src/main/java/org/cbioportal/legacy/web/ServerStatusController.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.service.ServerStatusService; -import org.cbioportal.service.impl.ServerStatusServiceImpl.ServerStatusMessage; -import org.cbioportal.web.config.annotation.PublicApi; +import org.cbioportal.legacy.service.ServerStatusService; +import org.cbioportal.legacy.service.impl.ServerStatusServiceImpl.ServerStatusMessage; +import org.cbioportal.legacy.web.config.annotation.PublicApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/SessionServiceController.java b/src/main/java/org/cbioportal/legacy/web/SessionServiceController.java similarity index 96% rename from src/main/java/org/cbioportal/web/SessionServiceController.java rename to src/main/java/org/cbioportal/legacy/web/SessionServiceController.java index d2ad7499c1f..d23f3528d80 100644 --- a/src/main/java/org/cbioportal/web/SessionServiceController.java +++ b/src/main/java/org/cbioportal/legacy/web/SessionServiceController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.annotation.JsonInclude.Include; import com.fasterxml.jackson.core.JsonProcessingException; @@ -12,24 +12,24 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import jakarta.servlet.http.HttpServletResponse; import jakarta.validation.constraints.Size; -import org.cbioportal.service.util.CustomAttributeWithData; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.utils.removeme.Session; -import org.cbioportal.web.parameter.CustomGeneList; -import org.cbioportal.web.parameter.CustomGeneListData; -import org.cbioportal.web.parameter.PageSettings; -import org.cbioportal.web.parameter.PageSettingsData; -import org.cbioportal.web.parameter.PageSettingsIdentifier; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.ResultsPageSettings; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.SessionPage; -import org.cbioportal.web.parameter.StudyPageSettings; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; -import org.cbioportal.web.parameter.VirtualStudySamples; -import org.cbioportal.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.service.util.CustomAttributeWithData; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.utils.removeme.Session; +import org.cbioportal.legacy.web.parameter.CustomGeneList; +import org.cbioportal.legacy.web.parameter.CustomGeneListData; +import org.cbioportal.legacy.web.parameter.PageSettings; +import org.cbioportal.legacy.web.parameter.PageSettingsData; +import org.cbioportal.legacy.web.parameter.PageSettingsIdentifier; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.ResultsPageSettings; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.SessionPage; +import org.cbioportal.legacy.web.parameter.StudyPageSettings; +import org.cbioportal.legacy.web.parameter.VirtualStudy; +import org.cbioportal.legacy.web.parameter.VirtualStudyData; +import org.cbioportal.legacy.web.parameter.VirtualStudySamples; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; import org.json.simple.JSONObject; import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; @@ -61,7 +61,7 @@ import java.util.regex.Pattern; import java.util.stream.Collectors; -import static org.cbioportal.web.PublicVirtualStudiesController.ALL_USERS; +import static org.cbioportal.legacy.web.PublicVirtualStudiesController.ALL_USERS; @Controller @RequestMapping("/api/session") diff --git a/src/main/java/org/cbioportal/web/SignificantCopyNumberRegionController.java b/src/main/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionController.java similarity index 84% rename from src/main/java/org/cbioportal/web/SignificantCopyNumberRegionController.java rename to src/main/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionController.java index 48c4919003a..86b0efa4594 100644 --- a/src/main/java/org/cbioportal/web/SignificantCopyNumberRegionController.java +++ b/src/main/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,15 +9,15 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.Gistic; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.SignificantCopyNumberRegionSortBy; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.SignificantCopyNumberRegionSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -43,7 +43,7 @@ public class SignificantCopyNumberRegionController { @Autowired private SignificantCopyNumberRegionService significantCopyNumberRegionService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/significant-copy-number-regions", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get significant copy number alteration regions in a study") diff --git a/src/main/java/org/cbioportal/web/SignificantlyMutatedGenesController.java b/src/main/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesController.java similarity index 84% rename from src/main/java/org/cbioportal/web/SignificantlyMutatedGenesController.java rename to src/main/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesController.java index 3a661feeae2..056408daf43 100644 --- a/src/main/java/org/cbioportal/web/SignificantlyMutatedGenesController.java +++ b/src/main/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,15 +9,15 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; -import org.cbioportal.model.MutSig; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.SignificantlyMutatedGeneSortBy; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.SignificantlyMutatedGeneSortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; @@ -43,7 +43,7 @@ public class SignificantlyMutatedGenesController { @Autowired private SignificantlyMutatedGeneService significantlyMutatedGeneService; - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}/significantly-mutated-genes", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get significantly mutated genes in a study") diff --git a/src/main/java/org/cbioportal/web/StaticDataTimestampController.java b/src/main/java/org/cbioportal/legacy/web/StaticDataTimestampController.java similarity index 90% rename from src/main/java/org/cbioportal/web/StaticDataTimestampController.java rename to src/main/java/org/cbioportal/legacy/web/StaticDataTimestampController.java index 39f3d5da978..b440f36dc18 100644 --- a/src/main/java/org/cbioportal/web/StaticDataTimestampController.java +++ b/src/main/java/org/cbioportal/legacy/web/StaticDataTimestampController.java @@ -1,12 +1,12 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.media.Content; import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; -import org.cbioportal.service.StaticDataTimestampService; -import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.legacy.service.StaticDataTimestampService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; diff --git a/src/main/java/org/cbioportal/web/StructuralVariantController.java b/src/main/java/org/cbioportal/legacy/web/StructuralVariantController.java similarity index 91% rename from src/main/java/org/cbioportal/web/StructuralVariantController.java rename to src/main/java/org/cbioportal/legacy/web/StructuralVariantController.java index 69e03bf3303..3701f6e3979 100644 --- a/src/main/java/org/cbioportal/web/StructuralVariantController.java +++ b/src/main/java/org/cbioportal/legacy/web/StructuralVariantController.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -31,11 +31,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.service.StructuralVariantService; -import org.cbioportal.web.config.InternalApiTags; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.StructuralVariantFilter; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.service.StructuralVariantService; +import org.cbioportal.legacy.web.config.InternalApiTags; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.StructuralVariantFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -61,7 +61,7 @@ public class StructuralVariantController { @Autowired private StructuralVariantService structuralVariantService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/structural-variant/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers") diff --git a/src/main/java/org/cbioportal/web/StudyController.java b/src/main/java/org/cbioportal/legacy/web/StudyController.java similarity index 90% rename from src/main/java/org/cbioportal/web/StudyController.java rename to src/main/java/org/cbioportal/legacy/web/StudyController.java index 253b591719d..b795153518b 100644 --- a/src/main/java/org/cbioportal/web/StudyController.java +++ b/src/main/java/org/cbioportal/legacy/web/StudyController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.core.JsonParseException; import com.fasterxml.jackson.databind.JsonMappingException; @@ -14,19 +14,19 @@ import jakarta.validation.constraints.Max; import jakarta.validation.constraints.Min; import jakarta.validation.constraints.Size; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; -import org.cbioportal.utils.security.PortalSecurityConfig; -import org.cbioportal.web.config.PublicApiTags; -import org.cbioportal.web.config.annotation.PublicApi; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.sort.StudySortBy; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; +import org.cbioportal.legacy.utils.security.PortalSecurityConfig; +import org.cbioportal.legacy.web.config.PublicApiTags; +import org.cbioportal.legacy.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.sort.StudySortBy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.HttpHeaders; @@ -136,7 +136,7 @@ public ResponseEntity> getAllStudies( } } - @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/{studyId}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get a study") @@ -149,7 +149,7 @@ public ResponseEntity getStudy( return new ResponseEntity<>(studyService.getStudy(studyId), HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch studies by IDs") @@ -194,8 +194,8 @@ public ResponseEntity getTags( return new ResponseEntity<>(map, HttpStatus.OK); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") - @PreFilter("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") + @PreFilter("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/studies/tags/fetch", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get the study tags by IDs") diff --git a/src/main/java/org/cbioportal/web/StudyViewController.java b/src/main/java/org/cbioportal/legacy/web/StudyViewController.java similarity index 93% rename from src/main/java/org/cbioportal/web/StudyViewController.java rename to src/main/java/org/cbioportal/legacy/web/StudyViewController.java index 90e53af20b7..2db202c5db9 100644 --- a/src/main/java/org/cbioportal/web/StudyViewController.java +++ b/src/main/java/org/cbioportal/legacy/web/StudyViewController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -16,61 +16,61 @@ import org.apache.commons.math3.stat.correlation.PearsonsCorrelation; import org.apache.commons.math3.stat.correlation.SpearmansCorrelation; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.ClinicalViolinPlotData; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DensityPlotBin; -import org.cbioportal.model.DensityPlotData; -import org.cbioportal.model.GenericAssayDataBin; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataBin; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Patient; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleClinicalDataCollection; -import org.cbioportal.model.SampleList; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyViewService; -import org.cbioportal.service.ViolinPlotService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataBinMethod; -import org.cbioportal.web.parameter.Direction; -import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinCountFilter; -import org.cbioportal.web.parameter.GenomicDataCountFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MutationOption; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.ClinicalDataBinUtil; -import org.cbioportal.web.util.ClinicalDataFetcher; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DensityPlotBin; +import org.cbioportal.legacy.model.DensityPlotData; +import org.cbioportal.legacy.model.GenericAssayDataBin; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataBin; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyViewService; +import org.cbioportal.legacy.service.ViolinPlotService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.Direction; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MutationOption; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.ClinicalDataBinUtil; +import org.cbioportal.legacy.web.util.ClinicalDataFetcher; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.context.ApplicationContext; @@ -144,7 +144,7 @@ private StudyViewController getInstance() { } return instance; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data counts by study view filter") @@ -198,7 +198,7 @@ public List cachedClinicalDataCounts(ClinicalDataCountFil return result; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data bin counts by study view filter") @@ -240,7 +240,7 @@ public List cachableFetchClinicalDataBinCounts(DataBinMethod da ); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/custom-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch custom data bin counts by study view filter") @@ -273,7 +273,7 @@ public ResponseEntity> fetchCustomDataBinCounts( return new ResponseEntity<>(clinicalDataBins, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection',T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection',T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/mutated-genes/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch mutated genes by study view filter") @@ -312,7 +312,7 @@ public List cachedFetchMutatedGenes(StudyViewFilter inter return alterationCountByGenes; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/structuralvariant-genes/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch structural variant genes by study view filter") @@ -353,7 +353,7 @@ public List cacheableFetchStructuralVariantGenes(StudyVie return alterationCountByGenes; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/structuralvariant-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch structural variant genes by study view filter") @@ -392,7 +392,7 @@ public List cacheableFetchStructuralVariantC return new ArrayList<>(); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/cna-genes/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch CNA genes by study view filter") @@ -431,7 +431,7 @@ public List cacheableFetchCNAGenes(StudyViewFilter interc return copyNumberCountByGenes; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/filtered-samples/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch sample IDs by study view filter") @@ -460,7 +460,7 @@ public ResponseEntity> fetchFilteredSamples( return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profile-sample-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch sample counts by study view filter") @@ -514,7 +514,7 @@ private static double parseValueLinear(ClinicalData c) { return Double.parseDouble(c.getAttrValue()); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-density-plot/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data density plot bins by study view filter") @@ -735,7 +735,7 @@ public ResponseEntity fetchClinicalDataDensityPlot( return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-violin-plots/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch violin plot curves per categorical clinical data value, filtered by study view filter") @@ -871,7 +871,7 @@ public ResponseEntity fetchClinicalDataViolinPlots( return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/sample-lists-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch case list sample counts by study view filter") @@ -929,7 +929,7 @@ public List fetchCaseListCounts( } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/genomic-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch genomic data bin counts by study view filter") @ApiResponse(responseCode = "200", description = "OK", @@ -946,7 +946,7 @@ public ResponseEntity> fetchGenomicDataBinCounts( return new ResponseEntity<>(studyViewFilterApplier.getDataBins(dataBinMethod, interceptedGenomicDataBinCountFilter), HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/genomic-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch genomic data counts by GenomicDataCountFilter") @@ -988,7 +988,7 @@ public ResponseEntity> fetchGenomicDataCounts( return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic-assay-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch generic assay data counts by study view filter") @ApiResponse(responseCode = "200", description = "OK", @@ -1028,7 +1028,7 @@ public ResponseEntity> fetchGenericAssayDataCoun return new ResponseEntity<>(result, HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/generic-assay-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch generic assay data bin counts by study view filter") @ApiResponse(responseCode = "200", description = "OK", @@ -1045,7 +1045,7 @@ public ResponseEntity> fetchGenericAssayDataBinCounts( return new ResponseEntity<>(studyViewFilterApplier.getDataBins(dataBinMethod, interceptedGenericAssayDataBinCountFilter), HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-data-table/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch clinical data for the Clinical Tab of Study View") @@ -1126,7 +1126,7 @@ public ImmutablePair cachedClinicalDataTa ); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/clinical-event-type-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get Counts of Clinical Event Types by Study View Filter") @@ -1167,7 +1167,7 @@ public List cachedClinicalEventTypeCounts(StudyViewFilte return clinicalEventService.getClinicalEventTypeCounts(studyIds, sampleIds); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/mutation-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch mutation data counts by GenomicDataCountFilter") diff --git a/src/main/java/org/cbioportal/web/SurvivalController.java b/src/main/java/org/cbioportal/legacy/web/SurvivalController.java similarity index 90% rename from src/main/java/org/cbioportal/web/SurvivalController.java rename to src/main/java/org/cbioportal/legacy/web/SurvivalController.java index 06e5e68b74d..8c4ab8c07d3 100644 --- a/src/main/java/org/cbioportal/web/SurvivalController.java +++ b/src/main/java/org/cbioportal/legacy/web/SurvivalController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.PatientIdentifier; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.http.HttpStatus; @@ -43,7 +43,7 @@ public SurvivalController(ClinicalEventService clinicalEventService) { this.clinicalEventService = clinicalEventService; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/survival-data/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, diff --git a/src/main/java/org/cbioportal/web/TestController.java b/src/main/java/org/cbioportal/legacy/web/TestController.java similarity index 89% rename from src/main/java/org/cbioportal/web/TestController.java rename to src/main/java/org/cbioportal/legacy/web/TestController.java index 3c227e7a97b..19c08642d6e 100644 --- a/src/main/java/org/cbioportal/web/TestController.java +++ b/src/main/java/org/cbioportal/legacy/web/TestController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.RestController; diff --git a/src/main/java/org/cbioportal/web/TreatmentController.java b/src/main/java/org/cbioportal/legacy/web/TreatmentController.java similarity index 91% rename from src/main/java/org/cbioportal/web/TreatmentController.java rename to src/main/java/org/cbioportal/legacy/web/TreatmentController.java index 370b7e9e99a..f4eba59e3e2 100644 --- a/src/main/java/org/cbioportal/web/TreatmentController.java +++ b/src/main/java/org/cbioportal/legacy/web/TreatmentController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -9,16 +9,16 @@ import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; import jakarta.validation.constraints.Size; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.PagingConstants; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.PagingConstants; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.context.ApplicationContext; @@ -68,7 +68,7 @@ private TreatmentController getInstance() { } return instance; } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/treatments/patient", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all patient level treatments") @ApiResponse(responseCode = "200", description = "OK", @@ -114,7 +114,7 @@ public List cachableGetAllPatientTreatments( } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/treatments/sample", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get all sample level treatments") @ApiResponse(responseCode = "200", description = "OK", @@ -160,7 +160,7 @@ public List cacheableGetAllSampleTreatments( return treatmentService.getAllSampleTreatmentRows(sampleIds, studyIds, tier); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/treatments/display-patient", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Should patient level treatments be displayed") @ApiResponse(responseCode = "200", description = "OK", @@ -186,7 +186,7 @@ public Boolean cacheableGetContainsTreatmentData(Set studyIds, ClinicalE return treatmentService.containsTreatmentData(new ArrayList<>(studyIds), tier); } - @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#studyIds, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/treatments/display-sample", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Should sample level treatments be displayed") @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/VariantCountController.java b/src/main/java/org/cbioportal/legacy/web/VariantCountController.java similarity index 87% rename from src/main/java/org/cbioportal/web/VariantCountController.java rename to src/main/java/org/cbioportal/legacy/web/VariantCountController.java index cff905808e4..ac6e7607cf8 100644 --- a/src/main/java/org/cbioportal/web/VariantCountController.java +++ b/src/main/java/org/cbioportal/legacy/web/VariantCountController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import io.swagger.v3.oas.annotations.Operation; import io.swagger.v3.oas.annotations.Parameter; @@ -8,11 +8,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.constraints.Size; -import org.cbioportal.model.VariantCount; -import org.cbioportal.service.VariantCountService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.VariantCountIdentifier; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.service.VariantCountService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.VariantCountIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -40,7 +40,7 @@ public class VariantCountController { @Autowired private VariantCountService variantCountService; - @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/molecular-profiles/{molecularProfileId}/variant-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/legacy/web/columnar/BasicDataBinner.java similarity index 91% rename from src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/columnar/BasicDataBinner.java index 1efaa2b01b9..5f9755830b6 100644 --- a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/BasicDataBinner.java @@ -1,15 +1,33 @@ -package org.cbioportal.web.columnar; +package org.cbioportal.legacy.web.columnar; -import org.cbioportal.model.*; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.StudyViewColumnarService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.columnar.util.CustomDataFilterUtil; -import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; -import org.cbioportal.web.parameter.*; -import org.cbioportal.web.util.DataBinner; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.model.GenericAssayDataBin; +import org.cbioportal.legacy.model.GenomicDataBin; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinCountFilter; +import org.cbioportal.legacy.web.parameter.DataBinFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.StudyViewColumnarService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.columnar.util.CustomDataFilterUtil; +import org.cbioportal.legacy.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.legacy.web.util.DataBinner; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java b/src/main/java/org/cbioportal/legacy/web/columnar/ClinicalDataBinner.java similarity index 86% rename from src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/columnar/ClinicalDataBinner.java index b14d6726dbc..2e8b9375b93 100644 --- a/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/ClinicalDataBinner.java @@ -1,19 +1,19 @@ -package org.cbioportal.web.columnar; - -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.service.StudyViewColumnarService; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.DataBinMethod; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DataBinner; +package org.cbioportal.legacy.web.columnar; + +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.service.StudyViewColumnarService; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DataBinner; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/legacy/web/columnar/StudyViewColumnStoreController.java similarity index 90% rename from src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java rename to src/main/java/org/cbioportal/legacy/web/columnar/StudyViewColumnStoreController.java index 39fc7001b8b..3686d3ad7f6 100644 --- a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/StudyViewColumnStoreController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.columnar; +package org.cbioportal.legacy.web.columnar; import io.swagger.v3.oas.annotations.Hidden; import io.swagger.v3.oas.annotations.Operation; @@ -8,51 +8,51 @@ import io.swagger.v3.oas.annotations.media.Schema; import io.swagger.v3.oas.annotations.responses.ApiResponse; import jakarta.validation.Valid; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.ClinicalViolinPlotData; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DensityPlotData; -import org.cbioportal.model.GenericAssayDataBin; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataBin; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.service.ClinicalDataDensityPlotService; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.StudyViewColumnarService; -import org.cbioportal.service.ViolinPlotService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; -import org.cbioportal.web.columnar.util.CustomDataFilterUtil; -import org.cbioportal.web.columnar.util.NewStudyViewFilterUtil; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataBinMethod; -import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinCountFilter; -import org.cbioportal.web.parameter.GenomicDataCountFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.MutationOption; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DensityPlotParameters; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DensityPlotData; +import org.cbioportal.legacy.model.GenericAssayDataBin; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataBin; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.PatientTreatmentReport; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleTreatmentReport; +import org.cbioportal.legacy.service.ClinicalDataDensityPlotService; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.StudyViewColumnarService; +import org.cbioportal.legacy.service.ViolinPlotService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.legacy.web.columnar.util.CustomDataFilterUtil; +import org.cbioportal.legacy.web.columnar.util.NewStudyViewFilterUtil; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.MutationOption; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DensityPlotParameters; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -112,7 +112,7 @@ public StudyViewColumnStoreController(StudyViewColumnarService studyViewColumnar @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/filtered-samples/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method=RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) public ResponseEntity> fetchFilteredSamples( @@ -127,7 +127,7 @@ public ResponseEntity> fetchFilteredSamples( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/mutated-genes/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method=RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) public ResponseEntity> fetchMutatedGenes( @@ -143,7 +143,7 @@ public ResponseEntity> fetchMutatedGenes( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/molecular-profile-sample-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch sample counts by study view filter") @@ -195,7 +195,7 @@ public ResponseEntity> fetchStructuralVariantGenes( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-data-counts/fetch", method=RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -218,7 +218,7 @@ public ResponseEntity> fetchClinicalDataCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/sample-lists-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch case list sample counts by study view filter") @@ -235,7 +235,7 @@ public List fetchCaseListCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) public ResponseEntity> fetchClinicalDataBinCounts( @@ -253,7 +253,7 @@ public ResponseEntity> fetchClinicalDataBinCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-data-density-plot/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, @@ -321,7 +321,7 @@ public ResponseEntity fetchClinicalDataDensityPlot( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-data-violin-plots/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -390,7 +390,7 @@ public ResponseEntity fetchClinicalDataViolinPlots( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/genomic-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -423,7 +423,7 @@ public ResponseEntity> fetchGenomicDataCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/generic-assay-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -452,7 +452,7 @@ public ResponseEntity> fetchGenericAssayDataCoun } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/mutation-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -488,7 +488,7 @@ public ResponseEntity> fetchMutationDataCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/clinical-event-type-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, @@ -514,7 +514,7 @@ public ResponseEntity> getClinicalEventTypeCounts( return new ResponseEntity<>(studyViewColumnarService.getClinicalEventTypeCounts(interceptedStudyViewFilter), HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/treatments/patient-counts/fetch", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @@ -544,7 +544,7 @@ public ResponseEntity fetchPatientTreatmentCounts( HttpStatus.OK); } - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/treatments/sample-counts/fetch", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @@ -574,7 +574,7 @@ public ResponseEntity fetchSampleTreatmentCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/custom-data-counts/fetch", method=RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @@ -612,7 +612,7 @@ public ResponseEntity> fetchCustomDataCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/custom-data-bin-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method= RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch custom data bin counts by study view filter") @@ -638,7 +638,7 @@ public ResponseEntity> fetchCustomDataBinCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/genomic-data-bin-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @ApiResponse(responseCode = "200", description = "OK", @@ -658,7 +658,7 @@ public ResponseEntity> fetchGenomicDataBinCounts( } @Hidden // should unhide when we remove legacy controller - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/column-store/generic-assay-data-bin-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java b/src/main/java/org/cbioportal/legacy/web/columnar/util/ClinicalDataXyPlotUtil.java similarity index 95% rename from src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java rename to src/main/java/org/cbioportal/legacy/web/columnar/util/ClinicalDataXyPlotUtil.java index 58b2d1e9c4e..5c75cf806a6 100644 --- a/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/util/ClinicalDataXyPlotUtil.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.columnar.util; +package org.cbioportal.legacy.web.columnar.util; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.Sample; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.Sample; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java b/src/main/java/org/cbioportal/legacy/web/columnar/util/CustomDataFilterUtil.java similarity index 95% rename from src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java rename to src/main/java/org/cbioportal/legacy/web/columnar/util/CustomDataFilterUtil.java index 9987bf510c1..786c695e5f3 100644 --- a/src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/util/CustomDataFilterUtil.java @@ -1,17 +1,21 @@ -package org.cbioportal.web.columnar.util; +package org.cbioportal.legacy.web.columnar.util; import com.google.common.collect.Range; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.Patient; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.web.parameter.*; -import org.cbioportal.web.util.CustomDatatype; -import org.cbioportal.web.util.DataBinHelper; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.CustomDatatype; +import org.cbioportal.legacy.web.util.DataBinHelper; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java b/src/main/java/org/cbioportal/legacy/web/columnar/util/NewClinicalDataBinUtil.java similarity index 90% rename from src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java rename to src/main/java/org/cbioportal/legacy/web/columnar/util/NewClinicalDataBinUtil.java index df1b9524c6e..8ea39ca19da 100644 --- a/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/util/NewClinicalDataBinUtil.java @@ -1,16 +1,16 @@ -package org.cbioportal.web.columnar.util; - -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.DataBin; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.DataBinner; +package org.cbioportal.legacy.web.columnar.util; + +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.DataBinner; import java.util.ArrayList; import java.util.HashMap; diff --git a/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java b/src/main/java/org/cbioportal/legacy/web/columnar/util/NewStudyViewFilterUtil.java similarity index 73% rename from src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java rename to src/main/java/org/cbioportal/legacy/web/columnar/util/NewStudyViewFilterUtil.java index 5363802afe2..d42bb7e8786 100644 --- a/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/columnar/util/NewStudyViewFilterUtil.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.columnar.util; +package org.cbioportal.legacy.web.columnar.util; -import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java b/src/main/java/org/cbioportal/legacy/web/config/CustomObjectMapper.java similarity index 56% rename from src/main/java/org/cbioportal/web/config/CustomObjectMapper.java rename to src/main/java/org/cbioportal/legacy/web/config/CustomObjectMapper.java index d5853d58218..8b72a455616 100644 --- a/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java +++ b/src/main/java/org/cbioportal/legacy/web/config/CustomObjectMapper.java @@ -30,77 +30,77 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.SerializationFeature; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.model.Patient; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.service.util.CustomAttributeWithData; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.utils.removeme.Session; -import org.cbioportal.web.mixin.CancerStudyMixin; -import org.cbioportal.web.mixin.ClinicalAttributeCountMixin; -import org.cbioportal.web.mixin.ClinicalAttributeMixin; -import org.cbioportal.web.mixin.ClinicalDataCountMixin; -import org.cbioportal.web.mixin.ClinicalDataMixin; -import org.cbioportal.web.mixin.ClinicalEventDataMixin; -import org.cbioportal.web.mixin.ClinicalEventMixin; -import org.cbioportal.web.mixin.CopyNumberSegMixin; -import org.cbioportal.web.mixin.DataAccessTokenMixin; -import org.cbioportal.web.mixin.DiscreteCopyNumberDataMixin; -import org.cbioportal.web.mixin.GeneMixin; -import org.cbioportal.web.mixin.GenePanelMixin; -import org.cbioportal.web.mixin.GenePanelToGeneMixin; -import org.cbioportal.web.mixin.GenesetCorrelationMixin; -import org.cbioportal.web.mixin.GenesetMixin; -import org.cbioportal.web.mixin.GenesetMolecularDataMixin; -import org.cbioportal.web.mixin.GisticMixin; -import org.cbioportal.web.mixin.GisticToGeneMixin; -import org.cbioportal.web.mixin.MolecularProfileMixin; -import org.cbioportal.web.mixin.MutSigMixin; -import org.cbioportal.web.mixin.MutationMixin; -import org.cbioportal.web.mixin.MutationSpectrumMixin; -import org.cbioportal.web.mixin.PatientMixin; -import org.cbioportal.web.mixin.ResourceDefinitionMixin; -import org.cbioportal.web.mixin.SampleListMixin; -import org.cbioportal.web.mixin.SampleMixin; -import org.cbioportal.web.mixin.SessionDataMixin; -import org.cbioportal.web.mixin.SessionMixin; -import org.cbioportal.web.mixin.StructuralVariantMixin; -import org.cbioportal.web.mixin.TypeOfCancerMixin; -import org.cbioportal.web.parameter.PageSettings; -import org.cbioportal.web.parameter.PageSettingsData; -import org.cbioportal.web.parameter.StudyPageSettings; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.service.util.CustomAttributeWithData; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.utils.removeme.Session; +import org.cbioportal.legacy.web.mixin.CancerStudyMixin; +import org.cbioportal.legacy.web.mixin.ClinicalAttributeCountMixin; +import org.cbioportal.legacy.web.mixin.ClinicalAttributeMixin; +import org.cbioportal.legacy.web.mixin.ClinicalDataCountMixin; +import org.cbioportal.legacy.web.mixin.ClinicalDataMixin; +import org.cbioportal.legacy.web.mixin.ClinicalEventDataMixin; +import org.cbioportal.legacy.web.mixin.ClinicalEventMixin; +import org.cbioportal.legacy.web.mixin.CopyNumberSegMixin; +import org.cbioportal.legacy.web.mixin.DataAccessTokenMixin; +import org.cbioportal.legacy.web.mixin.DiscreteCopyNumberDataMixin; +import org.cbioportal.legacy.web.mixin.GeneMixin; +import org.cbioportal.legacy.web.mixin.GenePanelMixin; +import org.cbioportal.legacy.web.mixin.GenePanelToGeneMixin; +import org.cbioportal.legacy.web.mixin.GenesetCorrelationMixin; +import org.cbioportal.legacy.web.mixin.GenesetMixin; +import org.cbioportal.legacy.web.mixin.GenesetMolecularDataMixin; +import org.cbioportal.legacy.web.mixin.GisticMixin; +import org.cbioportal.legacy.web.mixin.GisticToGeneMixin; +import org.cbioportal.legacy.web.mixin.MolecularProfileMixin; +import org.cbioportal.legacy.web.mixin.MutSigMixin; +import org.cbioportal.legacy.web.mixin.MutationMixin; +import org.cbioportal.legacy.web.mixin.MutationSpectrumMixin; +import org.cbioportal.legacy.web.mixin.PatientMixin; +import org.cbioportal.legacy.web.mixin.ResourceDefinitionMixin; +import org.cbioportal.legacy.web.mixin.SampleListMixin; +import org.cbioportal.legacy.web.mixin.SampleMixin; +import org.cbioportal.legacy.web.mixin.SessionDataMixin; +import org.cbioportal.legacy.web.mixin.SessionMixin; +import org.cbioportal.legacy.web.mixin.StructuralVariantMixin; +import org.cbioportal.legacy.web.mixin.TypeOfCancerMixin; +import org.cbioportal.legacy.web.parameter.PageSettings; +import org.cbioportal.legacy.web.parameter.PageSettingsData; +import org.cbioportal.legacy.web.parameter.StudyPageSettings; +import org.cbioportal.legacy.web.parameter.VirtualStudy; +import org.cbioportal.legacy.web.parameter.VirtualStudyData; import java.util.HashMap; import java.util.Map; diff --git a/src/main/java/org/cbioportal/web/config/DataAccessTokenConfig.java b/src/main/java/org/cbioportal/legacy/web/config/DataAccessTokenConfig.java similarity index 100% rename from src/main/java/org/cbioportal/web/config/DataAccessTokenConfig.java rename to src/main/java/org/cbioportal/legacy/web/config/DataAccessTokenConfig.java diff --git a/src/main/java/org/cbioportal/web/config/InternalApiTags.java b/src/main/java/org/cbioportal/legacy/web/config/InternalApiTags.java similarity index 94% rename from src/main/java/org/cbioportal/web/config/InternalApiTags.java rename to src/main/java/org/cbioportal/legacy/web/config/InternalApiTags.java index 810cbb21939..be1ee85a2db 100644 --- a/src/main/java/org/cbioportal/web/config/InternalApiTags.java +++ b/src/main/java/org/cbioportal/legacy/web/config/InternalApiTags.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; public class InternalApiTags { public static final String CLINICAL_EVENTS = "Clinical Events"; diff --git a/src/main/java/org/cbioportal/web/config/JacksonConfig.java b/src/main/java/org/cbioportal/legacy/web/config/JacksonConfig.java similarity index 90% rename from src/main/java/org/cbioportal/web/config/JacksonConfig.java rename to src/main/java/org/cbioportal/legacy/web/config/JacksonConfig.java index 6e0c7a00247..06ead7110e7 100644 --- a/src/main/java/org/cbioportal/web/config/JacksonConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/config/JacksonConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import com.fasterxml.jackson.databind.ObjectMapper; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/web/config/MethodValidationConfig.java b/src/main/java/org/cbioportal/legacy/web/config/MethodValidationConfig.java similarity index 94% rename from src/main/java/org/cbioportal/web/config/MethodValidationConfig.java rename to src/main/java/org/cbioportal/legacy/web/config/MethodValidationConfig.java index 52ec3c80cfb..14e447aa3f3 100644 --- a/src/main/java/org/cbioportal/web/config/MethodValidationConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/config/MethodValidationConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; diff --git a/src/main/java/org/cbioportal/web/config/PublicApiTags.java b/src/main/java/org/cbioportal/legacy/web/config/PublicApiTags.java similarity index 96% rename from src/main/java/org/cbioportal/web/config/PublicApiTags.java rename to src/main/java/org/cbioportal/legacy/web/config/PublicApiTags.java index 55952192cfa..3b8eeda1e89 100644 --- a/src/main/java/org/cbioportal/web/config/PublicApiTags.java +++ b/src/main/java/org/cbioportal/legacy/web/config/PublicApiTags.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; public class PublicApiTags { public static final String CANCER_TYPES = "Cancer Types"; diff --git a/src/main/java/org/cbioportal/web/config/SwaggerConfig.java b/src/main/java/org/cbioportal/legacy/web/config/SwaggerConfig.java similarity index 95% rename from src/main/java/org/cbioportal/web/config/SwaggerConfig.java rename to src/main/java/org/cbioportal/legacy/web/config/SwaggerConfig.java index 1c3b485865a..1468f14575d 100644 --- a/src/main/java/org/cbioportal/web/config/SwaggerConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/config/SwaggerConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import com.fasterxml.jackson.databind.ObjectMapper; import io.swagger.v3.core.converter.ModelConverters; @@ -8,8 +8,8 @@ import io.swagger.v3.oas.models.info.Contact; import io.swagger.v3.oas.models.info.Info; import io.swagger.v3.oas.models.info.License; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.config.annotation.PublicApi; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.config.annotation.PublicApi; import org.springdoc.core.customizers.OperationCustomizer; import org.springdoc.core.models.GroupedOpenApi; import org.springframework.context.annotation.Bean; diff --git a/src/main/java/org/cbioportal/web/config/WebServletContextListener.java b/src/main/java/org/cbioportal/legacy/web/config/WebServletContextListener.java similarity index 98% rename from src/main/java/org/cbioportal/web/config/WebServletContextListener.java rename to src/main/java/org/cbioportal/legacy/web/config/WebServletContextListener.java index 8311df288df..f770db7f400 100644 --- a/src/main/java/org/cbioportal/web/config/WebServletContextListener.java +++ b/src/main/java/org/cbioportal/legacy/web/config/WebServletContextListener.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import jakarta.servlet.ServletContextEvent; import jakarta.servlet.ServletContextListener; diff --git a/src/main/java/org/cbioportal/web/config/annotation/InternalApi.java b/src/main/java/org/cbioportal/legacy/web/config/annotation/InternalApi.java similarity index 74% rename from src/main/java/org/cbioportal/web/config/annotation/InternalApi.java rename to src/main/java/org/cbioportal/legacy/web/config/annotation/InternalApi.java index f9717fb0610..6e5ff9e37f8 100644 --- a/src/main/java/org/cbioportal/web/config/annotation/InternalApi.java +++ b/src/main/java/org/cbioportal/legacy/web/config/annotation/InternalApi.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config.annotation; +package org.cbioportal.legacy.web.config.annotation; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/src/main/java/org/cbioportal/web/config/annotation/PublicApi.java b/src/main/java/org/cbioportal/legacy/web/config/annotation/PublicApi.java similarity index 74% rename from src/main/java/org/cbioportal/web/config/annotation/PublicApi.java rename to src/main/java/org/cbioportal/legacy/web/config/annotation/PublicApi.java index 76dc021ee72..6fdfbbff2dd 100644 --- a/src/main/java/org/cbioportal/web/config/annotation/PublicApi.java +++ b/src/main/java/org/cbioportal/legacy/web/config/annotation/PublicApi.