From 2e9b9ca7d9f959c7a321d0014e1485cd6061191b Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Wed, 8 Dec 2004 12:50:39 +0000
Subject: [PATCH] deletes and reloads the meta_coord table with all featrue
tables it can find
---
sql/populate_meta_coord.pl | 68 ++++++++++++++++++++++++++++++++++++++
1 file changed, 68 insertions(+)
create mode 100644 sql/populate_meta_coord.pl
diff --git a/sql/populate_meta_coord.pl b/sql/populate_meta_coord.pl
new file mode 100644
index 0000000000..09b2314d0f
--- /dev/null
+++ b/sql/populate_meta_coord.pl
@@ -0,0 +1,68 @@
+# this script will repopulate the meta coord table
+# it makes an attempt to pick up all the right tables
+# (all those which have seq_region_id, seq_region_start and seq_region_end)
+
+# normally the API will populate the table ...
+
+
+use strict;
+use DBI;
+
+use Getopt::Long;
+
+my ($host, $user, $pass, $port, $dbname); #ensembl core db
+GetOptions('host=s' => \$host,
+ 'user=s' => \$user,
+ 'pass=s' => \$pass,
+ 'port=i' => \$port,
+ 'dbname=s' => \$dbname,
+ );
+
+
+my $dsn = "DBI:mysql:host=$host;dbname=$dbname";
+if( $port ) {
+ $dsn .= ";port=$port";
+}
+
+my $db = DBI->connect( $dsn, $user, $pass );
+
+$db->do( "delete from meta_coord" );
+
+my $res = $db->selectall_arrayref( "show tables" );
+
+my @tables = map { $_->[0] } @$res;
+
+my %need_cols = ( "seq_region_id" => 1,
+ "seq_region_start" => 1,
+ "seq_region_end" => 1 );
+
+for my $tablename ( @tables ) {
+ # skip empty tables
+ $res = $db->selectall_arrayref( "select count(*) from $tablename" );
+ next if( $res->[0]->[0] == 0 );
+
+ $res = $db->selectall_arrayref( "desc $tablename" );
+ my @columns = map { $_->[0] } @$res;
+ if( 3 == scalar( grep { exists $need_cols{$_}} @columns )) {
+ meta_coord_query( $db, $tablename );
+ }
+}
+
+
+
+
+sub meta_coord_query {
+ my $db = shift;
+ my $tablename = shift;
+
+ $db->do( qq{
+ INSERT INTO meta_coord
+ SELECT '$tablename', sr.coord_system_id,
+ MAX( f.seq_region_end - f.seq_region_start + 1)
+ FROM $tablename f, seq_region sr
+ WHERE sr.seq_region_id = f.seq_region_id
+ GROUP BY sr.coord_system_id
+ } );
+}
+
+
--
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