From 3d760cff156c94628b7734f16c4442dce9e116fa Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 17 Aug 2012 15:56:36 +0000
Subject: [PATCH] if there is no previous database, no mapping needed
---
misc-scripts/update_mapping_set.pl | 23 ++++++++++++++++++-----
1 file changed, 18 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/update_mapping_set.pl b/misc-scripts/update_mapping_set.pl
index 1b4a747577..4b9e41dd84 100644
--- a/misc-scripts/update_mapping_set.pl
+++ b/misc-scripts/update_mapping_set.pl
@@ -151,17 +151,30 @@ 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 $mapping_set_id = 1;
+ my $sth_seq_mapping = $dbh->prepare("INSERT INTO $db_name->[0].seq_region_mapping VALUES(?,?,?)");
+ my $sth_mapping_set = $dbh->prepare("INSERT INTO $db_name->[0].mapping_set VALUES(?,?)");
+ $schema_build = get_schema_and_build($db_name->[0]);
+
my $current_assembly = get_assembly($dbh, $db_name->[0]) ;
my $previous_dbname = &get_previous_dbname($old_dbh,$db_name->[0],$release);
+
+# If there is no previous database, no mapping needed
+ if (!defined($previous_dbname)) {
+ $sth_mapping_set->execute($mapping_set_id, $schema_build) unless $dry_run;
+ next;
+ }
my $old_assembly = get_assembly($old_dbh, $previous_dbname);
- if ($old_assembly ne $current_assembly) { next; }
- my $mapping_set_id;
+
+# If it is a new assembly, no mapping needed
+ if ($old_assembly ne $current_assembly) {
+ $sth_mapping_set->execute($mapping_set_id, $schema_build) unless $dry_run;
+ next;
+ }
+
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
- my $sth_seq_mapping = $dbh->prepare("INSERT INTO $db_name->[0].seq_region_mapping VALUES(?,?,?)");
- my $sth_mapping_set = $dbh->prepare("INSERT INTO $db_name->[0].mapping_set VALUES(?,?)");
$status = &mapping_status($dbh,$old_dbh, $db_name->[0],\$mapping_set_id,$release);
- $schema_build = get_schema_and_build($db_name->[0]);
## prune newly added mapping_set entries
# $dbh->do(qq(delete from $db_name->[0].mapping_set where schema_build = '$schema_build'));
--
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