Update tests and mappers in legacy

cBioPortal · Feb 6, 2025 · b03fef5 · b03fef5
1 parent c962ccc
commit b03fef5
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Showing 37 changed files with 9 additions and 8 deletions.
diff --git a/src/main/java/org/cbioportal/legacy/persistence/mybatis/config/PersistenceConfig.java b/src/main/java/org/cbioportal/legacy/persistence/mybatis/config/PersistenceConfig.java
@@ -51,7 +51,7 @@ private SqlSessionFactoryBean sqlSessionFactory(DataSource dataSource, Applicati
         SqlSessionFactoryBean sessionFactory = new SqlSessionFactoryBean();
         sessionFactory.setDataSource(dataSource);
         sessionFactory.setMapperLocations(
-            applicationContext.getResources("classpath:org/cbioportal/persistence/mybatis/*.xml")
+            applicationContext.getResources("classpath:org/cbioportal/legacy/persistence/mybatis/*.xml")
         );
         sessionFactory.setTypeHandlers(new SampleTypeTypeHandler());
         return sessionFactory;

diff --git a/src/main/java/org/cbioportal/legacy/web/error/GlobalExceptionHandler.java b/src/main/java/org/cbioportal/legacy/web/error/GlobalExceptionHandler.java
@@ -42,7 +42,7 @@
 // TODO
 // - consider extending extends ResponseEntityExceptionHandler
 // - check controllers for not catching exceptions themselves
-@ControllerAdvice("org.cbioportal.web")
+@ControllerAdvice("org.cbioportal.legacy.web")
 public class GlobalExceptionHandler {
 
     @ExceptionHandler(UnsupportedOperationException.class)

