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Fix clinical data NA count logic #10991

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merged 1 commit into from
Sep 17, 2024
Merged

Fix clinical data NA count logic #10991

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12 changes: 10 additions & 2 deletions src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@

import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.Map;

Expand Down Expand Up @@ -228,11 +229,13 @@ public static List<ClinicalDataCountItem> calculateMissingNaCountsForClinicalDat
}

// find "NA" or else create a new one
ClinicalDataCount naClinicalDataCount = clinicalDataCountItem
Optional<ClinicalDataCount> naClinicalDataCountOptional = clinicalDataCountItem
.getCounts()
.stream()
.filter(c -> c.getValue().equals("NA"))
.findFirst()
.findFirst();

ClinicalDataCount naClinicalDataCount = naClinicalDataCountOptional
.orElseGet(() -> {
// this should only happen when there are multiple studies
ClinicalDataCount count = new ClinicalDataCount();
Expand All @@ -242,6 +245,11 @@ public static List<ClinicalDataCountItem> calculateMissingNaCountsForClinicalDat
return count;
});

// if not present we need to add naClinicalDataCount to the existing counts
if (naClinicalDataCountOptional.isEmpty()) {
clinicalDataCountItem.getCounts().add(naClinicalDataCount);
}

naClinicalDataCount.setCount(naClinicalDataCount.getCount() + casesWithoutClinicalData);
}
}
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