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leexgh wants to merge 5 commits into from
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Add category for error messages #300

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1470d83
Add category for error messages
leexgh Jun 15, 2026
7e0d708
update comments
leexgh Jun 22, 2026
f5fa4cc
Add refseq to additional_transcript column
leexgh Jul 2, 2026
905fd91
Test and model update
leexgh Aug 4, 2026
5a7cbba
Update test - hgvsp changed because Splice_Region is removed from 'sp…
leexgh Aug 4, 2026
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54 changes: 45 additions & 9 deletions annotator/src/main/java/org/cbioportal/annotator/internal/AnnotationSummaryStatistics.java
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Original file line number Diff line number Diff line change
Expand Up @@ -51,9 +51,13 @@
* @author ochoaa
*/
public class AnnotationSummaryStatistics {
private final List<String> ERROR_FILE_HEADER = Arrays.asList("SAMPLE_ID", "CHR", "START",
public enum ErrorLevel {
ERROR, WARN, INFO
}

private final List<String> ERROR_FILE_HEADER = Arrays.asList("SAMPLE_ID", "CHR", "START",
"END", "REF", "Tumor_Seq_Allele1", "Tumor_Seq_Allele2", "VARIANT_CLASSIFICATION",
"FAILURE_REASON", "URL");
"LEVEL", "FAILURE_REASON", "URL");
private final String AMBIGUOUS_ALLELE_ERROR_MESSAGE = "Record contains ambiguous SNP and INDEL allele change - SNP allele will be used";
private final String NULL_VAR_CLASSIFICATION_ERROR_MESSGAE = "Record contains null HGVSp variant classification";
private final String UNKNOWN_ANNOTATION_ERROR_MESSAGE = "Failed to annotate variant";
Expand Down Expand Up @@ -113,6 +117,7 @@ public void addFailedAnnotatedRecordDueToServer(MutationRecord record, String se
failedAnnotatedRecords.add(record);
failedAnnotatedRecordsErrorMessages.add(constructErrorMessageFromRecord(record,
record.getVARIANT_CLASSIFICATION(),
ErrorLevel.ERROR,
serverErrorMessage,
annotator.getUrlForRecord(record, isoformOverride))
);
Expand All @@ -128,6 +133,7 @@ public Boolean isFailedAnnotatedRecord(AnnotatedRecord annotatedRecord, Mutation
this.failedAnnotatedRecordsErrorMessages.add(
constructErrorMessageFromRecord(record,
annotatedRecord.getVARIANT_CLASSIFICATION(),
ErrorLevel.WARN,
AMBIGUOUS_ALLELE_ERROR_MESSAGE,
annotator.getUrlForRecord(record, isoformOverride))
);
Expand All @@ -136,20 +142,40 @@ public Boolean isFailedAnnotatedRecord(AnnotatedRecord annotatedRecord, Mutation
}
if (annotatedRecord.getHGVSC().isEmpty() && annotatedRecord.getHGVSP().isEmpty()) {
if (annotator.isHgvspNullClassifications(annotatedRecord.getVARIANT_CLASSIFICATION())) {
// Expected: non-coding variants (UTR, IGR, Intron, etc.) have no HGVSc/HGVSp
this.nullVariantClassificationRecords++;
this.failedAnnotatedRecordsErrorMessages.add(
constructErrorMessageFromRecord(record,
annotatedRecord.getVARIANT_CLASSIFICATION(),
ErrorLevel.INFO,
NULL_VAR_CLASSIFICATION_ERROR_MESSGAE,
annotator.getUrlForRecord(record, isoformOverride))
);
failedAnnotation = Boolean.TRUE;
} else if (isVariantSpanningNonCodingRegion(annotatedRecord) && annotatedRecord.getErrorMessage() == null) {
// Multi-nucleotide deletion/insertion that spans a coding/UTR boundary:
// VEP classifies it as Frame_Shift or In_Frame (based on the coding portion)
// but cannot produce HGVSc/HGVSp because the variant extends past the stop codon
// or start codon into the UTR
this.nullVariantClassificationRecords++;
this.failedAnnotatedRecordsErrorMessages.add(
constructErrorMessageFromRecord(record,
annotatedRecord.getVARIANT_CLASSIFICATION(),
ErrorLevel.INFO,
"Variant spans coding/UTR boundary - HGVSc and HGVSp not computed by VEP for cross-boundary variants",
annotator.getUrlForRecord(record, isoformOverride))
);
failedAnnotation = Boolean.TRUE;
} else {
this.otherFailedAnnotatedRecords++;
String errorDetail = annotatedRecord.getErrorMessage() != null
? annotatedRecord.getErrorMessage()
: "no error details available - check genome nexus logs";
Comment on lines +170 to +172

@gemini-code-assist gemini-code-assist Bot Jun 22, 2026

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medium

If annotatedRecord.getErrorMessage() returns an empty string or whitespace, the resulting error message will be formatted as UNKNOWN_ANNOTATION_ERROR_MESSAGE + ";" + "", which is not very helpful. Using StringUtils.isNotBlank (from org.apache.commons.lang.StringUtils, which is already imported) ensures that we fall back to the default message if the error message is empty or blank.

