September 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c5a081: Retry job submissions in ShellJobRunner
by GitHub 13 Sep '17

13 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5a08186b7ff8090b5ec7191ed149c3e13c9aa90 https://github.com/galaxyproject/galaxy/commit/c5a08186b7ff8090b5ec7191ed14… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Retry job submissions in ShellJobRunner If I submit a large amount of jobs in a very short time I sometimes see ``` galaxy.jobs.runners.cli ERROR 2017-09-11 05:03:02,404 (17633) submission failed (stderr): qsub: submit error (Invalid credential) ``` in my logs for a minor subset of jobs (2 out of 120 in the last instance that this happened). In this case waiting a little while and trying again solves the problem. By default we will try submitting the job 3 times, and sleep 10 seconds before trying again. Commit: ecd8b90e44decbef60db4359bf4837ef5b12ed1f https://github.com/galaxyproject/galaxy/commit/ecd8b90e44decbef60db4359bf48… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Decrease log-level for resubmission msg and specifiy log level directly in if/else clause. Thx @erasche. Commit: 11d4380d2b40b4e18806f6b2d1e07f4a6eec1f8b https://github.com/galaxyproject/galaxy/commit/11d4380d2b40b4e18806f6b2d1e0… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #4599 from mvdbeek/make_qsub_submissions_more_robust Retry job submissions in ShellJobRunner Compare: https://github.com/galaxyproject/galaxy/compare/e33b35def345...11d4380d2b40

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[galaxyproject/galaxy] 60dd73: Remove unreachable statements
by GitHub 13 Sep '17

13 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 60dd7306d04c47aa4a9b2efed149cb3c4d259a10 https://github.com/galaxyproject/galaxy/commit/60dd7306d04c47aa4a9b2efed149… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Remove unreachable statements Commit: 61e05670c26cb75b9a76e3660e049a6f9383a644 https://github.com/galaxyproject/galaxy/commit/61e05670c26cb75b9a76e3660e04… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py Log Message: ----------- now unused imports Commit: e33b35def3453d6158bf6ed4109c3ec2dbffbc37 https://github.com/galaxyproject/galaxy/commit/e33b35def3453d6158bf6ed4109c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Merge pull request #4603 from erasche/dead-code Remove unreachable statements Compare: https://github.com/galaxyproject/galaxy/compare/26c7abb130ba...e33b35def345

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[galaxyproject/galaxy] 8adbf0: Add show/hide deleted/hidden links when history is...
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8adbf03f565b1d60fb42ca986d184387e19e94af https://github.com/galaxyproject/galaxy/commit/8adbf03f565b1d60fb42ca986d18… Author: chambm <matt.chambers42(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Add show/hide deleted/hidden links when history is filtered by find box; addresses #4103 Commit: 97264e3de8d9ea8cd0b4cec9bbe91b1b3d81636d https://github.com/galaxyproject/galaxy/commit/97264e3de8d9ea8cd0b4cec9bbe9… Author: chambm <matt.chambers42(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Try to start personal CI build Commit: 1aadd7866f6b94460a5703a8aa35949f7632adcf https://github.com/galaxyproject/galaxy/commit/1aadd7866f6b94460a5703a8aa35… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- Make client. Commit: fd1926767996a161cd2fc8bd184e6835fd688765 https://github.com/galaxyproject/galaxy/commit/fd1926767996a161cd2fc8bd184e… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- Merge pull request #2 from dannon/chambmdev Make client Commit: 26c7abb130bade73b64284956f0077f35067095f https://github.com/galaxyproject/galaxy/commit/26c7abb130bade73b64284956f00… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- Merge remote-tracking branch 'chambm/dev' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9468bef057f6...26c7abb130ba

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[galaxyproject/galaxy] 79a378: Small improvements to workflow editor Selenium tes...
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79a37830bb75ccd4d8c18236f7938a50a83f87c2 https://github.com/galaxyproject/galaxy/commit/79a37830bb75ccd4d8c18236f793… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Small improvements to workflow editor Selenium tests. I saw a failed test earlier that would have been fixed by a switch to wait_for_and_click in workflow_editor_click_options. This makes that switch and moves some of these workflow editor helper functions into navigates_galaxy.py for reuse by other test cases and by library users. Commit: 9468bef057f6372f75ceaee832457386c79e39cc https://github.com/galaxyproject/galaxy/commit/9468bef057f6372f75ceaee83245… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #4592 from jmchilton/workflow_click_fix Small improvements to workflow editor Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/2e160935d9ce...9468bef057f6