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config.annotation; +package org.cbioportal.legacy.web.config.annotation; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/src/main/java/org/cbioportal/web/error/ErrorResponse.java b/src/main/java/org/cbioportal/legacy/web/error/ErrorResponse.java similarity index 87% rename from src/main/java/org/cbioportal/web/error/ErrorResponse.java rename to src/main/java/org/cbioportal/legacy/web/error/ErrorResponse.java index cf37cafb850..4e9d7463fcd 100644 --- a/src/main/java/org/cbioportal/web/error/ErrorResponse.java +++ b/src/main/java/org/cbioportal/legacy/web/error/ErrorResponse.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.error; +package org.cbioportal.legacy.web.error; public class ErrorResponse { diff --git a/src/main/java/org/cbioportal/web/error/GlobalExceptionHandler.java b/src/main/java/org/cbioportal/legacy/web/error/GlobalExceptionHandler.java similarity index 87% rename from src/main/java/org/cbioportal/web/error/GlobalExceptionHandler.java rename to src/main/java/org/cbioportal/legacy/web/error/GlobalExceptionHandler.java index 1c24d60c431..1fca9669438 100644 --- a/src/main/java/org/cbioportal/web/error/GlobalExceptionHandler.java +++ b/src/main/java/org/cbioportal/legacy/web/error/GlobalExceptionHandler.java @@ -1,10 +1,28 @@ -package org.cbioportal.web.error; +package org.cbioportal.legacy.web.error; import jakarta.validation.ConstraintViolation; import jakarta.validation.ConstraintViolationException; import jakarta.validation.ElementKind; import jakarta.validation.Path; -import org.cbioportal.service.exception.*; +import org.cbioportal.legacy.service.exception.AccessForbiddenException; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.service.exception.CacheOperationException; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.DataAccessTokenNoUserIdentityException; +import org.cbioportal.legacy.service.exception.DataAccessTokenProhibitedUserException; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.service.exception.GeneWithMultipleEntrezIdsException; +import org.cbioportal.legacy.service.exception.GenericAssayNotFoundException; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.ResourceDefinitionNotFoundException; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.exception.TokenNotFoundException; import org.springframework.beans.TypeMismatchException; import org.springframework.http.HttpStatus; import org.springframework.http.ResponseEntity; diff --git a/src/main/java/org/cbioportal/web/interceptor/UniqueKeyInterceptor.java b/src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java similarity index 89% rename from src/main/java/org/cbioportal/web/interceptor/UniqueKeyInterceptor.java rename to src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java index baba716ecef..4422ddc1758 100644 --- a/src/main/java/org/cbioportal/web/interceptor/UniqueKeyInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java @@ -1,18 +1,18 @@ -package org.cbioportal.web.interceptor; +package org.cbioportal.legacy.web.interceptor; -import org.cbioportal.model.Alteration; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.MolecularData; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.model.NumericGeneMolecularData; -import org.cbioportal.model.Patient; -import org.cbioportal.model.ResourceData; -import org.cbioportal.model.Sample; -import org.cbioportal.model.StructuralVariant; +import org.cbioportal.legacy.model.Alteration; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.MolecularData; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.model.NumericGeneMolecularData; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.StructuralVariant; import org.springframework.core.MethodParameter; import org.springframework.http.MediaType; import org.springframework.http.converter.json.MappingJacksonValue; @@ -23,7 +23,7 @@ import java.util.List; -import static org.cbioportal.utils.Encoder.calculateBase64; +import static org.cbioportal.legacy.utils.Encoder.calculateBase64; @ControllerAdvice("org.cbioportal.web") public class UniqueKeyInterceptor extends AbstractMappingJacksonResponseBodyAdvice { diff --git a/src/main/java/org/cbioportal/web/mixin/CancerStudyMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/CancerStudyMixin.java similarity index 88% rename from src/main/java/org/cbioportal/web/mixin/CancerStudyMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/CancerStudyMixin.java index f8fc1045e66..631bdb7ab47 100644 --- a/src/main/java/org/cbioportal/web/mixin/CancerStudyMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/CancerStudyMixin.java @@ -1,9 +1,9 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonFormat; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; -import org.cbioportal.model.TypeOfCancer; +import org.cbioportal.legacy.model.TypeOfCancer; import java.util.Date; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalAttributeCountMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeCountMixin.java similarity index 80% rename from src/main/java/org/cbioportal/web/mixin/ClinicalAttributeCountMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeCountMixin.java index 4510c009639..de011b02113 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalAttributeCountMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeCountMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalAttributeMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeMixin.java similarity index 89% rename from src/main/java/org/cbioportal/web/mixin/ClinicalAttributeMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeMixin.java index e5b23cbc539..de07b86d37b 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalAttributeMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalAttributeMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalDataCountMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataCountMixin.java similarity index 77% rename from src/main/java/org/cbioportal/web/mixin/ClinicalDataCountMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataCountMixin.java index 92c5c657ccb..93ae2bdf58f 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalDataCountMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataCountMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataMixin.java similarity index 88% rename from src/main/java/org/cbioportal/web/mixin/ClinicalDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataMixin.java index 7f5e481fc4d..8cf37cb6378 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalEventDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventDataMixin.java similarity index 78% rename from src/main/java/org/cbioportal/web/mixin/ClinicalEventDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventDataMixin.java index c889e865a55..d15b7c840ba 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalEventDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/ClinicalEventMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventMixin.java similarity index 89% rename from src/main/java/org/cbioportal/web/mixin/ClinicalEventMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventMixin.java index 1b6c4fc4822..111649b73a8 100644 --- a/src/main/java/org/cbioportal/web/mixin/ClinicalEventMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ClinicalEventMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/CopyNumberSegMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/CopyNumberSegMixin.java similarity index 92% rename from src/main/java/org/cbioportal/web/mixin/CopyNumberSegMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/CopyNumberSegMixin.java index 896c371400e..9176a060b90 100644 --- a/src/main/java/org/cbioportal/web/mixin/CopyNumberSegMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/CopyNumberSegMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/DataAccessTokenMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/DataAccessTokenMixin.java similarity index 89% rename from src/main/java/org/cbioportal/web/mixin/DataAccessTokenMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/DataAccessTokenMixin.java index 119cae61c5a..72aa3a9dc40 100644 --- a/src/main/java/org/cbioportal/web/mixin/DataAccessTokenMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/DataAccessTokenMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonFormat; diff --git a/src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/DiscreteCopyNumberDataMixin.java similarity index 80% rename from src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/DiscreteCopyNumberDataMixin.java index ef9a17f3871..d10468dbde8 100644 --- a/src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/DiscreteCopyNumberDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/legacy/web/mixin/GeneMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GeneMixin.java new file mode 100644 index 00000000000..608583da0a7 --- /dev/null +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GeneMixin.java @@ -0,0 +1,5 @@ +package org.cbioportal.legacy.web.mixin; + +public class GeneMixin { + +} diff --git a/src/main/java/org/cbioportal/web/mixin/GenePanelMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenePanelMixin.java similarity index 85% rename from src/main/java/org/cbioportal/web/mixin/GenePanelMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenePanelMixin.java index 1ccbc6af9bd..fc440b14c66 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenePanelMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenePanelMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/GenePanelToGeneMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenePanelToGeneMixin.java similarity index 77% rename from src/main/java/org/cbioportal/web/mixin/GenePanelToGeneMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenePanelToGeneMixin.java index aacf2d62ba2..b851c55a543 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenePanelToGeneMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenePanelToGeneMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/GenesetCorrelationMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetCorrelationMixin.java similarity index 87% rename from src/main/java/org/cbioportal/web/mixin/GenesetCorrelationMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenesetCorrelationMixin.java index fa42833f5fe..9dbf25d51e4 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenesetCorrelationMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetCorrelationMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/GenesetMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetMixin.java similarity index 76% rename from src/main/java/org/cbioportal/web/mixin/GenesetMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenesetMixin.java index a1a2adecc67..f3b63b38f62 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenesetMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/GenesetMolecularDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetMolecularDataMixin.java similarity index 81% rename from src/main/java/org/cbioportal/web/mixin/GenesetMolecularDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GenesetMolecularDataMixin.java index ae836c19de1..c95d3e396fb 100644 --- a/src/main/java/org/cbioportal/web/mixin/GenesetMolecularDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GenesetMolecularDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/GisticMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GisticMixin.java similarity index 87% rename from src/main/java/org/cbioportal/web/mixin/GisticMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GisticMixin.java index 5913c07dbb5..e7e9d986198 100644 --- a/src/main/java/org/cbioportal/web/mixin/GisticMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GisticMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/GisticToGeneMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/GisticToGeneMixin.java similarity index 76% rename from src/main/java/org/cbioportal/web/mixin/GisticToGeneMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/GisticToGeneMixin.java index b43b1cebd75..3c7d4a19c7b 100644 --- a/src/main/java/org/cbioportal/web/mixin/GisticToGeneMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/GisticToGeneMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/MolecularProfileMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/MolecularProfileMixin.java similarity index 83% rename from src/main/java/org/cbioportal/web/mixin/MolecularProfileMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/MolecularProfileMixin.java index 78f58c76163..d16c96987f3 100644 --- a/src/main/java/org/cbioportal/web/mixin/MolecularProfileMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/MolecularProfileMixin.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; -import org.cbioportal.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudy; public class MolecularProfileMixin { diff --git a/src/main/java/org/cbioportal/web/mixin/MutSigMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/MutSigMixin.java similarity index 91% rename from src/main/java/org/cbioportal/web/mixin/MutSigMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/MutSigMixin.java index f837ef99240..89a830e1e45 100644 --- a/src/main/java/org/cbioportal/web/mixin/MutSigMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/MutSigMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/MutationMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/MutationMixin.java similarity index 93% rename from src/main/java/org/cbioportal/web/mixin/MutationMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/MutationMixin.java index 36e59eaba4e..37ce10a26d2 100644 --- a/src/main/java/org/cbioportal/web/mixin/MutationMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/MutationMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.annotation.JsonRawValue; diff --git a/src/main/java/org/cbioportal/web/mixin/MutationSpectrumMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/MutationSpectrumMixin.java similarity index 90% rename from src/main/java/org/cbioportal/web/mixin/MutationSpectrumMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/MutationSpectrumMixin.java index b4ef6b1dbe6..1dedaf5eadf 100644 --- a/src/main/java/org/cbioportal/web/mixin/MutationSpectrumMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/MutationSpectrumMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/PatientMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/PatientMixin.java similarity index 90% rename from src/main/java/org/cbioportal/web/mixin/PatientMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/PatientMixin.java index 3e555424e4e..ac743b7b0e2 100644 --- a/src/main/java/org/cbioportal/web/mixin/PatientMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/PatientMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ReferenceGenomeGeneMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ReferenceGenomeGeneMixin.java similarity index 83% rename from src/main/java/org/cbioportal/web/mixin/ReferenceGenomeGeneMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ReferenceGenomeGeneMixin.java index 0a333d11eb0..efa7ed39a2e 100644 --- a/src/main/java/org/cbioportal/web/mixin/ReferenceGenomeGeneMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ReferenceGenomeGeneMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/ResourceDefinitionMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/ResourceDefinitionMixin.java similarity index 80% rename from src/main/java/org/cbioportal/web/mixin/ResourceDefinitionMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/ResourceDefinitionMixin.java index b1c60d06509..5b4a3f2ffa2 100644 --- a/src/main/java/org/cbioportal/web/mixin/ResourceDefinitionMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/ResourceDefinitionMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/mixin/SampleListMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/SampleListMixin.java similarity index 82% rename from src/main/java/org/cbioportal/web/mixin/SampleListMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/SampleListMixin.java index d6919ae56aa..f57b40f92c2 100644 --- a/src/main/java/org/cbioportal/web/mixin/SampleListMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/SampleListMixin.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; -import org.cbioportal.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudy; public class SampleListMixin { diff --git a/src/main/java/org/cbioportal/web/mixin/SampleMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/SampleMixin.java similarity index 84% rename from src/main/java/org/cbioportal/web/mixin/SampleMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/SampleMixin.java index 4242a9f5d10..215d205072b 100644 --- a/src/main/java/org/cbioportal/web/mixin/SampleMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/SampleMixin.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; -import org.cbioportal.model.Patient; +import org.cbioportal.legacy.model.Patient; public class SampleMixin { diff --git a/src/main/java/org/cbioportal/web/mixin/SessionDataMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/SessionDataMixin.java similarity index 88% rename from src/main/java/org/cbioportal/web/mixin/SessionDataMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/SessionDataMixin.java index 60b4351eb2a..c65cdc76d2e 100644 --- a/src/main/java/org/cbioportal/web/mixin/SessionDataMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/SessionDataMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import java.util.Set; diff --git a/src/main/java/org/cbioportal/web/mixin/SessionMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/SessionMixin.java similarity index 83% rename from src/main/java/org/cbioportal/web/mixin/SessionMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/SessionMixin.java index 0d7e0a89d45..e76a61f0903 100644 --- a/src/main/java/org/cbioportal/web/mixin/SessionMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/SessionMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/src/main/java/org/cbioportal/web/mixin/StructuralVariantMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/StructuralVariantMixin.java similarity index 79% rename from src/main/java/org/cbioportal/web/mixin/StructuralVariantMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/StructuralVariantMixin.java index a0d840ed5ff..9fe36ab21be 100644 --- a/src/main/java/org/cbioportal/web/mixin/StructuralVariantMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/StructuralVariantMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.*; diff --git a/src/main/java/org/cbioportal/web/mixin/TypeOfCancerMixin.java b/src/main/java/org/cbioportal/legacy/web/mixin/TypeOfCancerMixin.java similarity index 79% rename from src/main/java/org/cbioportal/web/mixin/TypeOfCancerMixin.java rename to src/main/java/org/cbioportal/legacy/web/mixin/TypeOfCancerMixin.java index 73f4d8a1520..48268be7a08 100644 --- a/src/main/java/org/cbioportal/web/mixin/TypeOfCancerMixin.java +++ b/src/main/java/org/cbioportal/legacy/web/mixin/TypeOfCancerMixin.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.mixin; +package org.cbioportal.legacy.web.mixin; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/org/cbioportal/web/parameter/BinsGeneratorConfig.java b/src/main/java/org/cbioportal/legacy/web/parameter/BinsGeneratorConfig.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/BinsGeneratorConfig.java rename to src/main/java/org/cbioportal/legacy/web/parameter/BinsGeneratorConfig.java index 78b0de399e4..de6f54136b0 100644 --- a/src/main/java/org/cbioportal/web/parameter/BinsGeneratorConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/BinsGeneratorConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/CategorizedClinicalDataCountFilter.java similarity index 98% rename from src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CategorizedClinicalDataCountFilter.java index 22ce588453e..92dc23f6bbf 100644 --- a/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CategorizedClinicalDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/CategorizedGenericAssayDataCountFilter.java similarity index 98% rename from src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CategorizedGenericAssayDataCountFilter.java index 3d9face92c8..f46ff86da14 100644 --- a/src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CategorizedGenericAssayDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalAttributeCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalAttributeCountFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/ClinicalAttributeCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalAttributeCountFilter.java index 63e59aa5944..0e32556a484 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalAttributeCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalAttributeCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataBinCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinCountFilter.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataBinCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinCountFilter.java index 565b7286556..9e63e7fcdbb 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataBinCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataBinFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinFilter.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataBinFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinFilter.java index 4df9e8add07..854726c53eb 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataBinFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataBinFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataCountFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataCountFilter.java index 66679896da5..d49a9a8f210 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataFilter.java index 1b406b31532..2a59867b519 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import io.swagger.v3.oas.annotations.Hidden; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataIdentifier.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataIdentifier.java index 9b015f866b7..b7ada176860 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataMultiStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataMultiStudyFilter.java similarity index 81% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataMultiStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataMultiStudyFilter.java index 784331533e7..0bf1ec9726f 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataMultiStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataMultiStudyFilter.java @@ -1,12 +1,12 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; -import org.cbioportal.web.ClinicalDataController; +import org.cbioportal.legacy.web.ClinicalDataController; import jakarta.validation.constraints.Size; import java.util.List; import java.io.Serializable; -import static org.cbioportal.web.parameter.PagingConstants.MAX_PAGE_SIZE; +import static org.cbioportal.legacy.web.parameter.PagingConstants.MAX_PAGE_SIZE; public class ClinicalDataMultiStudyFilter implements Serializable { diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataSingleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataSingleStudyFilter.java similarity index 77% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataSingleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataSingleStudyFilter.java index f76f9daf0b7..76bab723b2c 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataSingleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataSingleStudyFilter.java @@ -1,11 +1,11 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.Size; -import org.cbioportal.web.ClinicalDataController; +import org.cbioportal.legacy.web.ClinicalDataController; import java.util.List; -import static org.cbioportal.web.parameter.PagingConstants.MAX_PAGE_SIZE; +import static org.cbioportal.legacy.web.parameter.PagingConstants.MAX_PAGE_SIZE; public class ClinicalDataSingleStudyFilter { diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataType.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataType.java similarity index 56% rename from src/main/java/org/cbioportal/web/parameter/ClinicalDataType.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataType.java index 6f7121c8fb2..5431a41dc26 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataType.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalDataType.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum ClinicalDataType { SAMPLE, diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalEventAttributeRequest.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventAttributeRequest.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/ClinicalEventAttributeRequest.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventAttributeRequest.java index 4cc2d6f254e..c6e22dbc817 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalEventAttributeRequest.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventAttributeRequest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalEventRequest.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequest.java similarity index 86% rename from src/main/java/org/cbioportal/web/parameter/ClinicalEventRequest.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequest.java index 1397e0dcb85..29db8c56ee4 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalEventRequest.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequest.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; -import org.cbioportal.model.ClinicalEventData; +import org.cbioportal.legacy.model.ClinicalEventData; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalEventRequestIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequestIdentifier.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/ClinicalEventRequestIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequestIdentifier.java index 2d38a85e91c..17162d9965b 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalEventRequestIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalEventRequestIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalTrackConfig.java b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalTrackConfig.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/ClinicalTrackConfig.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ClinicalTrackConfig.java index 9683a4b2fbe..6b33604d3f8 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalTrackConfig.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ClinicalTrackConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/org/cbioportal/web/parameter/CoExpressionFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/CoExpressionFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/CoExpressionFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CoExpressionFilter.java index 0bc03751278..5a97d8e8c69 100644 --- a/src/main/java/org/cbioportal/web/parameter/CoExpressionFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CoExpressionFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/CopyNumberCountIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/CopyNumberCountIdentifier.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/CopyNumberCountIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CopyNumberCountIdentifier.java index 20d14894d2e..8b23b101278 100644 --- a/src/main/java/org/cbioportal/web/parameter/CopyNumberCountIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CopyNumberCountIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public class CopyNumberCountIdentifier { diff --git a/src/main/java/org/cbioportal/web/parameter/CustomGeneList.java b/src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneList.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/CustomGeneList.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneList.java index ae762277a51..4738ac4a60a 100644 --- a/src/main/java/org/cbioportal/web/parameter/CustomGeneList.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneList.java @@ -1,9 +1,9 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.utils.removeme.Session; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/cbioportal/web/parameter/CustomGeneListData.java b/src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneListData.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/CustomGeneListData.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneListData.java index 6e9f1c5d194..dbf66fe8546 100644 --- a/src/main/java/org/cbioportal/web/parameter/CustomGeneListData.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CustomGeneListData.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; diff --git a/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/CustomSampleIdentifier.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/CustomSampleIdentifier.java index 51692168fcb..f8dbfda42ef 100644 --- a/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/CustomSampleIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/DataBinCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinCountFilter.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/DataBinCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataBinCountFilter.java index 4ed75c840d7..149059e0693 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataBinCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/DataBinFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinFilter.java similarity index 98% rename from src/main/java/org/cbioportal/web/parameter/DataBinFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataBinFilter.java index 4011b5547a4..de27ecdb7f3 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataBinFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/parameter/DataBinMethod.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinMethod.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/DataBinMethod.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataBinMethod.java index c63dda3c48c..e336647ae0c 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataBinMethod.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataBinMethod.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; /** * STATIC and DYNAMIC binning relate to the way bin boundaries are derived from numerical data of a sample cohort diff --git a/src/main/java/org/cbioportal/web/parameter/DataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataFilter.java similarity index 87% rename from src/main/java/org/cbioportal/web/parameter/DataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataFilter.java index 05d9c52c8b7..8a26dcf7b31 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/DataFilterValue.java b/src/main/java/org/cbioportal/legacy/web/parameter/DataFilterValue.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/DataFilterValue.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DataFilterValue.java index 47fdb0937e9..53e39525114 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataFilterValue.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DataFilterValue.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/parameter/Direction.java b/src/main/java/org/cbioportal/legacy/web/parameter/Direction.java similarity index 50% rename from src/main/java/org/cbioportal/web/parameter/Direction.java rename to src/main/java/org/cbioportal/legacy/web/parameter/Direction.java index 1453d856420..f8044124309 100644 --- a/src/main/java/org/cbioportal/web/parameter/Direction.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/Direction.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum Direction { diff --git a/src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberEventType.java b/src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberEventType.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberEventType.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberEventType.java index 520c58f98bb..d37d2c63917 100644 --- a/src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberEventType.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberEventType.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.Arrays; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberFilter.java index 859575119c4..ae11c289b94 100644 --- a/src/main/java/org/cbioportal/web/parameter/DiscreteCopyNumberFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/DiscreteCopyNumberFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/EnrichmentFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/EnrichmentFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/EnrichmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/EnrichmentFilter.java index 571f086a951..13a05367216 100644 --- a/src/main/java/org/cbioportal/web/parameter/EnrichmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/EnrichmentFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.NotNull; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GeneFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GeneFilter.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/GeneFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GeneFilter.java index a956f5a63c7..6936beb1b72 100644 --- a/src/main/java/org/cbioportal/web/parameter/GeneFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GeneFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.*; @@ -8,7 +8,7 @@ import jakarta.validation.constraints.AssertTrue; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.CNA; +import org.cbioportal.legacy.model.CNA; import com.fasterxml.jackson.annotation.JsonIgnore; public class GeneFilter implements Serializable { diff --git a/src/main/java/org/cbioportal/web/parameter/GeneIdType.java b/src/main/java/org/cbioportal/legacy/web/parameter/GeneIdType.java similarity index 60% rename from src/main/java/org/cbioportal/web/parameter/GeneIdType.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GeneIdType.java index a46435d1cdb..fe1f7a2da39 100644 --- a/src/main/java/org/cbioportal/web/parameter/GeneIdType.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GeneIdType.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum GeneIdType { diff --git a/src/main/java/org/cbioportal/web/parameter/GenePanelDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataFilter.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/GenePanelDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataFilter.java index 9b28bf8c510..783a5debace 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenePanelDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GenePanelDataMultipleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataMultipleStudyFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/GenePanelDataMultipleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataMultipleStudyFilter.java index f4e70978c6b..d3132930fbd 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenePanelDataMultipleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenePanelDataMultipleStudyFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinCountFilter.java similarity index 92% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinCountFilter.java index eb088eb6faa..078e80b9949 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinFilter.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinFilter.java index 0d30f34b7c0..d7f6dd89139 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataBinFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataBinFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataCountFilter.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataCountFilter.java index b4e60373894..c03153055ad 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataFilter.java index 14dfbf0a46d..a10b1966c5b 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataMultipleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataMultipleStudyFilter.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayDataMultipleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataMultipleStudyFilter.java index 35a1afb390f..60f3d9989c4 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataMultipleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayDataMultipleStudyFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayFilter.java index c0f4a75998c..ba5443d7461 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayMetaFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayMetaFilter.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/GenericAssayMetaFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayMetaFilter.java index f877912b2a2..7e9f2b9f285 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayMetaFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenericAssayMetaFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.Size; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenesetDataFilterCriteria.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenesetDataFilterCriteria.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/GenesetDataFilterCriteria.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenesetDataFilterCriteria.java index f0c9c3397f9..9ec3cfea761 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenesetDataFilterCriteria.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenesetDataFilterCriteria.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataBinCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinCountFilter.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/GenomicDataBinCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinCountFilter.java index b2e9ad1734a..a8d0e031c2c 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataBinCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataBinFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinFilter.java similarity index 92% rename from src/main/java/org/cbioportal/web/parameter/GenomicDataBinFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinFilter.java index 5629c027ec8..e58b06bcee0 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataBinFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataBinFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataCountFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataCountFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/GenomicDataCountFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataCountFilter.java index c01ec7696c1..c805d346c57 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataCountFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataCountFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataFilter.java index 34aca9c0894..3a1ed36f62d 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GenomicDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/Group.java b/src/main/java/org/cbioportal/legacy/web/parameter/Group.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/Group.java rename to src/main/java/org/cbioportal/legacy/web/parameter/Group.java index ae9e8c184e9..970f4592740 100644 --- a/src/main/java/org/cbioportal/web/parameter/Group.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/Group.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/GroupFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/GroupFilter.java similarity index 89% rename from src/main/java/org/cbioportal/web/parameter/GroupFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/GroupFilter.java index 8cfcba4859b..9cf85d87d4c 100644 --- a/src/main/java/org/cbioportal/web/parameter/GroupFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/GroupFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.Valid; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/HeaderKeyConstants.java b/src/main/java/org/cbioportal/legacy/web/parameter/HeaderKeyConstants.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/HeaderKeyConstants.java rename to src/main/java/org/cbioportal/legacy/web/parameter/HeaderKeyConstants.java index 89a51ea7e13..1fe54913a15 100644 --- a/src/main/java/org/cbioportal/web/parameter/HeaderKeyConstants.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/HeaderKeyConstants.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; /* When changing these edit them in portal/src/main/webapp/WEB-INF/web.xml as * well to expose the CORS headers */ diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/MolecularDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataFilter.java index d8765076905..821bd314977 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularDataMultipleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataMultipleStudyFilter.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/MolecularDataMultipleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataMultipleStudyFilter.java index 3527ca674c1..a065f4d804a 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularDataMultipleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularDataMultipleStudyFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java index a8d991ca95e..fbb4d340e09 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupAndAlterationTypeFilter.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import io.swagger.v3.oas.annotations.media.Schema; -import org.cbioportal.model.AlterationFilter; +import org.cbioportal.legacy.model.AlterationFilter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupFilter.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupFilter.java index decdc4748e5..87d975c7fcf 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularProfileCasesGroupFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileCasesGroupFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.ArrayList; import java.util.HashSet; @@ -6,7 +6,7 @@ import jakarta.validation.constraints.Size; -import org.cbioportal.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; public class MolecularProfileCasesGroupFilter { diff --git a/src/main/java/org/cbioportal/web/parameter/MolecularProfileFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/MolecularProfileFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileFilter.java index bc5a460dc9b..7c015b3bb19 100644 --- a/src/main/java/org/cbioportal/web/parameter/MolecularProfileFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MolecularProfileFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationDataFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationDataFilter.java index cb5401aaac6..6b5770bcfb6 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationDataFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/org/cbioportal/web/parameter/MutationFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/MutationFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationFilter.java index f9d10a3fccd..48fccdfeb2f 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MutationMultipleStudyFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationMultipleStudyFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/MutationMultipleStudyFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationMultipleStudyFilter.java index c487cf754fa..0305859ca9a 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationMultipleStudyFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationMultipleStudyFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/MutationOption.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationOption.java similarity index 81% rename from src/main/java/org/cbioportal/web/parameter/MutationOption.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationOption.java index 32d98555dce..f91e6a5cc5e 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationOption.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationOption.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum MutationOption { MUTATED, // fetch mutation data with MUTATED, NOT_MUTATED, NOT_PROFILED in MutationFilterOption diff --git a/src/main/java/org/cbioportal/web/parameter/MutationPositionIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationPositionIdentifier.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/MutationPositionIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationPositionIdentifier.java index a54854ecec9..ed8a5063c3f 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationPositionIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationPositionIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public class MutationPositionIdentifier { diff --git a/src/main/java/org/cbioportal/web/parameter/MutationSpectrumFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/MutationSpectrumFilter.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/MutationSpectrumFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/MutationSpectrumFilter.java index 8d97f0b85f8..9e401b08908 100644 --- a/src/main/java/org/cbioportal/web/parameter/MutationSpectrumFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/MutationSpectrumFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; diff --git a/src/main/java/org/cbioportal/web/parameter/OccurrencePosition.java b/src/main/java/org/cbioportal/legacy/web/parameter/OccurrencePosition.java similarity index 55% rename from src/main/java/org/cbioportal/web/parameter/OccurrencePosition.java rename to src/main/java/org/cbioportal/legacy/web/parameter/OccurrencePosition.java index b9a5dbc9aad..28f9378b0e3 100644 --- a/src/main/java/org/cbioportal/web/parameter/OccurrencePosition.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/OccurrencePosition.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum OccurrencePosition { FIRST, diff --git a/src/main/java/org/cbioportal/web/parameter/PageSettings.java b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettings.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/PageSettings.