Add tests for clinical data count merging

cBioPortal · Nov 11, 2024 · 43297f8 · 43297f8
1 parent 73b867f
commit 43297f8
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diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -161,6 +161,20 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
         List<Sample> filteredSamples = getFilteredSamples(studyViewFilter);
 
         var resultWithAllAttributes = StudyViewColumnarServiceUtil.addClinicalDataCountsForMissingAttributes(result, filteredAttributes, filteredSamples);
+
+        resultWithAllAttributes.stream().forEach(attr -> {
+            Map<String, List<ClinicalDataCount>> countsPerType = attr.getCounts().stream()
+                .collect(Collectors.groupingBy(ClinicalDataCount::getValue));
+            List<ClinicalDataCount> res = countsPerType.entrySet().stream().map((entry)->{
+                ClinicalDataCount mergedCount = new ClinicalDataCount();
+                mergedCount.setAttributeId(attr.getAttributeId());
+                mergedCount.setValue(entry.getKey());
+                mergedCount.setCount(entry.getValue().stream().mapToInt(ClinicalDataCount::getCount).sum());
+                return mergedCount;
+            }).collect(Collectors.toList());
+            attr.setCounts(res);
+        });
+
 
         return resultWithAllAttributes;
     }

diff --git a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java b/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java
@@ -32,4 +32,22 @@ public static List<ClinicalDataCountItem> addClinicalDataCountsForMissingAttribu
 
         return result;
     }
+
+    public static List<ClinicalDataCountItem> mergeClinicalDataCounts(List<ClinicalDataCountItem> items) {
+        items.forEach(attr -> {
+            Map<String, List<ClinicalDataCount>> countsPerType = attr.getCounts().stream()
+                .collect(Collectors.groupingBy(ClinicalDataCount::getValue));
+            List<ClinicalDataCount> res = countsPerType.entrySet().stream().map((entry) -> {
+                ClinicalDataCount mergedCount = new ClinicalDataCount();
+                mergedCount.setAttributeId(attr.getAttributeId());
+                mergedCount.setValue(entry.getKey());
+                mergedCount.setCount(entry.getValue().stream().mapToInt(ClinicalDataCount::getCount).sum());
+                return mergedCount;
+            }).collect(Collectors.toList());
+            attr.setCounts(res);
+        });
+        return items;
+    }
+
+
 }
diff --git a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java b/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java
@@ -9,6 +9,7 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.Optional;
 
 import static org.junit.Assert.*;
 
@@ -55,4 +56,59 @@ public void testAddClinicalDataCountsForMissingAttributes() {
         Assert.assertEquals(2, item3.getCounts().get(0).getCount().intValue());
     }
 
+    @Test
+    public void testMergeClinicalDataCounts() {
+
+        // first two counts are for same value (value1) and so should be 
+        // merged
+
+        ClinicalDataCount count1 = new ClinicalDataCount();
+        count1.setAttributeId("attr1");
+        count1.setValue("value1");
+        count1.setCount(1);
+
+        ClinicalDataCount count2 = new ClinicalDataCount();
+        count2.setAttributeId("attr1");
+        count2.setValue("value1");
+        count2.setCount(2);
+
+        ClinicalDataCount count3 = new ClinicalDataCount();
+        count3.setAttributeId("attr1");
+        count3.setValue("value3");
+        count3.setCount(6);
+
+        ClinicalDataCount count4 = new ClinicalDataCount();
+        count4.setAttributeId("attr1");
+        count4.setValue("value3");
+        count4.setCount(4);
+
+        ClinicalDataCount count5 = new ClinicalDataCount();
+        count5.setAttributeId("attr1");
+        count5.setValue("value2");
+        count5.setCount(4);
+
+        ClinicalDataCountItem item = new ClinicalDataCountItem();
+        item.setAttributeId("attr1");
+        item.setCounts(Arrays.asList(count1, count2, count3, count4, count5));
+
+        List<ClinicalDataCountItem> items = Collections.singletonList(item);
+
+        // Call the method under test
+        List<ClinicalDataCountItem> mergedItems = StudyViewColumnarServiceUtil.mergeClinicalDataCounts(items);
+
+        // it merged three count items to 2
+        Optional<ClinicalDataCount> mergedCount=mergedItems.get(0).getCounts().stream()
+            .filter(count->count.getValue().equals("value1")).findFirst();
+        Assert.assertEquals(3, mergedCount.get().getCount().intValue());
+
+        Optional<ClinicalDataCount> mergedCount2=mergedItems.get(0).getCounts().stream()
+            .filter(count->count.getValue().equals("value2")).findFirst();
+        Assert.assertEquals(4, mergedCount2.get().getCount().intValue());
+
+        Optional<ClinicalDataCount> mergedCount3=mergedItems.get(0).getCounts().stream()
+            .filter(count->count.getValue().equals("value3")).findFirst();
+        Assert.assertEquals(10, mergedCount3.get().getCount().intValue());
+
+    }
+
 }