January 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 59001c: Fix refactoring from 7587809b
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59001c61f2a3fa7ea0d1e132b98a9bb00ba91aa2 https://github.com/galaxyproject/galaxy/commit/59001c61f2a3fa7ea0d1e132b98a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Fix refactoring from 7587809b Commit: 923397df9a0678f9e16875716054b5e5d6d20699 https://github.com/galaxyproject/galaxy/commit/923397df9a0678f9e16875716054… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Merge pull request #1459 from dannon/tourfix Fix tour reloading Compare: https://github.com/galaxyproject/galaxy/compare/35c80067ab69...923397df9a06

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[galaxyproject/galaxy] 47361f: Reduce code duplication by reusing get_installed_r...
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 47361f12ecaad83d5d563be763320ae1b17edc3b https://github.com/galaxyproject/galaxy/commit/47361f12ecaad83d5d563be76332… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Conflicts: lib/galaxy/tools/toolbox/base.py Commit: e8e01bdfb19cf1cc8f8cf485762c68d3f8e2f352 https://github.com/galaxyproject/galaxy/commit/e8e01bdfb19cf1cc8f8cf485762c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Conflicts: lib/galaxy/tools/toolbox/base.py Commit: bb8f0f75efb971471fa65c2cc6951bfaa00b0fd0 https://github.com/galaxyproject/galaxy/commit/bb8f0f75efb971471fa65c2cc695… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1455 from jmchilton/release_16.01_merge_1 [16.01] Merge #1314 forward into 16.01. Compare: https://github.com/galaxyproject/galaxy/compare/e36d33ce74ba...bb8f0f75efb9

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[galaxyproject/galaxy] ed992b: A large assortment of escaping fixes to primarily ...
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ed992b3b28c7f6d9d637e82e88305b665733a50b https://github.com/galaxyproject/galaxy/commit/ed992b3b28c7f6d9d637e82e8830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). Commit: 90bed00ebe8a5b4a7e0aeb61c23c991daae03fb8 https://github.com/galaxyproject/galaxy/commit/90bed00ebe8a5b4a7e0aeb61c23c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge 15.07 into 15.10. Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Conflicts: client/galaxy/scripts/mvc/history/multi-panel.js lib/galaxy/webapps/galaxy/controllers/external_service.py lib/galaxy/webapps/galaxy/controllers/forms.py lib/galaxy/webapps/galaxy/controllers/library_admin.py lib/galaxy/webapps/galaxy/controllers/request_type.py lib/galaxy/webapps/galaxy/controllers/requests_admin.py lib/galaxy/webapps/galaxy/controllers/requests_common.py lib/galaxy/webapps/galaxy/controllers/visualization.py lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/controllers/sample_tracking.py lib/galaxy/webapps/reports/controllers/workflows.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/grids/repository_review_grids.py static/maps/mvc/history/multi-panel.js.map static/maps/mvc/ui/ui-select-default.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/collection/list-of-pairs-collection-creator.js static/scripts/mvc/dataset/dataset-li-edit.js static/scripts/mvc/dataset/dataset-li.js static/scripts/mvc/history/history-panel.js static/scripts/mvc/history/multi-panel.js static/scripts/mvc/list/list-panel.js static/scripts/mvc/ui/ui-select-default.js Commit: c13b1c088cfbb0c708b2ce1d9068c704aba6cc95 https://github.com/galaxyproject/galaxy/commit/c13b1c088cfbb0c708b2ce1d9068… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1458 from jmchilton/release_15.10_merge_0 [15.10] Merge 15.07 into 15.10. Compare: https://github.com/galaxyproject/galaxy/compare/7b45f7b40473...c13b1c088cfb

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[galaxyproject/galaxy] cd1cc9: Implement code from @natefoo comment
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd1cc96d5d565299168ac03371d664789bba783b https://github.com/galaxyproject/galaxy/commit/cd1cc96d5d565299168ac03371d6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M Makefile Log Message: ----------- Implement code from @natefoo comment https://github.com/galaxyproject/galaxy/issues/715#issuecomment-169148056 Commit: d848f83e8d0a49f108659838165dffaeeb2939cd https://github.com/galaxyproject/galaxy/commit/d848f83e8d0a49f108659838165d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M Makefile Log Message: ----------- Correct name, minor version Commit: f8072a8e486c4d3d36d946246faf647e3495a5c7 https://github.com/galaxyproject/galaxy/commit/f8072a8e486c4d3d36d946246faf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M Makefile Log Message: ----------- Configurable upstream Commit: 35c80067ab690bed89457c18ecc14fc5053a8dea https://github.com/galaxyproject/galaxy/commit/35c80067ab690bed89457c18ecc1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #1433 from erasche/release-process Add makefile target for release process Compare: https://github.com/galaxyproject/galaxy/compare/ca40d376f7e5...35c80067ab69