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PageSettings.java index 0d9c32dfe00..dcbb78024af 100644 --- a/src/main/java/org/cbioportal/web/parameter/PageSettings.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettings.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.IOException; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.utils.removeme.Session; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/cbioportal/web/parameter/PageSettingsData.java b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsData.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/PageSettingsData.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsData.java index 2a22e333bf8..33e25bc49fb 100644 --- a/src/main/java/org/cbioportal/web/parameter/PageSettingsData.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsData.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.Set; diff --git a/src/main/java/org/cbioportal/web/parameter/PageSettingsIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsIdentifier.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/PageSettingsIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsIdentifier.java index 6dbd479e2ad..a3b78b24d81 100644 --- a/src/main/java/org/cbioportal/web/parameter/PageSettingsIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PageSettingsIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.Set; diff --git a/src/main/java/org/cbioportal/web/parameter/PagingConstants.java b/src/main/java/org/cbioportal/legacy/web/parameter/PagingConstants.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/PagingConstants.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PagingConstants.java index 0c26098758c..a65cbcaa799 100644 --- a/src/main/java/org/cbioportal/web/parameter/PagingConstants.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PagingConstants.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public class PagingConstants { diff --git a/src/main/java/org/cbioportal/web/parameter/PatientFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/PatientFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/PatientFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PatientFilter.java index 7f69fb048de..3a44271b583 100644 --- a/src/main/java/org/cbioportal/web/parameter/PatientFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PatientFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/PatientIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/PatientIdentifier.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/PatientIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/PatientIdentifier.java index b7a9117a031..4109d747b02 100644 --- a/src/main/java/org/cbioportal/web/parameter/PatientIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/PatientIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/Projection.java b/src/main/java/org/cbioportal/legacy/web/parameter/Projection.java similarity index 61% rename from src/main/java/org/cbioportal/web/parameter/Projection.java rename to src/main/java/org/cbioportal/legacy/web/parameter/Projection.java index d17103c18ba..b62b2cbd2a7 100644 --- a/src/main/java/org/cbioportal/web/parameter/Projection.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/Projection.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum Projection { diff --git a/src/main/java/org/cbioportal/web/parameter/ResultsPageSettings.java b/src/main/java/org/cbioportal/legacy/web/parameter/ResultsPageSettings.java similarity index 94% rename from src/main/java/org/cbioportal/web/parameter/ResultsPageSettings.java rename to src/main/java/org/cbioportal/legacy/web/parameter/ResultsPageSettings.java index b549ed25c51..bb4205cf4f0 100644 --- a/src/main/java/org/cbioportal/web/parameter/ResultsPageSettings.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/ResultsPageSettings.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/org/cbioportal/web/parameter/SampleFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/SampleFilter.java similarity index 93% rename from src/main/java/org/cbioportal/web/parameter/SampleFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SampleFilter.java index 701dc6181ac..c8dea2bc1db 100644 --- a/src/main/java/org/cbioportal/web/parameter/SampleFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SampleFilter.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; -import org.cbioportal.web.SampleController; +import org.cbioportal.legacy.web.SampleController; import java.util.List; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/SampleIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/SampleIdentifier.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/SampleIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SampleIdentifier.java index 95b78e36763..71abb67cffb 100644 --- a/src/main/java/org/cbioportal/web/parameter/SampleIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SampleIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.Objects; diff --git a/src/main/java/org/cbioportal/web/parameter/SampleMolecularIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/SampleMolecularIdentifier.java similarity index 92% rename from src/main/java/org/cbioportal/web/parameter/SampleMolecularIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SampleMolecularIdentifier.java index 12103116941..9c484eae79d 100644 --- a/src/main/java/org/cbioportal/web/parameter/SampleMolecularIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SampleMolecularIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; diff --git a/src/main/java/org/cbioportal/web/parameter/SessionPage.java b/src/main/java/org/cbioportal/legacy/web/parameter/SessionPage.java similarity index 58% rename from src/main/java/org/cbioportal/web/parameter/SessionPage.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SessionPage.java index bdffd95307f..527f34f7371 100644 --- a/src/main/java/org/cbioportal/web/parameter/SessionPage.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SessionPage.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public enum SessionPage { results_view, diff --git a/src/main/java/org/cbioportal/web/parameter/StructuralVariantFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/StructuralVariantFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/parameter/StructuralVariantFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/StructuralVariantFilter.java index 7d3c831196c..ad87e3bc58a 100644 --- a/src/main/java/org/cbioportal/web/parameter/StructuralVariantFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/StructuralVariantFilter.java @@ -21,13 +21,13 @@ * along with this program. If not, see . */ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.Valid; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.StructuralVariantQuery; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/StudyPageSettings.java b/src/main/java/org/cbioportal/legacy/web/parameter/StudyPageSettings.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/StudyPageSettings.java rename to src/main/java/org/cbioportal/legacy/web/parameter/StudyPageSettings.java index 5dcbc8b3887..49a62f3274f 100644 --- a/src/main/java/org/cbioportal/web/parameter/StudyPageSettings.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/StudyPageSettings.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/StudyViewFilter.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/StudyViewFilter.java index 738d3632a70..61d3f7f5356 100644 --- a/src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/StudyViewFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.List; @@ -10,10 +10,11 @@ import jakarta.validation.Valid; import jakarta.validation.constraints.AssertTrue; import jakarta.validation.constraints.Size; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.GeneFilter; -import org.cbioportal.model.StudyViewStructuralVariantFilter; -import org.cbioportal.web.parameter.filter.*; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.GeneFilter; +import org.cbioportal.legacy.model.StudyViewStructuralVariantFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; @JsonIgnoreProperties(ignoreUnknown = true) @JsonInclude(Include.NON_NULL) diff --git a/src/main/java/org/cbioportal/web/parameter/SurvivalRequest.java b/src/main/java/org/cbioportal/legacy/web/parameter/SurvivalRequest.java similarity index 97% rename from src/main/java/org/cbioportal/web/parameter/SurvivalRequest.java rename to src/main/java/org/cbioportal/legacy/web/parameter/SurvivalRequest.java index 7f770d9cd42..c4301c52a98 100644 --- a/src/main/java/org/cbioportal/web/parameter/SurvivalRequest.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/SurvivalRequest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import jakarta.validation.Valid; import jakarta.validation.constraints.NotNull; diff --git a/src/main/java/org/cbioportal/web/parameter/VariantCountIdentifier.java b/src/main/java/org/cbioportal/legacy/web/parameter/VariantCountIdentifier.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/VariantCountIdentifier.java rename to src/main/java/org/cbioportal/legacy/web/parameter/VariantCountIdentifier.java index 1b6ace73404..4a9090ce935 100644 --- a/src/main/java/org/cbioportal/web/parameter/VariantCountIdentifier.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/VariantCountIdentifier.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; public class VariantCountIdentifier { diff --git a/src/main/java/org/cbioportal/web/parameter/VirtualStudy.java b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudy.java similarity index 91% rename from src/main/java/org/cbioportal/web/parameter/VirtualStudy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudy.java index d5613860982..c4a5e6a1593 100644 --- a/src/main/java/org/cbioportal/web/parameter/VirtualStudy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.IOException; @@ -8,7 +8,7 @@ import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.utils.removeme.Session; +import org.cbioportal.legacy.utils.removeme.Session; @JsonIgnoreProperties(ignoreUnknown = true) public class VirtualStudy extends Session { diff --git a/src/main/java/org/cbioportal/web/parameter/VirtualStudyData.java b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudyData.java similarity index 98% rename from src/main/java/org/cbioportal/web/parameter/VirtualStudyData.java rename to src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudyData.java index f3f60dfb360..b6add15bafd 100644 --- a/src/main/java/org/cbioportal/web/parameter/VirtualStudyData.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudyData.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.io.Serializable; import java.util.HashSet; diff --git a/src/main/java/org/cbioportal/web/parameter/VirtualStudySamples.java b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudySamples.java similarity index 89% rename from src/main/java/org/cbioportal/web/parameter/VirtualStudySamples.java rename to src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudySamples.java index 5cfb36afa3b..ed4e6e9d96c 100644 --- a/src/main/java/org/cbioportal/web/parameter/VirtualStudySamples.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/VirtualStudySamples.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter; +package org.cbioportal.legacy.web.parameter; import java.util.Set; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/AndedPatientTreatmentFilters.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedPatientTreatmentFilters.java similarity index 76% rename from src/main/java/org/cbioportal/web/parameter/filter/AndedPatientTreatmentFilters.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedPatientTreatmentFilters.java index eaf81744f5c..a06cd30d509 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/AndedPatientTreatmentFilters.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedPatientTreatmentFilters.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/AndedSampleTreatmentFilters.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedSampleTreatmentFilters.java similarity index 75% rename from src/main/java/org/cbioportal/web/parameter/filter/AndedSampleTreatmentFilters.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedSampleTreatmentFilters.java index 93960cc7541..1d0f23720fb 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/AndedSampleTreatmentFilters.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/AndedSampleTreatmentFilters.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/OredPatientTreatmentFilters.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/OredPatientTreatmentFilters.java similarity index 75% rename from src/main/java/org/cbioportal/web/parameter/filter/OredPatientTreatmentFilters.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/OredPatientTreatmentFilters.java index 57ae0d3797e..f41fb5faa6e 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/OredPatientTreatmentFilters.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/OredPatientTreatmentFilters.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/OredSampleTreatmentFilters.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/OredSampleTreatmentFilters.java similarity index 80% rename from src/main/java/org/cbioportal/web/parameter/filter/OredSampleTreatmentFilters.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/OredSampleTreatmentFilters.java index 388ab0113a4..497561e4a1e 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/OredSampleTreatmentFilters.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/OredSampleTreatmentFilters.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/PatientTreatmentFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/PatientTreatmentFilter.java similarity index 87% rename from src/main/java/org/cbioportal/web/parameter/filter/PatientTreatmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/PatientTreatmentFilter.java index fb4d8095ce9..d78da03a5cf 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/PatientTreatmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/PatientTreatmentFilter.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; import java.io.Serializable; import java.util.Map; import java.util.Set; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; public class PatientTreatmentFilter implements Serializable { private String treatment; diff --git a/src/main/java/org/cbioportal/web/parameter/filter/SampleTreatmentFilter.java b/src/main/java/org/cbioportal/legacy/web/parameter/filter/SampleTreatmentFilter.java similarity index 82% rename from src/main/java/org/cbioportal/web/parameter/filter/SampleTreatmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/parameter/filter/SampleTreatmentFilter.java index f4c2dcf1027..6975e744aac 100644 --- a/src/main/java/org/cbioportal/web/parameter/filter/SampleTreatmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/filter/SampleTreatmentFilter.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.parameter.filter; +package org.cbioportal.legacy.web.parameter.filter; -import org.cbioportal.model.TemporalRelation; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.io.Serializable; import java.util.Map; diff --git a/src/main/java/org/cbioportal/web/parameter/sort/CancerTypeSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/CancerTypeSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/CancerTypeSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/CancerTypeSortBy.java index 31305e393bd..68152cf1cde 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/CancerTypeSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/CancerTypeSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum CancerTypeSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalAttributeSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalAttributeSortBy.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/sort/ClinicalAttributeSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalAttributeSortBy.java index 5b6ef9c8021..b30e1e6374a 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalAttributeSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalAttributeSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ClinicalAttributeSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalDataSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalDataSortBy.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/sort/ClinicalDataSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalDataSortBy.java index 9da6465c5af..a738c93271c 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalDataSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalDataSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ClinicalDataSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalEventSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalEventSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/ClinicalEventSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalEventSortBy.java index 44508aba81f..84bba1dce25 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ClinicalEventSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ClinicalEventSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ClinicalEventSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/CopyNumberSegmentSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/CopyNumberSegmentSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/CopyNumberSegmentSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/CopyNumberSegmentSortBy.java index 2d662dbd005..b647b770c3e 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/CopyNumberSegmentSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/CopyNumberSegmentSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum CopyNumberSegmentSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/DiscreteCopyNumberSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/DiscreteCopyNumberSortBy.java similarity index 86% rename from src/main/java/org/cbioportal/web/parameter/sort/DiscreteCopyNumberSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/DiscreteCopyNumberSortBy.java index 41e4128c4a9..9cf89c89bfc 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/DiscreteCopyNumberSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/DiscreteCopyNumberSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum DiscreteCopyNumberSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/GenePanelSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/GenePanelSortBy.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/sort/GenePanelSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/GenePanelSortBy.java index 1b2750f9386..f554dcfb891 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/GenePanelSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/GenePanelSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum GenePanelSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/GeneSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/GeneSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/GeneSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/GeneSortBy.java index 233f92864b5..d5062e29314 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/GeneSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/GeneSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum GeneSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/MolecularProfileSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/MolecularProfileSortBy.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/sort/MolecularProfileSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/MolecularProfileSortBy.java index c089ee90fea..b7b063892b8 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/MolecularProfileSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/MolecularProfileSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum MolecularProfileSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/MutationSortBy.java similarity index 95% rename from src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/MutationSortBy.java index ce2caf51cdb..0e27aae5a7c 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/MutationSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum MutationSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/PatientSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/PatientSortBy.java similarity index 84% rename from src/main/java/org/cbioportal/web/parameter/sort/PatientSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/PatientSortBy.java index eca583a6e6e..885dc00b3d0 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/PatientSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/PatientSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum PatientSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ResourceDataSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDataSortBy.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/sort/ResourceDataSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDataSortBy.java index aa0d097020a..cc0fe176435 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ResourceDataSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDataSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ResourceDataSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/ResourceDefinitionSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDefinitionSortBy.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/sort/ResourceDefinitionSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDefinitionSortBy.java index 92163a2350b..2f02cfd4656 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/ResourceDefinitionSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/ResourceDefinitionSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum ResourceDefinitionSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/SampleListSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleListSortBy.java similarity index 88% rename from src/main/java/org/cbioportal/web/parameter/sort/SampleListSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleListSortBy.java index 924ca559177..838cabd135b 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/SampleListSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleListSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum SampleListSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/SampleSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleSortBy.java similarity index 85% rename from src/main/java/org/cbioportal/web/parameter/sort/SampleSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleSortBy.java index d42dc7b7f53..1730df00189 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/SampleSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SampleSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum SampleSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/SignificantCopyNumberRegionSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantCopyNumberRegionSortBy.java similarity index 89% rename from src/main/java/org/cbioportal/web/parameter/sort/SignificantCopyNumberRegionSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantCopyNumberRegionSortBy.java index 8003d56a9ef..823af50bd23 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/SignificantCopyNumberRegionSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantCopyNumberRegionSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum SignificantCopyNumberRegionSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/SignificantlyMutatedGeneSortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantlyMutatedGeneSortBy.java similarity index 89% rename from src/main/java/org/cbioportal/web/parameter/sort/SignificantlyMutatedGeneSortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantlyMutatedGeneSortBy.java index eb2a9003756..4fdb049969b 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/SignificantlyMutatedGeneSortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/SignificantlyMutatedGeneSortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum SignificantlyMutatedGeneSortBy { diff --git a/src/main/java/org/cbioportal/web/parameter/sort/StudySortBy.java b/src/main/java/org/cbioportal/legacy/web/parameter/sort/StudySortBy.java similarity index 90% rename from src/main/java/org/cbioportal/web/parameter/sort/StudySortBy.java rename to src/main/java/org/cbioportal/legacy/web/parameter/sort/StudySortBy.java index d13a09d9535..0f0122cf85f 100644 --- a/src/main/java/org/cbioportal/web/parameter/sort/StudySortBy.java +++ b/src/main/java/org/cbioportal/legacy/web/parameter/sort/StudySortBy.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.parameter.sort; +package org.cbioportal.legacy.web.parameter.sort; public enum StudySortBy { diff --git a/src/main/java/org/cbioportal/web/studyview/CustomDataController.java b/src/main/java/org/cbioportal/legacy/web/studyview/CustomDataController.java similarity index 85% rename from src/main/java/org/cbioportal/web/studyview/CustomDataController.java rename to src/main/java/org/cbioportal/legacy/web/studyview/CustomDataController.java index 9df5f7acf14..cc9544cbfa8 100644 --- a/src/main/java/org/cbioportal/web/studyview/CustomDataController.java +++ b/src/main/java/org/cbioportal/legacy/web/studyview/CustomDataController.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.studyview; +package org.cbioportal.legacy.web.studyview; import io.swagger.v3.oas.annotations.Operation; @@ -9,18 +9,18 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse; import io.swagger.v3.oas.annotations.tags.Tag; import jakarta.validation.Valid; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.Patient; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.web.config.annotation.InternalApi; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.web.config.annotation.InternalApi; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -56,7 +56,7 @@ public class CustomDataController { @Autowired private PatientService patientService; - @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)") @RequestMapping(value = "/custom-data-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Fetch custom data counts by study view filter") @ApiResponse(responseCode = "200", description = "OK", diff --git a/src/main/java/org/cbioportal/web/util/BinningData.java b/src/main/java/org/cbioportal/legacy/web/util/BinningData.java similarity index 88% rename from src/main/java/org/cbioportal/web/util/BinningData.java rename to src/main/java/org/cbioportal/legacy/web/util/BinningData.java index 82edafd1edd..e6d93f8eee1 100644 --- a/src/main/java/org/cbioportal/web/util/BinningData.java +++ b/src/main/java/org/cbioportal/legacy/web/util/BinningData.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.ImmutableList; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; import java.util.Collection; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/util/BinningIds.java b/src/main/java/org/cbioportal/legacy/web/util/BinningIds.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/BinningIds.java rename to src/main/java/org/cbioportal/legacy/web/util/BinningIds.java index 6d19d79051b..95c65c22070 100644 --- a/src/main/java/org/cbioportal/web/util/BinningIds.java +++ b/src/main/java/org/cbioportal/legacy/web/util/BinningIds.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtil.java similarity index 94% rename from src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtil.java index bf90b2de08b..f946b7a855b 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtil.java @@ -1,17 +1,22 @@ -package org.cbioportal.web.util; - -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.service.AttributeByStudyService; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.util.BinnableCustomDataValue; -import org.cbioportal.service.util.CustomAttributeWithData; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.CustomDataValue; -import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; -import org.cbioportal.web.parameter.*; +package org.cbioportal.legacy.web.util; + +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.service.AttributeByStudyService; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.util.BinnableCustomDataValue; +import org.cbioportal.legacy.service.util.CustomAttributeWithData; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.CustomDataValue; +import org.cbioportal.legacy.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtil.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtil.java similarity index 95% rename from src/main/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtil.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtil.java index 50ab61aafa1..ac07f9fce5e 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtil.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.math.BigDecimal; import java.util.*; @@ -7,15 +7,15 @@ import java.util.stream.Stream; import org.apache.commons.lang3.math.NumberUtils; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalDataEnrichment; -import org.cbioportal.model.Sample; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalDataEnrichment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEqualityFilterApplier.java similarity index 87% rename from src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEqualityFilterApplier.java index 251b9f96e56..b2842e8c078 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataEqualityFilterApplier.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataFetcher.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFetcher.java similarity index 93% rename from src/main/java/org/cbioportal/web/util/ClinicalDataFetcher.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFetcher.java index 56dcbef0573..943b511f3ae 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataFetcher.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFetcher.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.CollectionUtils; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.Projection; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFilterApplier.java similarity index 89% rename from src/main/java/org/cbioportal/web/util/ClinicalDataFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFilterApplier.java index 5a46baca9c2..af1fb6e97de 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataFilterApplier.java @@ -1,17 +1,17 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.ArrayList; import java.util.List; import java.util.stream.Collectors; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.Patient; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; public abstract class ClinicalDataFilterApplier implements DataFilterApplier { private PatientService patientService; diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataIntervalFilterApplier.java similarity index 93% rename from src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/ClinicalDataIntervalFilterApplier.java index 66d310a2511..9886c1af64d 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ClinicalDataIntervalFilterApplier.java @@ -1,12 +1,12 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.PatientService; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/CustomDataFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/CustomDataFilterApplier.java similarity index 94% rename from src/main/java/org/cbioportal/web/util/CustomDataFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/CustomDataFilterApplier.java index ed37c9a13a4..28be6574666 100644 --- a/src/main/java/org/cbioportal/web/util/CustomDataFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/CustomDataFilterApplier.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.service.CustomDataService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.service.CustomDataService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/CustomDatatype.java b/src/main/java/org/cbioportal/legacy/web/util/CustomDatatype.java similarity index 76% rename from src/main/java/org/cbioportal/web/util/CustomDatatype.java rename to src/main/java/org/cbioportal/legacy/web/util/CustomDatatype.java index 9aaac0ebd15..0e59d8c9bbc 100644 --- a/src/main/java/org/cbioportal/web/util/CustomDatatype.java +++ b/src/main/java/org/cbioportal/legacy/web/util/CustomDatatype.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; public enum CustomDatatype { /** diff --git a/src/main/java/org/cbioportal/web/util/DataBinHelper.java b/src/main/java/org/cbioportal/legacy/web/util/DataBinHelper.java similarity index 99% rename from src/main/java/org/cbioportal/web/util/DataBinHelper.java rename to src/main/java/org/cbioportal/legacy/web/util/DataBinHelper.java index 9138aef2572..d6a817afa70 100644 --- a/src/main/java/org/cbioportal/web/util/DataBinHelper.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DataBinHelper.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import com.google.common.collect.Range; import java.math.BigDecimal; import java.math.RoundingMode; diff --git a/src/main/java/org/cbioportal/web/util/DataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/DataBinner.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/DataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/DataBinner.java index 85e21f2e69c..d5340b47613 100644 --- a/src/main/java/org/cbioportal/web/util/DataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DataBinner.java @@ -1,13 +1,13 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; import org.apache.commons.lang3.math.NumberUtils; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.DataBin; -import org.cbioportal.web.parameter.BinsGeneratorConfig; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.DataBinFilter; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.web.parameter.BinsGeneratorConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/DataFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/DataFilterApplier.java similarity index 60% rename from src/main/java/org/cbioportal/web/util/DataFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/DataFilterApplier.java index ad5d6521658..62caf776304 100644 --- a/src/main/java/org/cbioportal/web/util/DataFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DataFilterApplier.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/util/DensityPlotParameters.java b/src/main/java/org/cbioportal/legacy/web/util/DensityPlotParameters.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/DensityPlotParameters.java rename to src/main/java/org/cbioportal/legacy/web/util/DensityPlotParameters.java index 47e65543680..fba7f8d0a6d 100644 --- a/src/main/java/org/cbioportal/web/util/DensityPlotParameters.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DensityPlotParameters.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/DiscreteDataBinner.java similarity index 91% rename from src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/DiscreteDataBinner.java index d6eaf334f82..b7a2552740c 100644 --- a/src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/DiscreteDataBinner.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import org.springframework.stereotype.Component; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/GoogleAnalyticsInterceptor.java b/src/main/java/org/cbioportal/legacy/web/util/GoogleAnalyticsInterceptor.java similarity index 99% rename from src/main/java/org/cbioportal/web/util/GoogleAnalyticsInterceptor.java rename to src/main/java/org/cbioportal/legacy/web/util/GoogleAnalyticsInterceptor.java index 540e8f2ab79..c40de9b87e3 100644 --- a/src/main/java/org/cbioportal/web/util/GoogleAnalyticsInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/util/GoogleAnalyticsInterceptor.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.Arrays; import java.util.concurrent.CompletableFuture; diff --git a/src/main/java/org/cbioportal/web/util/GzippedInputStreamRequestWrapper.java b/src/main/java/org/cbioportal/legacy/web/util/GzippedInputStreamRequestWrapper.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/GzippedInputStreamRequestWrapper.java rename to src/main/java/org/cbioportal/legacy/web/util/GzippedInputStreamRequestWrapper.java index 2d8b4bc9b90..5e0f3b74f20 100644 --- a/src/main/java/org/cbioportal/web/util/GzippedInputStreamRequestWrapper.java +++ b/src/main/java/org/cbioportal/legacy/web/util/GzippedInputStreamRequestWrapper.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import jakarta.servlet.ReadListener; import jakarta.servlet.ServletInputStream; diff --git a/src/main/java/org/cbioportal/web/util/HttpRequestUtils.java b/src/main/java/org/cbioportal/legacy/web/util/HttpRequestUtils.java similarity index 96% rename from src/main/java/org/cbioportal/web/util/HttpRequestUtils.java rename to src/main/java/org/cbioportal/legacy/web/util/HttpRequestUtils.java index 325a5cf35bf..f1e9318a448 100644 --- a/src/main/java/org/cbioportal/web/util/HttpRequestUtils.java +++ b/src/main/java/org/cbioportal/legacy/web/util/HttpRequestUtils.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.Enumeration; diff --git a/src/main/java/org/cbioportal/web/util/IdPopulator.java b/src/main/java/org/cbioportal/legacy/web/util/IdPopulator.java similarity index 89% rename from src/main/java/org/cbioportal/web/util/IdPopulator.java rename to src/main/java/org/cbioportal/legacy/web/util/IdPopulator.java index e7c02227bdf..d43f5a3286d 100644 --- a/src/main/java/org/cbioportal/web/util/IdPopulator.java +++ b/src/main/java/org/cbioportal/legacy/web/util/IdPopulator.java @@ -1,9 +1,9 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java b/src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java similarity index 96% rename from src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java rename to src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java index e0ee3961f71..9cc19225fe2 100644 --- a/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/util/InvolvedCancerStudyExtractorInterceptor.java @@ -30,43 +30,43 @@ * along with this program. If not, see . */ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.fasterxml.jackson.databind.ObjectMapper; import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; import org.apache.commons.lang3.StringUtils; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.SampleList; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.web.parameter.ClinicalAttributeCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataIdentifier; -import org.cbioportal.web.parameter.ClinicalDataMultiStudyFilter; -import org.cbioportal.web.parameter.ClinicalEventAttributeRequest; -import org.cbioportal.web.parameter.GenePanelDataMultipleStudyFilter; -import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataMultipleStudyFilter; -import org.cbioportal.web.parameter.GenomicDataBinCountFilter; -import org.cbioportal.web.parameter.GenomicDataCountFilter; -import org.cbioportal.web.parameter.GroupFilter; -import org.cbioportal.web.parameter.MolecularDataMultipleStudyFilter; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; -import org.cbioportal.web.parameter.MolecularProfileFilter; -import org.cbioportal.web.parameter.MutationMultipleStudyFilter; -import org.cbioportal.web.parameter.PatientFilter; -import org.cbioportal.web.parameter.PatientIdentifier; -import org.cbioportal.web.parameter.SampleFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; -import org.cbioportal.web.parameter.StructuralVariantFilter; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.web.parameter.ClinicalAttributeCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataIdentifier; +import org.cbioportal.legacy.web.parameter.ClinicalDataMultiStudyFilter; +import org.cbioportal.legacy.web.parameter.ClinicalEventAttributeRequest; +import org.cbioportal.legacy.web.parameter.GenePanelDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter; +import org.cbioportal.legacy.web.parameter.GroupFilter; +import org.cbioportal.legacy.web.parameter.MolecularDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileFilter; +import org.cbioportal.legacy.web.parameter.MutationMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.PatientFilter; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.SampleFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.web.parameter.StructuralVariantFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/cbioportal/web/util/LinearDataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/LinearDataBinner.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/LinearDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/LinearDataBinner.java index 34bea85d9e4..2af45cc9271 100644 --- a/src/main/java/org/cbioportal/web/util/LinearDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/LinearDataBinner.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import org.springframework.stereotype.Component; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/LogScaleDataBinner.java similarity index 97% rename from src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/LogScaleDataBinner.java index febeb34ebb8..8732533da92 100644 --- a/src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/LogScaleDataBinner.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import org.springframework.stereotype.Component; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/RequestBodyGZipFilter.java b/src/main/java/org/cbioportal/legacy/web/util/RequestBodyGZipFilter.java similarity index 98% rename from src/main/java/org/cbioportal/web/util/RequestBodyGZipFilter.java rename to src/main/java/org/cbioportal/legacy/web/util/RequestBodyGZipFilter.java index 7c68698c38c..7812abc932d 100644 --- a/src/main/java/org/cbioportal/web/util/RequestBodyGZipFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/util/RequestBodyGZipFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import jakarta.servlet.*; import jakarta.servlet.http.HttpServletRequest; diff --git a/src/main/java/org/cbioportal/web/util/ResettableHttpServletRequestFilter.java b/src/main/java/org/cbioportal/legacy/web/util/ResettableHttpServletRequestFilter.java similarity index 96% rename from src/main/java/org/cbioportal/web/util/ResettableHttpServletRequestFilter.java rename to src/main/java/org/cbioportal/legacy/web/util/ResettableHttpServletRequestFilter.java index b34fe2eaaab..0b65f6e148b 100644 --- a/src/main/java/org/cbioportal/web/util/ResettableHttpServletRequestFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ResettableHttpServletRequestFilter.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.io.IOException; diff --git a/src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java b/src/main/java/org/cbioportal/legacy/web/util/ScientificSmallDataBinner.java similarity index 97% rename from src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java rename to src/main/java/org/cbioportal/legacy/web/util/ScientificSmallDataBinner.java index f3766164ef8..854867db4d7 100644 --- a/src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java +++ b/src/main/java/org/cbioportal/legacy/web/util/ScientificSmallDataBinner.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.google.common.collect.Range; -import org.cbioportal.model.DataBin; +import org.cbioportal.legacy.model.DataBin; import org.springframework.stereotype.Component; import java.math.BigDecimal; diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java similarity index 95% rename from src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java index 43980c99f90..05a64c9f755 100644 --- a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterApplier.java @@ -1,63 +1,63 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.DataBin; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilter; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.GenericAssayDataBin; -import org.cbioportal.model.GenomicDataBin; -import org.cbioportal.model.MolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationFilterOption; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.UniqueKeyBase; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StructuralVariantService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.ClinicalDataType; -import org.cbioportal.web.parameter.DataBinCountFilter; -import org.cbioportal.web.parameter.DataBinFilter; -import org.cbioportal.web.parameter.DataBinMethod; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.DiscreteCopyNumberEventType; -import org.cbioportal.web.parameter.GeneIdType; -import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinCountFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.MutationDataFilter; -import org.cbioportal.web.parameter.MutationOption; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.appliers.StudyViewSubFilterApplier; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilter; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.GenericAssayDataBin; +import org.cbioportal.legacy.model.GenomicDataBin; +import org.cbioportal.legacy.model.MolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationFilterOption; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.UniqueKeyBase; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StructuralVariantService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.web.parameter.DataBinCountFilter; +import org.cbioportal.legacy.web.parameter.DataBinFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberEventType; +import org.cbioportal.legacy.web.parameter.GeneIdType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.MutationDataFilter; +import org.cbioportal.legacy.web.parameter.MutationOption; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.appliers.StudyViewSubFilterApplier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.context.ApplicationContext; diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java b/src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterUtil.java similarity index 92% rename from src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java rename to src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterUtil.java index b44b8bd8a63..1895e081225 100644 --- a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java +++ b/src/main/java/org/cbioportal/legacy/web/util/StudyViewFilterUtil.java @@ -1,20 +1,33 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.collections4.map.MultiKeyMap; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Patient; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariantSpecialValue; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.CustomDataValue; -import org.cbioportal.web.parameter.*; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantSpecialValue; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.util.CustomDataSession; +import org.cbioportal.legacy.service.util.CustomDataValue; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataBinFilter; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.GeneIdType; +import org.cbioportal.legacy.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.MutationDataFilter; +import org.cbioportal.legacy.web.parameter.MutationOption; +import org.cbioportal.legacy.web.parameter.Projection; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/UniqueKeyExtractor.java b/src/main/java/org/cbioportal/legacy/web/util/UniqueKeyExtractor.java similarity index 91% rename from src/main/java/org/cbioportal/web/util/UniqueKeyExtractor.java rename to src/main/java/org/cbioportal/legacy/web/util/UniqueKeyExtractor.java index 90d99dfe0a0..6e5ffce4049 100644 --- a/src/main/java/org/cbioportal/web/util/UniqueKeyExtractor.java +++ b/src/main/java/org/cbioportal/legacy/web/util/UniqueKeyExtractor.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.utils.Encoder; +import org.cbioportal.legacy.utils.Encoder; import java.util.List; import java.util.Collection; diff --git a/src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractPatientTreatmentFilter.java similarity index 81% rename from src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractPatientTreatmentFilter.java index 30d507d297a..0b8389fd522 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractPatientTreatmentFilter.java @@ -1,11 +1,11 @@ -package org.cbioportal.web.util.appliers; - -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +package org.cbioportal.legacy.web.util.appliers; + +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; import org.springframework.beans.factory.annotation.Autowired; import java.util.ArrayList; diff --git a/src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractSampleTreatmentFilter.java similarity index 80% rename from src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractSampleTreatmentFilter.java index c28dcefbcbd..e10673e7d50 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/AbstractSampleTreatmentFilter.java @@ -1,11 +1,11 @@ -package org.cbioportal.web.util.appliers; - -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +package org.cbioportal.legacy.web.util.appliers; + +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; import org.springframework.beans.factory.annotation.Autowired; import java.util.ArrayList; diff --git a/src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/ClinicalEventFilterApplier.java similarity index 89% rename from src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/ClinicalEventFilterApplier.java index adf70d4a782..65a93432d53 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/ClinicalEventFilterApplier.java @@ -1,10 +1,10 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.lang.NonNull; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentFilterApplier.java similarity index 62% rename from src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentFilterApplier.java index c97c313ec8b..b2377277368 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentGroupFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentGroupFilterApplier.java similarity index 63% rename from src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentGroupFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentGroupFilterApplier.java index 6110d4aa8e3..d63a68a65f7 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentGroupFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentGroupFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentTargetFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentTargetFilterApplier.java similarity index 63% rename from src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentTargetFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentTargetFilterApplier.java index 87c69ea8fbc..494bbd651d2 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/PatientTreatmentTargetFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/PatientTreatmentTargetFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentFilterApplier.java similarity index 62% rename from src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentFilterApplier.java index 83e6bd7301a..ed42f31a8a2 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentGroupFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentGroupFilterApplier.java similarity index 63% rename from src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentGroupFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentGroupFilterApplier.java index 9f0e3aa0b31..a2ed8cf5cbd 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentGroupFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentGroupFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentTargetFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentTargetFilterApplier.java similarity index 63% rename from src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentTargetFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentTargetFilterApplier.java index d7d6c37b449..6fbf49a044d 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/SampleTreatmentTargetFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/SampleTreatmentTargetFilterApplier.java @@ -1,8 +1,8 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; import org.springframework.stereotype.Component; @Component diff --git a/src/main/java/org/cbioportal/web/util/appliers/StructuralVariantSubFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/StructuralVariantSubFilterApplier.java similarity index 89% rename from src/main/java/org/cbioportal/web/util/appliers/StructuralVariantSubFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/StructuralVariantSubFilterApplier.java index 9367c54884b..716c4205b3b 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/StructuralVariantSubFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/StructuralVariantSubFilterApplier.java @@ -1,13 +1,13 @@ -package org.cbioportal.web.util.appliers; - -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StudyViewStructuralVariantFilter; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.StructuralVariantService; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.StudyViewFilterUtil; +package org.cbioportal.legacy.web.util.appliers; + +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StudyViewStructuralVariantFilter; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.StructuralVariantService; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/src/main/java/org/cbioportal/web/util/appliers/StudyViewSubFilterApplier.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/StudyViewSubFilterApplier.java similarity index 57% rename from src/main/java/org/cbioportal/web/util/appliers/StudyViewSubFilterApplier.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/StudyViewSubFilterApplier.java index 8ba7dc037ef..358df77207b 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/StudyViewSubFilterApplier.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/StudyViewSubFilterApplier.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import java.util.List; diff --git a/src/main/java/org/cbioportal/web/util/appliers/TreatmentRowExtractor.java b/src/main/java/org/cbioportal/legacy/web/util/appliers/TreatmentRowExtractor.java similarity index 69% rename from src/main/java/org/cbioportal/web/util/appliers/TreatmentRowExtractor.java rename to src/main/java/org/cbioportal/legacy/web/util/appliers/TreatmentRowExtractor.java index f260304356a..82d816dcf80 100644 --- a/src/main/java/org/cbioportal/web/util/appliers/TreatmentRowExtractor.java +++ b/src/main/java/org/cbioportal/legacy/web/util/appliers/TreatmentRowExtractor.java @@ -1,7 +1,7 @@ -package org.cbioportal.web.util.appliers; +package org.cbioportal.legacy.web.util.appliers; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.TreatmentRow; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.TreatmentRow; import org.springframework.stereotype.Service; import java.util.Set; diff --git a/src/main/java/org/cbioportal/service/ServerStatusService.java b/src/main/java/org/cbioportal/service/ServerStatusService.java deleted file mode 100644 index ac77b693c08..00000000000 --- a/src/main/java/org/cbioportal/service/ServerStatusService.java +++ /dev/null @@ -1,7 +0,0 @@ -package org.cbioportal.service; - -import org.cbioportal.service.impl.ServerStatusServiceImpl.ServerStatusMessage; - -public interface ServerStatusService { - ServerStatusMessage getServerStatus(); -} diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java deleted file mode 100644 index 66305eb5fe8..00000000000 --- a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.cbioportal.service.treatment; - -import org.cbioportal.model.PatientTreatmentReport; -import org.cbioportal.model.SampleTreatmentReport; -import org.cbioportal.model.StudyViewFilterContext; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; - -import java.util.List; - -public interface TreatmentCountReportService { - PatientTreatmentReport getPatientTreatmentReport(StudyViewFilterContext studyViewFilterContext); - SampleTreatmentReport getSampleTreatmentReport(StudyViewFilterContext studyViewFilterContext); -} diff --git a/src/main/java/org/cbioportal/utils/security/AccessLevel.java b/src/main/java/org/cbioportal/utils/security/AccessLevel.java deleted file mode 100644 index bdd3c9024f0..00000000000 --- a/src/main/java/org/cbioportal/utils/security/AccessLevel.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.cbioportal.utils.security; - -public enum AccessLevel { - READ, LIST -} diff --git a/src/main/java/org/cbioportal/web/mixin/GeneMixin.java b/src/main/java/org/cbioportal/web/mixin/GeneMixin.java deleted file mode 100644 index fb4445cfcb2..00000000000 --- a/src/main/java/org/cbioportal/web/mixin/GeneMixin.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.cbioportal.web.mixin; - -public class GeneMixin { - -} diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml index f9e53a35b08..c2bc086ada4 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml @@ -1,9 +1,9 @@ - + - SELECT ENTREZ_GENE_ID AS "entrezGeneId", HUGO_GENE_SYMBOL AS "hugoGeneSymbol", @@ -37,7 +37,7 @@ GROUP BY ENTREZ_GENE_ID, HUGO_GENE_SYMBOL; - SELECT ENTREZ_GENE_ID AS entrezGeneId, HUGO_GENE_SYMBOL AS hugoGeneSymbol, @@ -71,7 +71,7 @@ GROUP BY ENTREZ_GENE_ID, HUGO_GENE_SYMBOL; - SELECT cna_event.ENTREZ_GENE_ID AS entrezGeneId, gene.HUGO_GENE_SYMBOL AS hugoGeneSymbol, @@ -111,7 +111,7 @@ GROUP BY cna_event.ENTREZ_GENE_ID, cna_event.ALTERATION, reference_genome_gene.CYTOBAND, gene.HUGO_GENE_SYMBOL - SELECT cna_event.ENTREZ_GENE_ID AS entrezGeneId, gene.HUGO_GENE_SYMBOL AS hugoGeneSymbol, @@ -148,7 +148,7 @@ GROUP BY cna_event.ENTREZ_GENE_ID, cna_event.ALTERATION, gene.HUGO_GENE_SYMBOL - SELECT gene1.ENTREZ_GENE_ID AS gene1EntrezGeneId, gene1.HUGO_GENE_SYMBOL AS gene1HugoGeneSymbol, @@ -176,7 +176,7 @@ GROUP BY gene1.ENTREZ_GENE_ID, gene2.ENTREZ_GENE_ID - SELECT gene1.ENTREZ_GENE_ID AS gene1EntrezGeneId, gene1.HUGO_GENE_SYMBOL AS gene1HugoGeneSymbol, @@ -579,7 +579,7 @@ caseUniqueId - SELECT genetic_profile.GENETIC_PROFILE_ID AS molecularProfileId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.xml index 6d133f365d7..85e9d73a9e6 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.xml @@ -1,9 +1,9 @@ - + - SELECT alteration_driver_annotation.ALTERATION_EVENT_ID as alterationEventId, alteration_driver_annotation.GENETIC_PROFILE_ID as geneticProfileId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/CancerTypeMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/CancerTypeMapper.xml index 138ae3932bc..f1a93ec450a 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/CancerTypeMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/CancerTypeMapper.xml @@ -1,7 +1,7 @@ - + type_of_cancer.TYPE_OF_CANCER_ID AS "${prefix}typeOfCancerId" @@ -14,7 +14,7 @@ - SELECT @@ -31,13 +31,13 @@ - SELECT COUNT(*) AS "totalCount" FROM type_of_cancer - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml index 8dbdbc9a942..a552a83ffa2 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml @@ -1,7 +1,7 @@ - + clinical_attribute_meta.ATTR_ID AS "${prefix}attrId", @@ -64,7 +64,7 @@ - SELECT @@ -90,7 +90,7 @@ - SELECT COUNT(*) AS "totalCount" FROM clinical_attribute_meta @@ -105,7 +105,7 @@ - SELECT @@ -116,7 +116,7 @@ AND cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId} - SELECT count(*) as "count", clinical_sample.ATTR_ID as "attrId" FROM clinical_sample @@ -134,7 +134,7 @@ GROUP BY clinical_patient.ATTR_ID - SELECT count(*) as "count", clinical_sample.ATTR_ID as "attrId" FROM clinical_sample @@ -152,7 +152,7 @@ GROUP BY clinical_patient.ATTR_ID - SELECT clinical_attribute_meta.ATTR_ID AS "attrId", cancer_study.CANCER_STUDY_IDENTIFIER AS "cancerStudyIdentifier", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml index bfe06321aff..129fdce9494 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml @@ -1,7 +1,7 @@ - + clinical_sample.INTERNAL_ID AS "${prefix}internalId", @@ -15,7 +15,7 @@ , - + @@ -33,7 +33,7 @@ , - + @@ -115,7 +115,7 @@ - SELECT sample.INTERNAL_ID internalId, sample.STABLE_ID sampleId, patient.STABLE_ID patientId, cancer_study.CANCER_STUDY_IDENTIFIER studyId, clinical_patient.ATTR_ID attrId, clinical_patient.ATTR_VALUE attrValue FROM clinical_patient @@ -128,7 +128,7 @@ - SELECT sample.INTERNAL_ID internalId, sample.STABLE_ID sampleId, patient.STABLE_ID patientId, cancer_study.CANCER_STUDY_IDENTIFIER studyId, clinical_sample.ATTR_ID attrId, clinical_sample.ATTR_VALUE attrValue FROM clinical_sample @@ -141,7 +141,7 @@ - SELECT @@ -164,14 +164,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT @@ -194,7 +194,7 @@ - SELECT @@ -219,14 +219,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT count(*) as count, clinical_sample.ATTR_ID as attributeId, clinical_sample.ATTR_VALUE as value @@ -235,7 +235,7 @@ GROUP BY clinical_sample.ATTR_ID, clinical_sample.ATTR_VALUE - SELECT count(*) as count, clinical_patient.ATTR_ID as attributeId, clinical_patient.ATTR_VALUE as value diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml index 48e446aeccb..badc8b79702 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml @@ -1,7 +1,7 @@ - + clinical_event.CLINICAL_EVENT_ID AS "clinicalEventId", @@ -34,7 +34,7 @@ - SELECT @@ -50,14 +50,14 @@ - SELECT COUNT(*) AS totalCount - SELECT clinical_event_data.CLINICAL_EVENT_ID AS clinicalEventId, clinical_event_data.KEY AS "key", @@ -73,7 +73,7 @@ - SELECT @@ -89,14 +89,14 @@ - SELECT COUNT(*) AS totalCount - SELECT clinical_event.CLINICAL_EVENT_ID as clinicalEventId, clinical_event.EVENT_TYPE as eventType, @@ -140,7 +140,7 @@ - SELECT @@ -184,7 +184,7 @@ Group by clinical_event.EVENT_TYPE, patient.INTERNAL_ID - SELECT patient.STABLE_ID AS patientId, cancer_study.CANCER_STUDY_IDENTIFIER AS studyId, @@ -240,9 +240,9 @@ clinical_event.PATIENT_ID, cancer_study.CANCER_STUDY_IDENTIFIER; - + - + diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml index 58e2a37da07..0d3503c6fd5 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml @@ -1,7 +1,7 @@ - + copy_number_seg.SEG_ID AS "segId", @@ -50,7 +50,7 @@ - SELECT @@ -69,7 +69,7 @@ - SELECT COUNT(*) AS totalCount @@ -79,7 +79,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/CosmicCountMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/CosmicCountMapper.xml index df0fe7e0fe3..5541cb31f7b 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/CosmicCountMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/CosmicCountMapper.xml @@ -1,9 +1,9 @@ - + - SELECT cosmic_mutation.COSMIC_MUTATION_ID AS "cosmicMutationId", cosmic_mutation.PROTEIN_CHANGE AS "proteinChange", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.xml index f6aea8ca139..9aa8776df70 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/DataAccessTokenMapper.xml @@ -1,7 +1,7 @@ - + data_access_tokens.TOKEN AS "${prefix}token", @@ -10,7 +10,7 @@ data_access_tokens.CREATION AS "${prefix}creation" - SELECT @@ -20,7 +20,7 @@ ORDER BY data_access_tokens.EXPIRATION ASC - SELECT @@ -41,7 +41,7 @@ WHERE USERNAME = #{username} - + INSERT INTO data_access_tokens(TOKEN, USERNAME, EXPIRATION, CREATION) VALUES (#{token}, #{username}, #{expiration}, #{creation}) diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml index 3060a8a389e..338347d24ef 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml @@ -1,7 +1,7 @@ - + cna_event.ENTREZ_GENE_ID as entrezGeneId, @@ -17,7 +17,7 @@ alteration_driver_annotation.DRIVER_TIERS_FILTER_ANNOTATION AS "driverTiersFilterAnnotation" , - + @@ -193,7 +193,7 @@ - SELECT @@ -203,14 +203,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT @@ -220,7 +220,7 @@ - SELECT @@ -230,7 +230,7 @@ - SELECT @@ -240,14 +240,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT cna_event.ENTREZ_GENE_ID AS "entrezGeneId", gene.HUGO_GENE_SYMBOL AS "hugoGeneSymbol", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml index eb9bbf1f24a..eab4878cfb3 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml @@ -1,7 +1,7 @@ - + gene.ENTREZ_GENE_ID AS "${prefix}entrezGeneId", @@ -32,7 +32,7 @@ - SELECT @@ -53,14 +53,14 @@ - SELECT COUNT(*) AS "totalCount" - SELECT @@ -69,7 +69,7 @@ WHERE gene.GENETIC_ENTITY_ID = #{geneticEntityId} - SELECT @@ -78,7 +78,7 @@ WHERE gene.ENTREZ_GENE_ID = #{entrezGeneId} - SELECT @@ -100,14 +100,14 @@ WHERE gene.HUGO_GENE_SYMBOL = #{hugoGeneSymbol} - SELECT gene_alias.ENTREZ_GENE_ID AS "entrezGeneId", LOWER(gene_alias.GENE_ALIAS) AS "geneAlias" FROM gene_alias - SELECT @@ -126,7 +126,7 @@ - SELECT COUNT(*) AS "totalCount" FROM gene @@ -143,7 +143,7 @@ - SELECT @@ -162,7 +162,7 @@ - SELECT COUNT(*) AS totalCount FROM gene diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml index 96a1d434c15..289f4df0127 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml @@ -1,7 +1,7 @@ - + gene_panel.INTERNAL_ID AS "internalId", @@ -30,7 +30,7 @@ LEFT JOIN gene_panel ON sample_profile.PANEL_ID = gene_panel.INTERNAL_ID - SELECT FROM gene_panel @@ -45,20 +45,20 @@ - SELECT COUNT(*) AS totalCount FROM gene_panel - SELECT FROM gene_panel WHERE gene_panel.STABLE_ID = #{genePanelId} - SELECT FROM gene_panel @@ -72,7 +72,7 @@ - SELECT gene_panel.STABLE_ID AS genePanelId, gene_panel_list.GENE_ID AS entrezGeneId, @@ -91,7 +91,7 @@ ORDER BY hugoGeneSymbol ASC - SELECT @@ -102,7 +102,7 @@ AND sample_list_query.STABLE_ID = #{sampleListId} - SELECT @@ -116,7 +116,7 @@ - SELECT @@ -127,7 +127,7 @@ - SELECT @@ -157,7 +157,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GenericAssayMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/GenericAssayMapper.xml index 5b767fb93b3..461d855ef02 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GenericAssayMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/GenericAssayMapper.xml @@ -1,10 +1,10 @@ - + - SELECT genetic_entity.STABLE_ID as stableId, genetic_entity.ENTITY_TYPE as entityType FROM genetic_entity @@ -16,7 +16,7 @@ - SELECT generic_entity_properties.NAME as name, generic_entity_properties.VALUE as value, genetic_entity.STABLE_ID as stableId diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.xml index 6ed4252ada4..f8e105e4e64 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/GenesetHierarchyMapper.xml @@ -1,7 +1,7 @@ - + a.NODE_ID AS nodeId, @@ -10,7 +10,7 @@ b.NODE_NAME AS parentNodeName - SELECT FROM geneset_hierarchy_node as a left join geneset_hierarchy_node as b ON a.PARENT_ID = b.NODE_ID @@ -27,7 +27,7 @@ ORDER BY b.NODE_NAME, a.NODE_NAME - SELECT FROM geneset_hierarchy_node as a LEFT join geneset_hierarchy_node as b ON a.PARENT_ID = b.NODE_ID @@ -44,9 +44,9 @@ ORDER BY b.NODE_NAME, a.NODE_NAME - SELECT - + FROM geneset diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/GenesetMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/GenesetMapper.xml index 8c1fe553431..5a6674a2be4 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/GenesetMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/GenesetMapper.xml @@ -1,7 +1,7 @@ - + geneset.ID AS "${prefix}internalId", @@ -11,7 +11,7 @@ geneset.REF_LINK as "${prefix}refLink" - SELECT @@ -28,13 +28,13 @@ - SELECT COUNT(*) AS totalCount FROM geneset - SELECT @@ -43,7 +43,7 @@ WHERE geneset.EXTERNAL_ID = #{genesetId} - SELECT @@ -56,9 +56,9 @@ ORDER BY geneset.EXTERNAL_ID ASC - SELECT - + FROM gene diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml index 45a1e222e63..e6f22dcdf63 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml @@ -1,7 +1,7 @@ - + @@ -20,7 +20,7 @@ - SELECT genetic_profile.STABLE_ID AS "molecularProfileId", genetic_profile_samples.ORDERED_SAMPLE_LIST AS "commaSeparatedSampleIds" @@ -37,13 +37,13 @@ - SELECT gene.ENTREZ_GENE_ID AS "entrezGeneId", genetic_alteration.`VALUES` AS "values" , - + @@ -67,13 +67,13 @@ (Attempts where made to share getGeneMolecularAlterations between methods in MolecularDataMapper.java all of which have failed). --> - SELECT gene.ENTREZ_GENE_ID AS "entrezGeneId", genetic_alteration.`VALUES` AS "values" , - + @@ -92,7 +92,7 @@ - SELECT gene.ENTREZ_GENE_ID AS "entrezGeneId", genetic_alteration.`VALUES` AS "values" @@ -104,14 +104,14 @@ - SELECT gene.ENTREZ_GENE_ID AS "entrezGeneId", genetic_alteration.`VALUES` AS "values", genetic_profile.STABLE_ID AS "molecularProfileId" , - + @@ -121,7 +121,7 @@ - SELECT geneset.EXTERNAL_ID AS genesetId, @@ -145,7 +145,7 @@ - SELECT genetic_entity.STABLE_ID AS genericAssayStableId, genetic_profile.STABLE_ID AS molecularProfileId, @@ -175,7 +175,7 @@ (Attempts where made to share getGenericAssayMolecularAlterations between methods in MolecularDataMapper.java all of which have failed). --> - SELECT genetic_entity.STABLE_ID AS genericAssayStableId, genetic_profile.STABLE_ID AS molecularProfileId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml index b51a2f9b5ab..bf59ea76beb 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml @@ -1,7 +1,7 @@ - + genetic_profile.GENETIC_PROFILE_ID AS "${prefix}molecularProfileId", @@ -22,13 +22,13 @@ , - + - SELECT @@ -58,7 +58,7 @@ - SELECT COUNT(*) AS totalCount FROM genetic_profile @@ -72,7 +72,7 @@ - SELECT @@ -83,7 +83,7 @@ WHERE genetic_profile.STABLE_ID = #{molecularProfileId} - SELECT @@ -101,7 +101,7 @@ - SELECT COUNT(*) AS totalCount FROM genetic_profile @@ -115,7 +115,7 @@ - SELECT @@ -133,7 +133,7 @@ ) - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml index de6a18dc104..eb82f54b0e0 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml @@ -1,7 +1,7 @@ - + genetic_profile.STABLE_ID AS "molecularProfileId", @@ -40,7 +40,7 @@ , - + , @@ -275,13 +275,13 @@ AND mutation.SAMPLE_ID = allele_specific_copy_number.SAMPLE_ID - + - + - + @@ -289,7 +289,7 @@ - SELECT @@ -310,7 +310,7 @@ - SELECT COUNT(*) AS "totalCount", COUNT(DISTINCT(mutation.SAMPLE_ID)) AS "sampleCount" @@ -319,7 +319,7 @@ - SELECT @@ -332,7 +332,7 @@ - SELECT @@ -345,7 +345,7 @@ - SELECT COUNT(*) AS "totalCount", COUNT(DISTINCT(mutation.SAMPLE_ID)) AS "sampleCount" @@ -354,7 +354,7 @@ - SELECT COUNT(*) AS "totalCount", COUNT(DISTINCT(mutation.SAMPLE_ID)) AS "sampleCount" @@ -363,7 +363,7 @@ - SELECT mutation.ENTREZ_GENE_ID AS "entrezGeneId", gene.HUGO_GENE_SYMBOL AS "hugoGeneSymbol", @@ -378,7 +378,7 @@ GROUP BY mutation.ENTREZ_GENE_ID - SELECT #{entrezGeneId} AS "entrezGeneId", #{proteinPosStart} AS "proteinPosStart", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml index 3b396bdfa6a..009a363d46f 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml @@ -1,7 +1,7 @@ - + patient.INTERNAL_ID AS "${prefix}internalId", @@ -10,7 +10,7 @@ cancer_study.CANCER_STUDY_IDENTIFIER AS "${prefix}cancerStudyIdentifier" , - + @@ -45,7 +45,7 @@ - SELECT @@ -69,7 +69,7 @@ - SELECT COUNT(*) AS totalCount @@ -79,7 +79,7 @@ - SELECT @@ -89,7 +89,7 @@ AND cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId} - SELECT DISTINCT(patient.STABLE_ID) AS stableId, cancer_study.CANCER_STUDY_IDENTIFIER AS cancerStudyIdentifier FROM sample diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml index 0888d5d06be..0e2cbc981bd 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml @@ -1,7 +1,7 @@ - + @@ -18,7 +18,7 @@ - SELECT @@ -31,7 +31,7 @@ - SELECT @@ -53,7 +53,7 @@ - SELECT @@ -75,7 +75,7 @@ - SELECT @@ -89,7 +89,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml index 051634e0e86..cfba5e33523 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml @@ -1,7 +1,7 @@ - + sample.STABLE_ID AS "${prefix}sampleId", @@ -13,7 +13,7 @@ , - + @@ -28,7 +28,7 @@ , - + @@ -42,7 +42,7 @@ , - + @@ -105,7 +105,7 @@ - SELECT @@ -127,7 +127,7 @@ - SELECT @@ -149,7 +149,7 @@ - SELECT @@ -171,7 +171,7 @@ - SELECT @@ -188,7 +188,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.xml index a10818544ec..3910f6ce29c 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDefinitionMapper.xml @@ -1,7 +1,7 @@ - + resource_definition.RESOURCE_ID AS "${prefix}resourceId", @@ -17,7 +17,7 @@ - SELECT @@ -48,7 +48,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SampleListMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/SampleListMapper.xml index ffb47f850f5..3cbce6bf85c 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SampleListMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/SampleListMapper.xml @@ -1,7 +1,7 @@ - + sample_list.LIST_ID AS "${prefix}listId", @@ -16,13 +16,13 @@ , - + - SELECT @@ -53,7 +53,7 @@ - SELECT COUNT(*) AS totalCount FROM sample_list @@ -63,7 +63,7 @@ - SELECT @@ -74,7 +74,7 @@ WHERE sample_list.STABLE_ID = #{sampleListId} - SELECT @@ -101,7 +101,7 @@ WHERE sample_list.STABLE_ID = #{sampleListId} - SELECT sample_list_list.LIST_ID as sampleListId, sample.STABLE_ID as sampleId diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml index 21f4e86da37..291946fe0ed 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml @@ -1,7 +1,7 @@ - + sample.INTERNAL_ID AS "${prefix}internalId", @@ -15,7 +15,7 @@ , - + @@ -68,7 +68,7 @@ - SELECT @@ -89,7 +89,7 @@ - SELECT @@ -107,14 +107,14 @@ ) - SELECT COUNT(*) AS "totalCount" - SELECT COUNT(*) AS "totalCount" @@ -130,7 +130,7 @@ ) - SELECT @@ -140,7 +140,7 @@ AND cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId} - SELECT @@ -149,7 +149,7 @@ WHERE sample.INTERNAL_ID = #{internalId} - SELECT @@ -165,7 +165,7 @@ - SELECT @@ -181,7 +181,7 @@ - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SecurityMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/SecurityMapper.xml index 77eb4a73004..8c2c7694833 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SecurityMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/SecurityMapper.xml @@ -1,18 +1,18 @@ - + - + - SELECT LOWER(email) AS email, name, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.xml index eeea7c87f8c..c4cbfb34809 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMapper.xml @@ -1,7 +1,7 @@ - + gistic.GISTIC_ROI_ID AS "gisticRoiId", @@ -25,7 +25,7 @@ - SELECT @@ -41,14 +41,14 @@ - SELECT COUNT(*) AS totalCount - SELECT gistic_to_gene.GISTIC_ROI_ID AS gisticRoiId, gistic_to_gene.ENTREZ_GENE_ID AS entrezGeneId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.xml index 51d26473570..a3b4a463011 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMapper.xml @@ -1,7 +1,7 @@ - + mut_sig.ENTREZ_GENE_ID AS "entrezGeneId", @@ -26,7 +26,7 @@ - SELECT @@ -43,7 +43,7 @@ - SELECT COUNT(*) AS totalCount diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.xml index d1e69e5d8b7..fd058d34c0d 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/StaticDataTimestampMapper.xml @@ -1,9 +1,9 @@ - + - SELECT TABLE_NAME AS "tableName", diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/StructuralVariantMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/StructuralVariantMapper.xml index 0fe8bbe8955..6c5e15e7459 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/StructuralVariantMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/StructuralVariantMapper.xml @@ -1,7 +1,7 @@ - + genetic_profile.STABLE_ID AS "${prefix}molecularProfileId", @@ -243,7 +243,7 @@ - SELECT @@ -269,7 +269,7 @@ ORDER BY gene1.HUGO_GENE_SYMBOL, gene2.HUGO_GENE_SYMBOL - SELECT @@ -295,7 +295,7 @@ ORDER BY gene1.HUGO_GENE_SYMBOL, gene2.HUGO_GENE_SYMBOL - SELECT diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml index 9b580a23507..eff6ccbd3b5 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml @@ -1,7 +1,7 @@ - + cancer_study.CANCER_STUDY_ID AS "${prefix}cancerStudyId", @@ -95,7 +95,7 @@ - SELECT @@ -125,7 +125,7 @@ - SELECT COUNT(*) AS totalCount FROM cancer_study @@ -135,7 +135,7 @@ - SELECT @@ -152,7 +152,7 @@ GROUP BY cancer_study.CANCER_STUDY_ID - SELECT cancer_study_tags.CANCER_STUDY_ID AS cancerStudyId, cancer_study_tags.TAGS AS tags @@ -161,7 +161,7 @@ WHERE cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId} - SELECT cancer_study_tags.CANCER_STUDY_ID AS cancerStudyId, cancer_study_tags.TAGS AS tags, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/TreatmentMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/TreatmentMapper.xml index 58c93613077..91037a138f4 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/TreatmentMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/TreatmentMapper.xml @@ -1,9 +1,9 @@ - + - SELECT clinical_event_data.VALUE as treatment, patient.STABLE_ID as patientId, @@ -21,7 +21,7 @@ AND clinical_event_data.KEY = #{key} - SELECT sample.STABLE_ID as sampleId, patient.STABLE_ID as patientId, @@ -38,7 +38,7 @@ AND (clinical_event.EVENT_TYPE LIKE 'Sample Acquisition' OR clinical_event.EVENT_TYPE LIKE 'SPECIMEN') - SELECT sample.STABLE_ID as sampleId, patient.STABLE_ID as patientId, diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/VariantCountMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/VariantCountMapper.xml index 92dcfc2788b..35376d31c39 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/VariantCountMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/VariantCountMapper.xml @@ -1,9 +1,9 @@ - + - SELECT genetic_profile.STABLE_ID AS molecularProfileId, mutation_count_by_keyword.KEYWORD AS keyword, diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml index 7f003505381..ead231b0236 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml @@ -1,7 +1,7 @@ - + NULL diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml index 74eca303a81..1466b27727d 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml @@ -1,7 +1,7 @@ - + diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml index ce2fd9bf6ed..60ce0f90dce 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml @@ -1,10 +1,10 @@ - + - SELECT internal_id as internalId, patient_stable_id as patientStableId, @@ -33,7 +33,7 @@ - SELECT hugo_gene_symbol as hugoGeneSymbol, entrez_gene_id as entrezGeneId, @@ -55,7 +55,7 @@ - SELECT hugo_gene_symbol as hugoGeneSymbol, entrez_gene_id as entrezGeneId, @@ -76,7 +76,7 @@ GROUP BY entrez_gene_id, hugo_gene_symbol, alteration, cytoband - SELECT hugo_gene_symbol as hugoGeneSymbol, entrez_gene_id as entrezGeneId, @@ -92,7 +92,7 @@ GROUP BY entrez_gene_id, hugo_gene_symbol - SELECT internal_id as internalId, replaceOne(sample_unique_id, concat(cancer_study_identifier, '_'), '') as sampleId, @@ -115,7 +115,7 @@ AND type = 'sample' - SELECT internal_id as internalId, replaceOne(patient_unique_id, concat(cancer_study_identifier, '_'), '') as patientId, @@ -149,7 +149,7 @@ - --we need to derive the alteration type from the stable_id by removing cancer study id --this should probaby be refactored at some point but we need to maintain api interface SELECT replaceOne(genetic_profile.stable_id, @@ -168,7 +168,7 @@ - SELECT name AS label, REPLACE(stable_id, CONCAT(cancer_study_identifier, '_'), '') AS value, @@ -415,10 +415,10 @@ hugo_gene_symbol - + - + @@ -426,17 +426,17 @@ - + - + - + - + @@ -451,7 +451,7 @@ - SELECT attr_id as attrId, datatype as dataType, @@ -461,7 +461,7 @@ JOIN cancer_study cs on cs.cancer_study_id = cam.cancer_study_id - SELECT attr_id as attrId, datatype as dataType, @@ -486,7 +486,7 @@ We compute the WES counts by using the query getSampleProfileCountWithoutPanelData and adding this value to the totalProfiled Count per gene in java. --> - SELECT gene as hugoGeneSymbol, COUNT(*) as numberOfProfiledCases @@ -546,7 +546,7 @@ - SELECT gene as hugoGeneSymbol, gene_panel_id as genePanelId @@ -567,7 +567,7 @@ GROUP BY gene, gene_panel_id - SELECT event_type as eventType, count(DISTINCT patient_unique_id) as count @@ -601,7 +601,7 @@ - + @@ -649,7 +649,7 @@ - + @@ -699,7 +699,7 @@ GROUP BY treatments.treatment - WITH genomic_numerical_query AS ( @@ -742,7 +742,7 @@ cast(((SELECT * FROM ()) - coalesce((SELECT genomic_numerical_count FROM genomic_numerical_sum LIMIT 1), 0)) as INTEGER) as count - WITH generic_assay_query AS ( @@ -785,7 +785,7 @@ cast(((SELECT * FROM ()) - coalesce((SELECT generic_assay_count FROM generic_assay_sum LIMIT 1), 0)) as INTEGER) as count - SELECT genetic_profile.genetic_profile_id AS "molecularProfileId", genetic_profile.stable_id AS "stableId", @@ -806,7 +806,7 @@ WHERE genetic_profile.genetic_alteration_type = 'GENERIC_ASSAY' - WITH unique_study_ids AS ( SELECT DISTINCT cancer_study_identifier diff --git a/src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java b/src/test/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelperTest.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java rename to src/test/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelperTest.java index c2884acab53..ac88988613b 100644 --- a/src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/helper/AlterationFilterHelperTest.java @@ -1,7 +1,8 @@ -package org.cbioportal.persistence.helper; +package org.cbioportal.legacy.persistence.helper; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.MutationEventType; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; import org.junit.Test; import java.util.HashMap; diff --git a/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java b/src/test/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelperTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java rename to src/test/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelperTest.java index 1f0e10225a1..5be83440772 100644 --- a/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/helper/StudyViewFilterHelperTest.java @@ -1,7 +1,8 @@ -package org.cbioportal.persistence.helper; +package org.cbioportal.legacy.persistence.helper; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import org.junit.Test; import java.math.BigDecimal; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java similarity index 91% rename from src/test/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java index 242103d2f1d..fd9b171e1b1 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationDriverAnnotationMyBatisRepositoryTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.AlterationDriverAnnotation; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java index 440624b753b..b9e00e99dae 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/AlterationMyBatisRepositoryTest.java @@ -1,23 +1,18 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import java.sql.SQLException; -import java.util.ArrayList; import java.util.Arrays; -import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.TreeSet; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.QueryElement; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.h2.tools.Server; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java index bb071cb76bb..2ee0234598b 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CancerTypeMyBatisRepositoryTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.List; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java index 2166b2d0ab1..ea428caa1b4 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalAttributeMyBatisRepositoryTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Optional; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java index 254efa47463..539c16b2c2b 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; @@ -6,13 +6,12 @@ import java.util.Optional; import java.util.stream.Collectors; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.cbioportal.persistence.mybatis.util.PaginationCalculator; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java index 60a8d1067de..6d3f8f6ebda 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java index b8e72afac33..f8843db0725 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CopyNumberSegmentMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java similarity index 90% rename from src/test/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java index 585463834d3..7ff6bc65558 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java index 1bce1c32c8a..c9687bdd4ea 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/DataAccessTokenMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Calendar; import java.util.Date; import java.util.List; import java.util.UUID; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java index ef098188c8c..92687a9e770 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/DiscreteCopyNumberMyBatisRepositoryTest.java @@ -1,18 +1,18 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.Comparator; import java.util.List; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepositoryTest.java index 796bb0348aa..4359a729846 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GeneMyBatisRepositoryTest.java @@ -30,13 +30,13 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepositoryTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepositoryTest.java index 3e51b7bf9e5..a8b3b013126 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GenePanelMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenePanelMyBatisRepositoryTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java similarity index 89% rename from src/test/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java index 98dcdb0c8d6..c8637fae4f6 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenericAssayMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GenericAssayAdditionalProperty; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java index 8b27fe13768..3e3e0b96641 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetHierarchyMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepositoryTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepositoryTest.java index 7580baf8393..a40b5340c1d 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/GenesetMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/GenesetMyBatisRepositoryTest.java @@ -30,15 +30,15 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java index d3241bcd6cd..ee81451fb89 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.List; import java.util.Map; import java.util.stream.Collectors; import java.util.stream.Stream; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java index 2b4db775c3d..fa6d70a9438 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MolecularProfileMyBatisRepositoryTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepositoryTest.java index 723f200c30f..c589cf20ad3 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/MutationMyBatisRepositoryTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.mybatis; - -import org.cbioportal.model.AlleleSpecificCopyNumber; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +package org.cbioportal.legacy.persistence.mybatis; + +import org.cbioportal.legacy.model.AlleleSpecificCopyNumber; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepositoryTest.java index 3661a80043e..00b26192d96 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/PatientMyBatisRepositoryTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.stream.Collectors; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java similarity index 91% rename from src/test/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java index 939548f1135..ec62463d207 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ReferenceGenomeGeneMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.ReferenceGenome; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.ReferenceGenome; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java index 888c80e7602..01c451ca803 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDataMyBatisRepositoryTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ResourceData; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.model.ResourceType; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.model.ResourceType; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java index 36b3c5d7021..e10034dc65d 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/ResourceDefinitionMyBatisRepositoryTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.model.ResourceType; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.model.ResourceType; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepositoryTest.java index 9103ba5fc7d..4358ef95bfe 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/SampleListMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleListMyBatisRepositoryTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepositoryTest.java index 1d4614cecd4..a39b8ee0435 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/SampleMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepositoryTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.stream.Collectors; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Patient; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java index 197afb2dc6b..965f86ab722 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantCopyNumberRegionMyBatisRepositoryTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java similarity index 95% rename from src/test/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java index 3d92ac2ff52..216a0e93e8c 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/SignificantlyMutatedGeneMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.math.BigDecimal; import java.util.List; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java similarity index 98% rename from src/test/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java index 149d2327f01..48d4b7e48db 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/StructuralVariantMyBatisRepositoryTest.java @@ -21,21 +21,21 @@ * along with this program. If not, see . */ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantGeneSubQuery; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.model.StructuralVariantSpecialValue; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.mybatis.config.TestConfig; -import org.cbioportal.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantGeneSubQuery; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.StructuralVariantSpecialValue; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; @@ -44,12 +44,8 @@ import org.springframework.boot.test.context.SpringBootTest; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; -import java.util.List; import java.util.Objects; -import java.util.stream.Collectors; @RunWith(SpringJUnit4ClassRunner.class) @SpringBootTest(classes = {StructuralVariantMyBatisRepository.class, StructuralVariantMapper.class, diff --git a/src/test/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepositoryTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepositoryTest.java index f3bd2772229..9042c49aaa8 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/StudyMyBatisRepositoryTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.text.SimpleDateFormat; import java.util.Arrays; import java.util.List; import java.util.TimeZone; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepositoryTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepositoryTest.java index 5cdc3506c34..bbbb9859840 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/TreatmentMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/TreatmentMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; -import org.cbioportal.model.ClinicalEventKeyCode; -import org.cbioportal.model.ClinicalEventSample; -import org.cbioportal.model.Treatment; -import org.cbioportal.persistence.TreatmentRepository; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.Treatment; +import org.cbioportal.legacy.persistence.TreatmentRepository; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepositoryTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepositoryTest.java similarity index 92% rename from src/test/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepositoryTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepositoryTest.java index 1dd6b241105..1ae262a031a 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/VariantCountMyBatisRepositoryTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/VariantCountMyBatisRepositoryTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatis; +package org.cbioportal.legacy.persistence.mybatis; import java.util.Arrays; import java.util.List; import java.util.Optional; -import org.cbioportal.model.VariantCount; -import org.cbioportal.persistence.mybatis.config.TestConfig; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.persistence.mybatis.