Added from private repository.

misc-scripts/production_database/scripts/update_database_list.pl

+#!/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();