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[galaxyproject/galaxy] a964fc: Add run_toolshed_tests.html to .gitignore .
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a964fcc204eeebfaa5c193a8833e399b4abccee9 https://github.com/galaxyproject/galaxy/commit/a964fcc204eeebfaa5c193a8833e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M .gitignore Log Message: ----------- Add run_toolshed_tests.html to .gitignore . Commit: ca40d376f7e589f02605bb622444e7e3dd6ba934 https://github.com/galaxyproject/galaxy/commit/ca40d376f7e589f02605bb622444… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M .gitignore Log Message: ----------- Merge pull request #1456 from nsoranzo/gitignore Add run_toolshed_tests.html to .gitignore . Compare: https://github.com/galaxyproject/galaxy/compare/89781f74a593...ca40d376f7e5

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[galaxyproject/galaxy] 9b4ff6: Clean up: remove print statements in templates
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b4ff63a16edb651ada88a579dc4fbe839e7c85c https://github.com/galaxyproject/galaxy/commit/9b4ff63a16edb651ada88a579dc4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M templates/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Clean up: remove print statements in templates Commit: 89781f74a593943e7d1271a9a68ab0a770ef2bf6 https://github.com/galaxyproject/galaxy/commit/89781f74a593943e7d1271a9a68a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M templates/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Merge pull request #1454 from carlfeberhard/cleanup.grid_template Clean up: remove print statements in templates Compare: https://github.com/galaxyproject/galaxy/compare/7f81a8def003...89781f74a593

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[galaxyproject/galaxy] 07d574: Fix that typo.
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07d574c510611044a1f6bdba1de173ec1a0ad662 https://github.com/galaxyproject/galaxy/commit/07d574c510611044a1f6bdba1de1… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/tool_shed/dependencies/repository/relation_builder.py Log Message: ----------- Fix that typo. Commit: 7f81a8def003f46ba08c9a00b794674c371dc79b https://github.com/galaxyproject/galaxy/commit/7f81a8def003f46ba08c9a00b794… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/tool_shed/dependencies/repository/relation_builder.py Log Message: ----------- Merge pull request #1453 from davebx/that_typo Fix that typo in relation_builder. Compare: https://github.com/galaxyproject/galaxy/compare/33d533812920...7f81a8def003

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[galaxyproject/galaxy] d05ee5: Empty cherry-pick of 93c6d05 to cleanup merge.
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: d05ee507253901ef69a8892f6820b953c8d05725 https://github.com/galaxyproject/galaxy/commit/d05ee507253901ef69a8892f6820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Empty cherry-pick of 93c6d05 to cleanup merge. Commit: e36d33ce74babd939b3e70f30f0bf84f3cd2e527 https://github.com/galaxyproject/galaxy/commit/e36d33ce74babd939b3e70f30f0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1451 from jmchilton/release_16.01_merge_0 [16.01] Empty cherry-pick of 93c6d05 to cleanup merge 15.10 -> 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/88a1e636b8de...e36d33ce74ba

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[galaxyproject/galaxy] 7a3cc4: Fix optional watchdog handling.
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7a3cc410549474de18ff195c0e1dcd76fa92f64b https://github.com/galaxyproject/galaxy/commit/7a3cc410549474de18ff195c0e1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix optional watchdog handling. Broken with 4086dd61dafe562ec01a8b1fce687a539aedbcfe. Thanks for bug report from @nsoranzo. Commit: e611b8fdb80beb87196a685924abe8e71bedcbea https://github.com/galaxyproject/galaxy/commit/e611b8fdb80beb87196a685924ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Use a more typical optional default value for optional import in watcher.py. Thanks to @nsoranzo for the advice - https://github.com/galaxyproject/galaxy/pull/1448#discussion_r49210125. Commit: 88a1e636b8dea04a0db7d557fa6eb1483097b69d https://github.com/galaxyproject/galaxy/commit/88a1e636b8dea04a0db7d557fa6e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #1448 from jmchilton/watcher_fix [16.01] Fix optional watchdog handling. Compare: https://github.com/galaxyproject/galaxy/compare/5d32c9f8fc7e...88a1e636b8de

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[galaxyproject/galaxy] 2f760a: Fix formatting.
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2f760a2e6d3cc098e144a24931cf0af2369e2f44 https://github.com/galaxyproject/galaxy/commit/2f760a2e6d3cc098e144a24931cf… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Fix formatting. Commit: 33d533812920c1bc0e5998cd5564f5da716fc237 https://github.com/galaxyproject/galaxy/commit/33d533812920c1bc0e5998cd5564… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Merge pull request #1440 from davebx/proc_formatting Fix formatting in issues.rst Compare: https://github.com/galaxyproject/galaxy/compare/3b4fd544cecf...33d533812920

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