Merge pull request #11370 from dippindots/fix-11349

Add generic assay profiles checking in study view page
cBioPortal · Feb 5, 2025 · 1bb6601 · 1bb6601
2 parents 0b52896 + 73b6ac0
commit 1bb6601
Showing 1 changed file with 26 additions and 21 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
@@ -102,27 +102,32 @@ private CategorizedGenericAssayDataCountFilter extractGenericAssayDataCountFilte
         CategorizedGenericAssayDataCountFilter.Builder builder = CategorizedGenericAssayDataCountFilter.getBuilder();
 
         // No BINARY in the database yet
-        List<String> sampleNumericalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
-            .stream().filter(profile -> profile.getDatatype().equals("LIMIT-VALUE"))
-            .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
-            .toList();
-        builder.setSampleNumericalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
-            .filter(genericAssayDataFilter -> sampleNumericalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
-            .toList());
-        List<String> sampleCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
-            .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY"))
-            .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
-            .toList();
-        builder.setSampleCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
-            .filter(genericAssayDataFilter -> sampleCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
-            .toList());
-        List<String> patientCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.PATIENT)
-            .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY"))
-            .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
-            .toList();
-        builder.setPatientCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
-            .filter(genericAssayDataFilter -> patientCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
-            .toList());
+        if (genericAssayProfilesMap.containsKey(DataSource.SAMPLE)) {
+            List<String> sampleNumericalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
+                .stream().filter(profile -> profile.getDatatype().equals("LIMIT-VALUE"))
+                .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
+                .toList();
+            builder.setSampleNumericalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
+                .filter(genericAssayDataFilter -> sampleNumericalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
+                .toList());
+            List<String> sampleCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
+                .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY"))
+                .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
+                .toList();
+            builder.setSampleCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
+                .filter(genericAssayDataFilter -> sampleCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
+                .toList());
+        }
+        // patient level profile only have categorical for now
+        if (genericAssayProfilesMap.containsKey(DataSource.PATIENT)) {
+            List<String> patientCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.PATIENT)
+                .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY"))
+                .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
+                .toList();
+            builder.setPatientCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
+                .filter(genericAssayDataFilter -> patientCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
+                .toList());
+        }
         return builder.build();
     }