galaxy-commits March 2016

galaxy-commits@lists.galaxyproject.org

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208 discussions

[galaxyproject/usegalaxy-playbook] df8167: Update Test
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: df8167b2768a59d769adbafff5eebe94359b0007 https://github.com/galaxyproject/usegalaxy-playbook/commit/df8167b2768a59d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 0e0c1c: Fixing subworkflow migration (0131) to work with m...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e0c1caec4f14e0a5240763e697bd5d3613db719 https://github.com/galaxyproject/galaxy/commit/0e0c1caec4f14e0a5240763e697b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Fixing subworkflow migration (0131) to work with mysql Commit: 6442cbc3d4340ea3d03dad01c3ebf2dce05ed6e1 https://github.com/galaxyproject/galaxy/commit/6442cbc3d4340ea3d03dad01c3eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Fix downgrade attempting to drop parent_workflow_id off the wrong table. Commit: b23c354f91f9d1a572f488a4d49f25b8681e58ba https://github.com/galaxyproject/galaxy/commit/b23c354f91f9d1a572f488a4d49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Replace testing keynames with real ones. Commit: ad6273307da4b971ea4354d9ad33cb08ca912577 https://github.com/galaxyproject/galaxy/commit/ad6273307da4b971ea4354d9ad33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- We can't flip storedworkflow back to non-nullable in a downgrade step here, so don't try. Just leave it alone. Commit: 0f97b50e9ca8ca8b54e8d30769cd3fe46204f27c https://github.com/galaxyproject/galaxy/commit/0f97b50e9ca8ca8b54e8d30769cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Different logic for mysql (just don't worry about keys, due to the agony -- access to the database is entirely procedural and due to this we'd likely see any issues breaking these fk constraints in postgres before mysql (if ever) anyway. Commit: 30750c32e4817de18aecba8bc4f523f4369e7292 https://github.com/galaxyproject/galaxy/commit/30750c32e4817de18aecba8bc4f5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Merge pull request #1880 from dannon/fix_migration_0131_mysql [16.01] Fixes to subworkflow migration 0131 Commit: 45c17318889d03df39e7bda66403d169ea098778 https://github.com/galaxyproject/galaxy/commit/45c17318889d03df39e7bda66403… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/35403f2a91eb...45c17318889d

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[galaxyproject/galaxy] 0e0c1c: Fixing subworkflow migration (0131) to work with m...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 0e0c1caec4f14e0a5240763e697bd5d3613db719 https://github.com/galaxyproject/galaxy/commit/0e0c1caec4f14e0a5240763e697b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Fixing subworkflow migration (0131) to work with mysql Commit: 6442cbc3d4340ea3d03dad01c3ebf2dce05ed6e1 https://github.com/galaxyproject/galaxy/commit/6442cbc3d4340ea3d03dad01c3eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Fix downgrade attempting to drop parent_workflow_id off the wrong table. Commit: b23c354f91f9d1a572f488a4d49f25b8681e58ba https://github.com/galaxyproject/galaxy/commit/b23c354f91f9d1a572f488a4d49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Replace testing keynames with real ones. Commit: ad6273307da4b971ea4354d9ad33cb08ca912577 https://github.com/galaxyproject/galaxy/commit/ad6273307da4b971ea4354d9ad33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- We can't flip storedworkflow back to non-nullable in a downgrade step here, so don't try. Just leave it alone. Commit: 0f97b50e9ca8ca8b54e8d30769cd3fe46204f27c https://github.com/galaxyproject/galaxy/commit/0f97b50e9ca8ca8b54e8d30769cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Different logic for mysql (just don't worry about keys, due to the agony -- access to the database is entirely procedural and due to this we'd likely see any issues breaking these fk constraints in postgres before mysql (if ever) anyway. Commit: 30750c32e4817de18aecba8bc4f523f4369e7292 https://github.com/galaxyproject/galaxy/commit/30750c32e4817de18aecba8bc4f5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Merge pull request #1880 from dannon/fix_migration_0131_mysql [16.01] Fixes to subworkflow migration 0131 Compare: https://github.com/galaxyproject/galaxy/compare/566f556b076d...30750c32e481

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[galaxyproject/galaxy] e2a036: Fix farbtastic's use of deprecated jquery fns by l...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… Compare: https://github.com/galaxyproject/galaxy/compare/d225aebc8879...9cff686d6d94

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[galaxyproject/galaxy] 4b1b15: libraries: provide select all/none options when im...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b1b15aee85c4aed85fe91c72712f2f5086dfd23 https://github.com/galaxyproject/galaxy/commit/4b1b15aee85c4aed85fe91c72712… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- libraries: provide select all/none options when importing improve UX by using autofocus in modals fix a bug with selecting all folder items and deleting Commit: 35403f2a91eb33876c973f859fa038f9655dc297 https://github.com/galaxyproject/galaxy/commit/35403f2a91eb33876c973f859fa0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #1970 from martenson/select-all-from-history libraries: provide select all/none options when importing Compare: https://github.com/galaxyproject/galaxy/compare/c26788a267b9...35403f2a91eb

