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#!/usr/bin/perl -w
use strict;
use Getopt::Long;
#use lib '/home/cain/cvs_stuff/schema/chado/lib';
#use lib '/home/scott/cvs_stuff/schema/chado/lib';
use Bio::GMOD::Config;
use Bio::GMOD::DB::Config;
use ExtUtils::MakeMaker; #to get prompt
=head1 NAME
$0 - updates the schema of a Chado database if necessary
=head1 SYNOPSIS
% gmod_update_chado.pl [options]
=head1 COMMAND-LINE OPTIONS
--force Update the schema without prompt
--dbprofile Which database profile to use for updating
=head1 DESCRIPTION
=head1 AUTHOR
Scott Cain E<lt>scain@cpan.orgE<gt>
Copyright (c) 2011
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
my ($FORCE, $DBPROFILE, );
GetOptions(
'force' => \$FORCE,
'dbprofile=s' => \$DBPROFILE,
) or ( system( 'pod2text', $0 ), exit -1 );
$DBPROFILE ||= 'default';
my $gmod_conf = Bio::GMOD::Config->new();
my $version = $gmod_conf->version();
my $gmod_root = $gmod_conf->gmod_root();
my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf, $DBPROFILE);
my $dbh = $db_conf->dbh();
my $current_version = `gmod_chado_properties.pl --version --dbprof $DBPROFILE`;
chomp $current_version;
if ($current_version >= $version) {
print "This instance of the Chado schema does not need updating.\n";
exit(0);
}
if (!defined $FORCE) {
print <<END
The schema needs updating; this will add columns and/or tables, and should
not delete any data, but we still advise you to back up your database
before continuing.
END
;
my $YN = prompt ("Continue with update?", "y");
if ($YN =~ /^n/i) {
print "OK, exiting...\n";
exit(0);
}
}
#build path to get updates from
my $path = "$gmod_root/src/chado/schemas/$current_version-$version/diff.sql";
my $dbuser = $db_conf->user;
my $dbport = $db_conf->port;
my $dbhost = $db_conf->host;
my $dbname = $db_conf->name;
my $syscommand = "cat $path | psql -U $dbuser -p $dbport -h $dbhost $dbname";
system($syscommand) == 0 or die "failed updating database";
#now update the schema version in the chadoprop table
system("gmod_chado_properties.pl --version $version --force --dbprof $DBPROFILE");
print "Updating $dbname complete.\n";
exit(0);
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