Code review updates

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

@@ -38,7 +38,7 @@ 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

@@ -36,7 +36,7 @@ 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

@@ -110,34 +110,10 @@ public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
  return attributeDatatypeMap;
  }
 
- 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;
- }
-
  @Override
- public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter) {
+ public List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilter studyViewFilter) {
  CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
- var caseListDataCounts = mapper.getCaseListDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
- return mergeCaseListCounts(caseListDataCounts);
+ return mapper.getCaseListDataCountsPerStudy(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
  }
 
 

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

@@ -21,6 +21,7 @@
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
@@ -102,7 +103,10 @@ 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);
  }
 
 
@@ -115,4 +119,31 @@ public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter
  public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
  return studyViewRepository.getSampleClinicalData(studyViewFilter, attributeIds);
  }
+
+
+ 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 @@
 
 
  <!-- 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/CaseListSamplesCountsTest.java → src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java

@@ -1,8 +1,8 @@
 package org.cbioportal.persistence.mybatisclickhouse;
 
-import org.cbioportal.persistence.StudyViewRepository;
 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;
@@ -27,7 +27,7 @@
 @DirtiesContext
 @AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE)
 @ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class)
-public class CaseListSamplesCountsTest extends AbstractTestcontainers {
+public class StudyViewCaseListSamplesCountsTest extends AbstractTestcontainers {
 
  private static final String STUDY_TCGA_PUB = "study_tcga_pub";
  private static final String STUDY_ACC_TCGA = "acc_tcga";
@@ -45,7 +45,7 @@ public void getMolecularProfileCounts() {
 
  studyViewFilter.setCaseLists(caseListGroups);
 
- var sampleListCounts = studyViewMapper.getCaseListDataCounts(studyViewFilter,
+ var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(studyViewFilter,
  CategorizedClinicalDataCountFilter.getBuilder().build(), false );
 
  var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna"))
@@ -64,7 +64,7 @@ public void getMolecularProfileCountsMultipleListsOr() {
 
  studyViewFilter.setCaseLists(caseListGroups);
 
- var sampleListCounts = studyViewMapper.getCaseListDataCounts(studyViewFilter,
+ var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(studyViewFilter,
  CategorizedClinicalDataCountFilter.getBuilder().build(), false );
 
  var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna"))
@@ -84,7 +84,7 @@ public void getMolecularProfileCountsMultipleListsAnd() {
 
  studyViewFilter.setCaseLists(caseListGroups);
 
- var sampleListCounts = studyViewMapper.getCaseListDataCounts(studyViewFilter,
+ var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(studyViewFilter,
  CategorizedClinicalDataCountFilter.getBuilder().build(), false );
 
  var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna"))
@@ -103,10 +103,10 @@ public void getMolecularProfileCountsAcrossStudies() {
 
  studyViewFilter.setCaseLists(caseListGroups);
 
- var unMergedCounts = studyViewMapper.getCaseListDataCounts(studyViewFilter,
+ var unMergedCounts = studyViewMapper.getCaseListDataCountsPerStudy(studyViewFilter,
  CategorizedClinicalDataCountFilter.getBuilder().build(), false );
 
- var caseListCountsMerged = StudyViewMyBatisRepository.mergeCaseListCounts(
+ var caseListCountsMerged = StudyViewColumnarServiceImpl.mergeCaseListCounts(
  unMergedCounts
  );