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Migrate clinical-data endpoint to clean architecture with ClickHouse support (#11425)
* Implement clinical-data in clean arch with ClickHouse support * Add integration tests * Fix ResultMap * Rectify naming * Address comments
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‎src/integration/java/org/cbioportal/infrastructure/repository/clickhouse/clinical_data/ClickHouseClinicalDataRepositoryIntegrationTest.java‎

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package org.cbioportal.infrastructure.repository.clickhouse.clinical_data;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import java.util.Arrays;
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import java.util.List;
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import org.cbioportal.AbstractClickhouseIntegrationTest;
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import org.cbioportal.domain.clinical_data.ClinicalData;
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import org.cbioportal.domain.clinical_data.ClinicalDataType;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.test.context.junit.jupiter.SpringExtension;
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@ExtendWith(SpringExtension.class)
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class ClickHouseClinicalDataRepositoryIntegrationTest extends AbstractClickhouseIntegrationTest {
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private ClickhouseClinicalDataRepository repository;
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@Autowired
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private ClickhouseClinicalDataMapper mapper;
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// Test data based on actual cBioPortal public dataset
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private static final List<String> TEST_SAMPLE_UNIQUE_IDS = Arrays.asList(
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J1-01",
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J2-01",
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J3-01"
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);
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private static final List<String> TEST_PATIENT_UNIQUE_IDS = Arrays.asList(
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J1",
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J2",
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J3"
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);
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private static final List<String> COMMON_SAMPLE_ATTRIBUTES = Arrays.asList(
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"SAMPLE_TYPE",
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"ANEUPLOIDY_SCORE"
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);
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private static final List<String> COMMON_PATIENT_ATTRIBUTES = Arrays.asList(
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"AGE",
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"SEX",
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"PRIOR_DX"
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);
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@BeforeEach
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void setup() {
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repository = new ClickhouseClinicalDataRepository(mapper);
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}
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@Test
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void testFetchClinicalDataId_WithSampleData() {
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List<ClinicalData> result = repository.fetchClinicalDataId(
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TEST_SAMPLE_UNIQUE_IDS,
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COMMON_SAMPLE_ATTRIBUTES,
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ClinicalDataType.SAMPLE
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);
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assertFalse(result.isEmpty());
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result.forEach(clinicalData -> {
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assertNotNull(clinicalData.internalId());
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assertNotNull(clinicalData.sampleId());
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assertNotNull(clinicalData.studyId());
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assertNotNull(clinicalData.attrId());
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assertNull(clinicalData.attrValue());
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assertNull(clinicalData.clinicalAttribute());
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});
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}
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@Test
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void testFetchClinicalDataSummary_WithPatientData() {
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List<ClinicalData> result = repository.fetchClinicalDataSummary(
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TEST_PATIENT_UNIQUE_IDS,
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COMMON_PATIENT_ATTRIBUTES,
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ClinicalDataType.PATIENT
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);
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assertFalse(result.isEmpty());
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result.forEach(clinicalData -> {
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assertNotNull(clinicalData.internalId());
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assertNotNull(clinicalData.patientId());
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assertNotNull(clinicalData.studyId());
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assertNotNull(clinicalData.attrId());
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assertNotNull(clinicalData.attrValue());
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assertNull(clinicalData.clinicalAttribute());
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});
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}
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@Test
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void testFetchClinicalDataDetailed_WithSpecificValues() {
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// When - get detailed data for specific samples we know the values for
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List<ClinicalData> result = repository.fetchClinicalDataDetailed(
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Arrays.asList(
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J1-01",
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J2-01"
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),
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Arrays.asList("ANEUPLOIDY_SCORE", "SAMPLE_TYPE"),
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ClinicalDataType.SAMPLE
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);
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// Then - verify we get the expected values from real data
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assertFalse(result.isEmpty(), "Should return data for valid sample IDs");
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// Verify specific known values
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boolean foundJ1Aneuploidy = false;
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boolean foundJ2Aneuploidy = false;
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boolean foundSampleType = false;
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for (ClinicalData data : result) {
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if ("TCGA-OR-A5J1-01".equals(data.sampleId()) && "ANEUPLOIDY_SCORE".equals(data.attrId())) {
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assertEquals("2", data.attrValue(), "TCGA-OR-A5J1-01 should have ANEUPLOIDY_SCORE = 2");
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foundJ1Aneuploidy = true;
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}
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if ("TCGA-OR-A5J2-01".equals(data.sampleId()) && "ANEUPLOIDY_SCORE".equals(data.attrId())) {
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assertEquals("10", data.attrValue(), "TCGA-OR-A5J2-01 should have ANEUPLOIDY_SCORE = 10");
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foundJ2Aneuploidy = true;
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}
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if ("SAMPLE_TYPE".equals(data.attrId())) {
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assertEquals("Primary", data.attrValue(), "All samples should have SAMPLE_TYPE = Primary");
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foundSampleType = true;
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}
