From 08678ecf747dc2a8f95039b2f5bafd8e7049a462 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 9 Sep 2010 09:58:00 +0000
Subject: [PATCH] go_xref now ontology_xref in core database
---
misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm b/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
index 66373f48b0..d101e09239 100644
--- a/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
@@ -106,7 +106,7 @@ sub update{
$sth->bind_columns(\$name,\$count);
my $synonym_sth = $self->core->dbc->prepare('DELETE external_synonym FROM external_synonym, xref WHERE external_synonym.xref_id = xref.xref_id AND xref.external_db_id = ?');
- my $go_sth = $self->core->dbc->prepare('DELETE FROM go_xref');
+ my $go_sth = $self->core->dbc->prepare('DELETE FROM ontology_xref');
my $identity_sth = $self->core->dbc->prepare('DELETE identity_xref FROM identity_xref, object_xref, xref WHERE identity_xref.object_xref_id = object_xref.object_xref_id AND object_xref.xref_id = xref.xref_id AND xref.external_db_id = ?');
my $object_sth = $self->core->dbc->prepare('DELETE object_xref FROM object_xref, xref WHERE object_xref.xref_id = xref.xref_id AND xref.external_db_id = ?');
my $dependent_sth = $self->core->dbc->prepare('DELETE d FROM dependent_xref d, xref x WHERE d.dependent_xref_id = x.xref_id and x.external_db_id = ?');
@@ -224,7 +224,7 @@ GSQL
my $add_xref_sth = $self->core->dbc->prepare('insert into xref (xref_id, external_db_id, dbprimary_acc, display_label, version, description, info_type, info_text) values (?, ?, ?, ?, ?, ?, ?, ?)');
my $add_object_xref_sth = $self->core->dbc->prepare('insert into object_xref (object_xref_id, ensembl_id, ensembl_object_type, xref_id, analysis_id) values (?, ?, ?, ?, ?)');
my $add_identity_xref_sth = $self->core->dbc->prepare('insert into identity_xref (object_xref_id, xref_identity, ensembl_identity, xref_start, xref_end, ensembl_start, ensembl_end, cigar_line, score, evalue) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)');
- my $add_go_xref_sth = $self->core->dbc->prepare('insert into go_xref (object_xref_id, linkage_type) values (?, ?)');
+ my $add_go_xref_sth = $self->core->dbc->prepare('insert into ontology_xref (object_xref_id, linkage_type) values (?, ?)');
my $add_dependent_xref_sth = $self->core->dbc->prepare('insert ignore into dependent_xref (object_xref_id, master_xref_id, dependent_xref_id) values (?, ?, ?)');
my $add_syn_sth = $self->core->dbc->prepare('insert ignore into external_synonym (xref_id, synonym) values (?, ?)');
my $add_release_info_sth = $self->core->dbc->prepare('update external_db set db_release = ? where external_db_id = ?');
--
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