Add special case for null start end values for numerical study view filters (#11637)

* add case for null start end values for study filters

* add test

* fix issue with numerical and categorical filtering

* add comment

* add numerical and categorical test case where numerical filter is null

---------

Co-authored-by: Bryan Lai <[email protected]>

Author: 2 people

src/main/java/org/cbioportal/domain/studyview/StudyViewFilterContext.java

@@ -52,7 +52,16 @@ public String[] filteredSampleIdentifiers() {
   }
 
   public boolean isCategoricalClinicalDataFilter(ClinicalDataFilter clinicalDataFilter) {
-    var filterValue = clinicalDataFilter.getValues().getFirst();
+    var firstValue = clinicalDataFilter.getValues().getFirst();
+    var lastValue = clinicalDataFilter.getValues().getLast();
+    // there is a case where a categorical filter will have a set of null filter values first
+    // check if the first set of filter values is null. if so, use the last set of filter values
+    var filterValue =
+        firstValue.getStart() == null
+                && firstValue.getEnd() == null
+                && firstValue.getValue() == null
+            ? lastValue
+            : firstValue;
     return filterValue.getValue() != null;
   }
 }

src/main/resources/mappers/clickhouse/studyview/ClickhouseStudyViewFilterMapper.xml

@@ -280,6 +280,12 @@
                     AND 
                     ${attribute_value} ILIKE #{dataFilterValue.value}
                 </if>
+                <!--
+                    Special case: In case null start, end, and value values go through, don't apply filter.
+                -->
+                <if test="dataFilterValue.start == null and dataFilterValue.end == null">
+                    AND 1=1
+                </if>
                 <!--
                     Special case: Numerical range values such as <18, >=90, etc.
                     We need to make sure to treat these values as numerical for filtering purposes.

src/test/java/org/cbioportal/infrastructure/repository/clickhouse/sample/ClickhouseSampleMapperTest.java

@@ -149,6 +149,37 @@ public void getSamplesFilteredByClinicalData() {
                 studyViewFilter, List.of(), studyViewFilter.getStudyIds(), null));
     // 7 genuine NA samples from study_genie_pub + 1 UNKNOWN sample
     assertEquals(8, filteredSamples6.size());
+
+    // null age filter (start, end, and value are null)
+    // should return all samples with age attribute
+    studyViewFilter.setClinicalDataFilters(
+        List.of(newClinicalDataFilter("age", List.of(newDataFilterValue(null, null, null)))));
+    var filteredSamples7 =
+        mapper.getFilteredSamples(
+            StudyViewFilterFactory.make(
+                studyViewFilter, List.of(), studyViewFilter.getStudyIds(), null));
+    assertEquals(27, filteredSamples7.size());
+
+    // NA dead filter
+    studyViewFilter.setClinicalDataFilters(
+        List.of(newClinicalDataFilter("dead", List.of(newDataFilterValue(null, null, "NA")))));
+    var filteredSamples8 =
+        mapper.getFilteredSamples(
+            StudyViewFilterFactory.make(
+                studyViewFilter, List.of(), studyViewFilter.getStudyIds(), null));
+    assertEquals(17, filteredSamples8.size());
+
+    // null age filter + NA dead filter (test null numerical + any categorical filter)
+    // should return same as NA dead filter test
+    studyViewFilter.setClinicalDataFilters(
+        List.of(
+            newClinicalDataFilter("age", List.of(newDataFilterValue(null, null, null))),
+            newClinicalDataFilter("dead", List.of(newDataFilterValue(null, null, "NA")))));
+    var filteredSamples9 =
+        mapper.getFilteredSamples(
+            StudyViewFilterFactory.make(
+                studyViewFilter, List.of(), studyViewFilter.getStudyIds(), null));
+    assertEquals(17, filteredSamples9.size());
   }
 
   @Test