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[galaxyproject/galaxy] 4e3ca9: Fix nginx-based file upload
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e3ca993f213f17568324c98ba05aafe8efe8467 https://github.com/galaxyproject/galaxy/commit/4e3ca993f213f17568324c98ba05… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix nginx-based file upload Commit: c26788a267b9caec3bfb28ca752a6a0585535767 https://github.com/galaxyproject/galaxy/commit/c26788a267b9caec3bfb28ca752a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1971 from guerler/fix_nginx_upload_000 Fix nginx-based file upload Compare: https://github.com/galaxyproject/galaxy/compare/35e75d11cea6...c26788a267b9

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[galaxyproject/galaxy] bd0439: Fix tool access rights and forwarding
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd0439d9b724bb72c1fab4c27a4c72814abef0b9 https://github.com/galaxyproject/galaxy/commit/bd0439d9b724bb72c1fab4c27a4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix tool access rights and forwarding Commit: 054fdf76f09faf35662adf0f4a8a6f6428abab4f https://github.com/galaxyproject/galaxy/commit/054fdf76f09faf35662adf0f4a8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Parse user when filtering tools Commit: 566f556b076db164ce73750f33c9824fe0285530 https://github.com/galaxyproject/galaxy/commit/566f556b076db164ce73750f33c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #1952 from guerler/fix_tool_access_000 [16.01] Fix tool access rights and forwarding Commit: 35e75d11cea6e6b0e75fade9eabb1fd96bdd99af https://github.com/galaxyproject/galaxy/commit/35e75d11cea6e6b0e75fade9eabb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge branch 'release_16.01' into dev. Rebuild client. Compare: https://github.com/galaxyproject/galaxy/compare/c64c6754a84c...35e75d11cea6

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[galaxyproject/galaxy] bd0439: Fix tool access rights and forwarding
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bd0439d9b724bb72c1fab4c27a4c72814abef0b9 https://github.com/galaxyproject/galaxy/commit/bd0439d9b724bb72c1fab4c27a4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix tool access rights and forwarding Commit: 054fdf76f09faf35662adf0f4a8a6f6428abab4f https://github.com/galaxyproject/galaxy/commit/054fdf76f09faf35662adf0f4a8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Parse user when filtering tools Commit: 566f556b076db164ce73750f33c9824fe0285530 https://github.com/galaxyproject/galaxy/commit/566f556b076db164ce73750f33c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #1952 from guerler/fix_tool_access_000 [16.01] Fix tool access rights and forwarding Compare: https://github.com/galaxyproject/galaxy/compare/377ccbe23b71...566f556b076d

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[galaxyproject/galaxy] 9e9dfd: Fix workflow scheduler log message.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e9dfdfd55b2b8d2377f8ef4e288a1fa482105b9 https://github.com/galaxyproject/galaxy/commit/9e9dfdfd55b2b8d2377f8ef4e288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix workflow scheduler log message. Commit: 5f5f0af5cd5e21c64810d29202e149915226c34a https://github.com/galaxyproject/galaxy/commit/5f5f0af5cd5e21c64810d29202e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1955 from jmchilton/fix_wf_log_message [16.01] Fix workflow scheduler log message. Commit: 2efd9c2687d2ca818520249cdb3484e781659069 https://github.com/galaxyproject/galaxy/commit/2efd9c2687d2ca818520249cdb34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1721. TODO: write test... Commit: 377ccbe23b717f9c8cb0d571de9f0d6da08a1ee8 https://github.com/galaxyproject/galaxy/commit/377ccbe23b717f9c8cb0d571de9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1967 from jmchilton/fix_optional_numeric_params [16.01] Fix #1721. Commit: 8d37aeff507b2fa16a1164eeb64a771746d4767d https://github.com/galaxyproject/galaxy/commit/8d37aeff507b2fa16a1164eeb64a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/run.py Log Message: ----------- Manual merge to resolve conflict 16.01->dev Commit: c64c6754a84cfb399a9e3f230f08a6a6294406fa https://github.com/galaxyproject/galaxy/commit/c64c6754a84cfb399a9e3f230f08… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1969 from dannon/dev Merge 16.01->dev Compare: https://github.com/galaxyproject/galaxy/compare/67e6ced2118b...c64c6754a84c

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[galaxyproject/usegalaxy-playbook] 1cef1b: IE version update
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1cef1b4cd90ad8fb46cef0d4605569e692baa97a https://github.com/galaxyproject/usegalaxy-playbook/commit/1cef1b4cd90ad8fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- IE version update Commit: 31c916930b6a264dd7b34f92f2302f507b427a3e https://github.com/galaxyproject/usegalaxy-playbook/commit/31c916930b6a264d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs on test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/19f8ce2bcef0...…

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galaxy-commits March 2016