Fix exon annotation not showing (#484)

oncokb · Jan 10, 2025 · 63bbd18 · 63bbd18
1 parent 73006f5
commit 63bbd18
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/src/main/java/org/mskcc/oncokb/curation/service/MainService.java b/src/main/java/org/mskcc/oncokb/curation/service/MainService.java
@@ -214,6 +214,9 @@ public AlterationAnnotationStatus annotateAlteration(ReferenceGenome referenceGe
             alteration.setName(alteration.getAlteration());
         }
 
+        alterationWithStatus.setMessage(alterationWithEntityStatus.getMessage());
+        alterationWithStatus.setType(alterationWithEntityStatus.getType());
+
         // update reference genome
         if (alteration.getGenes().size() > 0 && PROTEIN_CHANGE.equals(alteration.getType())) {
             Gene gene = alteration.getGenes().iterator().next();
@@ -241,17 +244,13 @@ public AlterationAnnotationStatus annotateAlteration(ReferenceGenome referenceGe
                                     "The reference allele does not match with the transcript. It's supposed to be " + refRe
                                 );
                                 alterationWithStatus.setType(EntityStatusType.WARNING);
-                                return alterationWithStatus;
                             }
                         }
                     }
                 }
             }
         }
 
-        alterationWithStatus.setMessage(alterationWithEntityStatus.getMessage());
-        alterationWithStatus.setType(alterationWithEntityStatus.getType());
-
         // Provide annotation for the alteration
         // 1. check whether alteration is hotspot
         AnnotationDTO annotationDTO = new AnnotationDTO();

diff --git a/src/main/java/org/mskcc/oncokb/curation/util/parser/ProteinChangeParser.java b/src/main/java/org/mskcc/oncokb/curation/util/parser/ProteinChangeParser.java
@@ -2,7 +2,6 @@
 
 import static java.util.regex.Pattern.CASE_INSENSITIVE;
 import static org.mskcc.oncokb.curation.domain.enumeration.MutationConsequence.*;
-import static org.mskcc.oncokb.curation.domain.enumeration.MutationConsequence.INFRAME_DELETION;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -142,8 +141,8 @@ public static ParsingStatus<Alteration> parseInframe(String proteinChange) {
             if (m.group(1) != null && m.group(3) == null) {
                 // we only want to specify reference when it's one position ins/del
                 alteration.setRefResidues(m.group(1).toUpperCase());
-                revisedProteinChange += alteration.getRefResidues();
             }
+            revisedProteinChange += alteration.getRefResidues();
             alteration.setStart(Integer.valueOf(m.group(2)));
             revisedProteinChange += alteration.getStart();
             if (m.group(3) != null) {