Genomic data bin counts endpoint and Generic Assay data bin counts en…

…dpoint
dippindots · Aug 22, 2024 · 54b27ab · 54b27ab
1 parent 21f8990
commit 54b27ab
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Showing 13 changed files with 1,016 additions and 268 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -8,6 +8,7 @@
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenomicDataCount;
+import org.cbioportal.model.MolecularProfile;
 import org.cbioportal.model.Sample;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.StudyViewFilter;
@@ -33,7 +34,7 @@ public interface StudyViewRepository {
     List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter);
 
     List<ClinicalAttribute> getClinicalAttributes();
-
+    
     Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap();
 
     List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter);
@@ -47,4 +48,10 @@ public interface StudyViewRepository {
     int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, String alterationType);
 
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
+
+    List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
+
+    List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
+
+    List<MolecularProfile> getGenericAssayProfiles();
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -10,6 +10,7 @@
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenePanelToGene;
 import org.cbioportal.model.GenomicDataCount;
+import org.cbioportal.model.MolecularProfile;
 import org.cbioportal.model.Sample;
 import org.cbioportal.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
@@ -41,7 +42,7 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
     List<ClinicalAttribute> getClinicalAttributes();
 
     List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
-    
+
     List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
 
     @MapKey("hugoGeneSymbol")
@@ -54,4 +55,11 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
     int getTotalProfiledCountByAlterationType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
 
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+
+    List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
+                                                  boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
+    List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
+                                                    boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
+
+    List<MolecularProfile> getGenericAssayProfiles();
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
@@ -35,5 +35,9 @@ public interface StudyViewColumnarService {
     List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter);
 
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
+
+    List<ClinicalDataCountItem> getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
+
+    List<ClinicalDataCountItem> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
 
 }
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -57,6 +57,30 @@ public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter s
         return studyViewRepository.getClinicalEventTypeCounts(studyViewFilter);
     }
 
+    @Override
+    public List<ClinicalDataCountItem> getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
+        return studyViewRepository.getGenomicDataBinCounts(studyViewFilter, filteredAttributes)
+            .stream().collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId))
+            .entrySet().parallelStream().map(e -> {
+                ClinicalDataCountItem item = new ClinicalDataCountItem();
+                item.setAttributeId(e.getKey());
+                item.setCounts(e.getValue());
+                return item;
+            }).collect(Collectors.toList());
+    }
+
+    @Override
+    public List<ClinicalDataCountItem> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
+        return studyViewRepository.getGenericAssayDataBinCounts(studyViewFilter, filteredAttributes)
+            .stream().collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId))
+            .entrySet().parallelStream().map(e -> {
+                ClinicalDataCountItem item = new ClinicalDataCountItem();
+                item.setAttributeId(e.getKey());
+                item.setCounts(e.getValue());
+                return item;
+            }).collect(Collectors.toList());
+    }
+
     public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter) {
         return alterationCountService.getCnaGenes(studyViewFilter);
     }