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lib: improve log messages for ClinVar indexer, #TASK-6347
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On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java
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jtarraga committed Jun 25, 2024
1 parent f11f507 commit f820260
Showing 1 changed file with 4 additions and 4 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -270,28 +270,28 @@ private boolean updateRocksDB(AlleleLocationData alleleLocationData, PublicSetTy
try {
accession = publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc();
} catch (Exception e) {
logger.warn("Error getting accession\n" + StringUtils.join(e.getStackTrace(), "\n"));
logger.warn("Error getting accession. Ignore error and leave it as null.", e);
}
String clinicalSignficanceDescription = null;
try {
clinicalSignficanceDescription = publicSet.getReferenceClinVarAssertion()
.getClinicalSignificance()
.getDescription();
} catch (Exception e) {
logger.warn("Error getting clinical Significance description\n" + StringUtils.join(e.getStackTrace(), "\n"));
logger.warn("Error getting clinical significance description. Ignore error and leave it as null.", e);
}
String reviewStatusName = null;
try {
reviewStatusName = publicSet.getReferenceClinVarAssertion().getClinicalSignificance()
.getReviewStatus().name();
} catch (Exception e) {
logger.warn("Error getting review status name\n" + StringUtils.join(e.getStackTrace(), "\n"));
logger.warn("Error getting review status name. Ignore error and leave it as null.", e);
}
List<ObservationSet> getObservedIn = null;
try {
getObservedIn = publicSet.getReferenceClinVarAssertion().getObservedIn();
} catch (Exception e) {
logger.warn("Error getting observed in\n" + StringUtils.join(e.getStackTrace(), "\n"));
logger.warn("Error getting observed in. Ignore error and leave it as null.", e);
}

addNewEntries(variantAnnotation, publicSet, alleleLocationData.getAlleleId(), mateVariantString,
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