From 538379930093c52d4e5c47977c345755298af650 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 19 Oct 2011 10:13:30 +0000
Subject: [PATCH] Update to deal with schema 65.
---
.../utils/manage_id_mapping_tables.pl | 195 +++++++++---------
1 file changed, 102 insertions(+), 93 deletions(-)
diff --git a/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl b/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
index e34aa32169..71166f6c03 100755
--- a/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
+++ b/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
@@ -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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