diff --git a/...stence/mybatis/AlterationCountsMapper.xml → ...stence/mybatis/AlterationCountsMapper.xml b/...stence/mybatis/AlterationCountsMapper.xml → ...stence/mybatis/AlterationCountsMapper.xml
diff --git a/...atis/AlterationDriverAnnotationMapper.xml → ...atis/AlterationDriverAnnotationMapper.xml b/...atis/AlterationDriverAnnotationMapper.xml → ...atis/AlterationDriverAnnotationMapper.xml
diff --git a/.../persistence/mybatis/CancerTypeMapper.xml → .../persistence/mybatis/CancerTypeMapper.xml b/.../persistence/mybatis/CancerTypeMapper.xml → .../persistence/mybatis/CancerTypeMapper.xml
diff --git a/...tence/mybatis/ClinicalAttributeMapper.xml → ...tence/mybatis/ClinicalAttributeMapper.xml b/...tence/mybatis/ClinicalAttributeMapper.xml → ...tence/mybatis/ClinicalAttributeMapper.xml
diff --git a/...ersistence/mybatis/ClinicalDataMapper.xml → ...ersistence/mybatis/ClinicalDataMapper.xml b/...ersistence/mybatis/ClinicalDataMapper.xml → ...ersistence/mybatis/ClinicalDataMapper.xml
diff --git a/...rsistence/mybatis/ClinicalEventMapper.xml → ...rsistence/mybatis/ClinicalEventMapper.xml b/...rsistence/mybatis/ClinicalEventMapper.xml → ...rsistence/mybatis/ClinicalEventMapper.xml
diff --git a/...tence/mybatis/CopyNumberSegmentMapper.xml → ...tence/mybatis/CopyNumberSegmentMapper.xml b/...tence/mybatis/CopyNumberSegmentMapper.xml → ...tence/mybatis/CopyNumberSegmentMapper.xml
diff --git a/...persistence/mybatis/CosmicCountMapper.xml → ...persistence/mybatis/CosmicCountMapper.xml b/...persistence/mybatis/CosmicCountMapper.xml → ...persistence/mybatis/CosmicCountMapper.xml
diff --git a/...istence/mybatis/DataAccessTokenMapper.xml → ...istence/mybatis/DataAccessTokenMapper.xml b/...istence/mybatis/DataAccessTokenMapper.xml → ...istence/mybatis/DataAccessTokenMapper.xml
diff --git a/...ence/mybatis/DiscreteCopyNumberMapper.xml → ...ence/mybatis/DiscreteCopyNumberMapper.xml b/...ence/mybatis/DiscreteCopyNumberMapper.xml → ...ence/mybatis/DiscreteCopyNumberMapper.xml
diff --git a/...portal/persistence/mybatis/GeneMapper.xml → ...legacy/persistence/mybatis/GeneMapper.xml b/...portal/persistence/mybatis/GeneMapper.xml → ...legacy/persistence/mybatis/GeneMapper.xml
diff --git a/...l/persistence/mybatis/GenePanelMapper.xml → ...y/persistence/mybatis/GenePanelMapper.xml b/...l/persistence/mybatis/GenePanelMapper.xml → ...y/persistence/mybatis/GenePanelMapper.xml
diff --git a/...ersistence/mybatis/GenericAssayMapper.xml → ...ersistence/mybatis/GenericAssayMapper.xml b/...ersistence/mybatis/GenericAssayMapper.xml → ...ersistence/mybatis/GenericAssayMapper.xml
diff --git a/...stence/mybatis/GenesetHierarchyMapper.xml → ...stence/mybatis/GenesetHierarchyMapper.xml b/...stence/mybatis/GenesetHierarchyMapper.xml → ...stence/mybatis/GenesetHierarchyMapper.xml
diff --git a/...tal/persistence/mybatis/GenesetMapper.xml → ...acy/persistence/mybatis/GenesetMapper.xml b/...tal/persistence/mybatis/GenesetMapper.xml → ...acy/persistence/mybatis/GenesetMapper.xml
diff --git a/...rsistence/mybatis/MolecularDataMapper.xml → ...rsistence/mybatis/MolecularDataMapper.xml b/...rsistence/mybatis/MolecularDataMapper.xml → ...rsistence/mybatis/MolecularDataMapper.xml
diff --git a/...stence/mybatis/MolecularProfileMapper.xml → ...stence/mybatis/MolecularProfileMapper.xml b/...stence/mybatis/MolecularProfileMapper.xml → ...stence/mybatis/MolecularProfileMapper.xml
diff --git a/...al/persistence/mybatis/MutationMapper.xml → ...cy/persistence/mybatis/MutationMapper.xml b/...al/persistence/mybatis/MutationMapper.xml → ...cy/persistence/mybatis/MutationMapper.xml
diff --git a/...tal/persistence/mybatis/PatientMapper.xml → ...acy/persistence/mybatis/PatientMapper.xml b/...tal/persistence/mybatis/PatientMapper.xml → ...acy/persistence/mybatis/PatientMapper.xml
diff --git a/...nce/mybatis/ReferenceGenomeGeneMapper.xml → ...nce/mybatis/ReferenceGenomeGeneMapper.xml b/...nce/mybatis/ReferenceGenomeGeneMapper.xml → ...nce/mybatis/ReferenceGenomeGeneMapper.xml
diff --git a/...ersistence/mybatis/ResourceDataMapper.xml → ...ersistence/mybatis/ResourceDataMapper.xml b/...ersistence/mybatis/ResourceDataMapper.xml → ...ersistence/mybatis/ResourceDataMapper.xml
diff --git a/...ence/mybatis/ResourceDefinitionMapper.xml → ...ence/mybatis/ResourceDefinitionMapper.xml b/...ence/mybatis/ResourceDefinitionMapper.xml → ...ence/mybatis/ResourceDefinitionMapper.xml
diff --git a/.../persistence/mybatis/SampleListMapper.xml → .../persistence/mybatis/SampleListMapper.xml b/.../persistence/mybatis/SampleListMapper.xml → .../persistence/mybatis/SampleListMapper.xml
diff --git a/...rtal/persistence/mybatis/SampleMapper.xml → ...gacy/persistence/mybatis/SampleMapper.xml b/...rtal/persistence/mybatis/SampleMapper.xml → ...gacy/persistence/mybatis/SampleMapper.xml
diff --git a/...al/persistence/mybatis/SecurityMapper.xml → ...cy/persistence/mybatis/SecurityMapper.xml b/...al/persistence/mybatis/SecurityMapper.xml → ...cy/persistence/mybatis/SecurityMapper.xml
diff --git a/...tis/SignificantCopyNumberRegionMapper.xml → ...tis/SignificantCopyNumberRegionMapper.xml b/...tis/SignificantCopyNumberRegionMapper.xml → ...tis/SignificantCopyNumberRegionMapper.xml
diff --git a/...ybatis/SignificantlyMutatedGeneMapper.xml → ...ybatis/SignificantlyMutatedGeneMapper.xml b/...ybatis/SignificantlyMutatedGeneMapper.xml → ...ybatis/SignificantlyMutatedGeneMapper.xml
diff --git a/...nce/mybatis/StaticDataTimestampMapper.xml → ...nce/mybatis/StaticDataTimestampMapper.xml b/...nce/mybatis/StaticDataTimestampMapper.xml → ...nce/mybatis/StaticDataTimestampMapper.xml
diff --git a/...tence/mybatis/StructuralVariantMapper.xml → ...tence/mybatis/StructuralVariantMapper.xml b/...tence/mybatis/StructuralVariantMapper.xml → ...tence/mybatis/StructuralVariantMapper.xml
@@ -92,20 +92,20 @@
             <otherwise>
                 <trim prefix="" prefixOverrides="AND">
                      <choose>
-                        <when test="geneFilterQuery.getGene1Query().getSpecialValue() == @org.cbioportal.model.StructuralVariantSpecialValue@NO_GENE">
+                        <when test="geneFilterQuery.getGene1Query().getSpecialValue() == @org.cbioportal.legacy.model.StructuralVariantSpecialValue@NO_GENE">
                             AND structural_variant.SITE1_ENTREZ_GENE_ID IS NULL
                         </when>
-                        <when test="geneFilterQuery.getGene1Query().getSpecialValue() == @org.cbioportal.model.StructuralVariantSpecialValue@ANY_GENE" />
+                        <when test="geneFilterQuery.getGene1Query().getSpecialValue() == @org.cbioportal.legacy.model.StructuralVariantSpecialValue@ANY_GENE" />
                         <otherwise>
                             AND structural_variant.SITE1_ENTREZ_GENE_ID = ${geneFilterQuery.getGene1Query().getEntrezId()}
                         </otherwise>
                     </choose>
                     <choose>
-                        <when test="geneFilterQuery.getGene2Query().getSpecialValue() == @org.cbioportal.model.StructuralVariantSpecialValue@NO_GENE">
+                        <when test="geneFilterQuery.getGene2Query().getSpecialValue() == @org.cbioportal.legacy.model.StructuralVariantSpecialValue@NO_GENE">
                             AND
                             structural_variant.SITE2_ENTREZ_GENE_ID IS NULL
                         </when>
-                        <when test="geneFilterQuery.getGene2Query().getSpecialValue() == @org.cbioportal.model.StructuralVariantSpecialValue@ANY_GENE" />
+                        <when test="geneFilterQuery.getGene2Query().getSpecialValue() == @org.cbioportal.legacy.model.StructuralVariantSpecialValue@ANY_GENE" />
                         <otherwise>
                             AND
                             structural_variant.SITE2_ENTREZ_GENE_ID = ${geneFilterQuery.getGene2Query().getEntrezId()}

