Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f64d1597b84801dd48c2cdb5bc0c303355786942 https://github.com/galaxyproject/galaxy/commit/f64d1597b84801dd48c2cdb5bc0c3... Author: John Chilton <jmchilton@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/ea9f4a0467b6955ccc470da06eaf7... Author: John Chilton <jmchilton@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/7ce43a0463c3d98b757d78d0600aa... Author: John Chilton <jmchilton@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/77ed5681f8565b12ab1d5e5c7d030... Author: John Chilton <jmchilton@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/42778e27539d919ff11d67a07368c... Author: John Chilton <jmchilton@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/28501ab676f9df797bae316c3d24e... Author: John Chilton <jmchilton@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/4584a579a297ffd02bd77584b71a8... Author: John Chilton <jmchilton@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/21213ef70f535e06bc48537068680... Author: John Chilton <jmchilton@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/031a39aba83932fd0291f440a7e58... Author: John Chilton <jmchilton@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/8a01b42112ec32e5f978f3a424512... Author: John Chilton <jmchilton@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/cf367ff0c75454837359b74046c05... Author: John Chilton <jmchilton@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/7974c1f33486c0a66803004c5d788... Author: John Chilton <jmchilton@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/07c3d10f31e48f783baf05c133b11... Author: John Chilton <jmchilton@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/48340b5829fb5ca346060d9372ba7... Author: John Chilton <jmchilton@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/dd5f3aec52d1cec8e2a98dc9cf713... Author: John Chilton <jmchilton@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/20b96d883d9ef33b51d5a32d82ce2... Author: Nicola Soranzo <nsoranzo@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