Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 97415de3ce2bda54fb0730a41b4e0c7d8e93778a
https://github.com/galaxyproject/galaxy/commit/97415de3ce2bda54fb0730a41b4e…
Author: chambm <matt.chambers42(a)gmail.com>
Date: 2015-12-02 (Wed, 02 Dec 2015)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/test.idpDB
A lib/galaxy/datatypes/test/test.mz5
Log Message:
-----------
Move idpDB and MzSQlite formats from proteomics.py to binary.py, because the SQLite sniffer lives there, and more specialized formats must be registered for sniffing before the generic format
Add proper idpDB sniffing logic (akin to MzSQlite) and test case
Add H5 sniffing based on magic number and test case
Add SQLite/IdpDB/MzSQlite/GeminiSQLite and H5 to default datatypes in registry.py
Commit: 65e6a1c3b6ca26e9f0d760cb39be7ec177d6c40f
https://github.com/galaxyproject/galaxy/commit/65e6a1c3b6ca26e9f0d760cb39be…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/test.idpDB
A lib/galaxy/datatypes/test/test.mz5
Log Message:
-----------
Merge pull request #1209 from chambm/feature/idpdb_hdf5_sniffers
Add idpDB and HDF5 sniffers and fix MzSQlite sniffer
Compare: https://github.com/galaxyproject/galaxy/compare/c034dc3e33a4...65e6a1c3b6ca
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f64d1597b84801dd48c2cdb5bc0c303355786942
https://github.com/galaxyproject/galaxy/commit/f64d1597b84801dd48c2cdb5bc0c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Extension point for environment variables.
Commit: ea9f4a0467b6955ccc470da06eaf7c13e7643715
https://github.com/galaxyproject/galaxy/commit/ea9f4a0467b6955ccc470da06eaf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Initialize a ToolOutput.from_work_dir.
Commit: 7ce43a0463c3d98b757d78d0600aadf5d7876eb9
https://github.com/galaxyproject/galaxy/commit/7ce43a0463c3d98b757d78d0600a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Refactor run_request for downstream diff improvements.
Commit: 77ed5681f8565b12ab1d5e5c7d0302c938e9c73d
https://github.com/galaxyproject/galaxy/commit/77ed5681f8565b12ab1d5e5c7d03…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Extend base api workflow _run_jobs helper...
... to allow loading content from test-data files.
Commit: 42778e27539d919ff11d67a07368c0b6e4ebae75
https://github.com/galaxyproject/galaxy/commit/42778e27539d919ff11d67a07368…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/workflow/run.py
Log Message:
-----------
Improved error handling in workflow run code.
Commit: 28501ab676f9df797bae316c3d24e9ae8fd58a9b
https://github.com/galaxyproject/galaxy/commit/28501ab676f9df797bae316c3d24…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/managers/workflows.py
M test/unit/test_galaxy_mapping.py
Log Message:
-----------
Refactor workflow manager for extension.
Commit: 4584a579a297ffd02bd77584b71a8c17d85d261a
https://github.com/galaxyproject/galaxy/commit/4584a579a297ffd02bd77584b71a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix interface declaration for WorkflowModule.get_state.
Implementers all take this attribute.
Commit: 21213ef70f535e06bc485370686807a6d2850345
https://github.com/galaxyproject/galaxy/commit/21213ef70f535e06bc4853706868…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M test/unit/workflows/test_render.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Refactor workflow testing code to quickly bootstrap workflows.
Commit: 031a39aba83932fd0291f440a7e58c962deadfe8
https://github.com/galaxyproject/galaxy/commit/031a39aba83932fd0291f440a7e5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
A test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Basic unit tests for workflow progress tracking.
Commit: 8a01b42112ec32e5f978f3a4245127cad3219c45
https://github.com/galaxyproject/galaxy/commit/8a01b42112ec32e5f978f3a42451…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Refactor input_by_connections_name logic into model.
Continue to delay calculation of this but auto-compute it if requested and module injection code hasn't been called explicitly. Moves logic internal to class where it belongs also.
Commit: cf367ff0c75454837359b74046c05cc7cb456dc5
https://github.com/galaxyproject/galaxy/commit/cf367ff0c75454837359b74046c0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M test/unit/workflows/test_workflow_progress.py
Log Message:
-----------
Add another workflow progress test case.
This one for replacing a tool input with an input dataset.
Commit: 7974c1f33486c0a66803004c5d7885a9d91b9c70
https://github.com/galaxyproject/galaxy/commit/7974c1f33486c0a66803004c5d78…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M test/unit/workflows/test_workflow_progress.py
Log Message:
-----------
Add unit tests for workflow progress initialization.
Commit: 07c3d10f31e48f783baf05c133b117e7f3e7ee1a
https://github.com/galaxyproject/galaxy/commit/07c3d10f31e48f783baf05c133b1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M test/unit/workflows/test_workflow_progress.py
Log Message:
-----------
Extend workflow recovery progress test case to include replacement check.
Commit: 48340b5829fb5ca346060d9372ba7df7e3effcef
https://github.com/galaxyproject/galaxy/commit/48340b5829fb5ca346060d9372ba…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M test/unit/workflows/test_workflow_progress.py
Log Message:
-----------
Add TODO items to workflow progress unit tests.
Commit: dd5f3aec52d1cec8e2a98dc9cf7134cd9b381d84
https://github.com/galaxyproject/galaxy/commit/dd5f3aec52d1cec8e2a98dc9cf71…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Fix workflow extraction test cases broken with 77ed5681f8565b12ab1d5e5c7d0302c938e9c73d
Commit: 20b96d883d9ef33b51d5a32d82ce2d1251daf572
https://github.com/galaxyproject/galaxy/commit/20b96d883d9ef33b51d5a32d82ce…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M test/api/test_workflows.py
M test/unit/test_galaxy_mapping.py
M test/unit/workflows/test_render.py
A test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Merge pull request #1202 from jmchilton/workflow_tool_refactoring
Small Tool and Workflow Refactoring and Fixes
Compare: https://github.com/galaxyproject/galaxy/compare/ffb3de9ede51...20b96d883d9e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0c22d138891604d0df98784ab7edc43e9b541c1d
https://github.com/galaxyproject/galaxy/commit/0c22d138891604d0df98784ab7ed…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-11-20 (Fri, 20 Nov 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parser/xml.py
A test/functional/tools/collection_type_source.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Implement type_source on output collections.
Inherit collection_type from an input, the way metadata and format can be.
This commit includes a test tool demonstrating this functionality. The tool test for this tool can be executed using the following command:
```
./run_tests.sh -framework -id collection_type_source
```
Commit: ffb3de9ede515d10fbdf06519140a726e0cfa7d1
https://github.com/galaxyproject/galaxy/commit/ffb3de9ede515d10fbdf06519140…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-02 (Wed, 02 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parser/xml.py
A test/functional/tools/collection_type_source.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #1153 from jmchilton/collection_type_source
Implement type_source on output collections.
Compare: https://github.com/galaxyproject/galaxy/compare/67c98f54cad4...ffb3de9ede51
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 8597fdb06f69c4b0cade4b9e8f363aebe3c67704
https://github.com/galaxyproject/infrastructure-playbook/commit/8597fdb06f6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-01 (Tue, 01 Dec 2015)
Changed paths:
M galaxyenv/group_vars/starforgebuilders.yml
M galaxyenv/secret_group_vars/all.yml
M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml
M galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml
Log Message:
-----------
Allow jenkins to log in to mjolnir0 for building wheels