diff --git a/...ortal/persistence/mybatis/StudyMapper.xml → ...egacy/persistence/mybatis/StudyMapper.xml b/...ortal/persistence/mybatis/StudyMapper.xml → ...egacy/persistence/mybatis/StudyMapper.xml
diff --git a/...l/persistence/mybatis/TreatmentMapper.xml → ...y/persistence/mybatis/TreatmentMapper.xml b/...l/persistence/mybatis/TreatmentMapper.xml → ...y/persistence/mybatis/TreatmentMapper.xml
diff --git a/...ersistence/mybatis/VariantCountMapper.xml → ...ersistence/mybatis/VariantCountMapper.xml b/...ersistence/mybatis/VariantCountMapper.xml → ...ersistence/mybatis/VariantCountMapper.xml
diff --git a/src/test/java/org/cbioportal/legacy/persistence/mybatis/config/TestConfig.java b/src/test/java/org/cbioportal/legacy/persistence/mybatis/config/TestConfig.java
@@ -18,7 +18,7 @@
 import java.util.Properties;
 
 @TestConfiguration
-@MapperScan("org.cbioportal.persistence.mybatis")
+@MapperScan("org.cbioportal.legacy.persistence.mybatis")
 public class TestConfig {
 
     @Bean

diff --git a/...java/org/cbioportal/legacy/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java b/...java/org/cbioportal/legacy/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java
@@ -13,6 +13,7 @@
 import org.springframework.context.annotation.Import;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.context.junit4.SpringRunner;
 
 import java.util.List;

diff --git a/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/MyBatisConfig.java b/src/test/java/org/cbioportal/legacy/persistence/mybatisclickhouse/config/MyBatisConfig.java
@@ -12,7 +12,7 @@
 import java.io.IOException;
 
 @TestConfiguration
-@MapperScan("org.cbioportal.persistence.mybatisclickhouse")
+@MapperScan("org.cbioportal.legacy.persistence.mybatisclickhouse")
 public class MyBatisConfig {
 
     @Bean