galaxy-commits February 2016

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[galaxyproject/galaxy] 618189: Fix default option for repeats
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 61818948a163602b3c135937d053fe42c46bb4d2 https://github.com/galaxyproject/galaxy/commit/61818948a163602b3c135937d053… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js Log Message: ----------- Fix default option for repeats Commit: ee4f58ce7d6a81477e5e4fc3e544e5da909f1198 https://github.com/galaxyproject/galaxy/commit/ee4f58ce7d6a81477e5e4fc3e544… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js Log Message: ----------- Merge pull request #1635 from guerler/fix_repeat_default_001 [16.01] Fix default option for repeats Compare: https://github.com/galaxyproject/galaxy/compare/ade18b3cd23c...ee4f58ce7d6a

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[galaxyproject/galaxy] 2eb686: datalibs: introduce folder management; fix various...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2eb6868955ccf13c71802fd9a42db3bb3b859d05 https://github.com/galaxyproject/galaxy/commit/2eb6868955ccf13c71802fd9a42d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- datalibs: introduce folder management; fix various glitches; refactor Commit: 88ed6e93e84abe155292fc0ffbf21efd4043a9c9 https://github.com/galaxyproject/galaxy/commit/88ed6e93e84abe155292fc0ffbf2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py Log Message: ----------- extend API to show folder.description and dataset.message Commit: 11c5259f46b7d1774ecbee89e2459efa32b30099 https://github.com/galaxyproject/galaxy/commit/11c5259f46b7d1774ecbee89e245… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- fix librarydataset model detection; always show dataset.message and folder.description Commit: 17dcff96011f740d7e60ef09e451844ed39ea398 https://github.com/galaxyproject/galaxy/commit/17dcff96011f740d7e60ef09e451… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- datalib: show nice size after undeleting dataset Commit: cb1010682d5117737c62303aecfce0193088c8db https://github.com/galaxyproject/galaxy/commit/cb1010682d5117737c62303aecfc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py Log Message: ----------- remove abundant dict update Commit: dacb91907af7a885518d79f311e9e3115d3e87e5 https://github.com/galaxyproject/galaxy/commit/dacb91907af7a885518d79f311e9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/style/less/library.less M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #1562 from martenson/datalibs_better_foldermanagement datalibs: introduce folder management; fix various glitches; refactor Compare: https://github.com/galaxyproject/galaxy/compare/962fdc0eba0c...dacb91907af7

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[galaxyproject/usegalaxy-playbook] 376328: Update datatypes_conf.xml on Test
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 37632872d6b7ed9b805fa08fbf0dc0639daaccb3 https://github.com/galaxyproject/usegalaxy-playbook/commit/37632872d6b7ed9b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update datatypes_conf.xml on Test Commit: 37e7fcf578fc182e1fee943be0d244c0c53678b1 https://github.com/galaxyproject/usegalaxy-playbook/commit/37e7fcf578fc182e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Mutable configs (+ ie clone version I forgot to commit) on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d8c80fd42dd5...…

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[galaxyproject/galaxy] 981f90: Attempt to fix transiently failing test due to obj...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 981f904c3f8a501ffabaf7b83538151070bd8a21 https://github.com/galaxyproject/galaxy/commit/981f904c3f8a501ffabaf7b83538… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py Log Message: ----------- Attempt to fix transiently failing test due to object store makedirs call. Failing test - https://jenkins.galaxyproject.org/job/docker-api/2421/testReport/junit/api.…. If you look at the actual source code for os.makedirs - it does inconsistently handle errno.EEXIST - this is probably a better approach than raw os.makedirs for most cases. xref #1617 Commit: ade18b3cd23c54c347d38585736d32da5fccc4dd https://github.com/galaxyproject/galaxy/commit/ade18b3cd23c54c347d38585736d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1623 from jmchilton/makedirs [16.01] Attempt to fix transiently failing test due to objectstore makedirs … Compare: https://github.com/galaxyproject/galaxy/compare/44336b289bd5...ade18b3cd23c

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[galaxyproject/galaxy] 399e0c: Disable individual file metadata changes in upload
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 399e0ced6dd51733ee45c03ac558856e952706d4 https://github.com/galaxyproject/galaxy/commit/399e0ced6dd51733ee45c03ac558… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Disable individual file metadata changes in upload Commit: 962fdc0eba0c3436e034df3068b61e3eaa811c8f https://github.com/galaxyproject/galaxy/commit/962fdc0eba0c3436e034df3068b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #1625 from guerler/fix_upload_000 Disable individual file metadata changes in upload Compare: https://github.com/galaxyproject/galaxy/compare/3deb005e99c6...962fdc0eba0c

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galaxy-commits February 2016