Generic assay binary types (cBioPortal#10335)

* update possible valid binary types * Update ExpressionEnrichmentUtil.java * modify postypelist datatype
pughlab · Nov 8, 2023 · 6c76d44 · 6c76d44
1 parent 8cfd65a
commit 6c76d44
Showing 1 changed file with 11 additions and 3 deletions.
diff --git a/service/src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java b/service/src/main/java/org/cbioportal/service/util/ExpressionEnrichmentUtil.java
@@ -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 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(
@@ -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 (posTypeList.contains(a)) {
+                            return ALTERED;
+                        } else if (negTypeList.contains(a)) {
+                            return UNALTERED;
+                        } else {
+                            return a;
+                        }
+                    })
                     .collect(Collectors.toList());
 
                 // ignore group if there are less than 2 values