From 5fd827b1d767d4265168356eaf66b1299fd0a738 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 19 Oct 2011 10:49:04 +0000
Subject: [PATCH] Make this deal with release 65 schemas.
---
modules/Bio/EnsEMBL/IdMapping/Cache.pm | 41 +++++++++++++++++++++-----
1 file changed, 33 insertions(+), 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/Cache.pm b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
index 0c33503817..bdcb08f759 100644
--- a/modules/Bio/EnsEMBL/IdMapping/Cache.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
@@ -791,7 +791,8 @@ sub check_empty_tables {
}
eval {
- my @tables = qw(
+ my @tables =
+ qw(
gene_stable_id
transcript_stable_id
translation_stable_id
@@ -804,18 +805,42 @@ sub check_empty_tables {
my $dba = $self->get_DBAdaptor($dbtype);
foreach my $table (@tables) {
- if ($c = $self->fetch_value_from_db($dba, "SELECT COUNT(*) FROM $table")) {
- $self->logger->warning("$table table in $dbtype db has $c entries.\n");
- $err++;
+ if ( $table =~ /^([^_]+)_stable_id/ ) {
+ $table = $1;
+ if ( $c =
+ $self->fetch_value_from_db(
+ $dba,
+ "SELECT COUNT(*) FROM $table WHERE stable_id IS NOT NULL"
+ ) )
+ {
+ $self->logger->warning(
+ "$table table in $dbtype db has $c stable IDs.\n");
+ $err++;
+ }
}
- }
+ else {
+ if ( $c =
+ $self->fetch_value_from_db(
+ $dba, "SELECT COUNT(*) FROM $table"
+ ) )
+ {
+ $self->logger->warning(
+ "$table table in $dbtype db has $c entries.\n");
+ $err++;
+ }
+ }
+ } ## end foreach my $table (@tables)
};
if ($@) {
- $self->logger->warning("Error retrieving stable ID and archive table row counts from $dbtype db: $@\n");
+ $self->logger->warning(
+"Error retrieving stable ID and archive table row counts from $dbtype db: $@\n"
+ );
$err++;
- } elsif (!$err) {
- $self->logger->debug("All stable ID and archive tables in $dbtype db are empty.\n");
+ }
+ elsif ( !$err ) {
+ $self->logger->debug(
+ "All stable ID and archive tables in $dbtype db are empty.\n");
}
return $err;
}
--
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