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Commit dc47a1cf authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Rewritten. Now uses the species table in the production database to 

pick up all databases for a give release, and writes them into the db
table of the production database.  Relies on the db_list view.
parent 8efa0701
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misc-scripts/production_database/scripts/update_database_list.pl
+ 109
− 136
View file @ dc47a1cf
......@@ -55,21 +55,21 @@ my $master = 'ens-staging1';
my $dbport = '3306';
my ( $dbwuser, $dbwpass ) = ( 'ensadmin', undef );
my ( $duser, $dbass ) = ( 'ensro', undef );
my ( $dbuser, $dbpass ) = ( 'ensro', undef );
my $opt_help = 0;
my $opt_about = 0;
if ( !GetOptions( 'release|r=i' => \$release,
'master|m=s' => \$master,
'server|s=s@' => \@servers,
'dbuser|u=s' => \$dbuser,
'dbpass|p=s' => \$dbpass,
'dbport|P=s' => \$dbport,
'dbrouser|wu' => \$dbwuser,
'dbropass|wp' => \$dbwpass,
'help|h!' => \$opt_help,
'about!' => \$opt_about )
if ( !GetOptions( 'release|r=i' => \$release,
'master|m=s' => \$master,
'server|s=s@' => \@servers,
'dbuser|u=s' => \$dbuser,
'dbpass|p=s' => \$dbpass,
'dbport|P=s' => \$dbport,
'dbwuser|wu=s' => \$dbwuser,
'dbwpass|wp=s' => \$dbwpass,
'help|h!' => \$opt_help,
'about!' => \$opt_about )
|| $opt_help )
{
usage();
......@@ -83,156 +83,129 @@ if ( !GetOptions( 'release|r=i' => \$release,
exit();
}
my %databases;
foreach my $server (@servers) {
my $dsn = sprintf( 'DBI:mysql:host=%s;port=%d', $server, $dbport );
my $dbh = DBI->connect( $dsn, $dbuser, $dbpass,
{ '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;
}
my %species;
if ( $2 ne $dbtype ) {
carp( sprintf( "Strange database type '%s', expected '%s'",
$2, $dbtype ) );
next;
}
{
my $dsn = sprintf( 'DBI:mysql:host=%s;port=%d;database=%s',
$master, $dbport, 'ensembl_production' );
my $dbh = DBI->connect( $dsn, $dbuser, $dbpass,
{ 'PrintError' => 1, 'RaiseError' => 1 } );
my $cn_sth = $dbh->prepare(
sprintf(
"SELECT meta_value "
. "FROM %s.meta "
. "WHERE meta_key = 'species.common_name'",
$dbh->quote_identifier($dbname) ) );
my $statement =
'SELECT species_id, web_name, db_name '
. 'FROM species '
. 'WHERE is_current = 1';
$cn_sth->execute();
my $sth = $dbh->prepare($statement);
$sth->execute();
my $common_name;
if ( !$cn_sth->err() ) {
$cn_sth->bind_col( 1, \$common_name );
while ( $cn_sth->fetch() ) { }
}
my ( $species_id, $web_name, $db_name );
$sth->bind_columns( \( $species_id, $web_name, $db_name ) );
$databases{$1}{$2} = { 'db_release' => $3,
'db_assembly' => $4,
'db_suffix' => $5,
'db_host' => $server,
'common_name' => $common_name };
} ## end while ( $sth->fetch() )
} ## end foreach my $dbtype ( 'cdna'...)
while ( $sth->fetch() ) {
$species{$db_name} = { 'species_id' => $species_id,
'db_name' => $db_name,
'web_name' => $web_name };
}
$dbh->disconnect();
}
} ## end foreach my $server (@servers)
die;
my $dsn = sprintf( 'DBI:mysql:host=%s;port=%s;database=%s',
$master, $dbport,
sprintf( 'ensembl_production_%d', $release ) );
my $dbh = DBI->connect( $dsn, $dbwuser, $dbwpass,
{ '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 (?, ?, ?, ?, ?, ?)
