From b3bc2302e1c0e613262af9f486d26941427d705c Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 15 Oct 2012 14:08:02 +0000
Subject: [PATCH] default user is ensro and default port is 3306 if data_uri is
defined, all connection details can be read for vega and core databases
source_prefix is read from data_uri as well, so no need to hard-code it in
the module if there is a source_prefix, it is a merged species, else, skip
the module alltogether
---
.../XrefParser/curated_transcriptParser.pm | 36 ++++++-------------
1 file changed, 11 insertions(+), 25 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
index 226ab773ec..04a32d46f9 100644
--- a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
@@ -27,47 +27,33 @@ sub run_script {
my ($type, $my_args) = split(/:/,$file);
- my $host;
+ my ($host, $source_prefix);
my $user = "ensro";
if($my_args =~ /user[=][>](\S+?)[,]/){
$user = $1;
}
- my %id2name = $self->species_id2name;
- my $species_name = $id2name{$species_id}[0];
- my $source_prefix;
- if($species_name eq "homo_sapiens" ){
- $source_prefix = "HGNC";
- $host = "ens-staging1";
- }
- elsif($species_name eq "mus_musculus" ){
- $source_prefix = "MGI";
- $host = "ens-staging2";
- }
- elsif($species_name eq "danio_rerio" ){
- $source_prefix = "ZFIN_ID";
- $host = "ens-staging1";
+ if($my_args =~ /host[=][>](\S+?)[,]/){
+ $host = $1;
}
- if($species_name eq "sus_scrofa" ){
- $source_prefix = "PIGGY";
- $host = "ens-staging2";
+ if ($my_args =~ /source[=][>](\S+?)[,]/){
+ $source_prefix = $1;
}
- else{
+ my %id2name = $self->species_id2name;
+ my $species_name = $id2name{$species_id}[0];
+ if (!$source_prefix){
die "Species is $species_name and is not homo_sapiens, mus_musculus, danio_rerio or sus_scrofa, the only four valid species\n";
}
- if($my_args =~ /host[=][>](\S+?)[,]/){
- $host = $1;
- }
- my $vuser ="ensro";
+ my $vuser = "ensro";
my $vhost;
- my $vport;
+ my $vport = 3306;
my $vdbname;
my $vpass;
my $cuser ="ensro";
my $chost;
- my $cport;
+ my $cport = 3306;
my $cdbname;
my $cpass;
--
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