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Commit 53837993 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Update to deal with schema 65.

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misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
+ 102
− 93
View file @ 53837993
......@@ -36,16 +36,16 @@ Optional arguments:
This script will delete stable ID mapping data from a database. The script is
intended to be run interactively (your configuration will be overridden).
The tables that will be emptied are:
The tables that will be emptied or modified are:
gene_stable_id
transcript_stable_id
translation_stable_id
exon_stable_id
mapping_session
stable_id_event
gene_archive
peptide_archive
gene (modified)
transcript (modified)
translation (modified)
exon (modified)
mapping_session (emptied)
stable_id_event (emptied)
gene_archive (emptied)
peptide_archive (emptied)
Optionally (by interactive selection), the current tables can be backed up.
Backkup tables will get suffices of _bak_0, _bak_1, etc. (where the correct
......@@ -86,11 +86,13 @@ use Bio::EnsEMBL::Utils::Logger;
use Bio::EnsEMBL::Utils::ScriptUtils qw(user_proceed);
use Bio::EnsEMBL::DBSQL::DBAdaptor;
my @tables = qw(
gene_stable_id
transcript_stable_id
translation_stable_id
exon_stable_id
my @modify_tables = qw(
gene
transcript
translation
exon
);
my @empty_tables = qw(
mapping_session
stable_id_event
gene_archive
......@@ -100,42 +102,39 @@ my @tables = qw(
my %suffnum = ();
# parse configuration and commandline arguments
my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-SERVERROOT => "$Bin/../../../..",
-DEFAULT_CONF => ""
);
my $conf =
new Bio::EnsEMBL::Utils::ConfParser(-SERVERROOT => "$Bin/../../../..",
-DEFAULT_CONF => "" );
$conf->parse_options(
'host=s' => 1,
'port=n' => 1,
'user=s' => 1,
'pass=s' => 0,
'dbname=s' => 1,
);
$conf->parse_options( 'host=s' => 1,
'port=n' => 1,
'user=s' => 1,
'pass=s' => 0,
'dbname=s' => 1, );
# get log filehandle and print heading and parameters to logfile
my $logger = new Bio::EnsEMBL::Utils::Logger(
-LOGFILE => $conf->param('logfile'),
-LOGPATH => $conf->param('logpath'),
-LOGAPPEND => $conf->param('logappend'),
-VERBOSE => $conf->param('verbose'),
);
my $logger =
new Bio::EnsEMBL::Utils::Logger(
-LOGFILE => $conf->param('logfile'),
-LOGPATH => $conf->param('logpath'),
-LOGAPPEND => $conf->param('logappend'),
-VERBOSE => $conf->param('verbose'),
);
# always run interactively
$conf->param('interactive', 1);
$conf->param( 'interactive', 1 );
# initialise log
$logger->init_log($conf->list_param_values);
$logger->init_log( $conf->list_param_values );
# connect to database and get adaptors
my $dba = new Bio::EnsEMBL::DBSQL::DBAdaptor(
-host => $conf->param('host'),
-port => $conf->param('port'),
-user => $conf->param('user'),
-pass => $conf->param('pass'),
-dbname => $conf->param('dbname'),
-group => 'core',
);
my $dba =
new Bio::EnsEMBL::DBSQL::DBAdaptor( -host => $conf->param('host'),
-port => $conf->param('port'),
-user => $conf->param('user'),
-pass => $conf->param('pass'),
-dbname => $conf->param('dbname'),
-group => 'core', );
$dba->dnadb($dba);
my $dbh = $dba->dbc->db_handle;
......@@ -146,80 +145,84 @@ my $dbh = $dba->dbc->db_handle;
# then look for existing backup tables
my $sfx = &list_backup_counts;
# aks user if he wants to drop backup tables
if (%suffnum and user_proceed("Drop any backup tables? (you will be able chose which ones)", $conf->param('interactive'), 'n')) {
# ask user if he wants to drop backup tables
if ( %suffnum
and
user_proceed(
"Drop any backup tables? (you will be able chose which ones)",
$conf->param('interactive'), 'n' ) )
{
&drop_backup_tables;
}
# ask user if current tables should be backed up
if (user_proceed("Backup current tables?", $conf->param('interactive'), 'y')) {
if (user_proceed( "Backup current tables?", $conf->param('interactive'),
'y' ) )
{
&backup_tables($sfx);
}
# delete from tables
if (user_proceed("Delete from current tables?", $conf->param('interactive'), 'n')) {
if ( user_proceed( "Delete from current tables?",
$conf->param('interactive'),
'n' ) )
{
&delete_from_tables;
}
# finish logfile
$logger->finish_log;
