From e3b360a03c769d1781e7011365b8ca10b216df6b Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Fri, 29 Jul 2011 16:46:38 +0000
Subject: [PATCH] Added previous release to xref_config.ini
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 45 +++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 8ac2e6cda2..f28a80923d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -102,6 +102,25 @@ sub core{
return $self->{_core};
}
+=head2 previous_core
+
+ Arg [1] : (optional)
+ Example : $mapper->previous_core($old_core);
+ Description: Getter / Setter for the previous release of the core db.
+ Returntype : XrefMapper::db
+ Exceptions : none
+
+=cut
+
+sub previous_core{
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_previous_core} = $arg );
+ return $self->{_previous_core};
+}
+
+
sub add_meta_pair {
@@ -344,6 +363,32 @@ sub process_file {
}
}
$core->species($value);
+
+ #connect to previous release of core db if connection details specified in xref_input (pr_host, pr_port, pr_dbname, pr_user)
+ if (defined( $species_hash{'pr_host'}) && defined( $species_hash{'pr_user'}) && defined( $species_hash{'pr_dbname'}) ) {
+ my ($pr_host, $pr_port, $pr_user, $pr_dbname);
+ $pr_host = $species_hash{'pr_host'};
+ $pr_user = $species_hash{'pr_user'};
+ $pr_dbname = $species_hash{'pr_dbname'};
+ if(defined($species_hash{'pr_port'})){
+ $pr_port = $species_hash{'port'};
+ }
+ else{
+ $pr_port = '';
+ }
+
+ my $previous_core = new XrefMapper::db(-host => $pr_host,
+ -port => $pr_port,
+ -user => $pr_user,
+ -pass => '',
+ -group => 'core',
+ -dbname => $pr_dbname);
+
+ $mapper->previous_core($previous_core);
+
+ $mapper->add_meta_pair("species", $pr_host.":".$pr_dbname);
+
+ }
}
return $mapper;
--
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