From a24286702e1ee07800bf3b3438b2f67df4f01933 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 29 Sep 2009 12:54:19 +0000
Subject: [PATCH] if noxref_database is specified do not try to write to the
xref database. Needed for -recalc_display_xrefs option
---
.../xref_mapping/XrefMapper/DisplayXrefs.pm | 34 +++++++++++++------
1 file changed, 24 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
index 2c131d1f58..537ab4c782 100644
--- a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
@@ -120,18 +120,26 @@ sub genes_and_transcripts_attributes_set{
# build_meta_timestamp, and, if "-upload" is set, uses the SQL files
# produced to update the core database.
- my ($self,$fullmode) = @_;
+ my ($self, $fullmode, $noxref_database) = @_;
- my $status = $self->mapper->xref_latest_status();
-
+ my $status;
+ if(defined($noxref_database)){
+ $status = "none";
+ }
+ else{
+ $status = $self->mapper->xref_latest_status();
+ }
+
if(!$fullmode){
if($status ne "display_xref_done"){
$self->build_transcript_and_gene_display_xrefs();
- my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('display_xref_done',now())");
- $sth_stat->execute();
- $sth_stat->finish;
+ if(!defined($noxref_database)){
+ my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('display_xref_done',now())");
+ $sth_stat->execute();
+ $sth_stat->finish;
+ }
}
@@ -149,10 +157,12 @@ sub genes_and_transcripts_attributes_set{
$self->build_meta_timestamp;
- my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('gene_description_done',now())");
- $sth_stat->execute();
- $sth_stat->finish;
-
+ if(!defined($noxref_database)){
+ my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('gene_description_done',now())");
+ $sth_stat->execute();
+ $sth_stat->finish;
+ }
+
return 1;
}
@@ -722,6 +732,7 @@ GSQL
if ($filtered_description ne "") {
$xref_descriptions{$xref_id} = $description;
$xref_accessions{$xref_id} = $acc;
+ $ex_db{$xref_id} = $ex_db_id;
if($level{$ex_db_id} > $best_gene_level){
$best_gene_xref = $xref_id;
$best_gene_level = $level{$ex_db_id};
@@ -885,6 +896,9 @@ GSQL
$description =~ s/\"//ig; # remove " as they will cause problems in .sql files
+ if(!defined($ex_db_id_to_display_name{$ex_db{$best_gene_xref}})){
+ print STDERR "Could not find display name for gene $best_gene_xref for external db ".$ex_db{$best_gene_xref}."\n";
+ }
my $desc = $description . " [Source:".$ex_db_id_to_display_name{$ex_db{$best_gene_xref}}.";Acc:$acc]";
$update_gene_desc_sth->execute($desc, $gene_id) if($description);
--
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