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/config/TestConfig.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/config/TestConfig.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatis/config/TestConfig.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/config/TestConfig.java index bd86b27af83..779300b21a3 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/config/TestConfig.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/config/TestConfig.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatis.config; +package org.cbioportal.legacy.persistence.mybatis.config; import javax.sql.DataSource; import org.apache.ibatis.mapping.DatabaseIdProvider; import org.apache.ibatis.mapping.VendorDatabaseIdProvider; import org.apache.ibatis.session.SqlSessionFactory; -import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler; +import org.cbioportal.legacy.persistence.mybatis.typehandler.SampleTypeTypeHandler; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; import org.springframework.boot.test.context.TestConfiguration; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java index 7163f5300db..bb658c1957f 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/util/MolecularProfileCaseIdentifierUtilTest.java @@ -1,9 +1,11 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; import java.util.ArrayList; import java.util.Arrays; import java.util.Map; import java.util.Set; + +import org.cbioportal.legacy.persistence.mybatis.util.MolecularProfileCaseIdentifierUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/mybatis/util/PaginationCalculatorTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculatorTest.java similarity index 90% rename from src/test/java/org/cbioportal/persistence/mybatis/util/PaginationCalculatorTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculatorTest.java index 0f8bc654e1c..df3ccab4edc 100644 --- a/src/test/java/org/cbioportal/persistence/mybatis/util/PaginationCalculatorTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatis/util/PaginationCalculatorTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.persistence.mybatis.util; +package org.cbioportal.legacy.persistence.mybatis.util; +import org.cbioportal.legacy.persistence.mybatis.util.PaginationCalculator; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; @@ -7,7 +8,7 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; @RunWith(SpringJUnit4ClassRunner.class) -@ContextConfiguration(classes=PaginationCalculator.class) +@ContextConfiguration(classes= PaginationCalculator.class) public class PaginationCalculatorTest { diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/AbstractTestcontainers.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/AbstractTestcontainers.java index a4c04e4aedb..fb1d8117aff 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/AbstractTestcontainers.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; import org.junit.BeforeClass; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/CNAGenesTest.java similarity index 87% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/CNAGenesTest.java index 18df4041406..210d448534c 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/CNAGenesTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java similarity index 86% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java index 00bf968c29d..6b823a36ae4 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.DataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/FilteredSamplesTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/FilteredSamplesTest.java index d4926855e97..6d95950fafc 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/FilteredSamplesTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.CustomSampleIdentifier; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.CustomSampleIdentifier; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java similarity index 87% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java index 086b18593df..d1e5165ab86 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.GenericAssayDataCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.GenericAssayDataCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenomicDataCountsTest.java similarity index 87% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenomicDataCountsTest.java index 9e569b0e4a1..c2594b589a9 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/GenomicDataCountsTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MolecularProfileCountTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MolecularProfileCountTest.java index f9748a09110..b46492bf09a 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MolecularProfileCountTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutatedGenesTest.java similarity index 90% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutatedGenesTest.java index dd8001ded6f..86658bc8dfb 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutatedGenesTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutationDataCountsTest.java similarity index 87% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutationDataCountsTest.java index d04adb06575..a7c7959a0b4 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/MutationDataCountsTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java similarity index 84% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java index b23fc8f266f..f83ea3f263a 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; - -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; -import org.cbioportal.web.parameter.filter.OredPatientTreatmentFilters; -import org.cbioportal.web.parameter.filter.PatientTreatmentFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; + +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.OredPatientTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.PatientTreatmentFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProfiledCountsTest.java similarity index 97% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProfiledCountsTest.java index aa3e4a12f4f..6edfada6bec 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProfiledCountsTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java similarity index 89% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java index 332dff493b4..9d352d15b0e 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.persistence.mybatisclickhouse; - -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.StudyViewFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; + +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.GenomicDataBinFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java similarity index 83% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java index 5baa9149739..8cfd8977da4 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.persistence.mybatisclickhouse; - -import org.cbioportal.model.TemporalRelation; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; -import org.cbioportal.web.parameter.filter.OredSampleTreatmentFilters; -import org.cbioportal.web.parameter.filter.SampleTreatmentFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; + +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.OredSampleTreatmentFilters; +import org.cbioportal.legacy.web.parameter.filter.SampleTreatmentFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StructuralVariantGenesTest.java similarity index 86% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StructuralVariantGenesTest.java index f3a1dc6db00..f5abdcb578f 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StructuralVariantGenesTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.AlterationFilterHelper; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.persistence.helper.AlterationFilterHelper; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java index 66d72a34a88..4ec4993d5e2 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.persistence.mybatisclickhouse; +package org.cbioportal.legacy.persistence.mybatisclickhouse; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.service.util.StudyViewColumnarServiceUtil; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java index 2e48da4cb1d..a7d74ae3b3d 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.persistence.mybatisclickhouse; - -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.persistence.helper.StudyViewFilterHelper; -import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.StudyViewFilter; +package org.cbioportal.legacy.persistence.mybatisclickhouse; + +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/MyBatisConfig.java similarity index 96% rename from src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java rename to src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/MyBatisConfig.java index 25d1e098c64..4fcc1f3e8b7 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java +++ b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/MyBatisConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.mybatisclickhouse.config; +package org.cbioportal.legacy.persistence.mybatisclickhouse.config; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; diff --git a/src/test/java/org/cbioportal/persistence/util/CustomKeyGeneratorTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/CustomKeyGeneratorTest.java similarity index 93% rename from src/test/java/org/cbioportal/persistence/util/CustomKeyGeneratorTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/CustomKeyGeneratorTest.java index 94eb9170dd0..8606a4c0f96 100644 --- a/src/test/java/org/cbioportal/persistence/util/CustomKeyGeneratorTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/CustomKeyGeneratorTest.java @@ -1,8 +1,9 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.persistence.CacheEnabledConfig; -import org.cbioportal.persistence.StudyRepository; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.persistence.CacheEnabledConfig; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.util.CustomKeyGenerator; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheIntegrationTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheIntegrationTest.java similarity index 89% rename from src/test/java/org/cbioportal/persistence/util/CustomRedisCacheIntegrationTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheIntegrationTest.java index 0a52d338217..2c59ff38256 100644 --- a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheIntegrationTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheIntegrationTest.java @@ -1,6 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; -import org.cbioportal.persistence.util.fakeclient.MockInMemoryRedissonClient; +import org.cbioportal.legacy.persistence.util.fakeclient.MockInMemoryRedissonClient; import org.junit.Test; import static org.junit.Assert.assertEquals; diff --git a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheManagerTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManagerTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/util/CustomRedisCacheManagerTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManagerTest.java index 02578ed04df..975084d0cd5 100644 --- a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheManagerTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheManagerTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; +import org.cbioportal.legacy.persistence.util.CustomRedisCacheManager; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mock; diff --git a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheTest.java similarity index 99% rename from src/test/java/org/cbioportal/persistence/util/CustomRedisCacheTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheTest.java index e680e476a41..3e5ced0c2c0 100644 --- a/src/test/java/org/cbioportal/persistence/util/CustomRedisCacheTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/CustomRedisCacheTest.java @@ -1,8 +1,10 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; import java.util.Arrays; import java.util.HashMap; import java.util.List; + +import org.cbioportal.legacy.persistence.util.CustomRedisCache; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/util/EhCacheUtilsTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/EhCacheUtilsTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/util/EhCacheUtilsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/EhCacheUtilsTest.java index b60760037b8..c0c59f1fb18 100644 --- a/src/test/java/org/cbioportal/persistence/util/EhCacheUtilsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/EhCacheUtilsTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; +import org.cbioportal.legacy.persistence.util.EhCacheUtils; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/persistence/util/RedisCacheUtilsTest.java b/src/test/java/org/cbioportal/legacy/persistence/util/RedisCacheUtilsTest.java similarity index 94% rename from src/test/java/org/cbioportal/persistence/util/RedisCacheUtilsTest.java rename to src/test/java/org/cbioportal/legacy/persistence/util/RedisCacheUtilsTest.java index 8ea296623b8..12d32fae832 100644 --- a/src/test/java/org/cbioportal/persistence/util/RedisCacheUtilsTest.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/RedisCacheUtilsTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.persistence.util; +package org.cbioportal.legacy.persistence.util; +import org.cbioportal.legacy.persistence.util.RedisCacheUtils; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockInMemoryRedissonClient.java similarity index 99% rename from src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java rename to src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockInMemoryRedissonClient.java index 145be13601c..25ee4c46eae 100644 --- a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockInMemoryRedissonClient.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockInMemoryRedissonClient.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util.fakeclient; +package org.cbioportal.legacy.persistence.util.fakeclient; import org.redisson.api.*; import org.redisson.api.redisnode.BaseRedisNodes; diff --git a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockRBucket.java b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRBucket.java similarity index 99% rename from src/test/java/org/cbioportal/persistence/util/fakeclient/MockRBucket.java rename to src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRBucket.java index 642509fd28a..32c48bd8bf9 100644 --- a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockRBucket.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRBucket.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util.fakeclient; +package org.cbioportal.legacy.persistence.util.fakeclient; import org.redisson.api.ObjectListener; import org.redisson.api.RBucket; diff --git a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockRKeys.java b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRKeys.java similarity index 99% rename from src/test/java/org/cbioportal/persistence/util/fakeclient/MockRKeys.java rename to src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRKeys.java index 3866c31ddca..68fec768cf3 100644 --- a/src/test/java/org/cbioportal/persistence/util/fakeclient/MockRKeys.java +++ b/src/test/java/org/cbioportal/legacy/persistence/util/fakeclient/MockRKeys.java @@ -1,4 +1,4 @@ -package org.cbioportal.persistence.util.fakeclient; +package org.cbioportal.legacy.persistence.util.fakeclient; import org.redisson.api.*; diff --git a/src/test/java/org/cbioportal/proxy/MonkifierTest.java b/src/test/java/org/cbioportal/legacy/proxy/MonkifierTest.java similarity index 96% rename from src/test/java/org/cbioportal/proxy/MonkifierTest.java rename to src/test/java/org/cbioportal/legacy/proxy/MonkifierTest.java index 9fb7d5da515..85cc121b53a 100644 --- a/src/test/java/org/cbioportal/proxy/MonkifierTest.java +++ b/src/test/java/org/cbioportal/legacy/proxy/MonkifierTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.proxy; +package org.cbioportal.legacy.proxy; +import org.cbioportal.application.proxy.Monkifier; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImplTest.java index 0497e4e1d37..cd2c9e0648e 100644 --- a/src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/AlterationCountServiceImplTest.java @@ -1,22 +1,20 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.AlterationRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.StudyViewRepository; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.AlterationEnrichmentUtil; -import org.cbioportal.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.AlterationRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImplTest.java index 7fc93118464..da6445f678c 100644 --- a/src/test/java/org/cbioportal/service/impl/AlterationDriverAnnotationServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/AlterationDriverAnnotationServiceImplTest.java @@ -1,8 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.AlterationDriverAnnotation; -import org.cbioportal.model.CustomDriverAnnotationReport; -import org.cbioportal.persistence.AlterationDriverAnnotationRepository; +import org.cbioportal.legacy.model.AlterationDriverAnnotation; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.persistence.AlterationDriverAnnotationRepository; +import org.cbioportal.legacy.service.impl.AlterationDriverAnnotationServiceImpl; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImplTest.java similarity index 85% rename from src/test/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImplTest.java index 0c645bb2620..c1af5e5d2ad 100644 --- a/src/test/java/org/cbioportal/service/impl/AlterationEnrichmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/AlterationEnrichmentServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationCountByGene; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationCountByGene; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/BaseServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/BaseServiceImplTest.java similarity index 98% rename from src/test/java/org/cbioportal/service/impl/BaseServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/BaseServiceImplTest.java index 827a7b752a5..d6d0f436854 100644 --- a/src/test/java/org/cbioportal/service/impl/BaseServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/BaseServiceImplTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; public class BaseServiceImplTest { diff --git a/src/test/java/org/cbioportal/service/impl/CacheServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CacheServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/CacheServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CacheServiceImplTest.java index d2a686f9b1d..8e61eb38b9d 100644 --- a/src/test/java/org/cbioportal/service/impl/CacheServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CacheServiceImplTest.java @@ -1,10 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.persistence.cachemaputil.StaticRefCacheMapUtil; -import org.cbioportal.persistence.util.CacheUtils; -import org.cbioportal.service.exception.CacheOperationException; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.cachemaputil.StaticRefCacheMapUtil; +import org.cbioportal.legacy.persistence.util.CacheUtils; +import org.cbioportal.legacy.service.exception.CacheOperationException; +import org.cbioportal.legacy.service.impl.CacheServiceImpl; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/CancerTypeServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImplTest.java similarity index 88% rename from src/test/java/org/cbioportal/service/impl/CancerTypeServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImplTest.java index 72cd6eb40e0..40f30816ba4 100644 --- a/src/test/java/org/cbioportal/service/impl/CancerTypeServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CancerTypeServiceImplTest.java @@ -1,9 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/ClinicalAttributeServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/ClinicalAttributeServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImplTest.java index 8d07226f80d..759f2c4cbe4 100644 --- a/src/test/java/org/cbioportal/service/impl/ClinicalAttributeServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalAttributeServiceImplTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalAttributeRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalAttributeRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.Before; diff --git a/src/test/java/org/cbioportal/service/impl/ClinicalDataServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/ClinicalDataServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImplTest.java index 1a272ae3075..4d4f73ca0c5 100755 --- a/src/test/java/org/cbioportal/service/impl/ClinicalDataServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalDataServiceImplTest.java @@ -1,13 +1,23 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalDataRepository; -import org.cbioportal.service.*; -import org.cbioportal.service.exception.*; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.utils.Encoder; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalDataRepository; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.utils.Encoder; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/ClinicalEventServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/ClinicalEventServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImplTest.java index e6fe83f8c7e..a84e7471b41 100644 --- a/src/test/java/org/cbioportal/service/impl/ClinicalEventServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ClinicalEventServiceImplTest.java @@ -1,18 +1,18 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ClinicalEventRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.web.parameter.ClinicalEventRequest; -import org.cbioportal.web.parameter.ClinicalEventRequestIdentifier; -import org.cbioportal.web.parameter.OccurrencePosition; -import org.cbioportal.web.parameter.SurvivalRequest; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.ClinicalEventRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequest; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequestIdentifier; +import org.cbioportal.legacy.web.parameter.OccurrencePosition; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.InjectMocks; diff --git a/src/test/java/org/cbioportal/service/impl/CoExpressionServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImplTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/impl/CoExpressionServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImplTest.java index 711b5f43888..46b07fcc26d 100644 --- a/src/test/java/org/cbioportal/service/impl/CoExpressionServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CoExpressionServiceImplTest.java @@ -1,19 +1,19 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.CoExpression; -import org.cbioportal.model.EntityType; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.util.CoExpressionAsyncMethods; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.util.CoExpressionAsyncMethods; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImplTest.java index a5412473c32..876aecbbc8b 100644 --- a/src/test/java/org/cbioportal/service/impl/CopyNumberSegmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CopyNumberSegmentServiceImplTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/CosmicCountServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImplTest.java similarity index 87% rename from src/test/java/org/cbioportal/service/impl/CosmicCountServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImplTest.java index d8c1df4e26b..ef269ee4bd8 100644 --- a/src/test/java/org/cbioportal/service/impl/CosmicCountServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/CosmicCountServiceImplTest.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.persistence.CosmicCountRepository; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.persistence.CosmicCountRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImplTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImplTest.java index 199865c11bd..87448cccfed 100644 --- a/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/DiscreteCopyNumberServiceImplTest.java @@ -1,11 +1,16 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImplTest.java index 0b612d5f9ea..8aed57a4ef7 100644 --- a/src/test/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ExpressionEnrichmentServiceImplTest.java @@ -1,16 +1,30 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.math.BigDecimal; import java.util.*; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.ExpressionEnrichmentUtil; + +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.ExpressionEnrichment; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.GroupStatistics; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.ReferenceGenome; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.ExpressionEnrichmentUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GeneMemoizerServiceTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/GeneMemoizerServiceTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceTest.java index 04f81101215..13d1a52f437 100644 --- a/src/test/java/org/cbioportal/service/impl/GeneMemoizerServiceTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GeneMemoizerServiceTest.java @@ -1,7 +1,8 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.service.StaticDataTimestampService; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.service.StaticDataTimestampService; +import org.cbioportal.legacy.service.impl.GeneMemoizerServiceImpl; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/GenePanelServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenePanelServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/GenePanelServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenePanelServiceImplTest.java index 19b65920131..0a5944f0eea 100644 --- a/src/test/java/org/cbioportal/service/impl/GenePanelServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenePanelServiceImplTest.java @@ -1,14 +1,18 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.*; import java.util.stream.Collectors; -import org.cbioportal.model.*; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenePanelRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenePanelRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/GeneServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GeneServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/GeneServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GeneServiceImplTest.java index 10e3ada5269..d195b257136 100644 --- a/src/test/java/org/cbioportal/service/impl/GeneServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GeneServiceImplTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GeneRepository; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.service.util.ChromosomeCalculator; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GeneRepository; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.service.util.ChromosomeCalculator; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/GenericAssayEnrichmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenericAssayEnrichmentServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/GenericAssayEnrichmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenericAssayEnrichmentServiceImplTest.java index ea9e489e13a..9f3dd12f5bd 100644 --- a/src/test/java/org/cbioportal/service/impl/GenericAssayEnrichmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenericAssayEnrichmentServiceImplTest.java @@ -1,25 +1,25 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.ExpressionEnrichment; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.ReferenceGenome; -import org.cbioportal.model.Sample; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.GenericAssayBinaryEnrichment; -import org.cbioportal.model.GenericAssayCategoricalEnrichment; -import org.cbioportal.model.GroupStatistics; - -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.util.ExpressionEnrichmentUtil; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ExpressionEnrichment; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.ReferenceGenome; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.GenericAssayBinaryEnrichment; +import org.cbioportal.legacy.model.GenericAssayCategoricalEnrichment; +import org.cbioportal.legacy.model.GroupStatistics; + +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.util.ExpressionEnrichmentUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenericAssayServiceImpTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/GenericAssayServiceImpTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpTest.java index 14bcf9adbdf..db6b344a86d 100644 --- a/src/test/java/org/cbioportal/service/impl/GenericAssayServiceImpTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpTest.java @@ -1,24 +1,24 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; -import org.cbioportal.model.GenericAssayAdditionalProperty; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.GenericAssayMolecularAlteration; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.model.MolecularProfile.MolecularAlterationType; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.persistence.GenericAssayRepository; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.PersistenceConstants; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.GenericAssayNotFoundException; +import org.cbioportal.legacy.model.GenericAssayAdditionalProperty; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.GenericAssayMolecularAlteration; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.MolecularProfile.MolecularAlterationType; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.persistence.GenericAssayRepository; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.PersistenceConstants; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.GenericAssayNotFoundException; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenesetCorrelationServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImplTest.java similarity index 92% rename from src/test/java/org/cbioportal/service/impl/GenesetCorrelationServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImplTest.java index 65bc425fd04..27e35c359b7 100644 --- a/src/test/java/org/cbioportal/service/impl/GenesetCorrelationServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenesetCorrelationServiceImplTest.java @@ -1,19 +1,19 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenesetDataServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/GenesetDataServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImplTest.java index fc67d32bfba..c76233fea0b 100644 --- a/src/test/java/org/cbioportal/service/impl/GenesetDataServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenesetDataServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GenesetMolecularAlteration; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; +import org.cbioportal.legacy.model.GenesetMolecularAlteration; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenesetHierarchyServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/GenesetHierarchyServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImplTest.java index 5e13e9b2c9a..7e41f965ba0 100644 --- a/src/test/java/org/cbioportal/service/impl/GenesetHierarchyServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenesetHierarchyServiceImplTest.java @@ -1,19 +1,19 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.persistence.GenesetHierarchyRepository; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.service.GenesetService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.persistence.GenesetHierarchyRepository; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/GenesetServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/GenesetServiceImplTest.java similarity index 89% rename from src/test/java/org/cbioportal/service/impl/GenesetServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/GenesetServiceImplTest.java index 90a73ae3c3e..7186a7c7c8f 100644 --- a/src/test/java/org/cbioportal/service/impl/GenesetServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/GenesetServiceImplTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.GenesetRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.exception.GenesetNotFoundException; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.GenesetRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.exception.GenesetNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/MolecularDataServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/MolecularDataServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImplTest.java index d63ef1216c2..f58d8c6b913 100644 --- a/src/test/java/org/cbioportal/service/impl/MolecularDataServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MolecularDataServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.GeneMolecularAlteration; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileSamples; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.DiscreteCopyNumberRepository; -import org.cbioportal.persistence.MolecularDataRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.SampleService; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.GeneMolecularAlteration; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileSamples; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.DiscreteCopyNumberRepository; +import org.cbioportal.legacy.persistence.MolecularDataRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.SampleService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/MolecularProfileServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/MolecularProfileServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImplTest.java index ab68f88124a..5272283df94 100644 --- a/src/test/java/org/cbioportal/service/impl/MolecularProfileServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MolecularProfileServiceImplTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.service.util.MolecularProfileUtil; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/MrnaPercentileServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/MrnaPercentileServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImplTest.java index 4a21c6a8688..ce9f6469687 100644 --- a/src/test/java/org/cbioportal/service/impl/MrnaPercentileServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MrnaPercentileServiceImplTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/MutationServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MutationServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/MutationServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MutationServiceImplTest.java index e89edc0627f..b4f28bb14ce 100644 --- a/src/test/java/org/cbioportal/service/impl/MutationServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MutationServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.persistence.MutationRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.persistence.MutationRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/MutationSpectrumServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImplTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/impl/MutationSpectrumServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImplTest.java index c27bbcdb830..f4960f142d5 100644 --- a/src/test/java/org/cbioportal/service/impl/MutationSpectrumServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/MutationSpectrumServiceImplTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.MutationService; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.MutationService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/PatientServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/PatientServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/PatientServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/PatientServiceImplTest.java index 9d15499e55f..f2ecca2e8c8 100644 --- a/src/test/java/org/cbioportal/service/impl/PatientServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/PatientServiceImplTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/ReadPermissionServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImplTest.java similarity index 89% rename from src/test/java/org/cbioportal/service/impl/ReadPermissionServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImplTest.java index 5f781f0d9ce..406e8f22152 100644 --- a/src/test/java/org/cbioportal/service/impl/ReadPermissionServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ReadPermissionServiceImplTest.java @@ -1,8 +1,9 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.security.CancerStudyPermissionEvaluator; -import org.cbioportal.utils.security.AccessLevel; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.application.security.CancerStudyPermissionEvaluator; +import org.cbioportal.legacy.service.impl.ReadPermissionServiceImpl; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImplTest.java index 7ce4bb6a6bc..1d20e73e9e9 100644 --- a/src/test/java/org/cbioportal/service/impl/ReferenceGenomeGeneServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ReferenceGenomeGeneServiceImplTest.java @@ -1,11 +1,9 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.Gene; -import org.cbioportal.model.ReferenceGenome; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.ReferenceGenomeGeneRepository; -import org.cbioportal.service.exception.GeneNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.ReferenceGenome; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.persistence.ReferenceGenomeGeneRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; @@ -15,7 +13,6 @@ import org.mockito.junit.MockitoJUnitRunner; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; @RunWith(MockitoJUnitRunner.class) diff --git a/src/test/java/org/cbioportal/service/impl/SampleListServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/SampleListServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/SampleListServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/SampleListServiceImplTest.java index 42b639e5a0a..b6c64f0ceb3 100644 --- a/src/test/java/org/cbioportal/service/impl/SampleListServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/SampleListServiceImplTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.SampleList; -import org.cbioportal.model.SampleListToSampleId; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.SampleListToSampleId; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.Before; diff --git a/src/test/java/org/cbioportal/service/impl/SampleServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/SampleServiceImplTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/impl/SampleServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/SampleServiceImplTest.java index 374368d1718..c4dbb9f9060 100644 --- a/src/test/java/org/cbioportal/service/impl/SampleServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/SampleServiceImplTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.CopyNumberSegmentRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.SampleRepository; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.service.exception.StudyNotFoundException; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.CopyNumberSegmentRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.SampleRepository; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/ServerStatusServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImplTest.java similarity index 86% rename from src/test/java/org/cbioportal/service/impl/ServerStatusServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImplTest.java index 03fc7c35db0..e60862b7486 100644 --- a/src/test/java/org/cbioportal/service/impl/ServerStatusServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ServerStatusServiceImplTest.java @@ -1,11 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.service.impl.ServerStatusServiceImpl.ServerStatusMessage; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.persistence.CancerTypeRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImplTest.java similarity index 89% rename from src/test/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImplTest.java index cf7a4ae0e8b..ecbc2cf7aa4 100644 --- a/src/test/java/org/cbioportal/service/impl/SignificantCopyNumberRegionServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/SignificantCopyNumberRegionServiceImplTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantCopyNumberRegionRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantCopyNumberRegionRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImplTest.java similarity index 87% rename from src/test/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImplTest.java index 30076855c7f..1dcca401c3f 100644 --- a/src/test/java/org/cbioportal/service/impl/SignificantlyMutatedGeneServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/SignificantlyMutatedGeneServiceImplTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.SignificantlyMutatedGeneRepository; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.SignificantlyMutatedGeneRepository; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/StaticDataTimestampServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImplTest.java similarity index 86% rename from src/test/java/org/cbioportal/service/impl/StaticDataTimestampServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImplTest.java index 498ae771bb5..945d44fc899 100644 --- a/src/test/java/org/cbioportal/service/impl/StaticDataTimestampServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/StaticDataTimestampServiceImplTest.java @@ -1,7 +1,7 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.TableTimestampPair; -import org.cbioportal.persistence.StaticDataTimeStampRepository; +import org.cbioportal.legacy.model.TableTimestampPair; +import org.cbioportal.legacy.persistence.StaticDataTimeStampRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/StructuralVariantServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImplTest.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/StructuralVariantServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImplTest.java index 71e2d2d4efb..c7f1b1f1554 100644 --- a/src/test/java/org/cbioportal/service/impl/StructuralVariantServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/StructuralVariantServiceImplTest.java @@ -21,16 +21,16 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import java.util.ArrayList; import java.util.Collections; import java.util.List; -import org.cbioportal.model.GeneFilterQuery; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.persistence.StructuralVariantRepository; +import org.cbioportal.legacy.model.GeneFilterQuery; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.persistence.StructuralVariantRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/StudyServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/StudyServiceImplTest.java similarity index 88% rename from src/test/java/org/cbioportal/service/impl/StudyServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/StudyServiceImplTest.java index ae97ac38e4c..c5dbcec60f5 100644 --- a/src/test/java/org/cbioportal/service/impl/StudyServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/StudyServiceImplTest.java @@ -1,12 +1,12 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.ReadPermissionService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.utils.security.AccessLevel; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.ReadPermissionService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.utils.security.AccessLevel; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/StudyViewServiceImplTest.java similarity index 95% rename from src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/StudyViewServiceImplTest.java index e714ec3ea0d..c7d6e122e13 100644 --- a/src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/StudyViewServiceImplTest.java @@ -1,32 +1,32 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.GenericAssayDataCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.model.util.Select; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.model.GenericAssayDataCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/TreatmentServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/TreatmentServiceImplTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/impl/TreatmentServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/TreatmentServiceImplTest.java index 8a86e465d3f..cf4a01a066f 100644 --- a/src/test/java/org/cbioportal/service/impl/TreatmentServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/TreatmentServiceImplTest.java @@ -1,7 +1,13 @@ -package org.cbioportal.service.impl; - -import org.cbioportal.model.*; -import org.cbioportal.persistence.TreatmentRepository; +package org.cbioportal.legacy.service.impl; + +import org.cbioportal.legacy.model.ClinicalEventKeyCode; +import org.cbioportal.legacy.model.ClinicalEventSample; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.model.Treatment; +import org.cbioportal.legacy.service.impl.TreatmentServiceImpl; +import org.cbioportal.legacy.persistence.TreatmentRepository; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTest.java index 89b34a50c95..9a225e610f1 100644 --- a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTest.java @@ -46,31 +46,22 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; //TODO package org.cbioportal.security.spring.authentication.token; import java.util.