Commit 61deb3f4 authored by Leo Gordon's avatar Leo Gordon
Browse files

added Apache 2.0 license to all files

parent a55a3d94
=pod
=head1 NAME
MiniPecanMulti_conf
MiniPecanMulti_conf
=head1 SYNOPSIS
......@@ -25,12 +24,26 @@
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
package MiniPecanMulti_conf;
use strict;
......
=pod
=head1 NAME
MiniPecanSingle2_conf
MiniPecanSingle2_conf
=head1 SYNOPSIS
......@@ -25,12 +24,26 @@
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
package MiniPecanSingle2_conf;
use strict;
......
=pod
=head1 NAME
MiniPecanSingle3_conf
MiniPecanSingle3_conf
=head1 SYNOPSIS
......@@ -25,12 +24,26 @@
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
package MiniPecanSingle3_conf;
use strict;
......
=pod
=head1 NAME
MiniPecanSingle_conf
MiniPecanSingle_conf
=head1 SYNOPSIS
......@@ -25,12 +24,26 @@
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
package MiniPecanSingle_conf;
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
Bio::EnsEMBL::Hive
=head1 DESCRIPTION
......@@ -49,14 +44,22 @@
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
=head1 LICENSE
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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
=head1 APPENDIX
http://www.apache.org/licenses/LICENSE-2.0
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
......
......@@ -2,21 +2,33 @@
=head1 NAME
Bio::EnsEMBL::Hive::Accumulator
=head1 SYNOPSIS
Bio::EnsEMBL::Hive::Accumulator
=head1 DESCRIPTION
A data container object that defines parameters for accumulated dataflow.
This object is generated from specially designed datalow URLs.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
package Bio::EnsEMBL::Hive::Accumulator;
use strict;
......
......@@ -2,9 +2,7 @@
=head1 NAME
Bio::EnsEMBL::Hive::Analysis
=head1 SYNOPSIS
Bio::EnsEMBL::Hive::Analysis
=head1 DESCRIPTION
......@@ -15,12 +13,26 @@
Control rules unblock when their condition Analyses are done.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
package Bio::EnsEMBL::Hive::Analysis;
use strict;
......
# Perl module for Bio::EnsEMBL::Hive::AnalysisCtrlRule
#
# Creator: Jessica Severin <jessica@ebi.ac.uk>
# Date of creation: 22.03.2004
#
# Copyright EMBL-EBI 2000-2004
#
# You may distribute this module under the same terms as perl itself
=pod
=head1 NAME
Bio::EnsEMBL::Hive::AnalysisCtrlRule
=head1 SYNOPSIS
Bio::EnsEMBL::Hive::AnalysisCtrlRule
=head1 DESCRIPTION
An 'analysis control rule' is a high level blocking control structure where there is
a 'ctrled_analysis' which is 'BLOCKED' from running until all of its 'condition_analysis' are 'DONE'.
If a ctrled_analysis requires multiple analysis to be DONE before it can run, a separate
AnalysisCtrlRule must be created/stored for each condtion analysis.
Allows the 'condition' analysis to be specified with a network savy URL like
mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34'
An 'analysis control rule' is a high level blocking control structure where there is
a 'ctrled_analysis' which is 'BLOCKED' from running until all of its 'condition_analysis' are 'DONE'.
If a ctrled_analysis requires multiple analysis to be DONE before it can run, a separate
AnalysisCtrlRule must be created/stored for each condtion analysis.
Allows the 'condition' analysis to be specified with a network savy URL like
mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34'
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
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 _
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
use strict;
......
#
# You may distribute this module under the same terms as perl itself
=pod
=head1 NAME
Bio::EnsEMBL::Hive::AnalysisJob
Bio::EnsEMBL::Hive::AnalysisJob
=head1 DESCRIPTION
An AnalysisJob is the link between the input_id control data, the analysis and
the rule system. It also tracks the state of the job as it is processed
An AnalysisJob is the link between the input_id control data, the analysis and
the rule system. It also tracks the state of the job as it is processed
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
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 _
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
......
#
# You may distribute this module under the same terms as perl itself
=pod
=head1 NAME
Bio::EnsEMBL::Hive::AnalysisStats
=head1 SYNOPSIS
Bio::EnsEMBL::Hive::AnalysisStats
=head1 DESCRIPTION
An object that maintains counters for jobs in different states. This data is used by the Scheduler.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
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 _
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
......
# A base class for objects that we want to be configurable in the following sense:
# 1) have a pointer to the $config
# 2) know their context
# 3) automatically apply that context when getting and setting
=pod
=head1 NAME
Bio::EnsEMBL::Hive::Configurable
=head1 DESCRIPTION
A base class for objects that we want to be configurable in the following sense:
1) have a pointer to the $config
2) know their context
3) automatically apply that context when getting and setting
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
package Bio::EnsEMBL::Hive::Configurable;
......
......@@ -12,6 +12,19 @@
This is currently an "objectless" adaptor for building accumulated structures.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
......
......@@ -2,22 +2,35 @@
=head1 NAME
Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor
Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor
=head1 SYNOPSIS
$analysis_adaptor = $db_adaptor->get_AnalysisAdaptor;
$analysis_adaptor = $db_adaptor->get_AnalysisAdaptor;
$analysis_adaptor = $analysis_object->adaptor;
$analysis_adaptor = $analysis_object->adaptor;
=head1 DESCRIPTION
Module to encapsulate all db access for persistent class Analysis.
There should be just one such adaptor per application and database connection.
Module to encapsulate all db access for persistent class Analysis.
There should be just one such adaptor per application and database connection.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
......
......@@ -2,21 +2,34 @@
=head1 NAME
Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor
Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor
=head1 SYNOPSIS
$analysis_ctrl_rule_adaptor = $db_adaptor->get_AnalysisCtrlRuleAdaptor;
$analysis_ctrl_rule_adaptor = $analysisCtrlRuleObj->adaptor;
$analysis_ctrl_rule_adaptor = $db_adaptor->get_AnalysisCtrlRuleAdaptor;
$analysis_ctrl_rule_adaptor = $analysisCtrlRuleObj->adaptor;
=head1 DESCRIPTION
Module to encapsulate all db access for persistent class AnalysisCtrlRule.
There should be just one per application and database connection.
Module to encapsulate all db access for persistent class AnalysisCtrlRule.
There should be just one per application and database connection.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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 contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
......
# Perl module for Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
#
# Date of creation: 22.03.2004
# Original Creator : Jessica Severin <jessica@ebi.ac.uk>
#
# Copyright EMBL-EBI 2004
#
# You may distribute this module under the same terms as perl itself
=pod
=head1 NAME
Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
=head1 SYNOPSIS
$dataDBA = $db_adaptor->get_AnalysisDataAdaptor;
$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.
analysis_data table holds LONGTEXT data that is currently used as an extension of some fixed-width fields of 'job' table.
It is no longer general-purpose. Please avoid accessing this table directly or via the adaptor.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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.