From d63b60e940632161962cad5127fff76be0a1f1e8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 14 Sep 2011 10:51:09 +0000
Subject: [PATCH] In fetch_all_by_Slice_and_external_dbname_link(): Allow for
non-unique db_name in external_db. Clean up a few bugs while I'm at it.
Bugs corrected:
A list (rather than a list reference) was returned if the
external_db_id for the given db_name could not be found.
The list returned from list_gene_ids_by_external_db_id() (in
DBEntryAdaptor) was used as a hash.
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 79 ++++++++++++++----------
1 file changed, 48 insertions(+), 31 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index e4fd2b20a9..c6887e3db7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -446,52 +446,69 @@ sub fetch_all_by_domain {
=cut
sub fetch_all_by_Slice_and_external_dbname_link {
- my $self = shift;
- my $slice = shift;
- my $logic_name = shift;
- my $load_transcripts = shift;
- my $db_name = shift;
- my @genes_passed;
- my $external_db_id;
- #get the external_db_id from the name
+ my ( $self, $slice, $logic_name, $load_transcripts, $db_name ) = @_;
+
+ # Get the external_db_id(s) from the name.
my $sth = $self->prepare(
- "SELECT external_db_id from external_db where db_name = ?");
+ "SELECT external_db_id FROM external_db WHERE db_name = ?");
- $sth->bind_param(1,$db_name,SQL_VARCHAR);
+ $sth->bind_param( 1, $db_name, SQL_VARCHAR );
$sth->execute();
- $sth->bind_columns(\$external_db_id);
- $sth->fetch;
- if(!defined($external_db_id) || $external_db_id == 0){
- warn "Could not find external database $db_name in the external_db table\navailable are:-\n";
- $sth = $self->prepare(
- "SELECT db_name from external_db");
+
+ my $external_db_id;
+ $sth->bind_columns( \$external_db_id );
+
+ my @external_db_ids;
+ while ( $sth->fetch() ) {
+ push( @external_db_ids, $external_db_id );
+ }
+
+ if ( scalar(@external_db_id) == 0 ) {
+ warn sprintf( "Could not find external database "
+ . "'%s' in the external_db table\n"
+ . "Available are:\n",
+ $db_name );
+
+ $sth = $self->prepare("SELECT DISTINCT db_name FROM external_db");
+
$sth->execute();
- $sth->bind_columns(\$external_db_id);
- while($sth->fetch){
+ $sth->bind_columns( \$external_db_id );
+
+ while ( $sth->fetch() ) {
warn "\t$external_db_id\n";
}
- return @genes_passed;
+ return [];
}
-
- # get the gene_ids for those with links
+
+ # Get the gene_ids for those with links.
my $dbe_adaptor = $self->db()->get_DBEntryAdaptor();
- my %linked_genes= $dbe_adaptor->list_gene_ids_by_external_db_id($external_db_id);
- # get all the genes on the slice
+ my %linked_genes;
+ foreach $external_db_id (@external_db_ids) {
+ my @linked_genes =
+ q
+ $dbe_adaptor->list_gene_ids_by_external_db_id($external_db_id);
- my $genes = $self->SUPER::fetch_all_by_Slice_constraint($slice,
- 'g.is_current = 1', $logic_name);
+ foreach my $gene_id (@linked_genes) {
+ $linked_genes{$gene_id} = 1;
+ }
+ }
+
+ # Get all the genes on the slice.
+ my $genes = $self->SUPER::fetch_all_by_Slice_constraint( $slice,
+ 'g.is_current = 1', $logic_name );
- # create a list of those that are in the gene_ids list
- foreach my $gene (@$genes){
- if($linked_genes{$gene->dbID}){
- push @genes_passed, $gene;
+ # Create a list of those that are in the gene_ids list.
+ my @genes_passed;
+ foreach my $gene (@$genes) {
+ if ( exists( $linked_genes{ $gene->dbID() } ) ) {
+ push( @genes_passed, $gene );
}
}
- #return the list of those that passed
+ # Return the list of those that passed.
return \@genes_passed;
-}
+} ## end sub fetch_all_by_Slice_and_external_dbname_link
=head2 fetch_all_by_Slice
--
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