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 @@ ...@@ -49,11 +49,9 @@
It is also responsible for interfacing with the Queen to identify workers which died 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. unexpectantly so that she can free the dead workers unfinished jobs.
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX =head1 APPENDIX
......
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code =pod
=head1 NAME =head1 NAME
...@@ -28,8 +28,7 @@ ...@@ -28,8 +28,7 @@
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX =head1 APPENDIX
...@@ -39,8 +38,6 @@ ...@@ -39,8 +38,6 @@
=cut =cut
# Let the code begin...
package Bio::EnsEMBL::Hive::AnalysisCtrlRule; package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
......
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod =pod
...@@ -16,8 +14,7 @@ ...@@ -16,8 +14,7 @@
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX =head1 APPENDIX
...@@ -26,6 +23,7 @@ ...@@ -26,6 +23,7 @@
=cut =cut
package Bio::EnsEMBL::Hive::AnalysisJob; package Bio::EnsEMBL::Hive::AnalysisJob;
use strict; use strict;
......
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod =pod
=head1 NAME =head1 NAME
Bio::EnsEMBL::Hive::AnalysisStats Bio::EnsEMBL::Hive::AnalysisStats
=head1 SYNOPSIS =head1 SYNOPSIS
...@@ -13,14 +12,17 @@ ...@@ -13,14 +12,17 @@
=head1 DESCRIPTION =head1 DESCRIPTION
=head1 CONTACT =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 =head1 APPENDIX
The rest of the documentation details each of the object methods. The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _ Internal methods are usually preceded with a _
=cut =cut
package Bio::EnsEMBL::Hive::AnalysisStats; package Bio::EnsEMBL::Hive::AnalysisStats;
use strict; use strict;
......
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code =pod
=head1 NAME =head1 NAME
...@@ -25,8 +25,7 @@ ...@@ -25,8 +25,7 @@
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX =head1 APPENDIX
...@@ -36,8 +35,6 @@ ...@@ -36,8 +35,6 @@
=cut =cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor; package Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
......
...@@ -7,33 +7,35 @@ ...@@ -7,33 +7,35 @@
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code =pod
=head1 NAME =head1 NAME
Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
=head1 SYNOPSIS =head1 SYNOPSIS
$dataDBA = $db_adaptor->get_AnalysisDataAdaptor; $dataDBA = $db_adaptor->get_AnalysisDataAdaptor;
=head1 DESCRIPTION =head1 DESCRIPTION
analysis_data table holds LONGTEXT data for use by the analysis system. 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 This data is general purpose and it's up to each analysis to
determine how to use it. determine how to use it.
This Adaptor module is used to access/store this data. This Adaptor module is used to access/store this data.
=head1 CONTACT =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 =head1 APPENDIX
The rest of the documentation details each of the object methods. The rest of the documentation details each of the object methods.
Internal methods are preceded with a _ Internal methods are preceded with a _
=cut =cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor; package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
......
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code =pod
=head1 NAME =head1 NAME
...@@ -25,8 +25,7 @@ ...@@ -25,8 +25,7 @@
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX =head1 APPENDIX
...@@ -36,7 +35,6 @@ ...@@ -36,7 +35,6 @@
=cut =cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor; package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
......
...@@ -7,31 +7,34 @@ ...@@ -7,31 +7,34 @@
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code =pod
=head1 NAME =head1 NAME
Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor
=head1 SYNOPSIS =head1 SYNOPSIS
$analysisStatsAdaptor = $db_adaptor->get_AnalysisStatsAdaptor; $analysisStatsAdaptor = $db_adaptor->get_AnalysisStatsAdaptor;
$analysisStatsAdaptor = $analysisStats->adaptor; $analysisStatsAdaptor = $analysisStats->adaptor;
=head1 DESCRIPTION =head1 DESCRIPTION
Module to encapsulate all db access for persistent class AnalysisStats. Module to encapsulate all db access for persistent class AnalysisStats.
