Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d8edce33157e81112889ae7f241903747da3c92 https://github.com/galaxyproject/galaxy/commit/6d8edce33157e81112889ae7f2419... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Admin doc corrections Commit: f24043e8a74e3cb2070b06652d9a72be46e6a278 https://github.com/galaxyproject/galaxy/commit/f24043e8a74e3cb2070b06652d9a7... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5441 from natefoo/framework-dependencies-doc-update-18.01 [18.01] Admin doc corrections Commit: 7490fd452046b4a4578f6401501439773cbf2f28 https://github.com/galaxyproject/galaxy/commit/7490fd452046b4a4578f640150143... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- More robust nametag discovery and propagation. - Nametags weren't being picked up on collection inputs - so for instance tools that take in a single collection and produce a dataset or file weren't propagating nametags (unless the collection contents had tags). To see this create two unnamed datasets without tags, create a pair from them, add a tag to the pair, and run the pair through the "paired_test" test tool. - Nametags weren't being propagated to the outputs of collection operations. Commit: 6f40f7098d507895c6c6608aff6a698289f2eeb6 https://github.com/galaxyproject/galaxy/commit/6f40f7098d507895c6c6608aff6a6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cleanup collection operation tagging implementation thanks to @mvdbeek comments. Commit: 6022fe7d7e90b0da0cad83589d5d630f6dd1d386 https://github.com/galaxyproject/galaxy/commit/6022fe7d7e90b0da0cad83589d5d6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle optional inputs when collecting preserved tags. https://github.com/galaxyproject/galaxy/pull/5403/files#r165283450 Commit: 60561c20307cf0585e553d0fa5cd612716ab7975 https://github.com/galaxyproject/galaxy/commit/60561c20307cf0585e553d0fa5cd6... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- Merge pull request #5403 from jmchilton/collection_operation_tags [18.01] More robust nametag discovery and propagation. Commit: a392b5750aa776fbc8ba27736d78901ddf0db29d https://github.com/galaxyproject/galaxy/commit/a392b5750aa776fbc8ba27736d789... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail Commit: 2b8df110d0fad7c874c35c3176bf18d65cbcdbe3 https://github.com/galaxyproject/galaxy/commit/2b8df110d0fad7c874c35c3176bf1... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Apply rename PJA to collection outputs including $ replacements. Update PJA collection test to test HDCA is renamed also. Commit: f6f9f9a8914845c995d665dc5396ac5e43187324 https://github.com/galaxyproject/galaxy/commit/f6f9f9a8914845c995d665dc5396a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Extend mapped collection output rename PJAs to include # replacements. Also make sure output collections in non-mapping scenarios are also properly renamed as well. Commit: 0529153ac090de0601f38af2fbf4f9a4fcccb615 https://github.com/galaxyproject/galaxy/commit/0529153ac090de0601f38af2fbf4f... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix bug in PJAs for collection mapping. Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157). Commit: 6c013d0cb3eebffdb69c865a4cbe4019bd8ab95e https://github.com/galaxyproject/galaxy/commit/6c013d0cb3eebffdb69c865a4cbe4... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #5444 from dannon/multidelete_fix [18.01] Ensure jobStateSummariesCollection exists; Commit: fbfbdd51bb3e06754efc1ae9e0cec4c1c1db9ce4 https://github.com/galaxyproject/galaxy/commit/fbfbdd51bb3e06754efc1ae9e0cec... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5416 from jmchilton/rename_collections_pja [18.01] Fix rename post job actions to be more intuitive when mapping over collections. Commit: 245394acb694020c0f9f78185749fbccf45ec587 https://github.com/galaxyproject/galaxy/commit/245394acb694020c0f9f78185749f... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/988cab4db7ef...245394acb694