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

[galaxyproject/galaxy] 412d8e: Adding NGL viewer for molecule representation
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 412d8e1bb6c82a9aa8a86971e64e4242a5341419 https://github.com/galaxyproject/galaxy/commit/412d8e1bb6c82a9aa8a86971e64e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Adding NGL viewer for molecule representation Commit: 6864bc30b4a02495220d1552026c0cacb5d41af7 https://github.com/galaxyproject/galaxy/commit/6864bc30b4a02495220d1552026c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Replacing url by download_url to fetch files Commit: 48639028df5b59e7547a2e716b9c7e34e9743a41 https://github.com/galaxyproject/galaxy/commit/48639028df5b59e7547a2e716b9c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Removing utils.get to fetch pdb files Commit: c390da3cbd933c27ad0c731bc3b557ad916a72cd https://github.com/galaxyproject/galaxy/commit/c390da3cbd933c27ad0c731bc3b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Change default settings, avoid flickering on startup Commit: 7472568fe5102a77ff69c47db0f19d7fd0a8487a https://github.com/galaxyproject/galaxy/commit/7472568fe5102a77ff69c47db0f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Remove unused name from stage parameter Commit: 43f2a648230b5b0ee46c124cc3df95b758e50fb2 https://github.com/galaxyproject/galaxy/commit/43f2a648230b5b0ee46c124cc3df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Merge pull request #3601 from bgruening/ngl_viewer NGL Viewer for molecule representation Compare: https://github.com/galaxyproject/galaxy/compare/a7572145e9c0...43f2a648230b

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[galaxyproject/galaxy] 0e9eb7: deprecate repair repository feature
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0e9eb78636da19c68ff3c981ff8090b63a7d11ae https://github.com/galaxyproject/galaxy/commit/0e9eb78636da19c68ff3c981ff80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- deprecate repair repository feature Commit: 29d229cedd697ff79595b223d651dd0d97ded457 https://github.com/galaxyproject/galaxy/commit/29d229cedd697ff79595b223d651… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3615 from martenson/release_17.01 [17.01] deprecate repair repository feature Compare: https://github.com/galaxyproject/galaxy/compare/c82530fd2384...29d229cedd69

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[galaxyproject/galaxy] eb5ded: Remove likely un-needed check.
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb5ded2a439d1c9491700650842f9ece04cfad33 https://github.com/galaxyproject/galaxy/commit/eb5ded2a439d1c9491700650842f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Remove likely un-needed check. Commit: a7572145e9c0d4872cde027d547ef4c31c87af10 https://github.com/galaxyproject/galaxy/commit/a7572145e9c0d4872cde027d547e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #3618 from jmchilton/remove_unneeded_15 Remove un-needed check in histories manager code Compare: https://github.com/galaxyproject/galaxy/compare/149dfa007f70...a7572145e9c0

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[galaxyproject/galaxy] 452ab0: Implementation of slow query logging. Disabled by...
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 452ab0d509171033e901bf65cf2556ef411e5161 https://github.com/galaxyproject/galaxy/commit/452ab0d509171033e901bf65cf25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Implementation of slow query logging. Disabled by default. Commit: 78282a288bd1528dfd5222f47baaaeaaf1480f17 https://github.com/galaxyproject/galaxy/commit/78282a288bd1528dfd5222f47baa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Aarrghs spacing. Commit: 19e18dd5719abe08e361bf4b50a7bf4bbbd554e1 https://github.com/galaxyproject/galaxy/commit/19e18dd5719abe08e361bf4b50a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add forgotten sample change. Commit: 7810f5a8648c913045ae042a7c991642dbc045c8 https://github.com/galaxyproject/galaxy/commit/7810f5a8648c913045ae042a7c99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super. Commit: da24f4c8ad03a34da9323041e634d4bbe55617b4 https://github.com/galaxyproject/galaxy/commit/da24f4c8ad03a34da9323041e634… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Import formatting... Commit: 149dfa007f70fe6794b8c1f37708ac8fbb7cccef https://github.com/galaxyproject/galaxy/commit/149dfa007f70fe6794b8c1f37708… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3616 from dannon/slow_query_logging Slow query logging Compare: https://github.com/galaxyproject/galaxy/compare/8ce1291359c8...149dfa007f70

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[galaxyproject/galaxy] 255aa0: Fix workflow save-as url not using galaxy's prefix...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 255aa0470f44ea90d2b4d738e07b8f6d08874c3b https://github.com/galaxyproject/galaxy/commit/255aa0470f44ea90d2b4d738e07b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix workflow save-as url not using galaxy's prefix. Commit: c86d2ee8bcbdde82ac5e6f450241ef7fed076665 https://github.com/galaxyproject/galaxy/commit/c86d2ee8bcbdde82ac5e6f450241… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #3610 from dannon/fix-editor-save-as-url [17.01] Fix workflow save-as url not using galaxy's prefix. Commit: 4689cf16bf77b0e7b0d22d193b695d7d5df24d6c https://github.com/galaxyproject/galaxy/commit/4689cf16bf77b0e7b0d22d193b69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again' Commit: 43d80a0b6052b59f8be768ad810fee952a436ce3 https://github.com/galaxyproject/galaxy/commit/43d80a0b6052b59f8be768ad810f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Tooltips to suggest relog for quota correction. Commit: 966d578b47f4999ba0f8db874bf927e5f4246d7f https://github.com/galaxyproject/galaxy/commit/966d578b47f4999ba0f8db874bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Slightly more defensive programming -- we don't expose this in the UI unless there *is* a trans.user, but we might as well be careful here. Commit: 944feb2411d1381b1743f3365b6380e883c9cccb https://github.com/galaxyproject/galaxy/commit/944feb2411d1381b1743f3365b63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Minor tooltip tweaks. Commit: c82530fd2384f5df2457e8f5dd33368cc13abc48 https://github.com/galaxyproject/galaxy/commit/c82530fd2384f5df2457e8f5dd33… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #3614 from dannon/logout-recalc-backport [17.01] Logout recalc backport and additional logic Commit: 8ce1291359c88148023e5bb3f44a9eb38c78a864 https://github.com/galaxyproject/galaxy/commit/8ce1291359c88148023e5bb3f44a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/df22e40522d7...8ce1291359c8