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[galaxyproject/galaxy] 822678: Support for applying window title on display() of ...
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82267855ed3bc6d3f8911acf6e7e388023f6693d https://github.com/galaxyproject/galaxy/commit/82267855ed3bc6d3f8911acf6e7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/layout/page.js.map M static/maps/mvc/workflow/workflow.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/layout/page.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Support for applying window title on display() of views. Commit: 9a66adb4fe7a3be6e07baaec6cef8f553d6b486d https://github.com/galaxyproject/galaxy/commit/9a66adb4fe7a3be6e07baaec6cef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Standard (for now) paren spacing. Commit: 84de84294c95110f0ee3059ad8a5e9924daf6a9d https://github.com/galaxyproject/galaxy/commit/84de84294c95110f0ee3059ad8a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/history/history-list.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.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/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- History List, Tours, and User Preferences titles Commit: 6b2277e37dd0520de26442701407badcf792cfab https://github.com/galaxyproject/galaxy/commit/6b2277e37dd0520de26442701407… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Automatically append 'Galaxy | ' to title instead of requiring it for all view titles. Commit: 2cb8a28f7be2ff8b7076ef04a6d575d276e3bca6 https://github.com/galaxyproject/galaxy/commit/2cb8a28f7be2ff8b7076ef04a6d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M static/maps/layout/page.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.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/layout/page.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Rebuild. Commit: 9a0506c5c0832c93dcd7844ea9de92b619c00773 https://github.com/galaxyproject/galaxy/commit/9a0506c5c0832c93dcd7844ea9de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Include Galaxy brand in titles. Commit: 91eb849500faec57bebb35228a5a2e2638be70aa https://github.com/galaxyproject/galaxy/commit/91eb849500faec57bebb35228a5a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Use 'Galaxy / Brand' consistent styling instead of 'Galaxy | Brand' Commit: 935f25aa32b3a22a53de02d5bfe4b5f7de819a0b https://github.com/galaxyproject/galaxy/commit/935f25aa32b3a22a53de02d5bfe4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M static/maps/mvc/grid/grid-shared.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/grid/grid-shared.js Log Message: ----------- Titles for abstract grids w/ plural set. Commit: f83188e7f3c19a5686a623d9bb30f683cd04ff27 https://github.com/galaxyproject/galaxy/commit/f83188e7f3c19a5686a623d9bb30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/grid/grid-view.js Log Message: ----------- Normal grid title propagation. Commit: 928ad294936c4f6ca4ebc007963578527886af02 https://github.com/galaxyproject/galaxy/commit/928ad294936c4f6ca4ebc0079635… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-09 (Sat, 09 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Localize displayed titles. Commit: 6b14dda216d103da518a906f4eda018eb58bafbe https://github.com/galaxyproject/galaxy/commit/6b14dda216d103da518a906f4eda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/layout/page.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Grids do a late initialization and the title isn't available until this happens (after display()), so provide a way to allow views to set title late if necessary. Commit: 59d0e297f7217faed3d7c6d30e88678f1eaef600 https://github.com/galaxyproject/galaxy/commit/59d0e297f7217faed3d7c6d30e88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- When title isn't set, revert to the default -- otherwise display()'d contents without titles show up with the previous and incorrect titles. Commit: 2c40efb6c236220ccaffd7893fafa1b8969f1ad2 https://github.com/galaxyproject/galaxy/commit/2c40efb6c236220ccaffd7893faf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/utils/utils.js M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/layout/page.js M static/scripts/mvc/grid/grid-view.js M static/scripts/utils/utils.js Log Message: ----------- Minor refactor, use a single Utils.setWindowTitle() method. Commit: a5dbf29e13e1d558ac1c6798e7952963b0599e6e https://github.com/galaxyproject/galaxy/commit/a5dbf29e13e1d558ac1c6798e795… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use standard naming for Utils import. Commit: ecb4e06799fb61c4577e1a52276359149670cdf7 https://github.com/galaxyproject/galaxy/commit/ecb4e06799fb61c4577e1a522763… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/utils/utils.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- We apparently always use '|' in the title, even though masthead uses '/'. It does look better. Commit: ae1c68c7dbb9214def95e97a2f6714c68e23927b https://github.com/galaxyproject/galaxy/commit/ae1c68c7dbb9214def95e97a2f67… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Set title on base admin page. Commit: ff5b430319196a61e2a593b04a4bc60859062e3c https://github.com/galaxyproject/galaxy/commit/ff5b430319196a61e2a593b04a4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Workflow editor title fix (not new-style, to keep it simple and use the approach consistent with the .mako layout used. Commit: c71d3035ab7bbcdfb682a39e4e9e3cb49417289d https://github.com/galaxyproject/galaxy/commit/c71d3035ab7bbcdfb682a39e4e9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into titles_in_views Commit: 2e160935d9ceb3ca8441e3b51107594b9539573d https://github.com/galaxyproject/galaxy/commit/2e160935d9ceb3ca8441e3b51107… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #4578 from dannon/titles_in_views Delegate displaying of page titles to Layout.display() Compare: https://github.com/galaxyproject/galaxy/compare/36a3a6b3d9c0...2e160935d9ce