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; + import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; -import org.springframework.stereotype.Component; -import org.springframework.context.annotation.Import; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; import org.springframework.test.context.junit4.SpringRunner; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.Mockito; -import org.mockito.junit.MockitoJUnitRunner; -import org.cbioportal.persistence.DataAccessTokenRepository; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.impl.UuidDataAccessTokenServiceImpl; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; +import org.cbioportal.legacy.model.DataAccessToken; @TestPropertySource( properties = { "dat.jwt.secret_key = +NbopXzb/AIQNrVEGzxzP5CF42e5drvrXTQot3gfW/s=", diff --git a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java similarity index 97% rename from src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java rename to src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java index d83ff6994fe..c2905a58f87 100644 --- a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestConfiguration.java @@ -46,19 +46,20 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; //TODO package org.cbioportal.security.spring.authentication.token; import java.util.*; +import org.cbioportal.legacy.service.impl.UuidDataAccessTokenServiceImpl; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; import org.mockito.ArgumentMatchers; import org.mockito.Mockito; import org.mockito.stubbing.Answer; import org.mockito.invocation.InvocationOnMock; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.DataAccessTokenRepository; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; @TestConfiguration public class UuidDataAccessTokenServiceImplTestConfiguration { diff --git a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java similarity index 91% rename from src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java rename to src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java index 46a43245032..063a654a85d 100644 --- a/src/test/java/org/cbioportal/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/UuidDataAccessTokenServiceImplTestFiveTokenLimit.java @@ -46,31 +46,22 @@ * along with this program. If not, see . */ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; //TODO package org.cbioportal.security.spring.authentication.token; import java.util.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; + import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; -import org.springframework.stereotype.Component; -import org.springframework.context.annotation.Import; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; import org.springframework.test.context.junit4.SpringRunner; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.Mockito; -import org.mockito.junit.MockitoJUnitRunner; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.persistence.DataAccessTokenRepository; -import org.cbioportal.service.impl.UuidDataAccessTokenServiceImpl; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.persistence.DataAccessTokenRepository; @TestPropertySource( properties = { "dat.jwt.secret_key = +NbopXzb/AIQNrVEGzxzP5CF42e5drvrXTQot3gfW/s=", diff --git a/src/test/java/org/cbioportal/service/impl/VariantCountServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/VariantCountServiceImplTest.java similarity index 82% rename from src/test/java/org/cbioportal/service/impl/VariantCountServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/VariantCountServiceImplTest.java index 2b828629d62..14cd72b79ee 100644 --- a/src/test/java/org/cbioportal/service/impl/VariantCountServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/VariantCountServiceImplTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.VariantCount; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.persistence.VariantCountRepository; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.MutationService; -import org.cbioportal.service.SampleListService; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.persistence.VariantCountRepository; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.service.SampleListService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java b/src/test/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImplTest.java similarity index 97% rename from src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java rename to src/test/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImplTest.java index 2b00e7f2c66..e879097dccb 100644 --- a/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java +++ b/src/test/java/org/cbioportal/legacy/service/impl/ViolinPlotServiceImplTest.java @@ -1,10 +1,11 @@ -package org.cbioportal.service.impl; +package org.cbioportal.legacy.service.impl; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalViolinPlotData; -import org.cbioportal.model.ClinicalViolinPlotRowData; -import org.cbioportal.model.Sample; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalViolinPlotData; +import org.cbioportal.legacy.model.ClinicalViolinPlotRowData; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.impl.ViolinPlotServiceImpl; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java b/src/test/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtilTest.java similarity index 97% rename from src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java rename to src/test/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtilTest.java index 31f09303271..4ec37645110 100644 --- a/src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/AlterationCountServiceUtilTest.java @@ -1,13 +1,14 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationCountByStructuralVariant; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MutSig; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationCountByStructuralVariant; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.service.util.AlterationCountServiceUtil; import org.junit.Test; import java.math.BigDecimal; diff --git a/src/test/java/org/cbioportal/service/util/AlterationEnrichmentUtilTest.java b/src/test/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtilTest.java similarity index 94% rename from src/test/java/org/cbioportal/service/util/AlterationEnrichmentUtilTest.java rename to src/test/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtilTest.java index 7020d01ef0e..6751bfd1dd4 100644 --- a/src/test/java/org/cbioportal/service/util/AlterationEnrichmentUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/AlterationEnrichmentUtilTest.java @@ -1,11 +1,17 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.math.BigDecimal; import java.util.*; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.*; -import org.cbioportal.service.GeneService; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.util.AlterationEnrichmentUtil; +import org.cbioportal.legacy.service.util.FisherExactTestCalculator; +import org.cbioportal.legacy.service.util.ProfiledCasesCounter; +import org.cbioportal.legacy.service.GeneService; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/CoExpressionAsyncMethodsTest.java b/src/test/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethodsTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/util/CoExpressionAsyncMethodsTest.java rename to src/test/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethodsTest.java index 28fb4c43c13..9c2daebb3ec 100644 --- a/src/test/java/org/cbioportal/service/util/CoExpressionAsyncMethodsTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/CoExpressionAsyncMethodsTest.java @@ -1,6 +1,7 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import org.cbioportal.model.CoExpression; +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.service.util.CoExpressionAsyncMethods; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/JwtUtilsTest.java b/src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTest.java similarity index 98% rename from src/test/java/org/cbioportal/service/util/JwtUtilsTest.java rename to src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTest.java index 13d848d098d..954144b73de 100644 --- a/src/test/java/org/cbioportal/service/util/JwtUtilsTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTest.java @@ -46,11 +46,11 @@ * along with this program. If not, see . */ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; //TODO package org.cbioportal.security.spring.authentication.token; import java.util.*; -import org.cbioportal.service.exception.InvalidDataAccessTokenException; +import org.cbioportal.legacy.service.exception.InvalidDataAccessTokenException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; diff --git a/src/test/java/org/cbioportal/service/util/JwtUtilsTestConfiguration.java b/src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTestConfiguration.java similarity index 96% rename from src/test/java/org/cbioportal/service/util/JwtUtilsTestConfiguration.java rename to src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTestConfiguration.java index 5322922a2d6..5e235ffe341 100644 --- a/src/test/java/org/cbioportal/service/util/JwtUtilsTestConfiguration.java +++ b/src/test/java/org/cbioportal/legacy/service/util/JwtUtilsTestConfiguration.java @@ -46,9 +46,10 @@ * along with this program. If not, see . */ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; //TODO package org.cbioportal.security.spring.authentication.token; +import org.cbioportal.legacy.service.util.JwtUtils; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; diff --git a/src/test/java/org/cbioportal/service/util/MolecularProfileUtilTest.java b/src/test/java/org/cbioportal/legacy/service/util/MolecularProfileUtilTest.java similarity index 97% rename from src/test/java/org/cbioportal/service/util/MolecularProfileUtilTest.java rename to src/test/java/org/cbioportal/legacy/service/util/MolecularProfileUtilTest.java index 078acc83e06..5a23eef4325 100644 --- a/src/test/java/org/cbioportal/service/util/MolecularProfileUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/MolecularProfileUtilTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.service.impl.BaseServiceImplTest; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.service.impl.BaseServiceImplTest; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/ProfiledCasesCounterTest.java b/src/test/java/org/cbioportal/legacy/service/util/ProfiledCasesCounterTest.java similarity index 93% rename from src/test/java/org/cbioportal/service/util/ProfiledCasesCounterTest.java rename to src/test/java/org/cbioportal/legacy/service/util/ProfiledCasesCounterTest.java index a0303a80c7a..e5bc4fb1971 100644 --- a/src/test/java/org/cbioportal/service/util/ProfiledCasesCounterTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/ProfiledCasesCounterTest.java @@ -1,15 +1,16 @@ -package org.cbioportal.service.util; +package org.cbioportal.legacy.service.util; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.SampleListService; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.util.ProfiledCasesCounter; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java b/src/test/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtilTest.java similarity index 96% rename from src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java rename to src/test/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtilTest.java index 0c9687d6e59..cdbc893ecbb 100644 --- a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/service/util/StudyViewColumnarServiceUtilTest.java @@ -1,12 +1,13 @@ -package org.cbioportal.service.util; - -import org.cbioportal.model.CaseListDataCount; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.web.parameter.GenomicDataFilter; +package org.cbioportal.legacy.service.util; + +import org.cbioportal.legacy.model.CaseListDataCount; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; import org.junit.Assert; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/utils/config/PropertyConditionTest.java b/src/test/java/org/cbioportal/legacy/utils/config/PropertyConditionTest.java similarity index 97% rename from src/test/java/org/cbioportal/utils/config/PropertyConditionTest.java rename to src/test/java/org/cbioportal/legacy/utils/config/PropertyConditionTest.java index 79dd1ba5e48..b6a950fe7b4 100644 --- a/src/test/java/org/cbioportal/utils/config/PropertyConditionTest.java +++ b/src/test/java/org/cbioportal/legacy/utils/config/PropertyConditionTest.java @@ -1,5 +1,6 @@ -package org.cbioportal.utils.config; +package org.cbioportal.legacy.utils.config; +import org.cbioportal.legacy.utils.config.PropertyCondition; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/AlterationDriverAnnotationControllerTest.java b/src/test/java/org/cbioportal/legacy/web/AlterationDriverAnnotationControllerTest.java similarity index 93% rename from src/test/java/org/cbioportal/web/AlterationDriverAnnotationControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/AlterationDriverAnnotationControllerTest.java index cfa208c397f..7b0efce0839 100644 --- a/src/test/java/org/cbioportal/web/AlterationDriverAnnotationControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/AlterationDriverAnnotationControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.mockito.ArgumentMatchers.anyList; import static org.mockito.Mockito.when; @@ -11,9 +11,9 @@ import java.util.Collections; import java.util.HashSet; import java.util.List; -import org.cbioportal.model.CustomDriverAnnotationReport; -import org.cbioportal.service.AlterationDriverAnnotationService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.CustomDriverAnnotationReport; +import org.cbioportal.legacy.service.AlterationDriverAnnotationService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/AlterationEnrichmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/AlterationEnrichmentControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/AlterationEnrichmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/AlterationEnrichmentControllerTest.java index 54ab0b76405..25b39a16e93 100644 --- a/src/test/java/org/cbioportal/web/AlterationEnrichmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/AlterationEnrichmentControllerTest.java @@ -1,17 +1,17 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.AlterationEnrichment; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.CNA; -import org.cbioportal.model.CountSummary; -import org.cbioportal.model.MolecularProfileCaseIdentifier; -import org.cbioportal.model.MutationEventType; -import org.cbioportal.service.AlterationEnrichmentService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; -import org.cbioportal.web.parameter.MolecularProfileCasesGroupFilter; -import org.cbioportal.web.util.AlterationFilterMockitoArgumentMatcher; +import org.cbioportal.legacy.model.AlterationEnrichment; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.CNA; +import org.cbioportal.legacy.model.CountSummary; +import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier; +import org.cbioportal.legacy.model.MutationEventType; +import org.cbioportal.legacy.service.AlterationEnrichmentService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter; +import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupFilter; +import org.cbioportal.legacy.web.util.AlterationFilterMockitoArgumentMatcher; import org.hamcrest.Matchers; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/CacheControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CacheControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/CacheControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CacheControllerTest.java index cf40aee1d37..c09783784a7 100644 --- a/src/test/java/org/cbioportal/web/CacheControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CacheControllerTest.java @@ -1,7 +1,5 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import static org.mockito.ArgumentMatchers.anyBoolean; -import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.ArgumentMatchers.eq; import static org.mockito.Mockito.doThrow; import static org.mockito.Mockito.never; @@ -10,10 +8,8 @@ import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; -import org.cbioportal.service.CacheService; -import org.cbioportal.service.exception.CacheOperationException; -import org.junit.Ignore; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.service.CacheService; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/web/CacheStatsControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CacheStatsControllerTest.java similarity index 94% rename from src/test/java/org/cbioportal/web/CacheStatsControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CacheStatsControllerTest.java index 904b76f8d03..bfd5d45fc2a 100644 --- a/src/test/java/org/cbioportal/web/CacheStatsControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CacheStatsControllerTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.service.CacheStatisticsService; -import org.cbioportal.service.exception.CacheNotFoundException; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.service.CacheStatisticsService; +import org.cbioportal.legacy.service.exception.CacheNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/CancerTypeControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CancerTypeControllerTest.java similarity index 94% rename from src/test/java/org/cbioportal/web/CancerTypeControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CancerTypeControllerTest.java index fb53ae94c76..babad36579b 100644 --- a/src/test/java/org/cbioportal/web/CancerTypeControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CancerTypeControllerTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.CancerTypeService; -import org.cbioportal.service.exception.CancerTypeNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.CancerTypeService; +import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalAttributeControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalAttributeControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/ClinicalAttributeControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalAttributeControllerTest.java index 8433b5018fa..468f39accac 100644 --- a/src/test/java/org/cbioportal/web/ClinicalAttributeControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalAttributeControllerTest.java @@ -1,18 +1,15 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.ClinicalAttributeCountFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.exception.ClinicalAttributeNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalAttributeCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalAttributeCountControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/ClinicalAttributeCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalAttributeCountControllerTest.java index e59b46f760e..a074445caeb 100644 --- a/src/test/java/org/cbioportal/web/ClinicalAttributeCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalAttributeCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,15 +6,12 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalAttributeCount; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.exception.ClinicalAttributeNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalAttributeCountFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleIdentifier; + +import org.cbioportal.legacy.model.ClinicalAttributeCount; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalAttributeCountFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalDataControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/ClinicalDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalDataControllerTest.java index 86d56d7accb..7747ac721cb 100644 --- a/src/test/java/org/cbioportal/web/ClinicalDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalDataControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,15 +6,15 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.web.config.CustomObjectMapper; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalDataIdentifier; -import org.cbioportal.web.parameter.ClinicalDataMultiStudyFilter; -import org.cbioportal.web.parameter.ClinicalDataSingleStudyFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.web.config.CustomObjectMapper; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataIdentifier; +import org.cbioportal.legacy.web.parameter.ClinicalDataMultiStudyFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataSingleStudyFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalDataEnrichmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/ClinicalDataEnrichmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentControllerTest.java index 8e9ab0fa5ef..f7ea9e12e05 100644 --- a/src/test/java/org/cbioportal/web/ClinicalDataEnrichmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalDataEnrichmentControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -8,16 +8,16 @@ import java.util.Arrays; import java.util.List; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalDataEnrichment; -import org.cbioportal.model.Sample; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.SampleService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.Group; -import org.cbioportal.web.parameter.GroupFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.util.ClinicalDataEnrichmentUtil; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalDataEnrichment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.Group; +import org.cbioportal.legacy.web.parameter.GroupFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.util.ClinicalDataEnrichmentUtil; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ClinicalEventControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ClinicalEventControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/ClinicalEventControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ClinicalEventControllerTest.java index bdbda3ca306..b2d41aaff2e 100644 --- a/src/test/java/org/cbioportal/web/ClinicalEventControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ClinicalEventControllerTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.ClinicalEvent; -import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalEventAttributeRequest; -import org.cbioportal.web.parameter.ClinicalEventRequest; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.model.ClinicalEvent; +import org.cbioportal.legacy.model.ClinicalEventData; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalEventAttributeRequest; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequest; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/CoExpressionControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CoExpressionControllerTest.java similarity index 93% rename from src/test/java/org/cbioportal/web/CoExpressionControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CoExpressionControllerTest.java index ae97e59d1d6..a2b61a606cf 100644 --- a/src/test/java/org/cbioportal/web/CoExpressionControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CoExpressionControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -8,11 +8,11 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.CoExpression; -import org.cbioportal.model.EntityType; -import org.cbioportal.service.CoExpressionService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.CoExpressionFilter; +import org.cbioportal.legacy.model.CoExpression; +import org.cbioportal.legacy.model.EntityType; +import org.cbioportal.legacy.service.CoExpressionService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.CoExpressionFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/CopyNumberSegmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CopyNumberSegmentControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/CopyNumberSegmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CopyNumberSegmentControllerTest.java index 88e10e11eaa..cd242c8bed1 100644 --- a/src/test/java/org/cbioportal/web/CopyNumberSegmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CopyNumberSegmentControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,12 +7,12 @@ import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CopyNumberSeg; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.CopyNumberSegmentService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.CopyNumberSeg; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.CopyNumberSegmentService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/CosmicCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/CosmicCountControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/CosmicCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/CosmicCountControllerTest.java index e1cd3cb52e3..b39948136d7 100644 --- a/src/test/java/org/cbioportal/web/CosmicCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/CosmicCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,9 +6,9 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CosmicMutation; -import org.cbioportal.service.CosmicCountService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.CosmicMutation; +import org.cbioportal.legacy.service.CosmicCountService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/DataAccessTokenControllerTest.java b/src/test/java/org/cbioportal/legacy/web/DataAccessTokenControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/DataAccessTokenControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/DataAccessTokenControllerTest.java index 917a2908184..66065e76223 100644 --- a/src/test/java/org/cbioportal/web/DataAccessTokenControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/DataAccessTokenControllerTest.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.mockito.Mockito.*; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -23,12 +23,11 @@ import com.fasterxml.jackson.databind.ObjectMapper; import jakarta.servlet.http.HttpSession; -import org.cbioportal.model.DataAccessToken; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.service.exception.TokenNotFoundException; -import org.cbioportal.web.config.DataAccessTokenControllerConfig; -import org.cbioportal.web.config.DataAccessTokenControllerTestConfig; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.DataAccessToken; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.service.exception.TokenNotFoundException; +import org.cbioportal.legacy.web.config.DataAccessTokenControllerTestConfig; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; @@ -44,7 +43,6 @@ import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestPropertySource; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.util.ReflectionTestUtils; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.MvcResult; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; diff --git a/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java b/src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberControllerTest.java index 126c183c204..d0a5629ef84 100644 --- a/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,16 +6,15 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CopyNumberCount; -import org.cbioportal.model.DiscreteCopyNumberData; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.CopyNumberCountIdentifier; -import org.cbioportal.web.parameter.DiscreteCopyNumberEventType; -import org.cbioportal.web.parameter.DiscreteCopyNumberFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; + +import org.cbioportal.legacy.model.DiscreteCopyNumberData; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberEventType; +import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberFilter; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/DiscreteCopyNumberCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/DiscreteCopyNumberCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountControllerTest.java index e90866f12f8..81946bc5c1c 100644 --- a/src/test/java/org/cbioportal/web/DiscreteCopyNumberCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/DiscreteCopyNumberCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,10 +6,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CopyNumberCount; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.CopyNumberCountIdentifier; +import org.cbioportal.legacy.model.CopyNumberCount; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.CopyNumberCountIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/DocRedirectControllerTest.java b/src/test/java/org/cbioportal/legacy/web/DocRedirectControllerTest.java similarity index 85% rename from src/test/java/org/cbioportal/web/DocRedirectControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/DocRedirectControllerTest.java index 3765936985d..3c0257d37b9 100644 --- a/src/test/java/org/cbioportal/web/DocRedirectControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/DocRedirectControllerTest.java @@ -1,21 +1,15 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import junit.framework.TestCase; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Before; import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; -import org.mockito.Mockito; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.context.web.WebAppConfiguration; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; import org.springframework.test.web.servlet.result.MockMvcResultMatchers; diff --git a/src/test/java/org/cbioportal/web/ExpressionEnrichmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ExpressionEnrichmentControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/ExpressionEnrichmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ExpressionEnrichmentControllerTest.java index 2f73e1ca80b..f0742f96f07 100644 --- a/src/test/java/org/cbioportal/web/ExpressionEnrichmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ExpressionEnrichmentControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,12 +6,12 @@ import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.EnrichmentType; -import org.cbioportal.model.GenericAssayEnrichment; -import org.cbioportal.model.GenomicEnrichment; -import org.cbioportal.model.GroupStatistics; -import org.cbioportal.service.ExpressionEnrichmentService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.EnrichmentType; +import org.cbioportal.legacy.model.GenericAssayEnrichment; +import org.cbioportal.legacy.model.GenomicEnrichment; +import org.cbioportal.legacy.model.GroupStatistics; +import org.cbioportal.legacy.service.ExpressionEnrichmentService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GeneControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GeneControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/GeneControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GeneControllerTest.java index c4b78fb7fde..56498842a63 100644 --- a/src/test/java/org/cbioportal/web/GeneControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GeneControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.mockito.ArgumentMatchers.eq; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,14 +7,13 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.exception.GeneNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.exception.GeneNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mockito; diff --git a/src/test/java/org/cbioportal/web/GenePanelControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenePanelControllerTest.java similarity index 93% rename from src/test/java/org/cbioportal/web/GenePanelControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenePanelControllerTest.java index 50a5a7f09a5..20e3ea084c4 100644 --- a/src/test/java/org/cbioportal/web/GenePanelControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenePanelControllerTest.java @@ -1,22 +1,16 @@ -package org.cbioportal.web; - -import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenePanelDataFilter; -import org.cbioportal.web.parameter.GenePanelDataMultipleStudyFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GenePanel; +import org.cbioportal.legacy.model.GenePanelToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.exception.GenePanelNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenePanelDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenePanelDataControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/GenePanelDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenePanelDataControllerTest.java index 824223ef8a9..72d8b76b92a 100644 --- a/src/test/java/org/cbioportal/web/GenePanelDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenePanelDataControllerTest.java @@ -1,17 +1,12 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.GenePanel; -import org.cbioportal.model.GenePanelData; -import org.cbioportal.model.GenePanelToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.exception.GenePanelNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenePanelDataFilter; -import org.cbioportal.web.parameter.GenePanelDataMultipleStudyFilter; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GenePanelData; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.GenePanelDataFilter; +import org.cbioportal.legacy.web.parameter.GenePanelDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.hamcrest.Matchers; import org.junit.Before; import org.junit.Test; @@ -20,13 +15,10 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; import org.springframework.boot.test.mock.mockito.MockBean; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; import org.springframework.http.MediaType; import org.springframework.security.test.context.support.WithMockUser; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.context.web.WebAppConfiguration; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; import org.springframework.test.web.servlet.result.MockMvcResultMatchers; @@ -34,7 +26,6 @@ import org.springframework.web.context.WebApplicationContext; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; @RunWith(SpringJUnit4ClassRunner.class) diff --git a/src/test/java/org/cbioportal/web/GenericAssayControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenericAssayControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/GenericAssayControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenericAssayControllerTest.java index a3f81f70a38..8ee7612398a 100644 --- a/src/test/java/org/cbioportal/web/GenericAssayControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenericAssayControllerTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenericAssayMetaFilter; +import org.cbioportal.legacy.model.meta.GenericAssayMeta; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.GenericAssayMetaFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenericAssayDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenericAssayDataControllerTest.java similarity index 94% rename from src/test/java/org/cbioportal/web/GenericAssayDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenericAssayDataControllerTest.java index ee7fc0d285c..9a8742ba05d 100644 --- a/src/test/java/org/cbioportal/web/GenericAssayDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenericAssayDataControllerTest.java @@ -1,14 +1,12 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.GenericAssayData; -import org.cbioportal.model.meta.GenericAssayMeta; -import org.cbioportal.service.GenericAssayService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenericAssayDataMultipleStudyFilter; -import org.cbioportal.web.parameter.GenericAssayFilter; -import org.cbioportal.web.parameter.GenericAssayMetaFilter; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.GenericAssayData; +import org.cbioportal.legacy.service.GenericAssayService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.GenericAssayDataMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayFilter; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.hamcrest.Matchers; import org.junit.Before; import org.junit.Test; @@ -17,12 +15,9 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; import org.springframework.boot.test.mock.mockito.MockBean; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; import org.springframework.http.MediaType; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.context.web.WebAppConfiguration; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; import org.springframework.test.web.servlet.result.MockMvcResultMatchers; diff --git a/src/test/java/org/cbioportal/web/GenesetControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenesetControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/GenesetControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenesetControllerTest.java index e58da5d8fa0..426ccee931d 100644 --- a/src/test/java/org/cbioportal/web/GenesetControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenesetControllerTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.service.GenesetService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.service.GenesetService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenesetCorrelationControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenesetCorrelationControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/GenesetCorrelationControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenesetCorrelationControllerTest.java index a0bc3244d65..bc515cc5ec1 100644 --- a/src/test/java/org/cbioportal/web/GenesetCorrelationControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenesetCorrelationControllerTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.GenesetCorrelation; -import org.cbioportal.service.GenesetCorrelationService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.GenesetCorrelation; +import org.cbioportal.legacy.service.GenesetCorrelationService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenesetDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenesetDataControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/GenesetDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenesetDataControllerTest.java index 843d3aaa771..fcdf0b8b2d9 100644 --- a/src/test/java/org/cbioportal/web/GenesetDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenesetDataControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,10 +7,10 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GenesetMolecularData; -import org.cbioportal.service.GenesetDataService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.GenesetDataFilterCriteria; +import org.cbioportal.legacy.model.GenesetMolecularData; +import org.cbioportal.legacy.service.GenesetDataService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.GenesetDataFilterCriteria; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/GenesetHierarchyControllerTest.java b/src/test/java/org/cbioportal/legacy/web/GenesetHierarchyControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/GenesetHierarchyControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/GenesetHierarchyControllerTest.java index e9a951ce15d..c7674a50352 100644 --- a/src/test/java/org/cbioportal/web/GenesetHierarchyControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/GenesetHierarchyControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,10 +6,10 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.Geneset; -import org.cbioportal.model.GenesetHierarchyInfo; -import org.cbioportal.service.GenesetHierarchyService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.Geneset; +import org.cbioportal.legacy.model.GenesetHierarchyInfo; +import org.cbioportal.legacy.service.GenesetHierarchyService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/InfoControllerTest.java b/src/test/java/org/cbioportal/legacy/web/InfoControllerTest.java similarity index 94% rename from src/test/java/org/cbioportal/web/InfoControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/InfoControllerTest.java index af78e860bb1..c7cbe258570 100644 --- a/src/test/java/org/cbioportal/web/InfoControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/InfoControllerTest.java @@ -1,6 +1,6 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/test/java/org/cbioportal/web/MolecularDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MolecularDataControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/MolecularDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MolecularDataControllerTest.java index 3793079fe80..8fc0cdbc64b 100644 --- a/src/test/java/org/cbioportal/web/MolecularDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MolecularDataControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,12 +7,12 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.GeneMolecularData; -import org.cbioportal.service.MolecularDataService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MolecularDataFilter; -import org.cbioportal.web.parameter.MolecularDataMultipleStudyFilter; +import org.cbioportal.legacy.model.GeneMolecularData; +import org.cbioportal.legacy.service.MolecularDataService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MolecularDataFilter; +import org.cbioportal.legacy.web.parameter.MolecularDataMultipleStudyFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MolecularProfileControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MolecularProfileControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/MolecularProfileControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MolecularProfileControllerTest.java index b999ec5ebe8..0fd88754f6a 100644 --- a/src/test/java/org/cbioportal/web/MolecularProfileControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MolecularProfileControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,14 +7,14 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.MolecularProfile; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.exception.MolecularProfileNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MolecularProfileFilter; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.MolecularProfile; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MolecularProfileFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MrnaPercentileControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MrnaPercentileControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/MrnaPercentileControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MrnaPercentileControllerTest.java index 1056c2d0336..728b6ae2c60 100644 --- a/src/test/java/org/cbioportal/web/MrnaPercentileControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MrnaPercentileControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,9 +7,9 @@ import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.MrnaPercentile; -import org.cbioportal.service.MrnaPercentileService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.MrnaPercentile; +import org.cbioportal.legacy.service.MrnaPercentileService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MutationControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java similarity index 98% rename from src/test/java/org/cbioportal/web/MutationControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java index b68a15106ca..bf76fdf2e6b 100644 --- a/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MutationControllerTest.java @@ -1,18 +1,18 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.AlleleSpecificCopyNumber; -import org.cbioportal.model.Gene; -import org.cbioportal.model.Mutation; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.model.meta.MutationMeta; -import org.cbioportal.service.MutationService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.MutationFilter; -import org.cbioportal.web.parameter.MutationMultipleStudyFilter; -import org.cbioportal.web.parameter.MutationPositionIdentifier; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.model.AlleleSpecificCopyNumber; +import org.cbioportal.legacy.model.Gene; +import org.cbioportal.legacy.model.Mutation; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.model.meta.MutationMeta; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.MutationFilter; +import org.cbioportal.legacy.web.parameter.MutationMultipleStudyFilter; +import org.cbioportal.legacy.web.parameter.MutationPositionIdentifier; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MutationCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MutationCountControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/MutationCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MutationCountControllerTest.java index 26607dd2827..9bb8ed51c25 100644 --- a/src/test/java/org/cbioportal/web/MutationCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MutationCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,10 +6,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.MutationCountByPosition; -import org.cbioportal.service.MutationService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.MutationPositionIdentifier; +import org.cbioportal.legacy.model.MutationCountByPosition; +import org.cbioportal.legacy.service.MutationService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.MutationPositionIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/MutationSpectrumControllerTest.java b/src/test/java/org/cbioportal/legacy/web/MutationSpectrumControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/MutationSpectrumControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/MutationSpectrumControllerTest.java index 84b562c6a4e..a348e5cc1da 100644 --- a/src/test/java/org/cbioportal/web/MutationSpectrumControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/MutationSpectrumControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -7,10 +7,10 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.MutationSpectrum; -import org.cbioportal.service.MutationSpectrumService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.MutationSpectrumFilter; +import org.cbioportal.legacy.model.MutationSpectrum; +import org.cbioportal.legacy.service.MutationSpectrumService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.MutationSpectrumFilter; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/PatientControllerTest.java b/src/test/java/org/cbioportal/legacy/web/PatientControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/PatientControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/PatientControllerTest.java index 906e8df119e..cf4a1d3c409 100644 --- a/src/test/java/org/cbioportal/web/PatientControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/PatientControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,15 +6,15 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.Patient; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.exception.PatientNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.PatientFilter; -import org.cbioportal.