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[galaxyproject/galaxy] 4689cf: Recalculate user disk usage on logout. Not as ide...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 4689cf16bf77b0e7b0d22d193b695d7d5df24d6c https://github.com/galaxyproject/galaxy/commit/4689cf16bf77b0e7b0d22d193b69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again' Commit: 43d80a0b6052b59f8be768ad810fee952a436ce3 https://github.com/galaxyproject/galaxy/commit/43d80a0b6052b59f8be768ad810f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Tooltips to suggest relog for quota correction. Commit: 966d578b47f4999ba0f8db874bf927e5f4246d7f https://github.com/galaxyproject/galaxy/commit/966d578b47f4999ba0f8db874bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Slightly more defensive programming -- we don't expose this in the UI unless there *is* a trans.user, but we might as well be careful here. Commit: 944feb2411d1381b1743f3365b6380e883c9cccb https://github.com/galaxyproject/galaxy/commit/944feb2411d1381b1743f3365b63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Minor tooltip tweaks. Commit: c82530fd2384f5df2457e8f5dd33368cc13abc48 https://github.com/galaxyproject/galaxy/commit/c82530fd2384f5df2457e8f5dd33… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #3614 from dannon/logout-recalc-backport [17.01] Logout recalc backport and additional logic Compare: https://github.com/galaxyproject/galaxy/compare/c86d2ee8bcbd...c82530fd2384

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[galaxyproject/galaxy] 9bb9fe: Recalculate user disk usage on logout. Not as ide...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bb9feb0a8aeec36ded548aa8d28927e2b26d678 https://github.com/galaxyproject/galaxy/commit/9bb9feb0a8aeec36ded548aa8d28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again' Commit: fcbb7c3de17841027da5c2ec16cf11f78e709872 https://github.com/galaxyproject/galaxy/commit/fcbb7c3de17841027da5c2ec16cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Tooltips to suggest relog for quota correction. Commit: 3f07555173f89f39b4823767daaa25bd92ec7d68 https://github.com/galaxyproject/galaxy/commit/3f07555173f89f39b4823767daaa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/plugins/tours/core.galaxy_ui.yaml M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M lib/galaxy/datatypes/interval.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html 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.map M static/scripts/mvc/tool/tool-form-base.js M templates/admin/reload_tool.mako A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into recalc-on-logout Commit: df22e40522d7777cc3c82a4e32b64fe2d95d9273 https://github.com/galaxyproject/galaxy/commit/df22e40522d7777cc3c82a4e32b6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #3600 from dannon/recalc-on-logout Recalculate user disk usage on logout. Compare: https://github.com/galaxyproject/galaxy/compare/9597b9b62b66...df22e40522d7

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[galaxyproject/galaxy] 4f80b1: Revert "Set 'deleted' to True when purging a histo...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/revert-3572-fix_3548 Home: https://github.com/galaxyproject/galaxy Commit: 4f80b11e9c513b4ca1a9442fbf955a3116c07436 https://github.com/galaxyproject/galaxy/commit/4f80b11e9c513b4ca1a9442fbf95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/deletable.py R lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/webapps/galaxy/api/histories.py M test/api/test_histories.py M test/api/test_history_contents.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Revert "Set 'deleted' to True when purging a history dataset association"

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[galaxyproject/galaxy] 255aa0: Fix workflow save-as url not using galaxy's prefix...
by GitHub 14 Feb '17

14 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 255aa0470f44ea90d2b4d738e07b8f6d08874c3b https://github.com/galaxyproject/galaxy/commit/255aa0470f44ea90d2b4d738e07b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix workflow save-as url not using galaxy's prefix. Commit: c86d2ee8bcbdde82ac5e6f450241ef7fed076665 https://github.com/galaxyproject/galaxy/commit/c86d2ee8bcbdde82ac5e6f450241… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #3610 from dannon/fix-editor-save-as-url [17.01] Fix workflow save-as url not using galaxy's prefix. Compare: https://github.com/galaxyproject/galaxy/compare/5db0b7681bb6...c86d2ee8bcbd

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[galaxyproject/galaxy] ac4630: Minor fix of core.galaxy-ui tour in more robustly ...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac46305686c81a94b60a76dd6904a772a784ff24 https://github.com/galaxyproject/galaxy/commit/ac46305686c81a94b60a76dd6904… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Minor fix of core.galaxy-ui tour in more robustly selecting first reload icon in the active history. Commit: 9597b9b62b66d933ae5d891ff45550d23a86b6f2 https://github.com/galaxyproject/galaxy/commit/9597b9b62b66d933ae5d891ff455… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Merge pull request #3608 from dannon/minor-tour-fix Minor fix of core.galaxy-ui tour in more robustly selecting first rel… Compare: https://github.com/galaxyproject/galaxy/compare/4fc0b84910ad...9597b9b62b66

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