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cBioPortal · Jun 25, 2024 · 93e3fc5 · 93e3fc5
1 parent cd477b6
commit 93e3fc5
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Showing 3 changed files with 12 additions and 17 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -9,7 +9,6 @@
 import org.cbioportal.model.GenomicDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.Sample;
-import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 
@@ -45,9 +44,9 @@ public interface StudyViewRepository {
 
     int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, String alterationType);
 
-    List<GenomicDataCountItem> getCNAAlterationCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters);
+    List<GenomicDataCountItem> getCNAAlterationCounts(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);
 
-    Map<String, Integer> getMutationCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, GenomicDataFilter genomicDataFilter);
+    Map<String, Integer> getMutationCounts(StudyViewFilter studyViewFilter, GenomicDataFilter genomicDataFilter);
 
-    List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters);
+    List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -192,15 +192,18 @@ private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final
     }
 
     @Override
-    public List<GenomicDataCountItem> getCNAAlterationCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters) {
+    public List<GenomicDataCountItem> getCNAAlterationCounts(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         return mapper.getCNAAlterationCounts(studyViewFilter, categorizedClinicalDataCountFilter, genomicDataFilters);
     }
 
-    public Map<String, Integer> getMutationCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, GenomicDataFilter genomicDataFilter) {
+    public Map<String, Integer> getMutationCounts(StudyViewFilter studyViewFilter, GenomicDataFilter genomicDataFilter) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         return mapper.getMutationCounts(studyViewFilter, categorizedClinicalDataCountFilter, genomicDataFilter);
     }
 
-    public List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters) {
+    public List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         return mapper.getMutationCountsByType(studyViewFilter, categorizedClinicalDataCountFilter, genomicDataFilters);
     }
 

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -12,7 +12,6 @@
 import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.service.AlterationCountService;
 import org.cbioportal.service.StudyViewColumnarService;
-import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -93,18 +92,14 @@ public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter,
 
     @Override
     public List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
-        // CategorizedClinicalDataCountFilter is needed for all StudyViewFilter endpoints to work together in database queries. It may be removed in the future by architecture upgrade
-        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return studyViewRepository.getCNAAlterationCounts(studyViewFilter, categorizedClinicalDataCountFilter, genomicDataFilters);
+        return studyViewRepository.getCNAAlterationCounts(studyViewFilter, genomicDataFilters);
     }
 
     @Override
     public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
-        // CategorizedClinicalDataCountFilter is needed for all StudyViewFilter endpoints to work together in database queries. It may be removed in the future by architecture upgrade
-        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         List<GenomicDataCountItem> genomicDataCountItemList = new ArrayList<>();
         for (GenomicDataFilter genomicDataFilter : genomicDataFilters) {
-            Map<String, Integer> counts = studyViewRepository.getMutationCounts(studyViewFilter, categorizedClinicalDataCountFilter, genomicDataFilter);
+            Map<String, Integer> counts = studyViewRepository.getMutationCounts(studyViewFilter, genomicDataFilter);
             List<GenomicDataCount> genomicDataCountList = new ArrayList<>();
             if (counts.getOrDefault("mutatedCount", 0) > 0)
                 genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", counts.get("mutatedCount"), counts.get("mutatedCount")));
@@ -119,9 +114,7 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilte
 
     @Override
     public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
-        // CategorizedClinicalDataCountFilter is needed for all StudyViewFilter endpoints to work together in database queries. It may be removed in the future by architecture upgrade
-        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return studyViewRepository.getMutationCountsByType(studyViewFilter, categorizedClinicalDataCountFilter, genomicDataFilters);
+        return studyViewRepository.getMutationCountsByType(studyViewFilter, genomicDataFilters);
     }
 
 }