Add tests for case list sample counts endpoint

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -40,7 +40,7 @@ public interface StudyViewRepository {
 
     Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap();
 
-    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter);
+    List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilter studyViewFilter);
 
     Map<String, Integer> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType);
 

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java

@@ -39,7 +39,7 @@ List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewF
     List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
                                                   boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
 
-    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 
     List<ClinicalAttribute> getClinicalAttributes();
 

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java

@@ -134,11 +134,11 @@ public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
 
         return attributeDatatypeMap;
     }
-
+    
     @Override
-    public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter) {
+    public List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilter studyViewFilter) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return mapper.getCaseListDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
+        return mapper.getCaseListDataCountsPerStudy(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
     }
 
 

src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java

@@ -105,7 +105,10 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
 
     @Override
     public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter) {
-        return studyViewRepository.getCaseListDataCounts(studyViewFilter);
+        // the study view merges case lists by type across studies
+        // type is determined by the suffix of case list name (after study name)
+        var caseListDataCountsPerStudy = studyViewRepository.getCaseListDataCountsPerStudy(studyViewFilter);
+        return mergeCaseListCounts(caseListDataCountsPerStudy);
     }
 
 
@@ -146,4 +149,31 @@ public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(StudyViewF
         return studyViewRepository.getMutationCountsByType(studyViewFilter, genomicDataFilters);
     }
 
+
+
+    public static List<CaseListDataCount> mergeCaseListCounts(List<CaseListDataCount> counts) {
+        Map<String, List<CaseListDataCount>> countsPerListType = counts.stream()
+            .collect((Collectors.groupingBy(CaseListDataCount::getValue)));
+
+        // different cancer studies combined into one cohort will have separate case lists
+        // of a given type (e.g. rppa).  We need to merge the counts for these
+        // different lists based on the type and choose a label
+        // this code just picks the first label, which assumes that the labels will match for a give type
+        List<CaseListDataCount> mergedCounts = new ArrayList<>();
+        for (Map.Entry<String,List<CaseListDataCount>> entry : countsPerListType.entrySet()) {
+            var dc = new CaseListDataCount();
+            dc.setValue(entry.getKey());
+            // here just snatch the label of the first profile
+            dc.setLabel(entry.getValue().get(0).getLabel());
+            Integer sum = entry.getValue().stream()
+                .map(x -> x.getCount())
+                .collect(Collectors.summingInt(Integer::intValue));
+            dc.setCount(sum);
+            mergedCounts.add(dc);
+        }
+        return mergedCounts;
+    }
+
+
+
 }

src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml

@@ -148,7 +148,7 @@
     </select>
 
     <!-- for /sample-lists-counts/fetch (returns CaseListDataCount) -->
-    <select id="getCaseListDataCounts" resultType="org.cbioportal.model.CaseListDataCount">
+    <select id="getCaseListDataCountsPerStudy" resultType="org.cbioportal.model.CaseListDataCount">
         SELECT
             name AS label,
             REPLACE(stable_id, CONCAT(cancer_study_identifier, '_'), '') AS value,

src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java

@@ -0,0 +1,124 @@
+package org.cbioportal.persistence.mybatisclickhouse;
+
+import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig;
+
+import org.cbioportal.service.impl.StudyViewColumnarServiceImpl;
+import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
+import org.cbioportal.web.parameter.StudyViewFilter;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase;
+import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest;
+import org.springframework.context.annotation.Import;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+
+@RunWith(SpringRunner.class)
+@Import(MyBatisConfig.class)
+@DataJpaTest
+@DirtiesContext
+@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE)
+@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class)
+public class StudyViewCaseListSamplesCountsTest extends AbstractTestcontainers {
+
+    private static final String STUDY_TCGA_PUB = "study_tcga_pub";
+    private static final String STUDY_ACC_TCGA = "acc_tcga";
+
+    @Autowired
+    private StudyViewMapper studyViewMapper;
+
+    @Test
+    public void getMolecularProfileCounts() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
+
+        var caseList = new ArrayList<String>(Arrays.asList("pub_cna"));
+        var caseListGroups = new ArrayList(Arrays.asList(caseList));
+
+        studyViewFilter.setCaseLists(caseListGroups);
+
+        var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+
+        var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna"))
+            .findFirst().get().getCount().intValue();
+        assertEquals(7, size);
+
+    }
+
+    @Test
+    public void getMolecularProfileCountsMultipleListsOr() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
+
+        var caseList = new ArrayList<String>(Arrays.asList("mrna","pub_cna"));
+        var caseListGroups = new ArrayList(Arrays.asList(caseList));
+
+        studyViewFilter.setCaseLists(caseListGroups);
+
+        var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+
+        var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna"))
+            .findFirst().get().getCount().intValue();
+        assertEquals(8, size);
+
+    }
+
+    @Test
+    public void getMolecularProfileCountsMultipleListsAnd() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
+
+        var caseList1 = new ArrayList<String>(Arrays.asList("mrna"));
+        var caseList2 = new ArrayList<String>(Arrays.asList("pub_cna"));
+        var caseListGroups = new ArrayList(Arrays.asList(caseList1, caseList2));
+
+        studyViewFilter.setCaseLists(caseListGroups);
+
+        var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+
+        var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna"))
+            .findFirst().get().getCount().intValue();
+        assertEquals(7, size);
+
+    }
+
+    @Test
+    public void getMolecularProfileCountsAcrossStudies() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB, STUDY_ACC_TCGA));
+
+        var caseList1 = new ArrayList<String>(Arrays.asList("all"));
+        var caseListGroups = new ArrayList(Arrays.asList(caseList1));
+
+        studyViewFilter.setCaseLists(caseListGroups);
+
+        var unMergedCounts =  studyViewMapper.getCaseListDataCountsPerStudy(studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+
+        var caseListCountsMerged = StudyViewColumnarServiceImpl.mergeCaseListCounts(
+            unMergedCounts
+        );
+
+        var sizeUnmerged = unMergedCounts.stream().filter(gc->gc.getValue().equals("all"))
+            .findFirst().get().getCount().intValue();
+        assertEquals(14, sizeUnmerged);
+
+        // now we've combined the "all" from the two studies
+        var sizeMerged = caseListCountsMerged.stream().filter(gc->gc.getValue().equals("all"))
+            .findFirst().get().getCount().intValue();
+        assertEquals(15, sizeMerged);
+
+    }
+
+}