From ea2687565c591898aa3a7ad93bd4051ea9b6fd99 Mon Sep 17 00:00:00 2001
From: Will Spooner <whs@sanger.ac.uk>
Date: Thu, 14 Jun 2007 14:51:59 +0000
Subject: [PATCH] Added parameter checking to add_to_xrefs method
---
.../xref_mapping/XrefParser/BaseParser.pm | 23 ++++++++++++++++---
1 file changed, 20 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index fb71fd74dc..8350bbfc14 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -1426,6 +1426,7 @@ sub get_direct_xref{
return undef;
}
+
sub get_xref{
my ($self,$acc,$source) = @_;
@@ -1461,12 +1462,28 @@ sub add_xref {
sub add_to_xrefs{
my ($self,$master_xref,$acc,$version,$label,$description,$linkage,$source_id,$species_id) = @_;
+ $master_xref || die( "Need a master_xref_id on which this xref depends" );
+ $acc || die( "Need an accession of this dependent xref" );
+ $version ||= 0;
+ $label ||= $acc;
+ $description ||= undef;
+ $linkage ||= undef;
+ $source_id || die( "Need a source_id for this dependent xref" );
+ $species_id || die( "Need a species_id for this dependent xref" );
+
if(!defined($add_xref_sth)){
- $add_xref_sth = dbi->prepare("INSERT INTO xref (accession,version,label,description,source_id,species_id)".
- " VALUES(?,?,?,?,?,?)");
+ $add_xref_sth = dbi->prepare("
+INSERT INTO xref
+ (accession,version,label,description,source_id,species_id)
+VALUES
+ (?,?,?,?,?,?)");
}
if(!defined($add_dependent_xref_sth)){
- $add_dependent_xref_sth = dbi->prepare("INSERT INTO dependent_xref VALUES(?,?,?,?)");
+ $add_dependent_xref_sth = dbi->prepare("
+INSERT INTO dependent_xref
+ (master_xref_id,dependent_xref_id,linkage_annotation,linkage_source_id)
+VALUES
+ (?,?,?,?)");
}
my $dependent_id = $self->get_xref($acc, $source_id);
--
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