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.exception.PatientNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.PatientFilter; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ReferenceGenomeGeneControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ReferenceGenomeGeneControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/ReferenceGenomeGeneControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ReferenceGenomeGeneControllerTest.java index 958f4643ee4..1d01421497f 100644 --- a/src/test/java/org/cbioportal/web/ReferenceGenomeGeneControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ReferenceGenomeGeneControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.mockito.Mockito.times; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -8,10 +8,10 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import org.cbioportal.model.ReferenceGenomeGene; -import org.cbioportal.service.GeneMemoizerService; -import org.cbioportal.service.ReferenceGenomeGeneService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.ReferenceGenomeGene; +import org.cbioportal.legacy.service.GeneMemoizerService; +import org.cbioportal.legacy.service.ReferenceGenomeGeneService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ResourceDataControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ResourceDataControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/ResourceDataControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ResourceDataControllerTest.java index c5fb2af22a2..31c7df70063 100644 --- a/src/test/java/org/cbioportal/web/ResourceDataControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ResourceDataControllerTest.java @@ -1,11 +1,11 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.ResourceData; -import org.cbioportal.service.ResourceDataService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.ResourceData; +import org.cbioportal.legacy.service.ResourceDataService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ResourceDefinitionControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ResourceDefinitionControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/ResourceDefinitionControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ResourceDefinitionControllerTest.java index d76045645d2..b92849fffeb 100644 --- a/src/test/java/org/cbioportal/web/ResourceDefinitionControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ResourceDefinitionControllerTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.ResourceDefinition; -import org.cbioportal.service.ResourceDefinitionService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.model.ResourceDefinition; +import org.cbioportal.legacy.service.ResourceDefinitionService; +import org.cbioportal.legacy.web.config.TestConfig; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SampleControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SampleControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/SampleControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SampleControllerTest.java index 7756f33acdf..d8f8ffecb3c 100644 --- a/src/test/java/org/cbioportal/web/SampleControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SampleControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,16 +6,16 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Sample; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.SampleNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; -import org.cbioportal.web.parameter.SampleFilter; -import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.SampleNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.web.parameter.SampleFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SampleListControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SampleListControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/SampleListControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SampleListControllerTest.java index 5f2900fb057..579b5e5842f 100644 --- a/src/test/java/org/cbioportal/web/SampleListControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SampleListControllerTest.java @@ -1,15 +1,15 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.SampleList; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.exception.SampleListNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.SampleList; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.exception.SampleListNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/ServerStatusControllerTest.java b/src/test/java/org/cbioportal/legacy/web/ServerStatusControllerTest.java similarity index 93% rename from src/test/java/org/cbioportal/web/ServerStatusControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/ServerStatusControllerTest.java index f4ec9e1da59..5ad72442cd0 100644 --- a/src/test/java/org/cbioportal/web/ServerStatusControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/ServerStatusControllerTest.java @@ -1,6 +1,6 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.service.ServerStatusService; +import org.cbioportal.legacy.service.ServerStatusService; import org.junit.Before; import org.junit.Ignore; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SessionServiceControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SessionServiceControllerTest.java similarity index 91% rename from src/test/java/org/cbioportal/web/SessionServiceControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SessionServiceControllerTest.java index 0f9e751d826..dc1eb97c091 100644 --- a/src/test/java/org/cbioportal/web/SessionServiceControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SessionServiceControllerTest.java @@ -1,10 +1,10 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.utils.removeme.Session; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.utils.removeme.Session; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SignificantCopyNumberRegionControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/SignificantCopyNumberRegionControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionControllerTest.java index f91c5aaa539..d2aaa08abf9 100644 --- a/src/test/java/org/cbioportal/web/SignificantCopyNumberRegionControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SignificantCopyNumberRegionControllerTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.Gistic; -import org.cbioportal.model.GisticToGene; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SignificantCopyNumberRegionService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.Gistic; +import org.cbioportal.legacy.model.GisticToGene; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SignificantCopyNumberRegionService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/SignificantlyMutatedGenesControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/SignificantlyMutatedGenesControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesControllerTest.java index a8bd79a8fe2..22abdd4e06d 100644 --- a/src/test/java/org/cbioportal/web/SignificantlyMutatedGenesControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SignificantlyMutatedGenesControllerTest.java @@ -1,13 +1,13 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.MutSig; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.SignificantlyMutatedGeneService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.MutSig; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.SignificantlyMutatedGeneService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/StaticDataTimestampControllerTest.java b/src/test/java/org/cbioportal/legacy/web/StaticDataTimestampControllerTest.java similarity index 91% rename from src/test/java/org/cbioportal/web/StaticDataTimestampControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/StaticDataTimestampControllerTest.java index 1b555c2fbce..52bea19eaea 100644 --- a/src/test/java/org/cbioportal/web/StaticDataTimestampControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/StaticDataTimestampControllerTest.java @@ -1,8 +1,8 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import java.util.HashMap; -import org.cbioportal.service.StaticDataTimestampService; -import org.cbioportal.web.config.TestConfig; +import org.cbioportal.legacy.service.StaticDataTimestampService; +import org.cbioportal.legacy.web.config.TestConfig; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mockito; diff --git a/src/test/java/org/cbioportal/web/StructuralVariantControllerTest.java b/src/test/java/org/cbioportal/legacy/web/StructuralVariantControllerTest.java similarity index 98% rename from src/test/java/org/cbioportal/web/StructuralVariantControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/StructuralVariantControllerTest.java index 0be3faf380a..e2b29dc0189 100644 --- a/src/test/java/org/cbioportal/web/StructuralVariantControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/StructuralVariantControllerTest.java @@ -21,7 +21,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -32,16 +32,15 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.node.ObjectNode; -import org.cbioportal.model.StructuralVariant; -import org.cbioportal.model.StructuralVariantQuery; -import org.cbioportal.model.StructuralVariantSpecialValue; -import org.cbioportal.service.StructuralVariantService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.SampleMolecularIdentifier; -import org.cbioportal.web.parameter.StructuralVariantFilter; +import org.cbioportal.legacy.model.StructuralVariant; +import org.cbioportal.legacy.model.StructuralVariantQuery; +import org.cbioportal.legacy.model.StructuralVariantSpecialValue; +import org.cbioportal.legacy.service.StructuralVariantService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier; +import org.cbioportal.legacy.web.parameter.StructuralVariantFilter; import org.hamcrest.Matchers; import org.junit.Assert; -import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.ArgumentCaptor; @@ -54,8 +53,6 @@ import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.test.web.servlet.MockMvc; -import org.springframework.test.context.web.WebAppConfiguration; -import org.springframework.test.web.servlet.*; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; import org.springframework.test.web.servlet.result.MockMvcResultMatchers; diff --git a/src/test/java/org/cbioportal/web/StudyControllerTest.java b/src/test/java/org/cbioportal/legacy/web/StudyControllerTest.java similarity index 97% rename from src/test/java/org/cbioportal/web/StudyControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/StudyControllerTest.java index 1540bf6244c..29ff2258354 100644 --- a/src/test/java/org/cbioportal/web/StudyControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/StudyControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -10,15 +10,15 @@ import java.util.Arrays; import java.util.List; import java.util.TimeZone; -import org.cbioportal.model.CancerStudy; -import org.cbioportal.model.CancerStudyTags; -import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.model.meta.BaseMeta; -import org.cbioportal.service.StudyService; -import org.cbioportal.service.exception.StudyNotFoundException; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.utils.security.AccessLevel; -import org.cbioportal.web.parameter.HeaderKeyConstants; +import org.cbioportal.legacy.model.CancerStudy; +import org.cbioportal.legacy.model.CancerStudyTags; +import org.cbioportal.legacy.model.TypeOfCancer; +import org.cbioportal.legacy.model.meta.BaseMeta; +import org.cbioportal.legacy.service.StudyService; +import org.cbioportal.legacy.service.exception.StudyNotFoundException; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.utils.security.AccessLevel; +import org.cbioportal.legacy.web.parameter.HeaderKeyConstants; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; @@ -30,7 +30,6 @@ import org.springframework.security.test.context.support.WithMockUser; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.springframework.test.context.web.WebAppConfiguration; import org.springframework.test.util.ReflectionTestUtils; import org.springframework.test.web.servlet.MockMvc; import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; diff --git a/src/test/java/org/cbioportal/web/StudyViewControllerTest.java b/src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/StudyViewControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java index 19f607bf154..2956a6fb356 100644 --- a/src/test/java/org/cbioportal/web/StudyViewControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/StudyViewControllerTest.java @@ -1,64 +1,64 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.lang3.tuple.ImmutablePair; -import org.cbioportal.model.AlterationCountByGene; -import org.cbioportal.model.AlterationFilter; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalEventTypeCount; -import org.cbioportal.model.CopyNumberCountByGene; -import org.cbioportal.model.GenericAssayDataCount; -import org.cbioportal.model.GenericAssayDataCountItem; -import org.cbioportal.model.GenomicDataCount; -import org.cbioportal.model.GenomicDataCountItem; -import org.cbioportal.model.Sample; -import org.cbioportal.model.SampleClinicalDataCollection; -import org.cbioportal.model.StructuralVariantFilterQuery; -import org.cbioportal.model.StructuralVariantSpecialValue; -import org.cbioportal.model.StudyViewStructuralVariantFilter; -import org.cbioportal.model.util.Select; -import org.cbioportal.persistence.AlterationRepository; -import org.cbioportal.service.AlterationCountService; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.service.DiscreteCopyNumberService; -import org.cbioportal.service.GenePanelService; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.MolecularProfileService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.SampleListService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.StudyViewService; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.service.ViolinPlotService; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.utils.Encoder; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataCountFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.GenericAssayDataCountFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataCountFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.ClinicalDataBinUtil; -import org.cbioportal.web.util.ClinicalDataFetcher; -import org.cbioportal.web.util.DataBinHelper; -import org.cbioportal.web.util.DataBinner; -import org.cbioportal.web.util.DiscreteDataBinner; -import org.cbioportal.web.util.LinearDataBinner; -import org.cbioportal.web.util.LogScaleDataBinner; -import org.cbioportal.web.util.ScientificSmallDataBinner; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.AlterationCountByGene; +import org.cbioportal.legacy.model.AlterationFilter; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalEventTypeCount; +import org.cbioportal.legacy.model.CopyNumberCountByGene; +import org.cbioportal.legacy.model.GenericAssayDataCount; +import org.cbioportal.legacy.model.GenericAssayDataCountItem; +import org.cbioportal.legacy.model.GenomicDataCount; +import org.cbioportal.legacy.model.GenomicDataCountItem; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.model.SampleClinicalDataCollection; +import org.cbioportal.legacy.model.StructuralVariantFilterQuery; +import org.cbioportal.legacy.model.StructuralVariantSpecialValue; +import org.cbioportal.legacy.model.StudyViewStructuralVariantFilter; +import org.cbioportal.legacy.model.util.Select; +import org.cbioportal.legacy.persistence.AlterationRepository; +import org.cbioportal.legacy.service.AlterationCountService; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.service.DiscreteCopyNumberService; +import org.cbioportal.legacy.service.GenePanelService; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.MolecularProfileService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.SampleListService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.StudyViewService; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.service.ViolinPlotService; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.utils.Encoder; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter; +import org.cbioportal.legacy.web.parameter.GenomicDataFilter; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.ClinicalDataBinUtil; +import org.cbioportal.legacy.web.util.ClinicalDataFetcher; +import org.cbioportal.legacy.web.util.DataBinHelper; +import org.cbioportal.legacy.web.util.DataBinner; +import org.cbioportal.legacy.web.util.DiscreteDataBinner; +import org.cbioportal.legacy.web.util.LinearDataBinner; +import org.cbioportal.legacy.web.util.LogScaleDataBinner; +import org.cbioportal.legacy.web.util.ScientificSmallDataBinner; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.junit.Before; import org.junit.Ignore; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/SurvivalControllerTest.java b/src/test/java/org/cbioportal/legacy/web/SurvivalControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/SurvivalControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/SurvivalControllerTest.java index 7c8532c515d..0ae7f22e5aa 100644 --- a/src/test/java/org/cbioportal/web/SurvivalControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/SurvivalControllerTest.java @@ -1,14 +1,14 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.service.ClinicalEventService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.ClinicalEventRequest; -import org.cbioportal.web.parameter.ClinicalEventRequestIdentifier; -import org.cbioportal.web.parameter.OccurrencePosition; -import org.cbioportal.web.parameter.PatientIdentifier; -import org.cbioportal.web.parameter.SurvivalRequest; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.service.ClinicalEventService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequest; +import org.cbioportal.legacy.web.parameter.ClinicalEventRequestIdentifier; +import org.cbioportal.legacy.web.parameter.OccurrencePosition; +import org.cbioportal.legacy.web.parameter.PatientIdentifier; +import org.cbioportal.legacy.web.parameter.SurvivalRequest; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/TreatmentControllerTest.java b/src/test/java/org/cbioportal/legacy/web/TreatmentControllerTest.java similarity index 92% rename from src/test/java/org/cbioportal/web/TreatmentControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/TreatmentControllerTest.java index 85ba345b6fb..6a45b72d422 100644 --- a/src/test/java/org/cbioportal/web/TreatmentControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/TreatmentControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,15 +6,15 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.PatientTreatmentRow; -import org.cbioportal.model.SampleTreatmentRow; -import org.cbioportal.model.TemporalRelation; -import org.cbioportal.service.TreatmentService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; -import org.cbioportal.web.util.StudyViewFilterApplier; -import org.cbioportal.web.util.StudyViewFilterUtil; +import org.cbioportal.legacy.model.PatientTreatmentRow; +import org.cbioportal.legacy.model.SampleTreatmentRow; +import org.cbioportal.legacy.model.TemporalRelation; +import org.cbioportal.legacy.service.TreatmentService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.junit.Test; import org.junit.runner.RunWith; import org.mockito.Mockito; diff --git a/src/test/java/org/cbioportal/web/VariantCountControllerTest.java b/src/test/java/org/cbioportal/legacy/web/VariantCountControllerTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/VariantCountControllerTest.java rename to src/test/java/org/cbioportal/legacy/web/VariantCountControllerTest.java index 34a0f8753f2..6a973f433a9 100644 --- a/src/test/java/org/cbioportal/web/VariantCountControllerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/VariantCountControllerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web; +package org.cbioportal.legacy.web; import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; @@ -6,10 +6,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.ArrayList; import java.util.List; -import org.cbioportal.model.VariantCount; -import org.cbioportal.service.VariantCountService; -import org.cbioportal.web.config.TestConfig; -import org.cbioportal.web.parameter.VariantCountIdentifier; +import org.cbioportal.legacy.model.VariantCount; +import org.cbioportal.legacy.service.VariantCountService; +import org.cbioportal.legacy.web.config.TestConfig; +import org.cbioportal.legacy.web.parameter.VariantCountIdentifier; import org.hamcrest.Matchers; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/config/CacheMapUtilConfig.java b/src/test/java/org/cbioportal/legacy/web/config/CacheMapUtilConfig.java similarity index 78% rename from src/test/java/org/cbioportal/web/config/CacheMapUtilConfig.java rename to src/test/java/org/cbioportal/legacy/web/config/CacheMapUtilConfig.java index fe044aec44f..948be9ea9b2 100644 --- a/src/test/java/org/cbioportal/web/config/CacheMapUtilConfig.java +++ b/src/test/java/org/cbioportal/legacy/web/config/CacheMapUtilConfig.java @@ -15,16 +15,16 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; -import org.cbioportal.persistence.CancerTypeRepository; -import org.cbioportal.persistence.GenericAssayRepository; -import org.cbioportal.persistence.MolecularProfileRepository; -import org.cbioportal.persistence.PatientRepository; -import org.cbioportal.persistence.SampleListRepository; -import org.cbioportal.persistence.StudyRepository; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.service.StaticDataTimestampService; +import org.cbioportal.legacy.persistence.CancerTypeRepository; +import org.cbioportal.legacy.persistence.GenericAssayRepository; +import org.cbioportal.legacy.persistence.MolecularProfileRepository; +import org.cbioportal.legacy.persistence.PatientRepository; +import org.cbioportal.legacy.persistence.SampleListRepository; +import org.cbioportal.legacy.persistence.StudyRepository; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.service.StaticDataTimestampService; import org.mockito.Mockito; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; diff --git a/src/test/java/org/cbioportal/web/config/DataAccessTokenControllerConfig.java b/src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerConfig.java similarity index 91% rename from src/test/java/org/cbioportal/web/config/DataAccessTokenControllerConfig.java rename to src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerConfig.java index cf4f53f3efb..21efb05416d 100644 --- a/src/test/java/org/cbioportal/web/config/DataAccessTokenControllerConfig.java +++ b/src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerConfig.java @@ -30,10 +30,10 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; -import org.cbioportal.service.DataAccessTokenService; -import org.cbioportal.web.DataAccessTokenController; +import org.cbioportal.legacy.service.DataAccessTokenService; +import org.cbioportal.legacy.web.DataAccessTokenController; import org.mockito.Mockito; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; diff --git a/src/test/java/org/cbioportal/web/config/DataAccessTokenControllerTestConfig.java b/src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerTestConfig.java similarity index 98% rename from src/test/java/org/cbioportal/web/config/DataAccessTokenControllerTestConfig.java rename to src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerTestConfig.java index 484ab71b742..647f5edfb12 100644 --- a/src/test/java/org/cbioportal/web/config/DataAccessTokenControllerTestConfig.java +++ b/src/test/java/org/cbioportal/legacy/web/config/DataAccessTokenControllerTestConfig.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.context.annotation.Bean; diff --git a/src/test/java/org/cbioportal/web/config/RestAuthenticationEntryPoint.java b/src/test/java/org/cbioportal/legacy/web/config/RestAuthenticationEntryPoint.java similarity index 98% rename from src/test/java/org/cbioportal/web/config/RestAuthenticationEntryPoint.java rename to src/test/java/org/cbioportal/legacy/web/config/RestAuthenticationEntryPoint.java index 7984d3445df..d02e4ea6828 100644 --- a/src/test/java/org/cbioportal/web/config/RestAuthenticationEntryPoint.java +++ b/src/test/java/org/cbioportal/legacy/web/config/RestAuthenticationEntryPoint.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import java.io.IOException; diff --git a/src/test/java/org/cbioportal/web/config/TestConfig.java b/src/test/java/org/cbioportal/legacy/web/config/TestConfig.java similarity index 83% rename from src/test/java/org/cbioportal/web/config/TestConfig.java rename to src/test/java/org/cbioportal/legacy/web/config/TestConfig.java index dee57c0420d..f6ec8c650ae 100644 --- a/src/test/java/org/cbioportal/web/config/TestConfig.java +++ b/src/test/java/org/cbioportal/legacy/web/config/TestConfig.java @@ -1,8 +1,9 @@ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; -import org.cbioportal.persistence.cachemaputil.CacheMapUtil; -import org.cbioportal.web.error.GlobalExceptionHandler; -import org.cbioportal.web.util.InvolvedCancerStudyExtractorInterceptor; +import org.cbioportal.legacy.persistence.cachemaputil.CacheMapUtil; +import org.cbioportal.legacy.web.config.CustomObjectMapper; +import org.cbioportal.legacy.web.error.GlobalExceptionHandler; +import org.cbioportal.legacy.web.util.InvolvedCancerStudyExtractorInterceptor; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.context.TestConfiguration; import org.springframework.boot.test.mock.mockito.MockBean; diff --git a/src/test/java/org/cbioportal/web/config/TokenAuthenticationSuccessHandler.java b/src/test/java/org/cbioportal/legacy/web/config/TokenAuthenticationSuccessHandler.java similarity index 98% rename from src/test/java/org/cbioportal/web/config/TokenAuthenticationSuccessHandler.java rename to src/test/java/org/cbioportal/legacy/web/config/TokenAuthenticationSuccessHandler.java index 4fdadbc0c13..ce9ecba4d53 100644 --- a/src/test/java/org/cbioportal/web/config/TokenAuthenticationSuccessHandler.java +++ b/src/test/java/org/cbioportal/legacy/web/config/TokenAuthenticationSuccessHandler.java @@ -30,7 +30,7 @@ * along with this program. If not, see . */ -package org.cbioportal.web.config; +package org.cbioportal.legacy.web.config; import jakarta.servlet.http.HttpServletRequest; diff --git a/src/test/java/org/cbioportal/web/util/AlterationFilterMockitoArgumentMatcher.java b/src/test/java/org/cbioportal/legacy/web/util/AlterationFilterMockitoArgumentMatcher.java similarity index 94% rename from src/test/java/org/cbioportal/web/util/AlterationFilterMockitoArgumentMatcher.java rename to src/test/java/org/cbioportal/legacy/web/util/AlterationFilterMockitoArgumentMatcher.java index 59d97866bd2..c999e097ccc 100644 --- a/src/test/java/org/cbioportal/web/util/AlterationFilterMockitoArgumentMatcher.java +++ b/src/test/java/org/cbioportal/legacy/web/util/AlterationFilterMockitoArgumentMatcher.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.AlterationFilter; +import org.cbioportal.legacy.model.AlterationFilter; import org.mockito.ArgumentMatcher; public class AlterationFilterMockitoArgumentMatcher implements ArgumentMatcher { diff --git a/src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java b/src/test/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtilTest.java similarity index 95% rename from src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java rename to src/test/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtilTest.java index b25def51f5b..4b65b4c37bc 100644 --- a/src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/web/util/ClinicalDataBinUtilTest.java @@ -1,19 +1,37 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import com.fasterxml.jackson.core.TreeNode; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; -import org.cbioportal.model.Patient; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.PatientService; -import org.cbioportal.service.impl.CustomDataServiceImpl; -import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.service.util.SessionServiceRequestHandler; -import org.cbioportal.web.parameter.*; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataBin; +import org.cbioportal.legacy.model.Patient; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.PatientService; +import org.cbioportal.legacy.service.impl.CustomDataServiceImpl; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.service.util.SessionServiceRequestHandler; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataFilter; +import org.cbioportal.legacy.web.parameter.DataBinFilter; +import org.cbioportal.legacy.web.parameter.DataBinMethod; +import org.cbioportal.legacy.web.parameter.DataFilterValue; +import org.cbioportal.legacy.web.parameter.SampleIdentifier; +import org.cbioportal.legacy.web.parameter.StudyViewFilter; +import org.cbioportal.legacy.web.util.ClinicalDataBinUtil; +import org.cbioportal.legacy.web.util.ClinicalDataFetcher; +import org.cbioportal.legacy.web.util.DataBinHelper; +import org.cbioportal.legacy.web.util.DataBinner; +import org.cbioportal.legacy.web.util.DiscreteDataBinner; +import org.cbioportal.legacy.web.util.IdPopulator; +import org.cbioportal.legacy.web.util.LinearDataBinner; +import org.cbioportal.legacy.web.util.LogScaleDataBinner; +import org.cbioportal.legacy.web.util.ScientificSmallDataBinner; +import org.cbioportal.legacy.web.util.StudyViewFilterApplier; +import org.cbioportal.legacy.web.util.StudyViewFilterUtil; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtilTest.java b/src/test/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtilTest.java similarity index 96% rename from src/test/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtilTest.java rename to src/test/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtilTest.java index cc4cc5cf5d7..667143b008a 100644 --- a/src/test/java/org/cbioportal/web/util/ClinicalDataEnrichmentUtilTest.java +++ b/src/test/java/org/cbioportal/legacy/web/util/ClinicalDataEnrichmentUtilTest.java @@ -1,19 +1,20 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.ClinicalDataEnrichment; -import org.cbioportal.model.Sample; -import org.cbioportal.service.ClinicalAttributeService; -import org.cbioportal.service.ClinicalDataService; -import org.cbioportal.service.SampleService; -import org.cbioportal.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.model.ClinicalAttribute; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.ClinicalDataCount; +import org.cbioportal.legacy.model.ClinicalDataCountItem; +import org.cbioportal.legacy.model.ClinicalDataEnrichment; +import org.cbioportal.legacy.model.Sample; +import org.cbioportal.legacy.service.ClinicalAttributeService; +import org.cbioportal.legacy.service.ClinicalDataService; +import org.cbioportal.legacy.service.SampleService; +import org.cbioportal.legacy.service.util.ClinicalAttributeUtil; +import org.cbioportal.legacy.web.util.ClinicalDataEnrichmentUtil; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/util/DataBinHelperTest.java b/src/test/java/org/cbioportal/legacy/web/util/DataBinHelperTest.java similarity index 99% rename from src/test/java/org/cbioportal/web/util/DataBinHelperTest.java rename to src/test/java/org/cbioportal/legacy/web/util/DataBinHelperTest.java index 792cecfd6e2..934e2c22e5c 100644 --- a/src/test/java/org/cbioportal/web/util/DataBinHelperTest.java +++ b/src/test/java/org/cbioportal/legacy/web/util/DataBinHelperTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import static org.junit.Assert.*; @@ -9,6 +9,8 @@ import java.util.Collections; import java.util.List; import java.util.stream.Collectors; + +import org.cbioportal.legacy.web.util.DataBinHelper; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; diff --git a/src/test/java/org/cbioportal/web/util/DataBinnerMocker.java b/src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java similarity index 99% rename from src/test/java/org/cbioportal/web/util/DataBinnerMocker.java rename to src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java index e3090402073..c35ef521942 100644 --- a/src/test/java/org/cbioportal/web/util/DataBinnerMocker.java +++ b/src/test/java/org/cbioportal/legacy/web/util/DataBinnerMocker.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.util.LinkedHashMap; import java.util.Map; diff --git a/src/test/java/org/cbioportal/web/util/DataBinnerTest.java b/src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java similarity index 99% rename from src/test/java/org/cbioportal/web/util/DataBinnerTest.java rename to src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java index 5ed86de169b..d643891bf67 100644 --- a/src/test/java/org/cbioportal/web/util/DataBinnerTest.java +++ b/src/test/java/org/cbioportal/legacy/web/util/DataBinnerTest.java @@ -1,4 +1,4 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; import java.math.BigDecimal; import java.math.MathContext; @@ -9,19 +9,19 @@ import java.util.Map; import java.util.stream.Collectors; import java.util.stream.Stream; -import static org.cbioportal.web.parameter.DataBinFilter.*; +import static org.cbioportal.legacy.web.parameter.DataBinFilter.*; import java.util.stream.IntStream; -import org.cbioportal.model.Binnable; -import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.DataBin; -import org.cbioportal.service.GeneService; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.BinsGeneratorConfig; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.legacy.model.Binnable; +import org.cbioportal.legacy.model.ClinicalData; +import org.cbioportal.legacy.model.DataBin; +import org.cbioportal.legacy.service.GeneService; +import org.cbioportal.legacy.service.util.MolecularProfileUtil; +import org.cbioportal.legacy.web.parameter.BinsGeneratorConfig; +import org.cbioportal.legacy.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.legacy.web.parameter.ClinicalDataType; import org.junit.Assert; import org.junit.Before; import org.junit.Test; diff --git a/src/test/java/org/cbioportal/web/util/SelectMockitoArgumentMatcher.java b/src/test/java/org/cbioportal/legacy/web/util/SelectMockitoArgumentMatcher.java similarity index 87% rename from src/test/java/org/cbioportal/web/util/SelectMockitoArgumentMatcher.java rename to src/test/java/org/cbioportal/legacy/web/util/SelectMockitoArgumentMatcher.java index bcd6d021e1b..ca1ed05c043 100644 --- a/src/test/java/org/cbioportal/web/util/SelectMockitoArgumentMatcher.java +++ b/src/test/java/org/cbioportal/legacy/web/util/SelectMockitoArgumentMatcher.java @@ -1,6 +1,6 @@ -package org.cbioportal.web.util; +package org.cbioportal.legacy.web.util; -import org.cbioportal.model.util.Select; +import org.cbioportal.legacy.model.util.Select; import org.mockito.ArgumentMatcher; public class SelectMockitoArgumentMatcher implements ArgumentMatcher + WITH sample_counts as ( + SELECT + sample_list.cancer_study_id, + countIf(stable_id LIKE '%_all') as allSampleCount, + countIf(stable_id LIKE '%_sequenced') as sequencedSampleCount, + countIf(stable_id LIKE '%_cna') as cnaSampleCount, + countIf(stable_id LIKE '%_rna_seq_v2_mrna') as mrnaRnaSeqV2SampleCount, + countIf(stable_id LIKE '%_microrna') as miRnaSampleCount, + countIf(stable_id LIKE '%_mrna' AND stable_id NOT LIKE '%_rna_seq_v2_mrna') as mrnaMicroarraySampleCount, + countIf(stable_id LIKE '%_methylation_hm27') as methylationHm27SampleCount, + countIf(stable_id LIKE '%_rppa') as rppaSampleCount, + countIf(stable_id LIKE '%_protein_quantification') as massSpectrometrySampleCount, + countIf(stable_id LIKE '%_3way_complete') as completeSampleCount, + countIf(stable_id LIKE '%_rna_seq_mrna') as mrnaRnaSeqSampleCount + FROM sample_list_list + INNER JOIN sample_list ON sample_list_list.list_id = sample_list.list_id + GROUP BY sample_list.cancer_study_id + ), + treatment AS ( + SELECT + COUNT(DISTINCT patient_unique_id) as count, + cancer_study_identifier + FROM clinical_event_derived + + event_type IN ('Treatment', 'TREATMENT') + + GROUP BY cancer_study_identifier + ), + sv AS ( + SELECT + COUNT(DISTINCT sample_unique_id) as count, + cancer_study_identifier as cancer_study_identifier + FROM genomic_event_derived + + variant_type = 'structural_variant' + + GROUP BY cancer_study_identifier + ) + SELECT + cs.cancer_study_id AS cancerStudyId, + cs.cancer_study_identifier AS cancerStudyIdentifier, + cs.type_of_cancer_id AS typeOfCancerId, + cs.name AS name, + cs.description AS description, + cs.public AS publicStudy, + cs.pmid AS pmid, + cs.citation AS citation, + cs.groups AS groups, + cs.status AS status, + cs.import_date AS importDate, + reference_genome.name AS referenceGenome, + allSampleCount, + sequencedSampleCount, + cnaSampleCount, + mrnaRnaSeqV2SampleCount, + miRnaSampleCount, + mrnaMicroarraySampleCount, + methylationHm27SampleCount, + rppaSampleCount, + massSpectrometrySampleCount, + completeSampleCount, + mrnaRnaSeqSampleCount, + IFNULL(treatment.count, 0) AS treatmentCount, + IFNULL(sv.count, 0) AS structuralVariantCount, + type_of_cancer.name AS type_of_cancer_name, + type_of_cancer.dedicated_color AS type_of_cancer_dedicated_color, + type_of_cancer.short_name AS type_of_cancer_short_name, + type_of_cancer.parent AS type_of_cancer_parent + + FROM cancer_study AS cs + INNER JOIN reference_genome ON reference_genome.reference_genome_id = cs.reference_genome_id + INNER JOIN type_of_cancer ON cs.type_of_cancer_id = type_of_cancer.type_of_cancer_id + LEFT JOIN treatment ON cs.cancer_study_identifier = + treatment.cancer_study_identifier + LEFT JOIN sv ON sv.cancer_study_identifier = cs.cancer_study_identifier + INNER JOIN sample_counts ON sample_counts.cancer_study_id = cs.cancer_study_id + + + cancer_study.cancer_study_identifier IN + #{item} + + + GROUP BY cs.cancer_study_id, cs.cancer_study_identifier, cs.type_of_cancer_id, cs.name, + cs.description, cs.public, cs.pmid, cs.citation, cs.groups, cs.status, cs.import_date, + reference_genome.name, treatment.count, sv.count,allSampleCount, + sequencedSampleCount, cnaSampleCount, mrnaRnaSeqV2SampleCount, + miRnaSampleCount,mrnaMicroarraySampleCount, methylationHm27SampleCount, + rppaSampleCount, massSpectrometrySampleCount,completeSampleCount, + mrnaRnaSeqSampleCount,type_of_cancer.name, type_of_cancer.dedicated_color, + type_of_cancer.short_name, type_of_cancer.parent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From e9b304db968d0b84d29809b4c7a2a852fc862c57 Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Mon, 27 Jan 2025 13:47:50 -0500 Subject: [PATCH 04/12] Update Interceptor to use legacy package structure --- .../cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java b/src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java index 4422ddc1758..a216e24558b 100644 --- a/src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java +++ b/src/main/java/org/cbioportal/legacy/web/interceptor/UniqueKeyInterceptor.java @@ -25,7 +25,7 @@ import static org.cbioportal.legacy.utils.Encoder.calculateBase64; -@ControllerAdvice("org.cbioportal.web") +@ControllerAdvice("org.cbioportal.legacy.web") public class UniqueKeyInterceptor extends AbstractMappingJacksonResponseBodyAdvice { @Override From 27cab0dd42242a85120da5c080823e0fa2dce9d1 Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Tue, 28 Jan 2025 22:34:43 -0500 Subject: [PATCH 05/12] Update to support projection for cancerstudy endpoint --- pom.xml | 33 ++++++- .../mapper/CancerStudyMetadataMapper.java | 20 +++++ .../rest/response/CancerStudyMetadataDTO.java | 16 ++++ .../ColumnStoreStudyController.java | 66 ++++++++++---- .../cancerstudy/CancerStudyMetadata.java | 11 ++- .../cbioportal/cancerstudy/TypeOfCancer.java | 4 + .../cancerstudy/TypeOfCancerRecord.java | 4 - .../repository/CancerStudyRepository.java | 64 +++++++++++++- .../GetCancerStudyMetadataUseCase.java | 71 ++++++++++++++- .../ClickhouseCancerStudyMapper.java | 2 + .../ClickhouseCancerStudyRepository.java | 29 ++++-- .../shared/enums/ProjectionType.java | 88 +++++++++++++++++++ .../cancerstudy/CancerStudyMapper.xml | 59 ++++++++++++- 13 files changed, 428 insertions(+), 39 deletions(-) create mode 100644 src/main/java/org/cbioportal/application/rest/mapper/CancerStudyMetadataMapper.java create mode 100644 src/main/java/org/cbioportal/application/rest/response/CancerStudyMetadataDTO.java create mode 100644 src/main/java/org/cbioportal/cancerstudy/TypeOfCancer.java delete mode 100644 src/main/java/org/cbioportal/cancerstudy/TypeOfCancerRecord.java create mode 100644 src/main/java/org/cbioportal/shared/enums/ProjectionType.java diff --git a/pom.xml b/pom.xml index 9e8555525b2..3e9101ca711 100644 --- a/pom.xml +++ b/pom.xml @@ -17,7 +17,8 @@ cBioPortal for Cancer Genomics - 21 + jdt_apt + 21 21 21 @@ -100,6 +101,7 @@ 7.1.0 1.19.7 1.78 + 1.6.3 @@ -385,6 +387,18 @@ spring-boot-testcontainers test + + org.mapstruct + mapstruct + ${mapstruct.version} + + + + org.osgi + org.osgi.service.component.annotations + 1.5.1 + provided + @@ -470,6 +484,21 @@ + + org.apache.maven.plugins + maven-compiler-plugin + 3.13.0 + + 21 + + + org.mapstruct + mapstruct-processor + ${mapstruct.version} + + + + org.springframework.boot spring-boot-maven-plugin @@ -483,7 +512,7 @@ - + io.github.git-commit-id git-commit-id-maven-plugin diff --git a/src/main/java/org/cbioportal/application/rest/mapper/CancerStudyMetadataMapper.java b/src/main/java/org/cbioportal/application/rest/mapper/CancerStudyMetadataMapper.java new file mode 100644 index 00000000000..cbf1467d815 --- /dev/null +++ b/src/main/java/org/cbioportal/application/rest/mapper/CancerStudyMetadataMapper.java @@ -0,0 +1,20 @@ +package org.cbioportal.application.rest.mapper; + +import org.cbioportal.application.rest.response.CancerStudyMetadataDTO; +import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.mapstruct.Mapper; +import org.mapstruct.Mapping; +import org.mapstruct.factory.Mappers; + +import java.util.List; + +@Mapper +public interface CancerStudyMetadataMapper { + CancerStudyMetadataMapper INSTANCE = Mappers.getMapper(CancerStudyMetadataMapper.class); + + @Mapping(target = "importDate", source = "importDate", dateFormat = "yyyy-MM-dd HH:mm:ss") + CancerStudyMetadataDTO toDto(CancerStudyMetadata cancerStudyMetadata); + + @Mapping(target = "importDate", source = "importDate", dateFormat = "yyyy-MM-dd HH:mm:ss") + List toDtos(List cancerStudyMetadataList); +} diff --git a/src/main/java/org/cbioportal/application/rest/response/CancerStudyMetadataDTO.java b/src/main/java/org/cbioportal/application/rest/response/CancerStudyMetadataDTO.java new file mode 100644 index 00000000000..448de69ca28 --- /dev/null +++ b/src/main/java/org/cbioportal/application/rest/response/CancerStudyMetadataDTO.java @@ -0,0 +1,16 @@ +package org.cbioportal.application.rest.response; + +import io.swagger.v3.oas.annotations.media.Schema; +import org.cbioportal.cancerstudy.TypeOfCancer; + +@Schema(name = "CancerStudyMetadata", description = "Represents a cancer study") +public record CancerStudyMetadataDTO(String cancerStudyIdentifier, String typeOfCancerId, + String name, String description, Boolean publicStudy, String pmid, String citation, + String groups, Integer status, String importDate, Integer allSampleCount, + Integer sequencedSampleCount, Integer cnaSampleCount, Integer mrnaRnaSeqSampleCount, + Integer mrnaRnaSeqV2SampleCount, Integer mrnaMicroarraySampleCount, + Integer miRnaSampleCount, Integer methylationHm27SampleCount, Integer rppaSampleCount, + Integer massSpectrometrySampleCount, Integer completeSampleCount, + String referenceGenome, Integer treatmentCount, Integer structuralVariantCount, + TypeOfCancer typeOfCancer) { +} diff --git a/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java b/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java index 6c5aa85ab7a..b52242fca22 100644 --- a/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java +++ b/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java @@ -2,14 +2,12 @@ import io.swagger.v3.oas.annotations.Hidden; import io.swagger.v3.oas.annotations.Parameter; -import jakarta.validation.constraints.Max; -import jakarta.validation.constraints.Min; -import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.cbioportal.application.rest.mapper.CancerStudyMetadataMapper; +import org.cbioportal.application.rest.response.CancerStudyMetadataDTO; import org.cbioportal.cancerstudy.usecase.GetCancerStudyMetadataUseCase; import org.cbioportal.legacy.web.parameter.Direction; -import org.cbioportal.legacy.web.parameter.PagingConstants; -import org.cbioportal.legacy.web.parameter.Projection; import org.cbioportal.legacy.web.parameter.sort.StudySortBy; +import org.cbioportal.shared.enums.ProjectionType; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; import org.springframework.http.ResponseEntity; @@ -20,38 +18,72 @@ import java.util.List; +/** + * REST controller for managing and retrieving cancer study metadata from a column-store data source. + *

