make sure to go over all filtered attributes

cBioPortal · Sep 10, 2024 · 898020a · 898020a
1 parent 599ab3c
commit 898020a
Showing 1 changed file with 32 additions and 3 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -113,8 +113,28 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
                 return item;
             }).toList();
 
-        // This is postprocessing to adjust NA counts for multiple studies
-        for (ClinicalDataCountItem clinicalDataCountItem: clinicalDataCountItems) {
+        // This rest of the code is postprocessing to adjust NA counts for multiple studies
+        List<ClinicalDataCountItem> combinedClinicalDataCountItems = new ArrayList<>();
+
+        Map<String, ClinicalDataCountItem> clinicalDataCountItemMap = clinicalDataCountItems
+            .stream()
+            .collect(Collectors.toMap(
+                ClinicalDataCountItem::getAttributeId,
+                item -> item
+            ));
+
+        // go over all filtered attributes, not just attributes found in clinicalDataCountItems
+        for (String attributeId: filteredAttributes) {
+            ClinicalDataCountItem clinicalDataCountItem = clinicalDataCountItemMap.get(attributeId);
+            boolean isItemMissing = false;
+
+            if (clinicalDataCountItem == null) {
+                isItemMissing = true;
+                clinicalDataCountItem = new ClinicalDataCountItem();
+                clinicalDataCountItem.setAttributeId(attributeId);
+                clinicalDataCountItem.setCounts(new ArrayList<>());
+            }
+
             Integer totalClinicalDataCount = clinicalDataCountItem
                 .getCounts()
                 .stream()
@@ -126,6 +146,13 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
             int casesWithoutClinicalData = filteredCount - totalClinicalDataCount;
 
             if (casesWithoutClinicalData > 0) {
+                // some of these attributes may be completely missing in clinicalDataCountItem
+                // in case the only attribute value is NA.
+                // we need to manually add those missing items to make sure we have NA counts.
+                if (isItemMissing) {
+                    combinedClinicalDataCountItems.add(clinicalDataCountItem);
+                }
+
                 // find "NA"
                 ClinicalDataCount naClinicalDataCount = clinicalDataCountItem
                     .getCounts()
@@ -150,7 +177,9 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
             }
         }
 
-        return clinicalDataCountItems;
+        combinedClinicalDataCountItems.addAll(clinicalDataCountItems);
+
+        return combinedClinicalDataCountItems;
     }
 
     @Override