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Add back NA counts when corresponding samples are filtered out of stu…
…dy view (#11185) * Fix counting of clinical data na when filtered out * Add caching and cleanup * Fix Sonar issues
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63 changes: 63 additions & 0 deletions
63
src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| package org.cbioportal.service.util; | ||
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| import org.cbioportal.model.ClinicalAttribute; | ||
| import org.cbioportal.model.ClinicalDataCount; | ||
| import org.cbioportal.model.ClinicalDataCountItem; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.stream.Collectors; | ||
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| public class StudyViewColumnarServiceUtil { | ||
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| private StudyViewColumnarServiceUtil() {} | ||
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| 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; | ||
| }).toList(); | ||
| attr.setCounts(res); | ||
| }); | ||
| return items; | ||
| } | ||
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| public static List<ClinicalDataCountItem> addClinicalDataCountsForMissingAttributes( | ||
| List<ClinicalDataCountItem> counts, | ||
| List<ClinicalAttribute> attributes, | ||
| Integer filteredSampleCount, | ||
| Integer filteredPatientCount | ||
| ) { | ||
| Map<String, ClinicalDataCountItem> map = counts.stream() | ||
| .collect(Collectors.toMap(ClinicalDataCountItem::getAttributeId, item -> item)); | ||
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| List<ClinicalDataCountItem> result = new ArrayList<>(counts); | ||
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| attributes.forEach(attr -> { | ||
| Integer count = attr.getPatientAttribute().booleanValue() ? filteredPatientCount : filteredSampleCount; | ||
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| if (!map.containsKey(attr.getAttrId())) { | ||
| ClinicalDataCountItem newItem = new ClinicalDataCountItem(); | ||
| newItem.setAttributeId(attr.getAttrId()); | ||
| ClinicalDataCount countObj = new ClinicalDataCount(); | ||
| countObj.setCount(count); | ||
| countObj.setValue("NA"); | ||
| countObj.setAttributeId(attr.getAttrId()); | ||
| newItem.setCounts(List.of(countObj)); | ||
| result.add(newItem); | ||
| } | ||
| }); | ||
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| return result; | ||
| } | ||
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| } |
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131 changes: 131 additions & 0 deletions
131
src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,131 @@ | ||
| package org.cbioportal.service.util; | ||
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| import org.cbioportal.model.ClinicalAttribute; | ||
| import org.cbioportal.model.ClinicalDataCount; | ||
| import org.cbioportal.model.ClinicalDataCountItem; | ||
| import org.junit.Assert; | ||
| import org.junit.Test; | ||
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| import java.util.Arrays; | ||
| import java.util.Collections; | ||
| import java.util.List; | ||
| import java.util.Optional; | ||
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| import static org.junit.Assert.*; | ||
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| public class StudyViewColumnarServiceUtilTest { | ||
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| @Test | ||
| public void testMergeClinicalDataCounts() { | ||
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| // first two counts are for same value (value1) and so should be | ||
| // merged | ||
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| ClinicalDataCount count1 = new ClinicalDataCount(); | ||
| count1.setAttributeId("attr1"); | ||
| count1.setValue("value1"); | ||
| count1.setCount(1); | ||
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| ClinicalDataCount count2 = new ClinicalDataCount(); | ||
| count2.setAttributeId("attr1"); | ||
| count2.setValue("value1"); | ||
| count2.setCount(2); | ||
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| ClinicalDataCount count3 = new ClinicalDataCount(); | ||
| count3.setAttributeId("attr1"); | ||
| count3.setValue("value3"); | ||
| count3.setCount(6); | ||
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| ClinicalDataCount count4 = new ClinicalDataCount(); | ||
| count4.setAttributeId("attr1"); | ||
| count4.setValue("value3"); | ||
| count4.setCount(4); | ||
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| ClinicalDataCount count5 = new ClinicalDataCount(); | ||
| count5.setAttributeId("attr1"); | ||
| count5.setValue("value2"); | ||
| count5.setCount(4); | ||
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| ClinicalDataCountItem item = new ClinicalDataCountItem(); | ||
| item.setAttributeId("attr1"); | ||
| item.setCounts(Arrays.asList(count1, count2, count3, count4, count5)); | ||
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| List<ClinicalDataCountItem> items = Collections.singletonList(item); | ||
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| // Call the method under test | ||
| List<ClinicalDataCountItem> mergedItems = StudyViewColumnarServiceUtil.mergeClinicalDataCounts(items); | ||
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| // 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()); | ||
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| Optional<ClinicalDataCount> mergedCount2=mergedItems.get(0).getCounts().stream() | ||
| .filter(count->count.getValue().equals("value2")).findFirst(); | ||
| Assert.assertEquals(4, mergedCount2.get().getCount().intValue()); | ||
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| Optional<ClinicalDataCount> mergedCount3=mergedItems.get(0).getCounts().stream() | ||
| .filter(count->count.getValue().equals("value3")).findFirst(); | ||
| Assert.assertEquals(10, mergedCount3.get().getCount().intValue()); | ||
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| } | ||
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| @Test | ||
| public void testAddClinicalDataCountsForMissingAttributes() { | ||
| ClinicalDataCountItem existingItem = new ClinicalDataCountItem(); | ||
| existingItem.setAttributeId("attr1"); | ||
| ClinicalDataCount existingCount = new ClinicalDataCount(); | ||
| existingCount.setCount(5); | ||
| existingCount.setValue("value1"); | ||
| existingCount.setAttributeId("attr1"); | ||
| existingItem.setCounts(Collections.singletonList(existingCount)); | ||
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| List<ClinicalDataCountItem> counts = Collections.singletonList(existingItem); | ||
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| // we're gonna create two attributes which will not be represented in the passed result set | ||
| // test whether addClinicalDataCountsForMissingAttributes restores them | ||
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| ClinicalAttribute missingAttributeSample = new ClinicalAttribute(); | ||
| missingAttributeSample.setAttrId("attr2"); | ||
| missingAttributeSample.setPatientAttribute(false); | ||
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| ClinicalAttribute missingAttributePatient = new ClinicalAttribute(); | ||
| missingAttributePatient.setAttrId("attr3"); | ||
| missingAttributePatient.setPatientAttribute(true); | ||
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| List<ClinicalAttribute> attributes = Arrays.asList(missingAttributeSample, missingAttributePatient); | ||
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| List<ClinicalDataCountItem> result = StudyViewColumnarServiceUtil.addClinicalDataCountsForMissingAttributes( | ||
| counts, attributes, 10, 20 | ||
| ); | ||
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| assertEquals(3, result.size()); | ||
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| Optional<ClinicalDataCountItem> addedItemSample = result.stream() | ||
| .filter(item -> item.getAttributeId().equals("attr2")) | ||
| .findFirst(); | ||
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| assertTrue(addedItemSample.isPresent()); | ||
| assertEquals(1, addedItemSample.get().getCounts().size()); | ||
| assertEquals("NA", addedItemSample.get().getCounts().get(0).getValue()); | ||
| assertEquals(10, addedItemSample.get().getCounts().get(0).getCount().intValue()); | ||
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| Optional<ClinicalDataCountItem> addedItemPatient = result.stream() | ||
| .filter(item -> item.getAttributeId().equals("attr3")) | ||
| .findFirst(); | ||
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| assertTrue(addedItemPatient.isPresent()); | ||
| assertEquals(1, addedItemPatient.get().getCounts().size()); | ||
| assertEquals("NA", addedItemPatient.get().getCounts().get(0).getValue()); | ||
| assertEquals(20, addedItemPatient.get().getCounts().get(0).getCount().intValue()); | ||
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| } | ||
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| } |