add custom data filter for more endpoints

gblaih · Jul 8, 2024 · 0f95528 · 0f95528
1 parent 462315d
commit 0f95528
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Showing 7 changed files with 280 additions and 247 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -17,23 +17,23 @@
 
 public interface StudyViewRepository {
     List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, List<SampleIdentifier> customDataSamples);
-
-    List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
+    List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, List<SampleIdentifier> customDataSamples);
+
+    List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, List<SampleIdentifier> customDataSamples);
 
     List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter);
 
     List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter);
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter);
 
-    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
+    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes, List<SampleIdentifier> customDataSamples);
 
     List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter);
 
     List<ClinicalAttribute> getClinicalAttributes();
 
-    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter);
+    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter, List<SampleIdentifier> customDataSamples);
 
     Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -40,15 +40,15 @@ List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFil
                                                         boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues );
 
     List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
-                                                  boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
+                                                  boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues, List<SampleIdentifier> customDataSamples);
 
-    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<SampleIdentifier> customDataSamples);
 
     List<ClinicalAttribute> getClinicalAttributes();
 
-    List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
+    List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds, List<SampleIdentifier> customDataSamples);
 
-    List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
+    List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds, List<SampleIdentifier> customDataSamples);
 
     @MapKey("hugoGeneSymbol")
     Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -67,10 +67,10 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter stu
     }
 
     @Override
-    public List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
+    public List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes, List<SampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         return mapper.getClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
-            filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES );
+            filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES, customDataSamples );
     }
 
     @Override
@@ -85,27 +85,27 @@ public List<ClinicalAttribute> getClinicalAttributes() {
     }
 
     @Override
-    public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter) {
+    public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter, List<SampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return mapper.getCaseListDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
+        return mapper.getCaseListDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), customDataSamples);
     }
 
 
     private boolean shouldApplyPatientIdFilters(CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
         return categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters().isEmpty()
             || categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters().isEmpty();
     }
-
+    
     @Override
-    public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
+    public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, List<SampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return mapper.getSampleClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds);
+        return mapper.getSampleClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds, customDataSamples);
     }
 
     @Override
-    public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
+    public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, List<SampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return mapper.getPatientClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds);
+        return mapper.getPatientClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds, customDataSamples);
     }
 
     @Override