### END main ###
sub list_table_counts {
$logger->info("Current table counts:\n\n");
&list_counts(\@tables);
&list_counts( [ @modify_tables, @empty_tables ] );
}
sub list_backup_counts {
my $new_num = -1;
foreach my $table (@tables) {
foreach my $table ( @modify_tables, @empty_tables ) {
my $sth = $dbh->prepare(qq(SHOW TABLES LIKE "${table}_bak_%"));
$sth->execute;
while (my ($bak) = $sth->fetchrow_array) {
while ( my ($bak) = $sth->fetchrow_array ) {
$bak =~ /_bak_(\d+)$/;
my $num = $1;
$suffnum{$num} = 1;
$new_num = $num if ($num > $new_num);
$new_num = $num if ( $num > $new_num );
}
$sth->finish;
}
$logger->info("Backup tables found:\n\n") if (%suffnum);
foreach my $num (sort keys %suffnum) {
foreach my $num ( sort keys %suffnum ) {
my @t = ();
foreach my $table (@tables) {
foreach my $table ( @modify_tables, @empty_tables ) {
push @t, "${table}_bak_$num";
}
&list_counts(\@t);
&list_counts( \@t );
$logger->info("\n");
}
my $sfx = '_bak_' . ++$new_num;
return $sfx;
}
} ## end sub list_backup_counts
sub list_counts {
my $tabs = shift;
unless ($tabs and ref($tabs) eq 'ARRAY') {
unless ( $tabs and ref($tabs) eq 'ARRAY' ) {
throw("Need an arrayref.");
}
$logger->info(sprintf("%-30s%-8s\n", qw(TABLE COUNT)), 1);
$logger->info(('-'x38)."\n", 1);
$logger->info( sprintf( "%-30s%-8s\n", qw(TABLE COUNT) ), 1 );
$logger->info( ( '-' x 38 ) . "\n", 1 );
my $fmt = "%-30s%8d\n";
foreach my $table (@$tabs) {
......@@ -228,22 +231,23 @@ sub list_counts {
my $count = $sth->fetchrow_arrayref->[0];
$sth->finish;
$logger->info(sprintf($fmt, $table, $count), 1);
$logger->info( sprintf( $fmt, $table, $count ), 1 );
}
$logger->info("\n");
}
sub drop_backup_tables {
foreach my $num (sort keys %suffnum) {
foreach my $num ( sort keys %suffnum ) {
my $suffix = "_bak_$num";
if (user_proceed(qq(Drop backup tables with suffix ${suffix}?), $conf->param('interactive'), 'n')) {
foreach my $table (@tables) {
if ( user_proceed( qq(Drop backup tables with suffix ${suffix}?),
$conf->param('interactive'), 'n' ) )
{
foreach my $table ( @modify_tables, @empty_tables ) {
my $bak_table = "${table}${suffix}";
$logger->info("$bak_table\n", 1);
unless ($conf->param('dry_run')) {
$logger->info( "$bak_table\n", 1 );
unless ( $conf->param('dry_run') ) {
$dbh->do(qq(DROP TABLE $bak_table));
}
}
......@@ -258,14 +262,13 @@ sub drop_backup_tables {
# recalculate the suffix number to use for current backup
my $max_num = reverse sort keys %suffnum;
$sfx = '_bak_' . ++$max_num;
}
} ## end sub drop_backup_tables
sub backup_tables {
my $sfx = shift;
throw("Need a backup table suffix.") unless (defined($sfx));
throw("Need a backup table suffix.") unless ( defined($sfx) );
$logger->info(qq(\nWill use '$sfx' as suffix for backup tables\n));
$logger->info(qq(\nBacking up tables...\n));
......@@ -273,35 +276,41 @@ sub backup_tables {
my $fmt1 = "%-30s";
my $fmt2 = "%8d\n";
foreach my $table (@tables) {
$logger->info(sprintf($fmt1, $table), 1);
foreach my $table ( @modify_tables, @empty_tables ) {
$logger->info( sprintf( $fmt1, $table ), 1 );
my $c = 0;
unless ($conf->param('dry_run')) {
$c = $dbh->do(qq(CREATE TABLE ${table}${sfx} SELECT * FROM $table));
unless ( $conf->param('dry_run') ) {
$c =
$dbh->do(qq(CREATE TABLE ${table}${sfx} SELECT * FROM $table));
}
$logger->info(sprintf($fmt2, $c));
$logger->info( sprintf( $fmt2, $c ) );
}
$logger->info(qq(Done.\n));
}
sub delete_from_tables {
my $fmt1 = "%-30s";
my $fmt2 = "%8d\n";
$logger->info(qq(\nDeleting from current tables...\n));
foreach my $table (@tables) {
$logger->info(sprintf($fmt1, $table), 1);
foreach my $table (@modify_tables) {
$logger->info( sprintf( $fmt1, $table ), 1 );
my $c = 0;
unless ( $conf->param('dry_run') ) {
$c = $dbh->do(qq(UPDATE $table SET stable_id=NULL));
}
$logger->info( sprintf( $fmt2, $c ) );
}
foreach my $table (@empty_tables) {
$logger->info( sprintf( $fmt1, $table ), 1 );
my $c = 0;
unless ($conf->param('dry_run')) {
unless ( $conf->param('dry_run') ) {
$c = $dbh->do(qq(DELETE FROM $table));
}
$logger->info(sprintf($fmt2, $c));
$logger->info( sprintf( $fmt2, $c ) );
}
$logger->info(qq(Done.\n));
}
} ## end sub delete_from_tables
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