From 1b7b4c2c369505f334a88a2719d1e16773bfe336 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 13 Sep 2010 13:30:45 +0000
Subject: [PATCH] Added from private repository.
---
.../scripts/update_database_list.pl | 172 ++++++++++++++++++
1 file changed, 172 insertions(+)
create mode 100755 misc-scripts/production_database/scripts/update_database_list.pl
diff --git a/misc-scripts/production_database/scripts/update_database_list.pl b/misc-scripts/production_database/scripts/update_database_list.pl
new file mode 100755
index 0000000000..50f0800c7a
--- /dev/null
+++ b/misc-scripts/production_database/scripts/update_database_list.pl
@@ -0,0 +1,172 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use DBI qw(:sql_types);
+
+my @staging_servers = ( { 'dbhost' => 'ens-staging1',
+ 'dbport' => '3306' }, {
+ 'dbhost' => 'ens-staging2',
+ 'dbport' => '3306' } );
+
+my $master_server = $staging_servers[0];
+my $production_db_name = 'ensembl_production_60';
+
+my $dbuser = 'ensadmin';
+my $dbpass = 'ensembl';
+my $dbrouser = 'ensro';
+my $dbropass = undef;
+
+my %databases;
+foreach my $server (@staging_servers) {
+ my $dsn = sprintf( 'DBI:mysql:host=%s;port=%s',
+ $server->{'dbhost'}, $server->{'dbport'} );
+ my $dbh = DBI->connect( $dsn, $dbrouser, $dbropass,
+ { 'PrintError' => 1, 'RaiseError' => 0 } );
+
+ foreach my $dbtype ( 'cdna', 'core',
+ 'coreexpressionatlas', 'coreexpressionest',
+ 'coreexpressiongnf', 'funcgen',
+ 'otherfeatures', 'variation',
+ 'vega' )
+ {
+ my $sth = $dbh->prepare(
+ sprintf( "SHOW DATABASES LIKE '%%\\_%s\\_%%'", $dbtype ) );
+
+ $sth->execute();
+
+ my $dbname;
+ $sth->bind_col( 1, \$dbname );
+
+ while ( $sth->fetch() ) {
+ if ( $dbname !~
+ /^([a-z]+_[a-z]+)_([a-z]+)_([0-9]+)_([0-9]+)([a-z]?)$/
+ || exists( $databases{$1}{$2} ) )
+ {
+ next;
+ }
+
+ if ( $2 ne $dbtype ) {
+ carp( sprintf( "Strange database type '%s', expected '%s'",
+ $2, $dbtype ) );
+ next;
+ }
+
+ my $cn_sth = $dbh->prepare(
+ sprintf(
+ "SELECT meta_value "
+ . "FROM %s.meta "
+ . "WHERE meta_key = 'species.common_name'",
+ $dbh->quote_identifier($dbname) ) );
+
+ $cn_sth->execute();
+
+ my $common_name;
+ if ( !$cn_sth->err() ) {
+ $cn_sth->bind_col( 1, \$common_name );
+ while ( $cn_sth->fetch() ) { }
+ }
+
+ $databases{$1}{$2} = { 'db_release' => $3,
+ 'db_assembly' => $4,
+ 'db_suffix' => $5,
+ 'db_host' => $server->{'dbhost'},
+ 'common_name' => $common_name };
+
+ } ## end while ( $sth->fetch() )
+ } ## end foreach my $dbtype ( 'cdna'...)
+
+ $dbh->disconnect();
+
+} ## end foreach my $server (@staging_servers)
+
+my $dsn = sprintf( 'DBI:mysql:host=%s;port=%s;database=%s',
+ $master_server->{'dbhost'},
+ $master_server->{'dbport'},
+ $production_db_name );
+my $dbh = DBI->connect( $dsn, $dbuser, $dbpass,
+ { 'PrintError' => 0, 'RaiseError' => 0 } );
+
+my $sp_sel_sth = $dbh->prepare(
+ q(
+SELECT species_id
+FROM species
+WHERE db_name = ?
+) );
+
+my $sp_sth = $dbh->prepare(
+ q(
+INSERT INTO species
+ (db_name, common_name)
+VALUES (?, ?)
+) );
+
+my $db_sth = $dbh->prepare(
+ q(
+INSERT INTO db
+ (species_id, db_type, db_release, db_assembly, db_suffix, db_host)
+VALUES (?, ?, ?, ?, ?, ?)
+) );
+
+foreach my $db_name ( sort( keys(%databases) ) ) {
+ foreach my $db_type ( sort ( keys( %{ $databases{$db_name} } ) ) ) {
+ my $entry = $databases{$db_name}{$db_type};
+
+ $sp_sel_sth->bind_param( 1, $db_name, SQL_VARCHAR );
+
+ $sp_sel_sth->execute();
+
+ my $species_id;
+ $sp_sel_sth->bind_col( 1, \$species_id );
+
+ while ( $sp_sel_sth->fetch() ) { }
+
+ if ( !defined($species_id) ) {
+ $sp_sth->bind_param( 1, $db_name, SQL_VARCHAR );
+ $sp_sth->bind_param( 2, $entry->{'common_name'}, SQL_VARCHAR );
+
+ printf( "Inserting '%s' ('%s') into species_list table... ",
+ $db_name, $entry->{'common_name'} );
+
+ $sp_sth->execute();
+
+ if ( $sp_sth->err() ) {
+ print("failed\n");
+ next;
+ } else {
+ print("ok\n");
+ }
+
+ $species_id = $dbh->{'mysql_insertid'};
+ }
+
+ if ( !defined($species_id) ) {
+ die( sprintf( "No species_id for '%s'.", $db_name ) );
+ }
+
+ $db_sth->bind_param( 1, $species_id, SQL_INTEGER );
+ $db_sth->bind_param( 2, $db_type, SQL_VARCHAR );
+ $db_sth->bind_param( 3, $entry->{'db_release'}, SQL_INTEGER );
+ $db_sth->bind_param( 4, $entry->{'db_assembly'}, SQL_INTEGER );
+ $db_sth->bind_param( 5, $entry->{'db_suffix'}, SQL_VARCHAR );
+ $db_sth->bind_param( 6, $entry->{'db_host'}, SQL_VARCHAR );
+
+ printf( "Inserting database '%s_{%s}_%d_%d%s'... ",
+ $db_name, $db_type,
+ $entry->{'db_release'},
+ $entry->{'db_assembly'},
+ $entry->{'db_suffix'} );
+
+ $db_sth->execute();
+
+ if ( $db_sth->err() ) {
+ print("failed\n");
+ } else {
+ print("ok\n");
+ }
+ } ## end foreach my $db_type ( sort ...)
+
+} ## end foreach my $db_name ( sort(...))
+
+$dbh->disconnect();
--
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