From 3b0312b11835986bb9d911f91956742b214fd4c8 Mon Sep 17 00:00:00 2001 From: jweiser Date: Mon, 23 Feb 2026 13:04:02 -0500 Subject: [PATCH] adds name and GO: prefix for GO term to obsoletion report --- .../release/goupdate/GoTermsUpdater.java | 20 ++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java b/src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java index 7c7fbbe..c1a60e4 100644 --- a/src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java +++ b/src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java @@ -92,7 +92,7 @@ public GoTermsUpdater(MySQLAdaptor dba, List goLines, List 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") ); @@ -348,7 +348,14 @@ private int deleteFlaggedInstances(Map> 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 ++; } @@ -397,7 +404,14 @@ private void processObsoleteGOTerm(Map> 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)