From 90603cccc82e415ed7e60a31c11a7840344a44f9 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 15 Aug 2012 13:11:36 +0000
Subject: [PATCH] if assembly has changed between two releases, skip database
completely (no mapping required) password is not always required
---
misc-scripts/update_mapping_set.pl | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/update_mapping_set.pl b/misc-scripts/update_mapping_set.pl
index ca119de854..1b4a747577 100644
--- a/misc-scripts/update_mapping_set.pl
+++ b/misc-scripts/update_mapping_set.pl
@@ -125,7 +125,6 @@ GetOptions('host=s' => \$host,
pod2usage(1) if($help);
throw("--user argument required") if (!defined($user));
-throw("--pass argument required") if (!defined($pass));
throw("--release argument required") if(!defined($release));
my $database = 'information_schema';
@@ -152,6 +151,10 @@ foreach my $h ($host,$host2) {
my $schema_build;
foreach my $db_name (@{$dbs}){
print STDERR "Going to update mapping for $db_name->[0]....\n";
+ my $current_assembly = get_assembly($dbh, $db_name->[0]) ;
+ my $previous_dbname = &get_previous_dbname($old_dbh,$db_name->[0],$release);
+ my $old_assembly = get_assembly($old_dbh, $previous_dbname);
+ if ($old_assembly ne $current_assembly) { next; }
my $mapping_set_id;
my $current_seq_region = (); # hash containing the relation seq_region_name->seq_region_id for the current database
my $old_seq_region = (); #hash containing the previous database relation seq_region_name->seq_region_id
@@ -177,7 +180,6 @@ foreach my $h ($host,$host2) {
elsif ($status == NEW_MAPPING){
$sth_mapping_set->execute($mapping_set_id,$schema_build) unless $dry_run;
#there has been a seq_region change between releases, add a new mapping_set and the relation old_seq_region_id->new_seq_region_id
- my $previous_dbname = &get_previous_dbname($old_dbh,$db_name->[0],$release);
$current_seq_region = &read_seq_region($dbh,$db_name->[0]);
$old_seq_region = &read_seq_region($old_dbh,$previous_dbname);
#update the seq_region_mapping table with the old->new seq_region_id relation
@@ -317,3 +319,11 @@ sub get_schema_and_build{
my @dbname = split/_/, $dbname;
return join "_",$dbname[($#dbname -1)], $dbname[($#dbname)];
}
+
+
+sub get_assembly{
+ my ($dbh, $dbname) = @_;
+ my $sth = $dbh->prepare("select meta_value from $dbname.meta where meta_key = 'assembly.default'");
+ $sth->execute();
+ return $sth->fetchrow();
+}
--
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