Suggested change
String errorDetail = annotatedRecord.getErrorMessage() != null
? annotatedRecord.getErrorMessage()
: "no error details available - check genome nexus logs";
String errorDetail = StringUtils.isNotBlank(annotatedRecord.getErrorMessage())
? annotatedRecord.getErrorMessage()
: "no error details available - check genome nexus logs";

this.failedAnnotatedRecordsErrorMessages.add(
constructErrorMessageFromRecord(record,
record.getVARIANT_CLASSIFICATION(),
UNKNOWN_ANNOTATION_ERROR_MESSAGE + ";" + annotatedRecord.getErrorMessage(),
ErrorLevel.ERROR,
UNKNOWN_ANNOTATION_ERROR_MESSAGE + ";" + errorDetail,
annotator.getUrlForRecord(record, isoformOverride))
);
failedAnnotation = Boolean.TRUE;
Expand All @@ -162,14 +188,24 @@ public Boolean isFailedAnnotatedRecord(AnnotatedRecord annotatedRecord, Mutation
return failedAnnotation;
}

/**
* Returns true if this variant is a multi-nucleotide deletion or insertion that could
* physically span a coding/UTR boundary (Frame_Shift or In_Frame only).
*/
private boolean isVariantSpanningNonCodingRegion(AnnotatedRecord annotatedRecord) {
String varClass = annotatedRecord.getVARIANT_CLASSIFICATION();
if (varClass == null) return false;
return varClass.contains("Frame_Shift") || varClass.contains("In_Frame");
}
Comment on lines +191 to +195

@gemini-code-assist gemini-code-assist Bot Jun 22, 2026

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medium

The null check if (varClass == null) is redundant because getVARIANT_CLASSIFICATION() is guaranteed to return an empty string "" instead of null (as implemented in MutationRecord.java). We can simplify this method by removing the redundant null check.

    private boolean isVariantSpanningNonCodingRegion(AnnotatedRecord annotatedRecord) {
        String varClass = annotatedRecord.getVARIANT_CLASSIFICATION();
        return varClass.contains("Frame_Shift") || varClass.contains("In_Frame");
    }


public void printSummaryStatistics() {
StringBuilder builder = new StringBuilder();
builder.append("\nAnnotation Summary:")
.append("\n\tRecords with ambiguous SNP and INDEL allele changes: ").append(ambiguousTumorSeqAlleleRecords);
.append("\n\t[WARN] Records with ambiguous SNP and INDEL allele changes: ").append(ambiguousTumorSeqAlleleRecords);
if (totalFailedAnnotatedRecords > 0) {
builder.append("\n\n\tFailed annotations summary: ").append(totalFailedAnnotatedRecords).append(" total failed annotations")
.append("\n\t\tRecords with HGVSp null variant classification: ").append(nullVariantClassificationRecords)
.append("\n\t\tRecords that failed due to other unknown reason: ").append(otherFailedAnnotatedRecords);
builder.append("\n\n\tFailed annotations summary: ").append(totalFailedAnnotatedRecords).append(" total records in error report")
.append("\n\t\t[INFO] Records with expected empty HGVSc/HGVSp (non-coding variants or cross-boundary deletions/insertions): ").append(nullVariantClassificationRecords)
.append("\n\t\t[ERROR] Records that failed annotation: ").append(otherFailedAnnotatedRecords);
} else {
builder.append("\n\tAll variants annotated successfully without failures!");
}
Expand All @@ -179,11 +215,11 @@ public void printSummaryStatistics() {
System.out.print(builder.toString());
}

private String constructErrorMessageFromRecord(MutationRecord record, String variantClassification, String errorMessage, String url) {
private String constructErrorMessageFromRecord(MutationRecord record, String variantClassification, ErrorLevel level, String errorMessage, String url) {
List<String> msg = Arrays.asList(record.getTUMOR_SAMPLE_BARCODE(), record.getCHROMOSOME(),
record.getSTART_POSITION(), record.getEND_POSITION(), record.getREFERENCE_ALLELE(),
record.getTUMOR_SEQ_ALLELE1(), record.getTUMOR_SEQ_ALLELE2(), variantClassification,
errorMessage, url);
level.name(), errorMessage, url);
return StringUtils.join(msg, "\t");
}

Expand Down