Add tests

cBioPortal · Nov 11, 2024 · 73b867f · 73b867f
1 parent a597a8a
commit 73b867f
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Showing 3 changed files with 98 additions and 16 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -19,6 +19,7 @@
 import org.cbioportal.service.StudyViewColumnarService;
 import org.cbioportal.service.exception.StudyNotFoundException;
 import org.cbioportal.service.treatment.TreatmentCountReportService;
+import org.cbioportal.service.util.StudyViewColumnarServiceUtil;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.CustomSampleIdentifier;
 import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
@@ -159,24 +160,12 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
         // fetch the samples by using the provided study view filter
         List<Sample> filteredSamples = getFilteredSamples(studyViewFilter);
 
-        Map<String, ClinicalDataCountItem> map =
-            result.stream().collect(Collectors.toMap(ClinicalDataCountItem::getAttributeId, item -> item));
-
-        filteredAttributes.stream().forEach(attr -> {
-            if (!map.containsKey(attr)) {
-                ClinicalDataCountItem newItem = new ClinicalDataCountItem();
-                newItem.setAttributeId(attr);
-                ClinicalDataCount count = new ClinicalDataCount();
-                count.setCount(filteredSamples.size());
-                count.setValue("NA");
-                count.setAttributeId(attr);
-                newItem.setCounts(Arrays.asList(count));
-                result.add(newItem);
-            }
-        });
+        var resultWithAllAttributes = StudyViewColumnarServiceUtil.addClinicalDataCountsForMissingAttributes(result, filteredAttributes, filteredSamples);
 
-        return result;
+        return resultWithAllAttributes;
     }
+
+
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",

diff --git a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java b/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java
@@ -0,0 +1,35 @@
+package org.cbioportal.service.util;
+
+import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.ClinicalDataCountItem;
+import org.cbioportal.model.Sample;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+public class StudyViewColumnarServiceUtil {
+
+    public static List<ClinicalDataCountItem> addClinicalDataCountsForMissingAttributes(List<ClinicalDataCountItem> counts, List<String> filteredAttributes, List<Sample> filteredSamples) {
+        Map<String, ClinicalDataCountItem> map = counts.stream()
+            .collect(Collectors.toMap(ClinicalDataCountItem::getAttributeId, item -> item));
+
+        List<ClinicalDataCountItem> result = new ArrayList<>(counts);
+
+        filteredAttributes.forEach(attr -> {
+            if (!map.containsKey(attr)) {
+                ClinicalDataCountItem newItem = new ClinicalDataCountItem();
+                newItem.setAttributeId(attr);
+                ClinicalDataCount count = new ClinicalDataCount();
+                count.setCount(filteredSamples.size());
+                count.setValue("NA");
+                count.setAttributeId(attr);
+                newItem.setCounts(List.of(count));
+                result.add(newItem);
+            }
+        });
+
+        return result;
+    }
+}
diff --git a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java b/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java
@@ -0,0 +1,58 @@
+package org.cbioportal.service.util;
+
+import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.ClinicalDataCountItem;
+import org.cbioportal.model.Sample;
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import static org.junit.Assert.*;
+
+public class StudyViewColumnarServiceUtilTest {
+
+    @Test
+    public void testAddClinicalDataCountsForMissingAttributes() {
+        // Prepare the input data
+        ClinicalDataCountItem existingItem = new ClinicalDataCountItem();
+        existingItem.setAttributeId("existingAttr");
+        ClinicalDataCount existingCount = new ClinicalDataCount();
+        existingCount.setCount(1);
+        existingCount.setValue("value1");
+        existingItem.setCounts(Collections.singletonList(existingCount));
+        List<ClinicalDataCountItem> result = Collections.singletonList(existingItem);
+
+        List<String> filteredAttributes = Arrays.asList("existingAttr","attr1", "attr2");
+        List<Sample> filteredSamples = Arrays.asList(new Sample(), new Sample());
+
+        // Call the method under test
+        List<ClinicalDataCountItem> updatedResult = StudyViewColumnarServiceUtil.addClinicalDataCountsForMissingAttributes(result, filteredAttributes, filteredSamples);
+
+        // code adds missing attributes from filteredAttributes
+        Assert.assertEquals(3, updatedResult.size());
+
+        ClinicalDataCountItem item1 = updatedResult.get(0);
+        Assert.assertEquals("existingAttr", item1.getAttributeId());
+        Assert.assertEquals(1, item1.getCounts().size());
+        Assert.assertEquals("value1", item1.getCounts().get(0).getValue());
+
+        // the added attributes (they were filtered out)
+        // have counts for NA value equal to the total sample count
+        ClinicalDataCountItem item2 = updatedResult.get(1);
+        Assert.assertEquals("attr1", item2.getAttributeId());
+        Assert.assertEquals(1, item2.getCounts().size());
+        Assert.assertEquals("NA", item2.getCounts().get(0).getValue());
+        Assert.assertEquals(2, item2.getCounts().get(0).getCount().intValue());
+
+        // ditto the third item
+        ClinicalDataCountItem item3 = updatedResult.get(2);
+        Assert.assertEquals("attr2", item3.getAttributeId());
+        Assert.assertEquals(1, item3.getCounts().size());
+        Assert.assertEquals("NA", item3.getCounts().get(0).getValue());
+        Assert.assertEquals(2, item3.getCounts().get(0).getCount().intValue());
+    }
+
+}