From 4e3fc21a66344c0d5454e6115ca6aebb4654894d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 18 Apr 2012 13:20:46 +0000
Subject: [PATCH] In initial_stable_id():
Do not try to use ${type}_stable_id tables that do not any longer exist.
Reformat.
---
.../StableIdGenerator/EnsemblGeneric.pm | 51 +++++++++++--------
1 file changed, 29 insertions(+), 22 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
index cf6726e661..656645527d 100644
--- a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
@@ -117,54 +117,61 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
=cut
sub initial_stable_id {
- my $self = shift;
- my $type = shift;
+ my ( $self, $type ) = @_;
my $init_stable_id;
- # use stable ID from configuration if set
- if ($init_stable_id = $self->conf->param("starting_${type}_stable_id")) {
- $self->logger->debug("Using pre-configured $init_stable_id as base for new $type stable IDs.\n");
+ # Use stable ID from configuration if set.
+ $init_stable_id = $self->conf->param("starting_${type}_stable_id");
+ if ( defined($init_stable_id) ) {
+ $self->logger->debug( "Using pre-configured $init_stable_id " .
+ "as base for new $type stable IDs.\n" );
return $init_stable_id;
}
my $s_dba = $self->cache->get_DBAdaptor('source');
my $s_dbh = $s_dba->dbc->db_handle;
- # look in the ${type}_stable_id table first
+ # look in the ${type} table first
my $sql = qq(
SELECT MAX(stable_id)
- FROM ${type}_stable_id
+ FROM ${type}
WHERE stable_id LIKE "ENS%"
OR stable_id LIKE "ASMPATCH%"
);
- $init_stable_id = $self->fetch_value_from_db($s_dbh, $sql);
+ $init_stable_id = $self->fetch_value_from_db( $s_dbh, $sql );
- # also look in gene_archive to make sure there are no larger Ids there
- unless ($type eq 'exon') {
+ # Also look in gene_archive to make sure there are no larger IDs
+ # there.
+ if ( $type ne 'exon' ) {
$sql = qq(SELECT MAX(${type}_stable_id) FROM gene_archive);
- my $archived_stable_id = $self->fetch_value_from_db($s_dbh, $sql);
- if ($archived_stable_id and $self->is_valid($archived_stable_id) and
- ($archived_stable_id gt $init_stable_id)) {
+ my $archived_stable_id = $self->fetch_value_from_db( $s_dbh, $sql );
+ if ( $archived_stable_id &&
+ $self->is_valid($archived_stable_id) &&
+ ( $archived_stable_id gt $init_stable_id ) )
+ {
$init_stable_id = $archived_stable_id;
}
}
- if ($init_stable_id) {
- # since $init_stable_id now is the highest existing stable Id for this
- # object type, we need to increment it to find the first one we want to use
- # for new assignments
+ if ( defined($init_stable_id) ) {
+ # Since $init_stable_id now is the highest existing stable ID for
+ # this object type, we need to increment it to find the first one we
+ # want to use for new assignments.
$init_stable_id = $self->increment_stable_id($init_stable_id);
-
- $self->logger->debug("Using $init_stable_id as base for new $type stable IDs.\n");
- } else {
- $self->logger->warning("Can't find highest ${type}_stable_id in source db.\n");
+ $self->logger->debug(
+ "Using $init_stable_id as base for new $type stable IDs.\n");
+
+ }
+ else {
+ $self->logger->warning(
+ "Can't find highest ${type}_stable_id in source db.\n" );
}
return $init_stable_id;
-}
+} ## end sub initial_stable_id
=head2 increment_stable_id
--
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