There should be just one per application and database connection. There should be just one per application and database connection.
=head1 CONTACT =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 =head1 APPENDIX
The rest of the documentation details each of the object methods. The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _ Internal methods are usually preceded with a _
=cut =cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor; package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
......
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code =pod
=head1 NAME =head1 NAME
...@@ -22,20 +22,17 @@ Bio::EnsEMBL::Hive::DBSQL::DBAdaptor ...@@ -22,20 +22,17 @@ Bio::EnsEMBL::Hive::DBSQL::DBAdaptor
-driver => 'mysql', -driver => 'mysql',
); );
=head1 DESCRIPTION =head1 DESCRIPTION
This object represents the handle for a Hive system enabled database This object represents the handle for a Hive system enabled database
=head1 CONTACT =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 =cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor; package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
use vars qw(@ISA); use vars qw(@ISA);
......
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code =pod
=head1 NAME =head1 NAME
...@@ -25,8 +25,7 @@ ...@@ -25,8 +25,7 @@
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX =head1 APPENDIX
...@@ -36,9 +35,6 @@ ...@@ -36,9 +35,6 @@
=cut =cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor; package Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
use strict; use strict;
......
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code =pod
=head1 NAME =head1 NAME
...@@ -25,11 +25,9 @@ ...@@ -25,11 +25,9 @@
be specified with a network savy URL like be specified with a network savy URL like
mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34' mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34'
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX =head1 APPENDIX
...@@ -39,9 +37,6 @@ ...@@ -39,9 +37,6 @@
=cut =cut
# Let the code begin...
package Bio::EnsEMBL::Hive::DataflowRule; package Bio::EnsEMBL::Hive::DataflowRule;
use strict; use strict;
......
...@@ -9,24 +9,15 @@ ...@@ -9,24 +9,15 @@
Bio::EnsEMBL::Hive::Extensions Bio::EnsEMBL::Hive::Extensions
=cut
=head1 SYNOPSIS =head1 SYNOPSIS
Object categories to extend the functionality of existing classes Object categories to extend the functionality of existing classes
=cut
=head1 DESCRIPTION =head1 DESCRIPTION
=cut
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
=head1 APPENDIX =head1 APPENDIX
...@@ -35,6 +26,7 @@ ...@@ -35,6 +26,7 @@
=cut =cut
use strict; use strict;
use Bio::EnsEMBL::Utils::Exception; use Bio::EnsEMBL::Utils::Exception;
......
# You may distribute this module under the same terms as perl itself # # You may distribute this module under the same terms as perl itself #
# POD documentation - main docs before the code
=pod =pod
...@@ -7,8 +6,6 @@ ...@@ -7,8 +6,6 @@
Bio::EnsEMBL::Hive::Process Bio::EnsEMBL::Hive::Process
=cut
=head1 SYNOPSIS =head1 SYNOPSIS
Abstract superclass. Each Process makes up the individual building blocks Abstract superclass. Each Process makes up the individual building blocks
...@@ -73,14 +70,9 @@ ...@@ -73,14 +70,9 @@
http://en.wikipedia.org/wiki/Emergence http://en.wikipedia.org/wiki/Emergence
=cut
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
=head1 APPENDIX =head1 APPENDIX
...@@ -89,6 +81,8 @@ ...@@ -89,6 +81,8 @@
=cut =cut
my $g_hive_process_workdir; # a global directory location for the process using this module my $g_hive_process_workdir; # a global directory location for the process using this module
package Bio::EnsEMBL::Hive::Process; package Bio::EnsEMBL::Hive::Process;
......
# #
# You may distribute this module under the same terms as perl itself # You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod =pod
...@@ -49,8 +47,7 @@ ...@@ -49,8 +47,7 @@
=head1 CONTACT =head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX =head1 APPENDIX
...@@ -59,6 +56,7 @@ ...@@ -59,6 +56,7 @@