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Support patient ID swap to existing patient
Message handler now supports ability to swap to an existing patient node when handling CMO patient ID swaps Other updates: - updates to mocked data to bring it in sync with latest mock data in `cmo-metadb-common` Co-authored-by: Angelica Ochoa <[email protected]> Co-authored-by: Divya Madala <[email protected]> Signed-off-by: Angelica Ochoa <[email protected]>
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service/src/test/java/org/mskcc/cmo/metadb/service/CorrectCmoPatientIdHandlerTest.java
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| @@ -0,0 +1,126 @@ | ||
| package org.mskcc.cmo.metadb.service; | ||
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| import java.util.List; | ||
| import org.assertj.core.api.Assertions; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.mskcc.cmo.metadb.model.MetadbPatient; | ||
| import org.mskcc.cmo.metadb.model.MetadbRequest; | ||
| import org.mskcc.cmo.metadb.model.MetadbSample; | ||
| import org.mskcc.cmo.metadb.model.SampleMetadata; | ||
| import org.mskcc.cmo.metadb.persistence.neo4j.MetadbPatientRepository; | ||
| import org.mskcc.cmo.metadb.persistence.neo4j.MetadbRequestRepository; | ||
| import org.mskcc.cmo.metadb.persistence.neo4j.MetadbSampleRepository; | ||
| import org.mskcc.cmo.metadb.service.util.RequestDataFactory; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.boot.test.autoconfigure.data.neo4j.DataNeo4jTest; | ||
| import org.springframework.boot.test.context.TestConfiguration; | ||
| import org.springframework.context.annotation.Bean; | ||
| import org.springframework.context.annotation.Import; | ||
| import org.testcontainers.containers.Neo4jContainer; | ||
| import org.testcontainers.junit.jupiter.Container; | ||
| import org.testcontainers.junit.jupiter.Testcontainers; | ||
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| /** | ||
| * | ||
| * @author ochoaa | ||
| */ | ||
| @Testcontainers | ||
| @DataNeo4jTest | ||
| @Import(MockDataUtils.class) | ||
| public class CorrectCmoPatientIdHandlerTest { | ||
| @Autowired | ||
| private MockDataUtils mockDataUtils; | ||
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| @Autowired | ||
| private MetadbRequestService requestService; | ||
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| @Autowired | ||
| private MetadbSampleService sampleService; | ||
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| @Autowired | ||
| private MetadbPatientService patientService; | ||
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| @Container | ||
| private static final Neo4jContainer databaseServer = new Neo4jContainer<>() | ||
| .withEnv("NEO4J_dbms_security_procedures_unrestricted", "apoc.*,algo.*"); | ||
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| @TestConfiguration | ||
| static class Config { | ||
| @Bean | ||
| public org.neo4j.ogm.config.Configuration configuration() { | ||
| return new org.neo4j.ogm.config.Configuration.Builder() | ||
| .uri(databaseServer.getBoltUrl()) | ||
| .credentials("neo4j", databaseServer.getAdminPassword()) | ||
| .build(); | ||
| } | ||
| } | ||
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| private final MetadbRequestRepository requestRepository; | ||
| private final MetadbSampleRepository sampleRepository; | ||
| private final MetadbPatientRepository patientRepository; | ||
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| /** | ||
| * Persists the Mock Request data to the test database. | ||
| * @throws Exception | ||
| */ | ||
| @Autowired | ||
| public CorrectCmoPatientIdHandlerTest(MetadbRequestRepository requestRepository, | ||
| MetadbSampleRepository sampleRepository, MetadbPatientRepository patientRepository) { | ||
| this.requestRepository = requestRepository; | ||
| this.sampleRepository = sampleRepository; | ||
| this.patientRepository = patientRepository; | ||
| } | ||
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| /** | ||
| * Persists the Mock Request data to the test database. | ||
| * @throws Exception | ||
| */ | ||
| @Autowired | ||
| public void initializeMockDatabase() throws Exception { | ||
| // mock request id: MOCKREQUEST1_B | ||
| MockJsonTestData request1Data = mockDataUtils.mockedRequestJsonDataMap | ||
| .get("mockIncomingRequest1JsonDataWith2T2N"); | ||
| MetadbRequest request1 = RequestDataFactory.buildNewLimsRequestFromJson(request1Data.getJsonString()); | ||
| requestService.saveRequest(request1); | ||
| // mock request id: 145145_IM | ||
| MockJsonTestData request5Data = mockDataUtils.mockedRequestJsonDataMap | ||
| .get("mockIncomingRequest5JsonPtMultiSamples"); | ||
| MetadbRequest request5 = RequestDataFactory.buildNewLimsRequestFromJson(request5Data.getJsonString()); | ||
| requestService.saveRequest(request5); | ||
| } | ||
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| /** | ||
| * Tests sample fetch before patient swap and after the patient id swap in the | ||
| * event that the patient already exists by the new id. | ||
| */ | ||
| @Test | ||
| public void testPatientIdSwapWithExistingPatient() throws Exception { | ||
| String oldCmoPatientId = "C-MP789JR"; | ||
| String newCmoPatientId = "C-1MP6YY"; | ||
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| List<MetadbSample> samplesByNewCmoPatient = sampleService.getSamplesByCmoPatientId(newCmoPatientId); | ||
| System.out.println("Samples for new cmo patient id: " + samplesByNewCmoPatient.size()); | ||
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| String request1 = "MOCKREQUEST1_B"; | ||
| String sampleId1 = "MOCKREQUEST1_B_1"; | ||
| MetadbSample sample1 = sampleService.getResearchSampleByRequestAndIgoId(request1, sampleId1); | ||
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| MetadbPatient newPatient = patientService.getPatientByCmoPatientId(newCmoPatientId); | ||
| SampleMetadata newSample1Metadata = sample1.getLatestSampleMetadata(); | ||
| newSample1Metadata.setCmoPatientId(newCmoPatientId); | ||
| sample1.updateSampleMetadata(newSample1Metadata); | ||
| sample1.setPatient(newPatient); | ||
| sampleService.saveMetadbSample(sample1); | ||
| sampleService.updateSamplePatientRelationship(sample1.getMetaDbSampleId(), | ||
| newPatient.getMetaDbPatientId()); | ||
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| Integer expectedSampleCount = samplesByNewCmoPatient.size() + 1; | ||
| List<MetadbSample> samplesByNewCmoPatientAfterSwap = | ||
| sampleService.getSamplesByCmoPatientId(newCmoPatientId); | ||
| Assertions.assertThat(samplesByNewCmoPatientAfterSwap.size()) | ||
| .isEqualTo(expectedSampleCount); | ||
| } | ||
| } |
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