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// Verify DETAILED projection includes clinical attribute metadata
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assertNotNull(data.clinicalAttribute(), "DETAILED projection should include clinical attribute");
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assertEquals(data.attrId(), data.clinicalAttribute().attrId(), "Attribute IDs should match");
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}
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assertTrue(foundJ1Aneuploidy, "Should find ANEUPLOIDY_SCORE for TCGA-OR-A5J1-01");
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assertTrue(foundJ2Aneuploidy, "Should find ANEUPLOIDY_SCORE for TCGA-OR-A5J2-01");
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assertTrue(foundSampleType, "Should find SAMPLE_TYPE data");
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}
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@Test
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void testFetchClinicalDataMeta_WithSampleData() {
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Integer count = repository.fetchClinicalDataMeta(
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TEST_SAMPLE_UNIQUE_IDS,
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COMMON_SAMPLE_ATTRIBUTES,
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ClinicalDataType.SAMPLE
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);
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assertNotNull(count);
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assertEquals(54, count.intValue());
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List<ClinicalData> actualData = repository.fetchClinicalDataSummary(
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TEST_SAMPLE_UNIQUE_IDS,
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COMMON_SAMPLE_ATTRIBUTES,
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ClinicalDataType.SAMPLE
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);
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assertEquals(actualData.size(), count.intValue());
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}
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@Test
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void testFetchClinicalDataId_WithEmptyInput() {
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// When
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List<ClinicalData> result = repository.fetchClinicalDataId(
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List.of(),
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COMMON_SAMPLE_ATTRIBUTES,
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ClinicalDataType.SAMPLE
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);
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// Then
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assertTrue(result.isEmpty(), "Should return empty list for empty input");
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}
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@Test
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void testFetchClinicalDataMeta_WithEmptyInput() {
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// When
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Integer count = repository.fetchClinicalDataMeta(
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List.of(),
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COMMON_SAMPLE_ATTRIBUTES,
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ClinicalDataType.SAMPLE
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);
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// Then
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assertEquals(0, count.intValue(), "Should return 0 count for empty input");
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}
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@Test
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void testProjectionConsistency_SameEntitiesReturned() {
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// When - get data with different projections using subset for focused test
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List<String> testIds = Arrays.asList(
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J1-01",
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"acc_tcga_pan_can_atlas_2018_TCGA-OR-A5J2-01"
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);
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List<String> testAttrs = List.of("SAMPLE_TYPE");
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List<ClinicalData> idResults = repository.fetchClinicalDataId(
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testIds, testAttrs, ClinicalDataType.SAMPLE
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);
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List<ClinicalData> summaryResults = repository.fetchClinicalDataSummary(
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testIds, testAttrs, ClinicalDataType.SAMPLE
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);
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// Then - should return same entities with different levels of detail
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assertEquals(2, idResults.size(), "Should return 2 records for 2 samples with SAMPLE_TYPE");
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assertEquals(idResults.size(), summaryResults.size(),
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"Different projections should return same number of entities");
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// Verify entities match (same internal IDs and attribute IDs)
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for (int i = 0; i < idResults.size(); i++) {
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ClinicalData idData = idResults.get(i);
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ClinicalData summaryData = summaryResults.get(i);
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assertEquals(idData.internalId(), summaryData.internalId(),
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"Internal ID should match across projections");
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assertEquals(idData.attrId(), summaryData.attrId(),
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"Attribute ID should match across projections");
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assertEquals(idData.sampleId(), summaryData.sampleId(),
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"Sample ID should match across projections");
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// Verify projection differences
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assertNull(idData.attrValue(), "ID projection should not have attribute value");
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assertEquals("Primary", summaryData.attrValue(), "SUMMARY projection should have attribute value");
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}
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}
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@Test
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void testClinicalDataType_PatientVsSample() {
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// When
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List<ClinicalData> sampleData = repository.fetchClinicalDataSummary(
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TEST_SAMPLE_UNIQUE_IDS,
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COMMON_SAMPLE_ATTRIBUTES,
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ClinicalDataType.SAMPLE
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);
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List<ClinicalData> patientData = repository.fetchClinicalDataSummary(
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TEST_PATIENT_UNIQUE_IDS,
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COMMON_PATIENT_ATTRIBUTES,
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ClinicalDataType.PATIENT
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);
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// Then - verify correct data type returned
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sampleData.forEach(data -> {
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assertNotNull(data.sampleId(), "Sample data should have sample ID");
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assertNotNull(data.patientId(), "Sample data should also have patient ID");
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});
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patientData.forEach(data -> {
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assertNotNull(data.patientId(), "Patient data should have patient ID");
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// Sample ID may be null or empty for patient-level data
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});
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}
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}