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[galaxyproject/galaxy] 87b798: FAST5 archive support
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87b798d40a5acb78ddf428d82639f2d5a7f40098 https://github.com/galaxyproject/galaxy/commit/87b798d40a5acb78ddf428d82639… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- FAST5 archive support Commit: 9e6cb13e314d451cba7e0eaf841f05410ac19750 https://github.com/galaxyproject/galaxy/commit/9e6cb13e314d451cba7e0eaf841f… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A SECURITY_POLICY.md M 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config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M 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config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css R config/reports.ini.sample A config/reports.yml.sample A config/swarm_manager_conf.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_destinations.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A config/user_preferences_extra_conf.yml.sample M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M cron/updateucsc.sh.sample M display_applications/igv/bigwig.xml M doc/Makefile R doc/patch.py A doc/source/admin/authentication.md R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R 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doc/source/admin/special_topics/performance_tracking.rst A doc/source/admin/special_topics/webhooks.rst A doc/source/admin/tool_panel.rst M doc/source/admin/useful_scripts.rst R doc/source/admin/webhooks.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/dev/build_a_job_runner.rst A doc/source/dev/finding_and_improving_slow_code.rst M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst M doc/source/index.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M 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tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/wc_gnu.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fast5 Commit: 2fc60430a187cc4a95e2d935b89b65f52acd86b8 https://github.com/galaxyproject/galaxy/commit/2fc60430a187cc4a95e2d935b89b… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix formatting to make tox happy Commit: f07c6a98431f1a4c2a2d81f99d3b54a23f0a901e https://github.com/galaxyproject/galaxy/commit/f07c6a98431f1a4c2a2d81f99d3b… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- optimized sniffing, subclassed different tarball types Commit: 297d2353ce594b3325d029fb72c3ffd825c07f57 https://github.com/galaxyproject/galaxy/commit/297d2353ce594b3325d029fb72c3… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz Log Message: ----------- add datatype tests Commit: 49258a7df8bb0f8c489c06dc2a77c27b2244b5f9 https://github.com/galaxyproject/galaxy/commit/49258a7df8bb0f8c489c06dc2a77… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fixed sniff order and misc linting errors Commit: 08b5a47c396d38d288d54806edb87e9e717b799d https://github.com/galaxyproject/galaxy/commit/08b5a47c396d38d288d54806edb8… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/utils/uploadbox.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/utils/uploadbox.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/history/options-menu.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/utils/uploadbox.js A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_published_histories_grid.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fast5 Commit: 36a3a6b3d9c0b00c26ae861649983a441f725ae8 https://github.com/galaxyproject/galaxy/commit/36a3a6b3d9c0b00c26ae86164998… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz Log Message: ----------- Merge pull request #4569 from jvolkening/fast5 fast5_archive datatype Compare: https://github.com/galaxyproject/galaxy/compare/c0e2db2d98ea...36a3a6b3d9c0

