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Generic assay binary types #10335

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merged 3 commits into from
Aug 22, 2023
Merged

Generic assay binary types #10335

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f35d859
update possible valid binary types
Djokovic0311 Aug 22, 2023
b843182
Update ExpressionEnrichmentUtil.java
Djokovic0311 Aug 22, 2023
b75df08
modify postypelist datatype
Djokovic0311 Aug 22, 2023
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14 changes: 11 additions & 3 deletions service/src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,8 +48,8 @@ public class ExpressionEnrichmentUtil {

private static final double LOG2 = Math.log(2);
private static final String RNA_SEQ = "rna_seq";
private static final String POS = "true";
private static final String NEG = "false";
private static final String[] posTypeList = {"true", "yes"};
private static final String[] negTypeList = {"false", "no"};
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How about doing this, so we can avoid doing the conversion every time?

Suggested change
private static final String[] posTypeList = {"true", "yes"};
private static final String[] negTypeList = {"false", "no"};
private static final List<String> posTypeList = Arrays.asList("true", "yes");
private static final List<String> negTypeList = Arrays.asList("false", "no");

private static final String ALTERED = "1";
private static final String UNALTERED = "0";
public <T extends MolecularAlteration, S extends ExpressionEnrichment> List<S> getEnrichments(
Expand Down Expand Up @@ -205,7 +205,15 @@ public <T extends MolecularAlteration, S extends ExpressionEnrichment> List<S> g
List<String> molecularDataValues = group.getValue().stream()
.map(sampleIndex -> ma.getSplitValues()[sampleIndex])
.filter(StringUtils::isNotEmpty)
.map(a -> a.equals(POS) ? ALTERED : UNALTERED)
.map(a ->{
if (Arrays.asList(posTypeList).contains(a)) {
return ALTERED;
} else if (Arrays.asList(negTypeList).contains(a)) {
return UNALTERED;
} else {
return a;
}
})
.collect(Collectors.toList());

// ignore group if there are less than 2 values
Expand Down
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