Put non-numerical values to the end

cBioPortal · Dec 6, 2024 · ceb19a5 · ceb19a5
1 parent 31a3b0d
commit ceb19a5
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Showing 2 changed files with 12 additions and 6 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
@@ -37,6 +37,10 @@ public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFil
             List<GenomicDataFilter> mergedGenomicDataFilters = mergeDataFilters(studyViewFilter.getGenomicDataFilters());
             studyViewFilter.setGenomicDataFilters(mergedGenomicDataFilters);
         }
+        if (studyViewFilter.getClinicalDataFilters() != null && !studyViewFilter.getClinicalDataFilters().isEmpty()) {
+            List<ClinicalDataFilter> mergedClinicalDataFilters = mergeDataFilters(studyViewFilter.getClinicalDataFilters());
+            studyViewFilter.setClinicalDataFilters(mergedClinicalDataFilters);
+        }
         if (studyViewFilter.getGenericAssayDataFilters() != null && !studyViewFilter.getGenericAssayDataFilters().isEmpty()) {
             List<GenericAssayDataFilter> mergedGenericAssayDataFilters = mergeDataFilters(studyViewFilter.getGenericAssayDataFilters());
             studyViewFilter.setGenericAssayDataFilters(mergedGenericAssayDataFilters);
@@ -114,13 +118,14 @@ public static <T extends DataFilter> List<T> mergeDataFilters(List<T> filters) {
 
         for (T filter : filters) {
             List<DataFilterValue> mergedValues = new ArrayList<>();
+            List<DataFilterValue> nonNumericalValues = new ArrayList<>();
 
             BigDecimal mergedStart = null;
             BigDecimal mergedEnd = null;
             for (DataFilterValue dataFilterValue : filter.getValues()) {
                 // leave non-numerical values as they are
                 if (dataFilterValue.getValue() != null) {
-                    mergedValues.add(dataFilterValue);
+                    nonNumericalValues.add(dataFilterValue);
                 }
                 // merge adjacent numerical bins
                 else {
@@ -142,6 +147,7 @@ else if (mergedEnd.equals(start)) {
             }
 
             mergedValues.add(new DataFilterValue(mergedStart, mergedEnd, null));
+            mergedValues.addAll(nonNumericalValues);
             filter.setValues(mergedValues);
             mergedDataFilters.add(filter);
         }

diff --git a/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java b/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java
@@ -73,7 +73,7 @@ public void testMergeDataFilterNumericalInfiniteValues() {
         assertNull(end);
     }
 
-    // (-2.5, -2.25], (-2.25, -2], "NA" -> "NA", (-2.5, -1.75]
+    // (-2.5, -2.25], (-2.25, -2], "NA" -> (-2.5, -1.75], "NA"
     @Test
     public void testMergeDataFilterNumericalNonNumericalValues() {
         List<GenomicDataFilter> genomicDataFilters = new ArrayList<>();
@@ -85,11 +85,11 @@ public void testMergeDataFilterNumericalNonNumericalValues() {
 
         List<GenomicDataFilter> mergedGenomicDataFilters = StudyViewFilterHelper.mergeDataFilters(genomicDataFilters);
         List<DataFilterValue> mergedDataFilterValues = mergedGenomicDataFilters.getFirst().getValues();
-        String value = mergedDataFilterValues.getFirst().getValue();
-        BigDecimal start = mergedDataFilterValues.get(1).getStart();
-        BigDecimal end = mergedDataFilterValues.get(1).getEnd();
-        assertEquals("NA", value);
+        BigDecimal start = mergedDataFilterValues.getFirst().getStart();
+        BigDecimal end = mergedDataFilterValues.getFirst().getEnd();
+        String value = mergedDataFilterValues.get(1).getValue();
         assertEquals(0, BigDecimal.valueOf(-2.5).compareTo(start));
         assertEquals(0, BigDecimal.valueOf(-2).compareTo(end));
+        assertEquals("NA", value);
     }
 }