Commit 2ce7ebc1 authored by Andy Yates's avatar Andy Yates
Browse files

Removed as specified in release declarations

parent 2837f49c
#!/usr/local/ensembl/bin/perl -w
=head1 NAME - automagically apply schema patches to Ensembl dbs
=head1 SYNOPSIS [arguments]
Required arguments:
--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
--pattern, --dbpattern=PATTERN patch databases where name matches PATTERN
Note that this is a database pattern of
the form %core_41% rather than a regexp
--schema, --dbschema=NUM patch to schema version NUM
--schema_type Schema type to patch e.g. core|variation|funcgen
Optional arguments:
--conffile, --conf=FILE read parameters from FILE
(default: conf/Conversion.ini)
--bindir=DIR mysql binary directory (default:
--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, --dry_run=0|1 don't write results to database
-h, --help, -? print help (this message)
Please note that where an argument expects a value, this is true for all
alternative argument styles.
This is a script to facilitate patching databases to the next schema version.
It will connect to a database server and apply schema patches to all databases
where the name matches a pattern. The pattern is a string that can be used in an
'IN' clause in SQL (e.g. "%_core_%"; if you want to patch only a single
database, use a pattern without % expansion, e.g. "homo_sapiens_core_38_36").
If you only want to check which patches need to be applied, use --dry_run=1
(best done in combination with --interactive=0).
=head1 LICENCE
This code is distributed under an Apache style licence:
Please see for details
=head1 AUTHOR
Patrick Meidl <>, Ensembl core API team
=head1 CONTACT
Please post comments/questions to the Ensembl development list
# Should really add explicit --schema_type param to avoid applying core patches to non-core DBs
# Could also validate this against meta schema.type = core|funcgen|variation
use strict;
use warnings;
no warnings 'uninitialized';
use FindBin qw($Bin);
use vars qw($SERVERROOT);
$SERVERROOT = "$Bin/../..";
unshift(@INC, "$SERVERROOT/ensembl/modules");
use Getopt::Long;
use Pod::Usage;
use Bio::EnsEMBL::Utils::ConversionSupport;
use DBI;
$| = 1;
my $support = new Bio::EnsEMBL::Utils::ConversionSupport($SERVERROOT);
# parse options
$support->param('dbname', undef);
my @params = map { $_ unless ($_ =~ /dbname/) } $support->get_common_params;
if ($support->param('help') or $support->error) {
warn $support->error if $support->error;
unless ($support->param('bindir')) {
$support->param('bindir', '/usr/local/ensembl/bin');
# ask user to confirm parameters to proceed
# get log filehandle and print heading and parameters to logfile
my $schema_type = $support->param('schema_type');
my %patch_dirs = (
'core' => "$SERVERROOT/ensembl/sql",
'funcgen' => "$SERVERROOT/ensembl-functgenomics/sql",
'variation' => "$SERVERROOT/ensembl-variation/sql",
#check schema_type is valid
if(! (defined $schema_type && exists $patch_dirs{$schema_type})){
$support->log_error('You must specify a valid --schema_type parameter e.g. core|variation|funcgen');
# connect to database
my $dbh = $support->get_dbconnection;
# read patches from file
$support->log("Reading patches from file...\n");
my $patchdir = $patch_dirs{$schema_type};
my $schema = $support->param('schema');
my @patches;
opendir(DIR, $patchdir) or
$support->log_error("Can't opendir $patchdir: $!");
while (my $file = readdir(DIR)) {
if ($file =~ /^patch_\d+_${schema}.*\.sql$/) {
$support->log("$file\n", 1);
push @patches, $file;
# get all database names that match pattern
my ($sth, $sql);
$sql = "SHOW DATABASES LIKE '".$support->param('pattern')."'";
$sth = $dbh->prepare($sql);
# loop over databases
while (my ($dbname) = $sth->fetchrow_array) {
my $failure = 0;
if ($support->user_proceed("\nPatch $dbname?")) {
# check which patches have already been applied
$sql = qq(SELECT meta_value FROM $dbname.meta WHERE meta_key = 'patch');
my $sth1 = $dbh->prepare($sql);
my %applied;
while (my ($val) = $sth1->fetchrow_array) {
my ($file) = split(/\|/, $val);
$applied{$file} = 1;
# apply the missing ones
foreach my $patch (sort @patches) {
# if a patch has failed do not continue with other patches as there may be dependencies.
$support->log("$patch... ", 1);
if ($applied{$patch}) {
$support->log("already applied.\n")
} elsif ($support->param('dry_run')) {
$support->log("needs applying.\n")
} else {
$support->log("applying... ");
my $cmd = $support->param('bindir')."/mysql".
" -h ".$support->param('host').
" -P ".$support->param('port').
" -u ".$support->param('user').
" -p".$support->param('pass').
" $dbname < $patchdir/$patch";
if (system($cmd) == 0) {
} else {
$support->log_warning("Error applying patch. Please check patch file.\n", 1);
$failure = 1;
} else {
$support->log("Skipping on user's request.\n", 1);
# finish logfile
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