From bde83ea1b18a40d8cf8e00b6ace55829255b0b13 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 19 Jan 2018 16:50:27 +0000
Subject: [PATCH] clean up GOs
---
misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm b/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
index 377a0e2e28..fbd8a8fb6d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
@@ -70,10 +70,12 @@ sub update{
my $affected_rows = $sth->execute();
print "\tDeleted $affected_rows PROJECTED external_synonym row(s)\n" if $verbose;
+ # Delete all ontologies, as they are done by a separate pipeline
$sql = <<SQL;
-DELETE ontology_xref
+DELETE ontology_xref, object_xref, xref, dependent_xref
FROM ontology_xref, object_xref, xref
-WHERE ontology_xref.object_xref_id = object_xref.object_xref_id AND object_xref.xref_id = xref.xref_id AND xref.info_type = 'PROJECTION'
+LEFT JOIN dependent_xref on xref_id = dependent_xref_id
+WHERE ontology_xref.object_xref_id = object_xref.object_xref_id AND object_xref.xref_id = xref.xref_id
SQL
$sth = $core_dbi->prepare($sql);
$affected_rows = $sth->execute();
--
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