refresh_guest_languages.pl

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#!/usr/bin/env perl
use strict;
use warnings;
 
    # Finding out own path in order to reference own components (including own modules):
use Cwd            ();
use File::Basename ();
BEGIN {
    $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
    unshift @INC, $ENV{'EHIVE_ROOT_DIR'}.'/modules';
}
 
use Getopt::Long qw(:config no_auto_abbrev);
use Pod::Usage;
 
use Bio::EnsEMBL::Hive::HivePipeline;
use Bio::EnsEMBL::Hive::GuestProcess;
 
Bio::EnsEMBL::Hive::Utils::URL::hide_url_password();
 
main();
 
 
sub main {
    my ($url, $reg_conf, $reg_type, $reg_alias, $nosqlvc, $job_id, $help);
    my @languages;
 
    GetOptions(
 
        # Connection parameters:
               'url=s'                        => \$url,
               'reg_conf|regfile|reg_file=s'  => \$reg_conf,
               'reg_type=s'                   => \$reg_type,
               'reg_alias|regname|reg_name=s' => \$reg_alias,
               'nosqlvc'                      => \$nosqlvc,       # using "nosqlvc" instead of "sqlvc!" for consistency with scripts where it is a propagated option
 
        # Other commands
               'language=s@'                => \@languages,
               'h|help'                     => \$help,
    ) or die "Error in command line arguments\n";
 
    if (@ARGV) {
        die "ERROR: There are invalid arguments on the command-line: ". join(" ", @ARGV). "\n";
    }
 
    if ($help) {
        pod2usage({-exitvalue => 0, -verbose => 2});
    }
 
    # All the languages that are registered
    my $wrappers = Bio::EnsEMBL::Hive::GuestProcess::_get_all_registered_wrappers;
 
    my %requested_languages;
 
    if($url or $reg_alias) {
 
        my $pipeline = Bio::EnsEMBL::Hive::HivePipeline->new(
            -url                            => $url,
            -reg_conf                       => $reg_conf,
            -reg_type                       => $reg_type,
            -reg_alias                      => $reg_alias,
            -no_sql_schema_version_check    => $nosqlvc,
        );
 
        my $found = 0;
        foreach my $analysis ($pipeline->collection_of('Analysis')->list()) {
            if ($analysis->language) {
                $found = 1;
                if ($wrappers->{$analysis->language}) {
                    $requested_languages{$analysis->language} = 1;
                } else {
                    warn sprintf("Anaylsis '%s' is implemented in %s, but this wrapper is not registered.\n", $analysis->logic_name, $analysis->language);
                }
            }
        }
 
        unless ($found) {
            warn "All the analyses of this pipeline are implemented with the default language.\n";
        }
 
    } elsif (scalar(@languages)) {
        foreach my $language (@languages) {
            if ($wrappers->{$language}) {
                $requested_languages{$language} = 1;
            } else {
                warn "No wrapper for '$language' is registered.\n";
            }
        }
 
    } else {
        $requested_languages{$_} = 1 for keys %$wrappers;
 
    }
 
    foreach my $language (keys %requested_languages) {
        print "** $language **\n";
        Bio::EnsEMBL::Hive::GuestProcess::build_wrapper_for_language($language);
        print "\n\n";
    }
}
 
 
__DATA__
 
=pod
 
=head1 NAME
 
refresh_guest_languages.pl [options]
 
=head1 DESCRIPTION
 
refresh_guest_languages.pl is an eHive component script that simplifies rebuilding the wrappers for guest languages
 
=head1 USAGE EXAMPLES
 
        # Rebuild all the wrappers needed for an existing pipeline
    refresh_guest_languages.pl --url mysql://username:secret@hostname:port/ehive_dbname
 
        # Rebuild one wrapper
    refresh_guest_languages.pl --language python
 
        # Rebuild all the wrappers
    refresh_guest_languages.pl
 
=head1 OPTIONS
 
=head2 Connection parameters:
 
=over
 
=item --reg_conf <path>
 
path to a Registry configuration file
 
=item --reg_alias <string>
 
species/alias name for the eHive DBAdaptor
 
=item --reg_type <string>
 
type of the registry entry ("hive", "core", "compara", etc - defaults to "hive")
 
=item --url <url string>
 
URL defining where database is located
 
=item --nosqlvc
 
"No SQL Version Check" - set if you want to force working with a database created by a potentially schema-incompatible API
 
=back
 
=head2 Task specification parameters:
 
=over
 
=item --language <name>
 
The name of a language whose wrapper has to be rebuilt.
The option can be repeated
 
=back
 
=head2 Other options:
 
=over
 
=item --help
 
print this help
 
=back
 
=head1 LICENSE
 
    See the NOTICE file distributed with this work for additional information
    regarding copyright ownership.
 
    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at
 
         http://www.apache.org/licenses/LICENSE-2.0
 
    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.
 
=head1 CONTACT
 
Please subscribe to the eHive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss eHive-related questions or to be notified of our updates
 
=cut