Commit 9be30f46 authored by Leo Gordon's avatar Leo Gordon
Browse files

bulk fixing of PODs - may have accidentally broken something?

parent d7f1818f
......@@ -49,11 +49,9 @@
It is also responsible for interfacing with the Queen to identify workers which died
unexpectantly so that she can free the dead workers unfinished jobs.
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......
......@@ -7,7 +7,7 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
......@@ -28,8 +28,7 @@
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -39,8 +38,6 @@
=cut
# Let the code begin...
package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
......
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
......@@ -16,8 +14,7 @@
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -26,6 +23,7 @@
=cut
package Bio::EnsEMBL::Hive::AnalysisJob;
use strict;
......
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Hive::AnalysisStats
=head1 SYNOPSIS
......@@ -13,14 +12,17 @@
=head1 DESCRIPTION
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Hive::AnalysisStats;
use strict;
......
......@@ -7,7 +7,7 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
......@@ -25,8 +25,7 @@
=head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -36,8 +35,6 @@
=cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
......
......@@ -7,33 +7,35 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
=head1 SYNOPSIS
$dataDBA = $db_adaptor->get_AnalysisDataAdaptor;
=head1 DESCRIPTION
analysis_data table holds LONGTEXT data for use by the analysis system.
This data is general purpose and it's up to each analysis to
determine how to use it.
This Adaptor module is used to access/store this data.
=head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
......
......@@ -7,7 +7,7 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
......@@ -25,8 +25,7 @@
=head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -36,7 +35,6 @@
=cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
......
......@@ -7,31 +7,34 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor
=head1 SYNOPSIS
$analysisStatsAdaptor = $db_adaptor->get_AnalysisStatsAdaptor;
$analysisStatsAdaptor = $analysisStats->adaptor;
=head1 DESCRIPTION
Module to encapsulate all db access for persistent class AnalysisStats.
There should be just one per application and database connection.
=head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
......
......@@ -7,7 +7,7 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
......@@ -22,20 +22,17 @@ Bio::EnsEMBL::Hive::DBSQL::DBAdaptor
-driver => 'mysql',
);
=head1 DESCRIPTION
This object represents the handle for a Hive system enabled database
=head1 CONTACT
Post questions the the EnsEMBL developer list: <ensembl-dev@ebi.ac.uk>
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
use vars qw(@ISA);
......
......@@ -7,7 +7,7 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
......@@ -25,8 +25,7 @@
=head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -36,9 +35,6 @@
=cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
use strict;
......
......@@ -7,7 +7,7 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
......@@ -25,11 +25,9 @@
be specified with a network savy URL like
mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34'
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -39,9 +37,6 @@
=cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DataflowRule;
use strict;
......
......@@ -9,24 +9,15 @@
Bio::EnsEMBL::Hive::Extensions
=cut
=head1 SYNOPSIS
Object categories to extend the functionality of existing classes
=cut
=head1 DESCRIPTION
=cut
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -35,6 +26,7 @@
=cut
use strict;
use Bio::EnsEMBL::Utils::Exception;
......
# You may distribute this module under the same terms as perl itself #
# POD documentation - main docs before the code
=pod
......@@ -7,8 +6,6 @@
Bio::EnsEMBL::Hive::Process
=cut
=head1 SYNOPSIS
Abstract superclass. Each Process makes up the individual building blocks
......@@ -73,14 +70,9 @@
http://en.wikipedia.org/wiki/Emergence
=cut
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -89,6 +81,8 @@
=cut
my $g_hive_process_workdir; # a global directory location for the process using this module
package Bio::EnsEMBL::Hive::Process;
......
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
......@@ -49,8 +47,7 @@
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -59,6 +56,7 @@
=cut
package Bio::EnsEMBL::Hive::Queen;
use strict;
......
......@@ -9,8 +9,6 @@
Bio::EnsEMBL::Hive::RunnableDB::Dummy
=cut
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::DBAdaptor->new($locator);
......@@ -23,8 +21,6 @@ $repmask->run();
$repmask->output();
$repmask->write_output(); #writes to DB
=cut
=head1 DESCRIPTION
This object is used as a place holder in the hive system.
......@@ -32,13 +28,9 @@ It does nothing, but is needed so that a Worker can grab
a job, pass the input through to output, and create the
next layer of jobs in the system.
=cut
=head1 CONTACT
jessica@ebi.ac.uk
=cut
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......
......@@ -9,8 +9,6 @@
Bio::EnsEMBL::Hive::RunnableDB::SystemCmd
=cut
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::DBAdaptor->new($locator);
......@@ -23,20 +21,14 @@ $runDB->run();
$runDB->output();
$runDB->write_output(); #writes to DB
=cut
=head1 DESCRIPTION
This object is a very simple module. It takes the input_id
and runs it as a system command.
=cut
=head1 CONTACT
jessica@ebi.ac.uk
=cut
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -45,6 +37,7 @@ Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Hive::RunnableDB::SystemCmd;
use strict;
......
......@@ -9,8 +9,6 @@
Bio::EnsEMBL::Hive::RunnableDB::Test
=cut
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::DBAdaptor->new($locator);
......@@ -23,8 +21,6 @@ $repmask->run();
$repmask->output();
$repmask->write_output(); #writes to DB
=cut
=head1 DESCRIPTION
This object is used to test failure of jobs in the hive system.
......@@ -35,13 +31,9 @@ It parses the analysis.parameters and analysis_job.input_id as
(string representing) hasrefs and extracts the divisor and the value.
If the modulo (value % divisor) is 0, the job will fail.
=cut
=head1 CONTACT
ensembl-dev@ebi.ac.uk
=cut
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......@@ -50,6 +42,8 @@ Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Hive::RunnableDB::Test;
use strict;
......
......@@ -7,30 +7,33 @@
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Hive::URLFactory
=head1 SYNOPSIS
$someObj = Bio::EnsEMBL::Hive::URLFactory->fetch($url_string);
Bio::EnsEMBL::Hive::URLFactory->store($object);
=head1 DESCRIPTION
Module to parse URL strings and return EnsEMBL objects be them
DBConnections, DBAdaptors, or specifics like Analysis, Member, Gene, ....
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
=cut
# Let the code begin...
# global instance to cache connection to limit the number of open DB connections
my $_URLFactory_global_instance;
......
......@@ -9,8 +9,6 @@
Bio::EnsEMBL::Hive::Worker
=cut
=head1 DESCRIPTION
Object which encapsulates the details of how to find jobs, how to run those
......@@ -51,14 +49,9 @@
It is also responsible for interfacing with the Queen to identify workers which died
unexpectantly so that she can free the dead workers unfinished jobs.
=cut
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=head1 APPENDIX
......
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