#!perl
use Config;
use File::Basename qw(&basename &dirname);
use Cwd;
$origdir = cwd;
chdir dirname($0);
$file = basename($0, '.PL','.PLS');
$file .= $^O eq 'VMS' ? '.com' : '.pl';
open OUT,">$file" or die "Can't create $file: $!";
print "Extracting $file (with variable substitutions)\n";
print OUT <<"!GROK!THIS!";
$Config{startperl}
!GROK!THIS!
# In the following, perl variables are not expanded during extraction.
print OUT <<'!NO!SUBS!';
use strict;
use Getopt::Long;
use Bio::GMOD::Admin::Update;
my $USAGE = <<USAGE;
This script provides a convenient mechanism to maintain a MOD
installation. It should be excecuted with super user privileges.
% gmod_update_installation.pl [options]
For a full description of options, see:
% perldoc gmod_update_installation.pl
USAGE
my ($MOD,$VERSION,$SYNC_TO,$FORCE,$HELP,$TMP,$PURGE);
GetOptions( 'mod=s' => \$MOD,
'version=s' => \$VERSION,
'sync_to=s' => \$SYNC_TO, # one of live or dev
'force' => \$FORCE,
'purge' => \$PURGE,
'tmp=s' => \$TMP,
'help' => \$HELP);
die $USAGE if ($HELP || !$MOD);
my @options = @ARGV;
my $gmod = Bio::GMOD::Admin::Update->new(-mod => $MOD,@options);
# Fetch the current live, local, and development versions of the MOD
# Each method will return a hash reference with keys of:
# status, url, title, version, versiond
my %live = $gmod->live_version();
my %dev = $gmod->development_version();
my %local = $gmod->local_version();
if (keys %live < 1) {
print "WARNING: Could not check the live versions. You must be online to update your $MOD installation.\n";
die;
}
print "LIVE SITE ($live{url})\n";
print "----------------------------\n";
print_keys(\%live);
print "DEV SITE ($dev{url})\n";
print "----------------------------\n";
print_keys(\%dev);
print "LOCAL INSTALLATION\n";
print "----------------------------\n";
print_keys(\%local);
# The desired version, fetched automatically or provided with --version
my $desired_version = ($SYNC_TO eq 'dev') ? $dev{version} : $live{version};
$desired_version = $VERSION if $VERSION;
unless ($FORCE) {
if ($local{version} eq $desired_version) {
print "Your $MOD installation is up-to-date: " . $local{version};
exit;
}
}
$gmod->update(-version => $desired_version,@options);
$gmod->cleanup() if $PURGE;
sub print_keys {
my $hash = shift;
print "Status : $hash->{status}\n";
print "Title : $hash->{title}\n";
print "Version : $hash->{version}\n";
print "Released : $hash->{released}\n\n";
}
__END__
=pod
=head1 NAME
gmod_update_installation.pl - Maintain a MOD installation
=head1 USAGE
This script provides a convenient mechanism to maintain a MOD
installation. It should be excecuted with super user privileges.
$ gmod_update_installation.pl [options]
=head1 OPTIONS
The following options are generically available for any MOD (default
values in parenthesis):
MOD:
--mod One of WormBase, FlyBase, SGD, etc
Versions:
--sync_to [live || dev] Sync to the current live or development version (live)
--force [boolean] Force an update to the live or development version as appropriate (false)
--version Update to the provided version (the current live version)
System paths:
--tmp Full path to the temporary directory to hold downloads (/usr/local/gmod/tmp)
Miscellaneous:
--purge [boolean] Purge the tmp download folder following upgrade (false)
--help Display this message
Due to the wide variety of installation paths and MOD structures, each
MOD may offer specialized options. These can be provided as
"--option_name OPTION" which will be passed directly to the
Bio::GMOD::Update::"MOD" object's update() method. For example, a
typical command to maintain a WormBase installation looks like:
% gmod_update_installation.pl --analyze_logs --mysql_path /usr/local/mysql/data
For a full description of all available system paths and update
options for your particular MOD, see L<Bio::GMOD::Adaptor> and
L<GMOD::Adaptor::your_mod>.
=head1 Running under cron
You may wish to run this script under cron to ensure that your
installation is always up-to-date. For my personal installation of
WormBase, I use the following settings:
0 2 * * * /usr/local/bin/gmod_update_installation.pl --sync_to dev
This will check for and install a new version if present at 2 AM in
the morning.
I keep my installation in sync with the development version. You will
want to use the more stable live version, which you can specify using
"--sync_to live" or by simply leaving off the "--sync_to" option
altogether.
A suggested crontab entry for a simple local installation is:
gmod_update_intallation.pl --sync_to live --purge 1
A suggested crontab entry for official WormBase mirror sites is:
gmod_update_intallation.pl --sync_to live --purge 1 --analyze_logs 1
=head1 SEE ALSO
L<Bio::GMOD>, L<Bio::GMOD::Update>
=head1 AUTHOR
Todd Harris <harris@cshl.edu>.
Copyright (c) 2003-2005 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;