Add script to peek at job parameters

peekJob.pl allows us to check which params a job has access to

modules/Bio/EnsEMBL/Hive/Scripts/PeekJob.pm

+=head1 LICENSE
+
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2018] EMBL-European Bioinformatics Institute
+
+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.
+
+=cut
+
+
+package Bio::EnsEMBL::Hive::Scripts::PeekJob;
+
+use strict;
+use warnings;
+
+use Data::Dumper;
+
+sub peek {
+    my ($pipeline, $job_id) = @_;
+
+    my $hive_dba = $pipeline->hive_dba;
+    die "Hive's DBAdaptor is not a defined Bio::EnsEMBL::Hive::DBSQL::DBAdaptor\n" unless $hive_dba and $hive_dba->isa('Bio::EnsEMBL::Hive::DBSQL::DBAdaptor');
+
+    # fetch job and populate params
+    my $job_adaptor = $hive_dba->get_AnalysisJobAdaptor;
+    my $job = $job_adaptor->fetch_by_dbID( $job_id );
+    $job->load_parameters;
+
+    my $unsub_params = $job->{'_unsubstituted_param_hash'};
+    print Dumper $unsub_params;
+    
+    # my @ordered_params = sort { lc($a) cmp lc($b) } keys %$unsub_params;
+    # print "{\n";
+    # foreach my $param ( @ordered_params ) {
+    #     print "\t'$param' => '" . $unsub_params->{$param} . "',\n";
+    # }
+    # print "}\n";
+}
+
+1;

scripts/peekJob.pl

+#!/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, $ENV{'EHIVE_ROOT_DIR'}.'/modules';
+}
+
+use Getopt::Long qw(:config no_auto_abbrev);
+use Pod::Usage;
+
+use Bio::EnsEMBL::Hive::Version qw(report_versions);
+use Bio::EnsEMBL::Hive::HivePipeline;
+use Bio::EnsEMBL::Hive::Scripts::PeekJob;
+use Bio::EnsEMBL::Hive::Utils::URL;
+
+Bio::EnsEMBL::Hive::Utils::URL::hide_url_password();
+
+main();
+
+
+sub main {
+    my ($url, $reg_conf, $reg_type, $reg_alias, $nosqlvc, $job_id); 
+    my ($help, $report_versions);
+
+    $|=1;   # make STDOUT unbuffered (STDERR is unbuffered anyway)
+
+    GetOptions(
+
+    # Connection parameters:
+               'url=s'                        => \$url,
+               'reg_conf|regfile|reg_file=s'  => \$reg_conf,
+               'reg_type=s'                   => \$reg_type,
+               'reg_alias|regname|reg_name=s' => \$reg_alias,
+               'nosqlvc'                      => \$nosqlvc,       # using "nosqlvc" instead of "sqlvc!" for consistency with scripts where it is a propagated option
+
+    # Task specification parameters:
+               'job_id=i'                   => \$job_id,
+
+    # Other commands
+               'h|help'                     => \$help,
+               'v|version|versions'         => \$report_versions,
+    ) or die "Error in command line arguments\n";
+
+    if (@ARGV) {
+        die "ERROR: There are invalid arguments on the command-line: ". join(" ", @ARGV). "\n";
+    }
+
+    if ($help || !$job_id) {
+        pod2usage({-exitvalue => 0, -verbose => 2});
+    }
+
+    if($report_versions) {
+        report_versions();
+        exit(0);
+    }
+
+    my $pipeline;
+
+    if($url or $reg_alias) {
+
+        $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,
+        );
+        # $pipeline->hive_dba()->dbc->requires_write_access();
+
+    } else {
+        die "\nERROR: Connection parameters (url or reg_conf+reg_alias) need to be specified\n";
+    }
+
+    unless($pipeline->hive_dba) {
+        die "ERROR : no database connection, the pipeline could not be accessed\n\n";
+    }
+
+    Bio::EnsEMBL::Hive::Scripts::PeekJob::peek($pipeline, $job_id);
+}
+
+
+__DATA__
+
+=pod
+
+=head1 NAME
+
+peekJob.pl [options]
+
+=head1 DESCRIPTION
+
+peekJob.pl is an eHive component script that allows us to peek into the parameters of a given job.
+
+=head1 USAGE EXAMPLES
+
+        # Check the params for job 123456
+    runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -job_id 12345
+
+=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 --job_id <id>
+
+run a specific Job defined by its database id
+
+=head2 Other options:
+
+=over
+
+=item --help
+
+print this help
+
+=item --versions
+
+report both eHive code version and eHive database schema version
+
+=back
+
+=head1 LICENSE
+
+    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+    Copyright [2016-2018] EMBL-European Bioinformatics Institute
+
+    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
+