script to interactively delete temporary and backup tables from a database

misc-scripts/cleanup_tmp_tables.pl

+#!/usr/local/bin/perl
+
+=head1 NAME
+
+cleanup_tmp_tables.pl - delete temporary and backup tables from a database
+
+=head1 SYNOPSIS
+
+cleanup_tmp_tables.pl [arguments]
+
+Required arguments:
+
+  --dbname, db_name=NAME              database name NAME
+  --host, --dbhost, --db_host=HOST    database host HOST
+  --port, --dbport, --db_port=PORT    database port PORT
+  --user, --dbuser, --db_user=USER    database username USER
+  --pass, --dbpass, --db_pass=PASS    database passwort PASS
+
+Optional arguments:
+
+  --conffile, --conf=FILE             read parameters from FILE
+                                      (default: conf/Conversion.ini)
+
+  --logfile, --log=FILE               log to FILE (default: *STDOUT)
+  --logpath=PATH                      write logfile to PATH (default: .)
+  --logappend, --log_append           append to logfile (default: truncate)
+
+  -v, --verbose=0|1                   verbose logging (default: false)
+  -i, --interactive=0|1               run script interactively (default: true)
+  -n, --dry_run, --dry=0|1            don't write results to database
+  -h, --help, -?                      print help (this message)
+
+=head1 DESCRIPTION
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence:
+Please see http://www.ensembl.org/code_licence.html for details
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use FindBin qw($Bin);
+use vars qw($SERVERROOT);
+
+BEGIN {
+    $SERVERROOT = "$Bin/../..";
+    unshift(@INC, "$SERVERROOT/ensembl/modules");
+    unshift(@INC, "$SERVERROOT/bioperl-live");
+}
+
+use Getopt::Long;
+use Pod::Usage;
+use Bio::EnsEMBL::Utils::ConversionSupport;
+
+$| = 1;
+
+my $support = new Bio::EnsEMBL::Utils::ConversionSupport($SERVERROOT);
+
+# parse options
+$support->parse_common_options(@_);
+$support->allowed_params(
+  $support->get_common_params,
+);
+
+if ($support->param('help') or $support->error) {
+    warn $support->error if $support->error;
+    pod2usage(1);
+}
+
+# ask user to confirm parameters to proceed
+$support->confirm_params;
+
+# get log filehandle and print heading and parameters to logfile
+$support->init_log;
+
+$support->check_required_params;
+
+# connect to database and get adaptors
+my $dba = $support->get_database('ensembl');
+my $dbh = $dba->dbc->db_handle;
+
+# find all temporary and backup tables
+my @tables;
+
+foreach my $pattern (qw(tmp temp bak backup)) {
+  my $sql = qq(SHOW TABLES LIKE '\%$pattern\%');
+  my $sth = $dbh->prepare($sql);
+  $sth->execute;
+  while (my ($table) = $sth->fetchrow_array) {
+    push @tables, $table;
+  }
+}
+
+if ($support->param('dry_run')) {
+  # for a dry run, only show which databases would be deleted
+  $support->log("Temporary and backup tables found:\n");
+  foreach my $table (sort @tables) {
+    $support->log("$table\n", 1);
+  }
+
+} else {
+  # delete tables
+  foreach my $table (sort @tables) {
+    if ($support->user_proceed("Drop table $table?")) {
+      $support->log("Dropping table $table...\n");
+      $dbh->do("DROP TABLE $table");
+      $support->log("Done.\n");
+    }
+  }
+}
+
+# finish logfile
+$support->finish_log;
+