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[galaxyproject/galaxy] 7e2727: Remove bam to bai converter
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e2727bc0a74868198e7e457f99df3d1e39f1ddb https://github.com/galaxyproject/galaxy/commit/7e2727bc0a74868198e7e457f99d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Remove bam to bai converter This converter served no real purpose (you can download bam index files by clicking on the floppy icon, and we never had a bai datatype). Commit: c0e2db2d98ead7f9d532ad0f5106d644019d5265 https://github.com/galaxyproject/galaxy/commit/c0e2db2d98ead7f9d532ad0f5106… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge pull request #4598 from mvdbeek/remove_bai_converter Remove bam to bai converter Compare: https://github.com/galaxyproject/galaxy/compare/e1cdb740cb43...c0e2db2d98ea

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[galaxyproject/galaxy] 5da62c: Cancel workflow invocations when histories are del...
by GitHub 11 Sep '17

11 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5da62ca264826bca0318a08f10d9d5e0ab6a3cc8 https://github.com/galaxyproject/galaxy/commit/5da62ca264826bca0318a08f10d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Cancel workflow invocations when histories are deleted. With test case, rebased with spelling fixes thanks to @nsoranzo. xref #3555 (third point) Commit: 7efe561867b7c5a3a16e873c215889c58d225277 https://github.com/galaxyproject/galaxy/commit/7efe561867b7c5a3a16e873c2158… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Rework invocation state tracking in API tests. At the insistence of @nsoranzo, be more explicit about waiting for workflow test in API tests. While I was in there I also setup new abstractions for waiting on state and updated various workflow cancelling tests to use test_history context for better error reporting. Commit: e1cdb740cb431104439dbbd63c2f1c0472d2c16b https://github.com/galaxyproject/galaxy/commit/e1cdb740cb431104439dbbd63c2f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #4580 from jmchilton/deleted_history Cancel workflow invocations when histories are deleted. Compare: https://github.com/galaxyproject/galaxy/compare/74a486084bcb...e1cdb740cb43

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[galaxyproject/galaxy] 0a54a3: remove unneeded property, fix import from history ...
by GitHub 11 Sep '17

11 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a54a313b77b7c47cf57d5f7365cd37231b879ea https://github.com/galaxyproject/galaxy/commit/0a54a313b77b7c47cf57d5f7365c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map 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/bundled/login.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- remove unneeded property, fix import from history targets some refactoring Commit: 5b87754ab77dbba1aab632345517e404bc421295 https://github.com/galaxyproject/galaxy/commit/5b87754ab77dbba1aab632345517… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- refactor traversing to use latest() instead Commit: 74a486084bcb5d0aef50bebe499b9b39b8a68a74 https://github.com/galaxyproject/galaxy/commit/74a486084bcb5d0aef50bebe499b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-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-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map 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/bundled/login.bundled.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #4579 from martenson/fix-reload-error datalibs: fix two bugs, refactor Compare: https://github.com/galaxyproject/galaxy/compare/a190903bd031...74a486084bcb

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[galaxyproject/galaxy] b61ca4: Make history sharing tests more robust and informa...
by GitHub 11 Sep '17

11 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b61ca47c99da6661dee64d6612f8aa30daa464f8 https://github.com/galaxyproject/galaxy/commit/b61ca47c99da6661dee64d6612f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/selenium_tests/test_history_sharing.py Log Message: ----------- Make history sharing tests more robust and informative. - Be sure when sharing a history with a user we wait to actually see that user's e-mail address appear in the history's sharing list after submission. - Print something for the failed history sharing assertions (I'm pretty sure they are 403 errors because some aspect of the sharing or login didn't work - but might as well verify). Commit: a190903bd031ff78f286977cdb7eaca04884de4c https://github.com/galaxyproject/galaxy/commit/a190903bd031ff78f286977cdb7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/selenium_tests/test_history_sharing.py Log Message: ----------- Merge pull request #4588 from jmchilton/selenium_fixes_25 Make history sharing Selenium tests more robust and informative. Compare: https://github.com/galaxyproject/galaxy/compare/31f2168c3d7f...a190903bd031

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