‎src/main/java/org/cbioportal/application/rest/mapper/ClinicalAttributeMapper.java‎

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package org.cbioportal.application.rest.mapper;
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import java.util.List;
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import org.cbioportal.application.rest.response.ClinicalAttributeDTO;
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import org.cbioportal.domain.clinical_attributes.ClinicalAttribute;
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import org.mapstruct.Mapper;
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import org.mapstruct.Mapping;
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import org.mapstruct.factory.Mappers;
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@Mapper
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public interface ClinicalAttributeMapper {
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ClinicalAttributeMapper INSTANCE = Mappers.getMapper(ClinicalAttributeMapper.class);
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@Mapping(target = "clinicalAttributeId", source = "attrId")
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@Mapping(target = "studyId", source = "cancerStudyIdentifier")
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ClinicalAttributeDTO toClinicalAttributeDTO(ClinicalAttribute clinicalAttribute);
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List<ClinicalAttributeDTO> toClinicalAttributeDTOs(List<ClinicalAttribute> clinicalAttributes);
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}

‎src/main/java/org/cbioportal/application/rest/mapper/ClinicalDataMapper.java‎

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package org.cbioportal.application.rest.mapper;
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import java.util.List;
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import org.cbioportal.application.rest.response.ClinicalDataDTO;
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import org.cbioportal.domain.clinical_data.ClinicalData;
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import org.cbioportal.legacy.utils.Encoder;
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import org.mapstruct.Mapper;
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import org.mapstruct.Mapping;
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import org.mapstruct.factory.Mappers;
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@Mapper(imports = Encoder.class, uses = ClinicalAttributeMapper.class)
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public interface ClinicalDataMapper {
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ClinicalDataMapper INSTANCE = Mappers.getMapper(ClinicalDataMapper.class);
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@Mapping(
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target = "uniqueSampleKey",
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expression =
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"java( Encoder.calculateBase64(clinicalData.sampleId()," + "clinicalData.studyId()) )")
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@Mapping(
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target = "uniquePatientKey",
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expression =
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"java( Encoder.calculateBase64(clinicalData.patientId(), " + "clinicalData.studyId()) )")
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@Mapping(target = "patientAttribute", source = "clinicalAttribute.patientAttribute")
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@Mapping(target = "clinicalAttributeId", source = "attrId")
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@Mapping(target = "value", source = "attrValue")
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ClinicalDataDTO toClinicalDataDTO(ClinicalData clinicalData);
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List<ClinicalDataDTO> toDTOs(List<ClinicalData> clinicalDataList);
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}

‎src/main/java/org/cbioportal/application/rest/response/ClinicalAttributeDTO.java‎

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package org.cbioportal.application.rest.response;
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public record ClinicalAttributeDTO(
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String displayName,
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String description,
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String datatype,
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Boolean patientAttribute,
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String priority,
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String clinicalAttributeId,
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String studyId) {}

‎src/main/java/org/cbioportal/application/rest/response/ClinicalDataDTO.java‎

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package org.cbioportal.application.rest.response;
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public record ClinicalDataDTO(
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String uniqueSampleKey,
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String uniquePatientKey,
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String sampleId,
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String patientId,
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String studyId,
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ClinicalAttributeDTO clinicalAttribute,
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Boolean patientAttribute,
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String clinicalAttributeId,
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String value) {}

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