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Generic Assay categorical patient level filtering - legacy #11381

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merged 1 commit into from
Feb 10, 2025
+49 −19
Merged

Generic Assay categorical patient level filtering - legacy #11381

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10 changes: 10 additions & 0 deletions src/main/java/org/cbioportal/legacy/model/GenericAssayData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@ public class GenericAssayData extends MolecularData implements Serializable {

@NotNull
private String genericAssayStableId;

private boolean patientLevel;

/**
* @return the genericAssayStableId
Expand All @@ -26,4 +28,12 @@ public void setGenericAssayStableId(String genericAssayStableId) {
public String getStableId() {
return genericAssayStableId;
}

public void setPatientLevel(boolean patientLevel) {
this.patientLevel = patientLevel;
}

public boolean getPatientLevel() {
return patientLevel;
}
}
3 changes: 3 additions & 0 deletions src/main/java/org/cbioportal/legacy/service/impl/GenericAssayServiceImpl.java
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Expand Up @@ -169,6 +169,9 @@ public List<GenericAssayData> fetchGenericAssayData(List<String> molecularProfil
molecularData.setStudyId(sample.getCancerStudyIdentifier());
molecularData.setGenericAssayStableId(molecularAlteration.getGenericAssayStableId());
molecularData.setValue(molecularAlteration.getSplitValues()[indexOfSampleId]);
if (molecularProfile.getPatientLevel() != null) {
molecularData.setPatientLevel(molecularProfile.getPatientLevel());
}
result.add(molecularData);
}
}
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55 changes: 36 additions & 19 deletions src/main/java/org/cbioportal/legacy/service/impl/StudyViewServiceImpl.java
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Expand Up @@ -440,36 +440,53 @@ public List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String>

return data
.stream()
.filter(g -> StringUtils.isNotEmpty(g.getValue()) && !g.getValue().equals("NA"))
.collect(Collectors.groupingBy(GenericAssayData::getGenericAssayStableId))
.entrySet()
.stream()
.map(entry -> {
int totalCount = entry.getValue().size();
int naCount = sampleIds.size() - totalCount;
List<GenericAssayDataCount> counts = entry.getValue()
.stream()
List<GenericAssayData> groupData = entry.getValue();
boolean isPatientLevel = !groupData.isEmpty() && groupData.get(0).getPatientLevel();

List<GenericAssayData> filteredData;
int totalIds;

if (isPatientLevel) {
Set<String> uniquePatientIds = data.stream()
.map(GenericAssayData::getPatientId)
.collect(Collectors.toSet());
totalIds = uniquePatientIds.size();

filteredData = groupData.stream()
.filter(g -> StringUtils.isNotEmpty(g.getValue()) && !g.getValue().equals("NA"))
.collect(Collectors.groupingBy(GenericAssayData::getPatientId))
.values()
.stream()
.map(patientSamples -> patientSamples.get(0))
.toList();
} else {
totalIds = sampleIds.size();
filteredData = groupData.stream()
.filter(g -> StringUtils.isNotEmpty(g.getValue()) && !g.getValue().equals("NA"))
.toList();
}

int naCount = totalIds - filteredData.size();

List<GenericAssayDataCount> counts = filteredData.stream()
.collect(Collectors.groupingBy(GenericAssayData::getValue))
.entrySet()
.stream()
.map(datum -> {
GenericAssayDataCount dataCount = new GenericAssayDataCount();
dataCount.setValue(datum.getKey());
dataCount.setCount(datum.getValue().size());
return dataCount;
}).collect(Collectors.toList());
.map(datum -> new GenericAssayDataCount(datum.getKey(), datum.getValue().size()))
.collect(Collectors.toList());

if (naCount > 0) {
GenericAssayDataCount dataCount = new GenericAssayDataCount();
dataCount.setValue("NA");
dataCount.setCount(naCount);
counts.add(dataCount);
counts.add(new GenericAssayDataCount("NA", naCount));
}

GenericAssayDataCountItem genericAssayDataCountItem = new GenericAssayDataCountItem();
genericAssayDataCountItem.setStableId(entry.getKey());
genericAssayDataCountItem.setCounts(counts);
return genericAssayDataCountItem;
GenericAssayDataCountItem countItem = new GenericAssayDataCountItem();
countItem.setStableId(entry.getKey());
countItem.setCounts(counts);
return countItem;
}).toList();
}

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