+ * This controller provides an endpoint to fetch cancer study metadata with support for filtering, + * sorting, and controlling the level of detail in the response. It is designed to work with a + * column-store database, which is optimized for querying large datasets efficiently. + *

+ * + * @see GetCancerStudyMetadataUseCase + * @see CancerStudyMetadataDTO + * @see ProjectionType + * @see StudySortBy + * @see Direction + */ @RestController @RequestMapping("/api/column-store") public class ColumnStoreStudyController { private final GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase; + /** + * Constructs a new {@link ColumnStoreStudyController} with the specified use case. + * + * @param getCancerStudyMetadataUseCase the use case responsible for retrieving cancer study metadata. + */ public ColumnStoreStudyController(GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase) { this.getCancerStudyMetadataUseCase = getCancerStudyMetadataUseCase; } -// Projection return same type best case would be to return types that reflect this + + /** + * Retrieves a list of cancer study metadata based on the specified criteria. + *

+ * This endpoint supports filtering by keyword, controlling the level of detail in the response + * through the projection parameter, and sorting the results by a specified property and direction. + *

+ *

+ * Note: This endpoint is marked as {@link Hidden} and will not be exposed in the API documentation. + *

+ * + * @param keyword the search keyword that applies to the name and cancer type of the studies. + * This parameter is optional. + * @param projection the level of detail of the response. Defaults to {@link ProjectionType#SUMMARY}. + * @param sortBy the name of the property that the result list is sorted by. This parameter is optional. + * @param direction the direction of the sort. Defaults to {@link Direction#ASC}. + * @return a {@link ResponseEntity} containing a list of {@link CancerStudyMetadataDTO} objects + * and an HTTP status code {@link HttpStatus#OK}. + * + * @see ProjectionType + * @see StudySortBy + * @see Direction + */ @Hidden @GetMapping(value = "/studies", produces = MediaType.APPLICATION_JSON_VALUE) - public ResponseEntity> getAllStudies( + public ResponseEntity> getAllStudies( @Parameter(description = "Search keyword that applies to name and cancer type of the studies") @RequestParam(required = false) String keyword, @Parameter(description = "Level of detail of the response") - @RequestParam(defaultValue = "SUMMARY") Projection projection, - @Parameter(description = "Page size of the result list") - @Max(PagingConstants.MAX_PAGE_SIZE) - @Min(PagingConstants.MIN_PAGE_SIZE) - @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_SIZE) Integer pageSize, - @Parameter(description = "Page number of the result list") - @Min(PagingConstants.MIN_PAGE_NUMBER) - @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER) Integer pageNumber, + @RequestParam(defaultValue = "SUMMARY") ProjectionType projection, @Parameter(description = "Name of the property that the result list is sorted by") @RequestParam(required = false) StudySortBy sortBy, @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC") Direction direction) { - return new ResponseEntity<>(getCancerStudyMetadataUseCase.execute() - , HttpStatus.OK); + return new ResponseEntity<>(CancerStudyMetadataMapper.INSTANCE.toDtos(getCancerStudyMetadataUseCase.execute(projection)) + ,HttpStatus.OK); } } diff --git a/src/main/java/org/cbioportal/cancerstudy/CancerStudyMetadata.java b/src/main/java/org/cbioportal/cancerstudy/CancerStudyMetadata.java index c593396653c..4631e559084 100644 --- a/src/main/java/org/cbioportal/cancerstudy/CancerStudyMetadata.java +++ b/src/main/java/org/cbioportal/cancerstudy/CancerStudyMetadata.java @@ -10,6 +10,15 @@ public record CancerStudyMetadata(Integer cancerStudyId, String cancerStudyIdent Integer miRnaSampleCount, Integer methylationHm27SampleCount, Integer rppaSampleCount, Integer massSpectrometrySampleCount, Integer completeSampleCount, String referenceGenome, Integer treatmentCount, Integer structuralVariantCount, - TypeOfCancerRecord typeOfCancer) { + TypeOfCancer typeOfCancer) { + + public CancerStudyMetadata(Integer cancerStudyId, String cancerStudyIdentifier, String typeOfCancerId, + String name, String description, Boolean publicStudy, String pmid, String citation, + String groups, Integer status, Date importDate, String referenceGenome, TypeOfCancer typeOfCancer){ + this(cancerStudyId, cancerStudyIdentifier, typeOfCancerId, name, description, publicStudy, pmid,citation, groups, + status, importDate, null, null, null, null, null, + null, null, null, null, null, + null, referenceGenome, null, null, typeOfCancer); + } } diff --git a/src/main/java/org/cbioportal/cancerstudy/TypeOfCancer.java b/src/main/java/org/cbioportal/cancerstudy/TypeOfCancer.java new file mode 100644 index 00000000000..a1265421641 --- /dev/null +++ b/src/main/java/org/cbioportal/cancerstudy/TypeOfCancer.java @@ -0,0 +1,4 @@ +package org.cbioportal.cancerstudy; + +public record TypeOfCancer(String id, String name, String dedicatedColor, String shortName, String parent) { +} diff --git a/src/main/java/org/cbioportal/cancerstudy/TypeOfCancerRecord.java b/src/main/java/org/cbioportal/cancerstudy/TypeOfCancerRecord.java deleted file mode 100644 index 9d59cfc4767..00000000000 --- a/src/main/java/org/cbioportal/cancerstudy/TypeOfCancerRecord.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.cbioportal.cancerstudy; - -public record TypeOfCancerRecord(String id, String name, String dedicatedColor, String shortName, String parent) { -} diff --git a/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java b/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java index 680936e58bd..11923cacfa2 100644 --- a/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java +++ b/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java @@ -5,14 +5,72 @@ import java.util.List; /** - * Repository interface for accessing cancer study. + * Repository interface for accessing and managing cancer study data. + *

+ * This repository provides methods to retrieve metadata and summary information + * about cancer studies. It serves as an abstraction layer between the domain + * logic and the data source, allowing for flexible and maintainable data access. + *

+ *

+ * Usage Example: + * 

+ * {@code
+ * // Inject the repository into a service
+ * private final CancerStudyRepository cancerStudyRepository;
+ *
+ * public CancerStudyService(CancerStudyRepository cancerStudyRepository) {
+ *     this.cancerStudyRepository = cancerStudyRepository;
+ * }
+ *
+ * // Retrieve metadata for all cancer studies
+ * List metadata = cancerStudyRepository.getCancerStudiesMetadata();
+ *
+ * // Retrieve summary metadata for cancer studies
+ * List summaryMetadata = cancerStudyRepository.getCancerStudiesMetadataSummary();
+ * }
+ *
+ *

+ * + * @see CancerStudyMetadata */ public interface CancerStudyRepository { - + /** * Retrieves a list of metadata for all cancer studies. + *

+ * This method returns detailed metadata for all available cancer studies, + * including information such as study identifiers, descriptions, and + * associated data sources. The metadata can be used for comprehensive + * analysis or display purposes. + *

+ *

+ * Note: The returned list may be large, depending on the number of + * cancer studies in the database. Consider using pagination or filtering + * if performance is a concern. + *

* - * @return a list of {@link CancerStudyMetadata} objects containing metadata for cancer studies. + * @return a list of {@link CancerStudyMetadata} objects containing detailed + * metadata for all cancer studies. The list may be empty if no + * studies are found. */ List getCancerStudiesMetadata(); + + /** + * Retrieves a list of summary metadata for cancer studies. + *

+ * This method returns a lightweight representation of cancer study metadata, + * containing only the most essential fields. It is suitable for scenarios + * where a high-level overview of the studies is sufficient, such as displaying + * a list of studies in a UI or performing quick lookups. + *

+ *

+ * Note: The summary metadata typically excludes detailed information + * to reduce the size of the response and improve performance. + *

+ * + * @return a list of {@link CancerStudyMetadata} objects containing summary + * metadata for cancer studies. The list may be empty if no studies + * are found. + */ + List getCancerStudiesMetadataSummary(); } diff --git a/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java b/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java index 88e33c6719d..e8c78083e74 100644 --- a/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java +++ b/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java @@ -2,19 +2,82 @@ import org.cbioportal.cancerstudy.CancerStudyMetadata; import org.cbioportal.cancerstudy.repository.CancerStudyRepository; +import org.cbioportal.shared.enums.ProjectionType; import org.springframework.stereotype.Service; +import java.util.Collections; import java.util.List; +/** + * Service class responsible for retrieving cancer study metadata based on the specified projection type. + *

+ * This use case encapsulates the logic for fetching cancer study metadata from the repository + * and returning the appropriate data based on the requested level of detail (projection). + * It acts as an intermediary between the controller and the repository, ensuring that the + * domain logic is decoupled from the data access layer. + *

+ *

+ * Usage Example: + * 

+ * {@code
+ * // Inject the use case into a controller or service
+ * private final GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase;
+ *
+ * public CancerStudyController(GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase) {
+ *     this.getCancerStudyMetadataUseCase = getCancerStudyMetadataUseCase;
+ * }
+ *
+ * // Retrieve detailed metadata for cancer studies
+ * List detailedMetadata = getCancerStudyMetadataUseCase.execute(ProjectionType.DETAILED);
+ *
+ * // Retrieve summary metadata for cancer studies
+ * List summaryMetadata = getCancerStudyMetadataUseCase.execute(ProjectionType.SUMMARY);
+ * }
+ *
+ *

+ * + * @see CancerStudyRepository + * @see ProjectionType + * @see CancerStudyMetadata + */ @Service public final class GetCancerStudyMetadataUseCase { private final CancerStudyRepository studyRepository; - + + + /** + * Constructs a new {@link GetCancerStudyMetadataUseCase} with the specified repository. + * + * @param studyRepository the repository used to access cancer study metadata. + */ public GetCancerStudyMetadataUseCase(CancerStudyRepository studyRepository) { this.studyRepository = studyRepository; } - - public List execute(){ - return studyRepository.getCancerStudiesMetadata(); + + /** + * Executes the use case to retrieve cancer study metadata based on the specified projection type. + *

+ * This method determines the level of detail to fetch from the repository based on the + * provided {@link ProjectionType}. It supports the following projections: + *

    + *
  • {@link ProjectionType#DETAILED}: Fetches all available metadata for cancer studies.
    • + *
  • {@link ProjectionType#SUMMARY}: Fetches a summarized version of the metadata.
    • + *
  • Other projection types: Returns an empty list.
    • + *
+ *

+ * + * @param projectionType the level of detail to fetch. Determines which repository method is called. + * @return a list of {@link CancerStudyMetadata} objects based on the specified projection type. + * Returns an empty list if the projection type is not supported. + * + * @see ProjectionType + * @see CancerStudyMetadata + */ + public List execute(ProjectionType projectionType) { + return switch (projectionType) { + case DETAILED -> studyRepository.getCancerStudiesMetadata(); + case SUMMARY -> studyRepository.getCancerStudiesMetadataSummary(); + default -> Collections.emptyList(); + }; } } diff --git a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java index 127a7fd861d..d245fdb331c 100644 --- a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java +++ b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java @@ -6,4 +6,6 @@ public interface ClickhouseCancerStudyMapper { List getCancerStudiesMetadata(); + + List getCancerStudiesMetadataSummary(); } diff --git a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java index e9639010f3e..17c9a937151 100644 --- a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java +++ b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java @@ -2,26 +2,45 @@ import org.cbioportal.cancerstudy.CancerStudyMetadata; import org.cbioportal.cancerstudy.repository.CancerStudyRepository; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; import java.util.List; +/** + * Repository implementation for accessing cancer study metadata from ClickHouse. + * This class delegates database queries to {@link ClickhouseCancerStudyMapper}. + */ @Repository public class ClickhouseCancerStudyRepository implements CancerStudyRepository { private final ClickhouseCancerStudyMapper cancerStudyMapper; - - @Autowired + + /** + * Constructs a new {@code ClickhouseCancerStudyRepository} with the required mapper. + * + * @param cancerStudyMapper the mapper responsible for executing ClickHouse queries + */ public ClickhouseCancerStudyRepository(ClickhouseCancerStudyMapper cancerStudyMapper) { this.cancerStudyMapper = cancerStudyMapper; } - + /** - * @return + * Retrieves detailed metadata for all cancer studies. + * + * @return a list of {@link CancerStudyMetadata} containing detailed metadata for each study */ @Override public List getCancerStudiesMetadata() { return cancerStudyMapper.getCancerStudiesMetadata(); } + + /** + * Retrieves a summarized version of cancer study metadata. + * + * @return a list of {@link CancerStudyMetadata} containing summarized metadata for each study + */ + @Override + public List getCancerStudiesMetadataSummary() { + return cancerStudyMapper.getCancerStudiesMetadataSummary(); + } } diff --git a/src/main/java/org/cbioportal/shared/enums/ProjectionType.java b/src/main/java/org/cbioportal/shared/enums/ProjectionType.java new file mode 100644 index 00000000000..21f12e0d7ba --- /dev/null +++ b/src/main/java/org/cbioportal/shared/enums/ProjectionType.java @@ -0,0 +1,88 @@ +package org.cbioportal.shared.enums; +/** + * Enum representing different levels of data projection for API responses. + *

+ * This enum is used in the domain layer to control the amount of data + * included in API responses, ensuring that only the necessary fields are + * returned based on the specific use case. By limiting the data returned, + * this enum helps improve performance, reduce network overhead, and simplify + * client-side processing. + *

+ *

+ * Each projection level corresponds to a specific set of fields or data + * representation, allowing the domain layer to tailor responses to the + * requirements of the client or the context of the request. + *

+ *

+ * Usage Example: + * 

+ * {@code
+ * public ResponseEntity getEntity(@RequestParam Projection projection) {
+ *     Entity entity = entityService.getEntity(projection);
+ *     EntityDto dto = entityMapper.toDto(entity, projection);
+ *     return ResponseEntity.ok(dto);
+ * }
+ * }
+ *
+ *

+ */ +public enum ProjectionType { + + /** + * ID Projection - Includes only the essential identifier fields of the entity. + *

+ * This projection is suitable for scenarios where only the unique identifier + * of the entity is required, such as when referencing the entity in another + * context or performing lightweight operations. + *

+ *

+ * Example Use Case: Fetching entity IDs for batch processing or + * creating relationships between entities. + *

+ */ + ID, + + /** + * SUMMARY Projection - Includes a limited set of fields to provide + * a high-level overview of the entity. + *

+ * This projection is useful for lightweight data representations, such as + * displaying a list of entities in a UI or providing a quick summary without + * the full details. + *

+ *

+ * Example Use Case: Displaying a list of entities in a dropdown or + * search results. + *

+ */ + SUMMARY, + + /** + * DETAILED Projection - Includes all available fields of the entity. + *

+ * This projection provides a complete representation of the entity, including + * all attributes and relationships. It is best suited for scenarios where + * the client requires a full view of the entity. + *

+ *

+ * Example Use Case: Viewing the full details of an entity in a + * detailed view or edit form. + *

+ */ + DETAILED, + + /** + * META Projection - Focuses on metadata, such as counts, statistics, + * or aggregated information about the underlying data. + *

+ * This projection is useful for scenarios where the client needs summary + * information rather than individual records, such as displaying totals, + * averages, or other aggregated data. + *

+ *

+ * Example Use Case: Displaying dashboard metrics or summary reports. + *

+ */ + META +} + diff --git a/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml b/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml index a3720de8b2f..c3e7a810126 100644 --- a/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml +++ b/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml @@ -98,9 +98,42 @@ type_of_cancer.short_name, type_of_cancer.parent + + - @@ -127,10 +160,30 @@ - + + + + + + + + + + + + + + + + + + + - + + From 3318b167146c44d0a50d7b111c7a02f361a2d477 Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Wed, 29 Jan 2025 12:38:43 -0500 Subject: [PATCH 06/12] Add Tests for GetCancerStudyUseCase --- .../GetCancerStudyMetadataUseCaseTest.java | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 src/test/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCaseTest.java diff --git a/src/test/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCaseTest.java b/src/test/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCaseTest.java new file mode 100644 index 00000000000..ed7381d8e8d --- /dev/null +++ b/src/test/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCaseTest.java @@ -0,0 +1,38 @@ +package org.cbioportal.cancerstudy.usecase; + +import org.cbioportal.cancerstudy.repository.CancerStudyRepository; +import org.cbioportal.shared.enums.ProjectionType; +import org.junit.Assert; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.junit.MockitoJUnitRunner; + +import static org.mockito.Mockito.verify; + + +@RunWith(MockitoJUnitRunner.class) +public class GetCancerStudyMetadataUseCaseTest { + + @InjectMocks + private GetCancerStudyMetadataUseCase getCancerStudyMetadataUseCase; + + @Mock + CancerStudyRepository cancerStudyRepository; + + @Test + public void testExecuteWithProjectionTypeSummary() { + getCancerStudyMetadataUseCase.execute(ProjectionType.SUMMARY); + verify(cancerStudyRepository).getCancerStudiesMetadataSummary(); + } + @Test + public void testExecuteWithProjectionTypeDetailed() { + getCancerStudyMetadataUseCase.execute(ProjectionType.DETAILED); + verify(cancerStudyRepository).getCancerStudiesMetadata(); + } + @Test + public void testExecuteWithProjectionTypeDefault() { + Assert.assertTrue(getCancerStudyMetadataUseCase.execute(ProjectionType.META).isEmpty()); + } +} \ No newline at end of file From d9613eb323f6d67be971ea0edce20d2e523f8b82 Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Wed, 29 Jan 2025 12:39:02 -0500 Subject: [PATCH 07/12] Update return of getAllStudies --- .../rest/vcolumnstore/ColumnStoreStudyController.java | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java b/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java index b52242fca22..543b3bb965f 100644 --- a/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java +++ b/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java @@ -82,8 +82,7 @@ public ResponseEntity> getAllStudies( @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC") Direction direction) { - return new ResponseEntity<>(CancerStudyMetadataMapper.INSTANCE.toDtos(getCancerStudyMetadataUseCase.execute(projection)) - ,HttpStatus.OK); + return ResponseEntity.ok(CancerStudyMetadataMapper.INSTANCE.toDtos(getCancerStudyMetadataUseCase.execute(projection))); } } From 23ad14433ed5b772ca3a26b22f74e32ec1ff0946 Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Mon, 3 Feb 2025 01:22:34 -0500 Subject: [PATCH 08/12] ;dd Sort Feature to cancerStudy endpoint --- pom.xml | 3 +- .../ColumnStoreStudyController.java | 6 ++- .../repository/CancerStudyRepository.java | 5 ++- .../GetCancerStudyMetadataUseCase.java | 9 +++-- .../ClickhouseCancerStudyMapper.java | 39 ++++++++++++++++++- .../ClickhouseCancerStudyRepository.java | 13 +++++-- .../shared/SortAndSearchCriteria.java | 12 ++++++ .../cancerstudy/CancerStudyMapper.xml | 6 ++- .../GetCancerStudyMetadataUseCaseTest.java | 13 ++++--- 9 files changed, 87 insertions(+), 19 deletions(-) create mode 100644 src/main/java/org/cbioportal/shared/SortAndSearchCriteria.java diff --git a/pom.xml b/pom.xml index 3e9101ca711..e68469d013b 100644 --- a/pom.xml +++ b/pom.xml @@ -392,7 +392,8 @@ mapstruct ${mapstruct.version} - + + org.osgi org.osgi.service.component.annotations diff --git a/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java b/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java index 543b3bb965f..2f5a15cb0d1 100644 --- a/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java +++ b/src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java @@ -7,6 +7,7 @@ import org.cbioportal.cancerstudy.usecase.GetCancerStudyMetadataUseCase; import org.cbioportal.legacy.web.parameter.Direction; import org.cbioportal.legacy.web.parameter.sort.StudySortBy; +import org.cbioportal.shared.SortAndSearchCriteria; import org.cbioportal.shared.enums.ProjectionType; import org.springframework.http.HttpStatus; import org.springframework.http.MediaType; @@ -82,7 +83,10 @@ public ResponseEntity> getAllStudies( @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC") Direction direction) { - return ResponseEntity.ok(CancerStudyMetadataMapper.INSTANCE.toDtos(getCancerStudyMetadataUseCase.execute(projection))); + + var sortAndSearchCriteria = new SortAndSearchCriteria(keyword, (sortBy != null ? sortBy.getOriginalValue(): ""), + direction.toString()); + return ResponseEntity.ok(CancerStudyMetadataMapper.INSTANCE.toDtos(getCancerStudyMetadataUseCase.execute(projection, sortAndSearchCriteria))); } } diff --git a/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java b/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java index 11923cacfa2..fe9856e7c9c 100644 --- a/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java +++ b/src/main/java/org/cbioportal/cancerstudy/repository/CancerStudyRepository.java @@ -1,6 +1,7 @@ package org.cbioportal.cancerstudy.repository; import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.cbioportal.shared.SortAndSearchCriteria; import java.util.List; @@ -53,7 +54,7 @@ public interface CancerStudyRepository { * metadata for all cancer studies. The list may be empty if no * studies are found. */ - List getCancerStudiesMetadata(); + List getCancerStudiesMetadata(SortAndSearchCriteria sortAndSearchCriteria); /** * Retrieves a list of summary metadata for cancer studies. @@ -72,5 +73,5 @@ public interface CancerStudyRepository { * metadata for cancer studies. The list may be empty if no studies * are found. */ - List getCancerStudiesMetadataSummary(); + List getCancerStudiesMetadataSummary(SortAndSearchCriteria sortAndSearchCriteria); } diff --git a/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java b/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java index e8c78083e74..049e6c62305 100644 --- a/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java +++ b/src/main/java/org/cbioportal/cancerstudy/usecase/GetCancerStudyMetadataUseCase.java @@ -2,6 +2,7 @@ import org.cbioportal.cancerstudy.CancerStudyMetadata; import org.cbioportal.cancerstudy.repository.CancerStudyRepository; +import org.cbioportal.shared.SortAndSearchCriteria; import org.cbioportal.shared.enums.ProjectionType; import org.springframework.stereotype.Service; @@ -42,6 +43,7 @@ */ @Service public final class GetCancerStudyMetadataUseCase { + private final CancerStudyRepository studyRepository; @@ -67,16 +69,17 @@ public GetCancerStudyMetadataUseCase(CancerStudyRepository studyRepository) { *

* * @param projectionType the level of detail to fetch. Determines which repository method is called. + * @param sortAndSearchCriteria enables sorting and searching feature within persistence layer. {@link SortAndSearchCriteria} * @return a list of {@link CancerStudyMetadata} objects based on the specified projection type. * Returns an empty list if the projection type is not supported. * * @see ProjectionType * @see CancerStudyMetadata */ - public List execute(ProjectionType projectionType) { + public List execute(ProjectionType projectionType, SortAndSearchCriteria sortAndSearchCriteria) { return switch (projectionType) { - case DETAILED -> studyRepository.getCancerStudiesMetadata(); - case SUMMARY -> studyRepository.getCancerStudiesMetadataSummary(); + case DETAILED -> studyRepository.getCancerStudiesMetadata(sortAndSearchCriteria); + case SUMMARY -> studyRepository.getCancerStudiesMetadataSummary(sortAndSearchCriteria); default -> Collections.emptyList(); }; } diff --git a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java index d245fdb331c..68ae7968782 100644 --- a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java +++ b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyMapper.java @@ -1,11 +1,46 @@ package org.cbioportal.infrastructure.repository.clickhouse.cancerstudy; import org.cbioportal.cancerstudy.CancerStudyMetadata; +import org.cbioportal.shared.SortAndSearchCriteria; import java.util.List; +/** + * Provides methods for retrieving cancer study metadata from a ClickHouse database. + * This interface defines the contract for fetching detailed and summarized metadata + * for cancer studies based on specified criteria. + */ public interface ClickhouseCancerStudyMapper { - List getCancerStudiesMetadata(); + /** + * Retrieves detailed metadata for cancer studies based on the provided sorting, + * search criteria, and a list of study IDs. This method is intended to return + * comprehensive information about each study. + * + * @param sortAndSearchCriteria the criteria used for sorting and searching the + * cancer study metadata. This includes parameters + * such as sort direction, sort by field, and search keywords. + * @param studyIds a list of study IDs to filter the results. If empty, all studies + * matching the criteria should be returned. + * @return a list of {@link CancerStudyMetadata} containing detailed metadata + * for each study that matches the provided criteria and study IDs. + * The list may be empty if no studies match the criteria. + */ + List getCancerStudiesMetadata(SortAndSearchCriteria sortAndSearchCriteria, List studyIds); - List getCancerStudiesMetadataSummary(); + + /** + * Retrieves a summarized version of cancer study metadata based on the provided + * sorting, search criteria, and a list of study IDs. This method is intended to + * return a concise overview of each study. + * + * @param sortAndSearchCriteria the criteria used for sorting and searching the + * cancer study metadata. This includes parameters + * such as sort direction, sort by field, and search keywords. + * @param studyIds a list of study IDs to filter the results. If empty, all studies + * matching the criteria should be returned. + * @return a list of {@link CancerStudyMetadata} containing summarized metadata + * for each study that matches the provided criteria and study IDs. + * The list may be empty if no studies match the criteria. + */ + List getCancerStudiesMetadataSummary(SortAndSearchCriteria sortAndSearchCriteria, List studyIds); } diff --git a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java index 17c9a937151..e889a6c8715 100644 --- a/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java +++ b/src/main/java/org/cbioportal/infrastructure/repository/clickhouse/cancerstudy/ClickhouseCancerStudyRepository.java @@ -2,6 +2,7 @@ import org.cbioportal.cancerstudy.CancerStudyMetadata; import org.cbioportal.cancerstudy.repository.CancerStudyRepository; +import org.cbioportal.shared.SortAndSearchCriteria; import org.springframework.stereotype.Repository; import java.util.List; @@ -26,21 +27,25 @@ public ClickhouseCancerStudyRepository(ClickhouseCancerStudyMapper cancerStudyMa /** * Retrieves detailed metadata for all cancer studies. + * @param sortAndSearchCriteria the criteria used for sorting and searching the cancer study metadata. + * This includes parameters such as sort direction, sort by field, and search keywords. * * @return a list of {@link CancerStudyMetadata} containing detailed metadata for each study */ @Override - public List getCancerStudiesMetadata() { - return cancerStudyMapper.getCancerStudiesMetadata(); + public List getCancerStudiesMetadata(SortAndSearchCriteria sortAndSearchCriteria) { + return cancerStudyMapper.getCancerStudiesMetadata(sortAndSearchCriteria, List.of()); } /** * Retrieves a summarized version of cancer study metadata. * + * @param sortAndSearchCriteria the criteria used for sorting and searching the cancer study metadata. + * This includes parameters such as sort direction, sort by field, and search keywords. * @return a list of {@link CancerStudyMetadata} containing summarized metadata for each study */ @Override - public List getCancerStudiesMetadataSummary() { - return cancerStudyMapper.getCancerStudiesMetadataSummary(); + public List getCancerStudiesMetadataSummary(SortAndSearchCriteria sortAndSearchCriteria) { + return cancerStudyMapper.getCancerStudiesMetadataSummary(sortAndSearchCriteria, List.of()); } } diff --git a/src/main/java/org/cbioportal/shared/SortAndSearchCriteria.java b/src/main/java/org/cbioportal/shared/SortAndSearchCriteria.java new file mode 100644 index 00000000000..49c4aa6ae43 --- /dev/null +++ b/src/main/java/org/cbioportal/shared/SortAndSearchCriteria.java @@ -0,0 +1,12 @@ +package org.cbioportal.shared; + +public record SortAndSearchCriteria(String searchTerm, String sortField, String sortOrder) { + boolean isSortable() { + return (sortField != null && !sortField.isEmpty()) + && (sortOrder != null && !sortOrder.isEmpty()); + } + + boolean isSearchable() { + return searchTerm != null && !searchTerm.isEmpty(); + } +} diff --git a/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml b/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml index c3e7a810126..fbdc8b4c720 100644 --- a/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml +++ b/src/main/resources/mappers/clickhouse/cancerstudy/CancerStudyMapper.xml @@ -95,7 +95,11 @@ miRnaSampleCount,mrnaMicroarraySampleCount, methylationHm27SampleCount, rppaSampleCount, massSpectrometrySampleCount,completeSampleCount, mrnaRnaSeqSampleCount,type_of_cancer.name, type_of_cancer.dedicated_color, - type_of_cancer.short_name, type_of_cancer.parent + type_of_cancer.short_name, type_of_cancer.parent + + + ORDER BY ${sortAndSearchCriteria.sortField} ${sortAndSearchCriteria.sortOrder} +