) );
my %databases;
foreach my $db_name ( sort( keys(%databases) ) ) {
foreach my $db_type ( sort ( keys( %{ $databases{$db_name} } ) ) ) {
my $entry = $databases{$db_name}{$db_type};
foreach my $server (@servers) {
my $dsn = sprintf( 'DBI:mysql:host=%s;port=%d', $server, $dbport );
my $dbh = DBI->connect( $dsn, $dbuser, $dbpass,
{ 'PrintError' => 1, 'RaiseError' => 0 } );
$sp_sel_sth->bind_param( 1, $db_name, SQL_VARCHAR );
my $statement = 'SHOW DATABASES LIKE ?';
$sp_sel_sth->execute();
my $sth = $dbh->prepare($statement);
my $species_id;
$sp_sel_sth->bind_col( 1, \$species_id );
foreach my $species ( keys(%species) ) {
$sth->bind_param( 1, sprintf( '%s%%\_%d\_%%', $species, $release ),
SQL_VARCHAR );
while ( $sp_sel_sth->fetch() ) { }
$sth->execute();
if ( !defined($species_id) ) {
$sp_sth->bind_param( 1, $db_name, SQL_VARCHAR );
$sp_sth->bind_param( 2, $entry->{'common_name'}, SQL_VARCHAR );
my $database;
printf( "Inserting '%s' ('%s') into species_list table... ",
$db_name, $entry->{'common_name'} );
$sth->bind_col( 1, \$database );
$sp_sth->execute();
while ( $sth->fetch() ) {
my ( $db_type, $db_assembly, $db_suffix ) = ( $database =~
/^[a-z]+_[a-z]+_([a-z]+)_([0-9]+)_([0-9]+[a-z]?)$/ );
if ( $sp_sth->err() ) {
print("failed\n");
next;
} else {
print("ok\n");
if ( !defined($db_type)
|| !defined($db_assembly)
|| !defined($db_suffix) )
{
die(
sprintf( "Failed to parse database name '%s'", $database ) );
}
$species_id = $dbh->{'mysql_insertid'};
$databases{$database} = {
'species_id' => $species{$species}{'species_id'},
'db_type' => $db_type,
'db_assembly' => $db_assembly,
'db_suffix' => $db_suffix,
'db_host' => $server };
}
} ## end foreach my $species ( keys(...))
if ( !defined($species_id) ) {
die( sprintf( "No species_id for '%s'.", $db_name ) );
$dbh->disconnect();
} ## end foreach my $server (@servers)
{
my $dsn = sprintf( 'DBI:mysql:host=%s;port=%d;database=%s',
$master, $dbport, 'ensembl_production' );
my $dbh = DBI->connect( $dsn, $dbwuser, $dbwpass,
{ 'PrintError' => 1, 'RaiseError' => 1 } );
my $select_stmt = 'SELECT db_id FROM db_list WHERE full_db_name = ?';
my $select_sth = $dbh->prepare($select_stmt);
my $insert_stmt =
'INSERT INTO db '
. '(species_id, db_type, db_release, db_assembly, db_suffix, db_host) '
. 'VALUES (?, ?, ?, ?, ?, ?)';
my $insert_sth = $dbh->prepare($insert_stmt);
foreach my $database ( keys(%databases) ) {
$select_sth->bind_param( 1, $database, SQL_VARCHAR );
$select_sth->execute();
my $db_id;
$select_sth->bind_col( 1, \$db_id );
my $is_found = 0;
while ( $select_sth->fetch() ) {
$is_found = 1;
last;
}
$select_sth->finish();
$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, $entry->{'db_host'}, SQL_VARCHAR );
if ($is_found) {
# printf( "The database '%s' is already in "
# . "the production database (id %d)\n",
# $database, $db_id );
} else {
my $db = $databases{$database};
printf( "Inserting database '%s_{%s}_%d_%d%s'... ",
$db_name, $db_type,
$entry->{'db_release'},
$entry->{'db_assembly'},
$entry->{'db_suffix'} );
printf( "Inserting database '%s' into "
. "the production database\n",
$database );
$db_sth->execute();
$insert_sth->bind_param( 1, $db->{'species_id'}, SQL_INTEGER );
$insert_sth->bind_param( 2, $db->{'db_type'}, SQL_VARCHAR );
$insert_sth->bind_param( 3, $release, SQL_INTEGER );
$insert_sth->bind_param( 4, $db->{'db_assembly'}, SQL_INTEGER );
$insert_sth->bind_param( 5, $db->{'db_suffix'}, SQL_VARCHAR );
$insert_sth->bind_param( 6, $db->{'db_host'}, SQL_VARCHAR );
if ( $db_sth->err() ) {
print("failed\n");
} else {
print("ok\n");
$insert_sth->execute();
}
} ## end foreach my $db_type ( sort ...)
} ## end foreach my $db_name ( sort(...))
} ## end foreach my $database ( keys...)
$dbh->disconnect();
$dbh->disconnect();
}
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