add unit tests for fetchClinicalDataCounts / fetchClinicalDataBinCounts

cBioPortal · Jan 3, 2025 · 82cc2b6 · 82cc2b6
1 parent 2c489b4
commit 82cc2b6
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Showing 3 changed files with 276 additions and 55 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java b/src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java
@@ -177,6 +177,7 @@ public List<ClinicalDataCountItem> fetchClinicalDataCounts(List<String> studyIds
         Map<String, List<ClinicalDataCount>> clinicalDataCountMap = clinicalDataCounts.stream()
                 .collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId));
 
+        // Used to calculate number of missing values for patient attributes
         List<Patient> patients = new ArrayList<Patient>();
         if (!patientAttributeIds.isEmpty()) {
             patients.addAll(patientService.getPatientsOfSamples(studyIds, sampleIds));

diff --git a/src/main/java/org/cbioportal/service/impl/FederatedDataSourceService.java b/src/main/java/org/cbioportal/service/impl/FederatedDataSourceService.java
@@ -66,14 +66,14 @@ public List<ClinicalDataCountItem> cachedClinicalDataCounts(ClinicalDataCountFil
             studyViewFilterUtil.removeSelfFromFilter(attributes.get(0).getAttributeId(), studyViewFilter);
         }
         List<SampleIdentifier> filteredSampleIdentifiers = studyViewFilterApplier.apply(studyViewFilter);
-
+        
         if (filteredSampleIdentifiers.isEmpty()) {
             return new ArrayList<>();
         }
         List<String> studyIds = new ArrayList<>();
         List<String> sampleIds = new ArrayList<>();
         studyViewFilterUtil.extractStudyAndSampleIds(filteredSampleIdentifiers, studyIds, sampleIds);
-
+        
         List<ClinicalDataCountItem> result = clinicalDataService.fetchClinicalDataCounts(
             studyIds, sampleIds, attributes.stream().map(a -> a.getAttributeId()).collect(Collectors.toList()));
 
@@ -97,4 +97,14 @@ public List<ClinicalDataBin> cachedFetchClinicalDataBinCounts(ClinicalDataBinCou
             false
         );
     }
+
+    private List<String> filterStudyIds(List<String> requestedStudyIds) {
+        var result = new ArrayList<String>();
+        for (String studyId : requestedStudyIds) {
+            if (visibleStudies.contains(studyId)) {
+                result.add(studyId);
+            }
+        }
+        return requestedStudyIds;
+    }
 }