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adds name and GO: prefix for GO term to obsoletion report #30

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Merged
jweiser merged 1 commit into from
Feb 24, 2026
Merged

adds name and GO: prefix for GO term to obsoletion report #30

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20 changes: 17 additions & 3 deletions src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ public GoTermsUpdater(MySQLAdaptor dba, List<String> goLines, List<String> ec2Go
}
String dateString = LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyyMMdd_HHmmss"));
this.newMFPrinter = new CSVPrinter(Files.newBufferedWriter(Paths.get("reports/new_molecular_functions_"+dateString+".csv")), GO_REPORT_FORMAT.withHeader("DB_ID", "GO ID", "GO Term Name", "Definition") );
this.obsoleteAccessionPrinter = new CSVPrinter(Files.newBufferedWriter(Paths.get("reports/obsolete_GO_terms_"+dateString+".csv")), GO_REPORT_FORMAT.withHeader("DB_ID", "GO Type", "Obsolete Term", "Suggested action", "New/replacement GO Terms") );
this.obsoleteAccessionPrinter = new CSVPrinter(Files.newBufferedWriter(Paths.get("reports/obsolete_GO_terms_"+dateString+".csv")), GO_REPORT_FORMAT.withHeader("DB_ID", "GO Type", "Obsolete GO Accession", "Obsolete GO Term Name", "Suggested action", "New/replacement GO Terms") );
this.newGOTermsPrinter = new CSVPrinter(Files.newBufferedWriter(Paths.get("reports/new_GO_terms_"+dateString+".csv")), GO_REPORT_FORMAT.withHeader("DB_ID", "GO Term Name", "GO Term ID", "GO Term Type", "Definition") );
this.categoryMismatchPrinter = new CSVPrinter(Files.newBufferedWriter(Paths.get("reports/category_mismatch_"+dateString+".csv")), GO_REPORT_FORMAT.withHeader("DB_ID", "GO ID", "Category in Database", "Category in file") );
this.replacedGOTermsPrinter = new CSVPrinter(Files.newBufferedWriter(Paths.get("reports/replaced_GO_terms_"+dateString+".csv")), GO_REPORT_FORMAT.withHeader("DB_ID", "GO Term Name", "Primary accession", "Primary Class", "DB_ID (Secondary; to be deleted)", "Secondary accession (to be deleted)", "Secondary Class", "Referrers to be automatically redirected to Primary accession") );
Expand Down Expand Up @@ -348,7 +348,14 @@ private int deleteFlaggedInstances(Map<String, Map<String, Object>> goTermsFromF
{
action = "Automatic Deletion (no referrers)";
}
this.obsoleteAccessionPrinter.printRecord(instance.getDBID(), instance.getSchemClass().getName(), instance.getAttributeValue(ReactomeJavaConstants.accession), action, replacementGOTermAccession);
this.obsoleteAccessionPrinter.printRecord(
instance.getDBID(),
instance.getSchemClass().getName(),
"GO:" + instance.getAttributeValue(ReactomeJavaConstants.accession),
instance.getDisplayName(),
action,
replacementGOTermAccession
);
goTermModifier.deleteGoInstance(goTermsFromFile, allGoInstances, this.deletionStringBuilder);
deletedCount ++;
}
Expand Down Expand Up @@ -397,7 +404,14 @@ private void processObsoleteGOTerm(Map<String, Map<String, Object>> goTermsFromF
consider = considerList != null && !considerList.isEmpty() ? "Consider: " + String.join(", ", considerList) : "";
String replacementTermString = replaceBy + consider;
replacementTermString = replacementTermString.length() == 0 ? "N/A" : replacementTermString;
obsoleteAccessionPrinter.printRecord(inst.getDBID(), inst.getSchemClass().getName(), inst.getAttributeValue(ReactomeJavaConstants.accession), "Manual cleanup (referrers exist)", replacementTermString);
obsoleteAccessionPrinter.printRecord(
inst.getDBID(),
inst.getSchemClass().getName(),
"GO:" + inst.getAttributeValue(ReactomeJavaConstants.accession),
inst.getDisplayName(),
"Manual cleanup (referrers exist)",
replacementTermString
);
}
}
catch (Exception e)
Expand Down