From 1692acb01d714c0b20bf6b2d8623f5079cbc31a8 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 15 Oct 2012 14:25:30 +0000
Subject: [PATCH] load vega and core databases independently both can be loaded
via the registry or via the parameters set up in the xref_config.ini file
---
.../XrefParser/curated_transcriptParser.pm | 27 +++++++++++--------
1 file changed, 16 insertions(+), 11 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
index 04a32d46f9..53b37e4fb1 100644
--- a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
@@ -91,7 +91,7 @@ sub run_script {
my $vega_dbc;
my $core_dbc;
if(defined($vdbname)){
- print "Using $host $vdbname for Vega and $cdbname for Core\n";
+ print "Using $vhost $vdbname for Vega\n";
my $vega_db = XrefParser::Database->new({ host => $vhost,
port => $vport,
@@ -104,7 +104,21 @@ sub run_script {
print "Problem could not open connection to $vhost, $vport, $vuser, $vdbname, $vpass\n";
return 1;
}
+ } else {
+ $reg->load_registry_from_db(
+ -host => $host,
+ -user => $user,
+ -species => $species_name);
+
+ $vega_dbc = $reg->get_adaptor($species_name,"vega","slice");
+ if(!defined($vega_dbc)){
+ print "Could not connect to $species_name vega database using load_registry_from_db $host $user\n";
+ return 1;
+ }
+ $vega_dbc = $vega_dbc->dbc;
+ }
+ if (defined($cdbname)){
my $core_db = XrefParser::Database->new({ host => $chost,
port => $cport,
user => $cuser,
@@ -115,21 +129,12 @@ sub run_script {
print "Problem could not open connectipn to $chost, $cport, $cuser, $cdbname, $cpass\n";
return 1;
}
-
- }
- else{
-
+ } else{
$reg->load_registry_from_db(
-host => $host,
-user => $user,
-species => $species_name);
- $vega_dbc = $reg->get_adaptor($species_name,"vega","slice");
- if(!defined($vega_dbc)){
- print "Could not connect to $species_name vega database using load_registry_from_db $host $user\n";
- return 1;
- }
- $vega_dbc = $vega_dbc->dbc;
$core_dbc = $reg->get_adaptor($species_name,"core","slice");
if(!defined($core_dbc)){
print "Could not connect to $species_name core database using load_registry_from_db $host $user\n";
--
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