January 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 34ada9: Use regular js-event handling instead of jquery fo...
by GitHub 02 Jan '19

02 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 34ada99915c63943bac4630ebb461b54c37b9838 https://github.com/galaxyproject/galaxy/commit/34ada99915c63943bac4630ebb46… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use regular js-event handling instead of jquery for uploader Commit: 8f10178e43d1ca001a0a02291ef7b01c3891cc30 https://github.com/galaxyproject/galaxy/commit/8f10178e43d1ca001a0a02291ef7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix dragover highlighting for composite dataset uploader Commit: 2f8a62344e66194e3a8d37a8539a8540abbbb494 https://github.com/galaxyproject/galaxy/commit/2f8a62344e66194e3a8d37a8539a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Use default js to handle drop events in tool form Commit: e906ca1ffdd92f2b7709373b0e82c84a5218b077 https://github.com/galaxyproject/galaxy/commit/e906ca1ffdd92f2b7709373b0e82… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/scss/upload.scss Log Message: ----------- Merge pull request #7145 from guerler/fix_drop Use regular js-event handling instead of jquery for uploader Compare: https://github.com/galaxyproject/galaxy/compare/65419bd3763d...e906ca1ffdd9 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dd5e3c: Move error stack controller endpoint to tools api
by GitHub 02 Jan '19

02 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd5e3c6c68077268d3d551857e508d914ed1d3f9 https://github.com/galaxyproject/galaxy/commit/dd5e3c6c68077268d3d551857e50… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Move error stack controller endpoint to tools api Commit: 3665ef056d377960edd92b558fcf903f9280a204 https://github.com/galaxyproject/galaxy/commit/3665ef056d377960edd92b558fcf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/ErrorStack.vue M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add error stack vue component and client side routes Commit: 8eceb76ee1e36ae14403ccfbaf082ed6395451b6 https://github.com/galaxyproject/galaxy/commit/8eceb76ee1e36ae14403ccfbaf08… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: R templates/admin/tool_errors.mako Log Message: ----------- Remove legacy tool error mako file Commit: 481243c3ed0a31ebde7a4ed85592e7068e5e4b45 https://github.com/galaxyproject/galaxy/commit/481243c3ed0a31ebde7a4ed85592… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue Log Message: ----------- Remove unused attribute Commit: 462303043d47437486fb0d6df5b65d43f8235790 https://github.com/galaxyproject/galaxy/commit/462303043d47437486fb0d6df5b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue Log Message: ----------- Remove unused tag in vue component Commit: 8a439cfb0f81e2ca8a7ab8c2526452c27a875046 https://github.com/galaxyproject/galaxy/commit/8a439cfb0f81e2ca8a7ab8c25264… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue Log Message: ----------- Allow sorting by file name in error log table Commit: 30d5baf90978f79b57fbd7f8008a76c05fe5c11d https://github.com/galaxyproject/galaxy/commit/30d5baf90978f79b57fbd7f8008a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix comment section of error stack api endpoint Commit: bc695f898c3f7098cc6cef1acb68bcbec2c77f0b https://github.com/galaxyproject/galaxy/commit/bc695f898c3f7098cc6cef1acb68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue Log Message: ----------- Use bootstrap vue message alerts Commit: d53e33cf9f814700d14743d8addd4e059b380ebd https://github.com/galaxyproject/galaxy/commit/d53e33cf9f814700d14743d8addd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/DisplayApplications.vue M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-view.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/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M config/datatypes_conf.xml.sample M config/tool_conf.xml.sample M doc/source/dev/build_a_job_runner.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/__init__.py A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/webapps/galaxy/admin/view_display_applications.mako M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml M test/selenium_tests/test_admin_app.py Log Message: ----------- Merge branch 'dev' into admin_error_log Commit: d385be993a4939f5741c54296a041ab994731f50 https://github.com/galaxyproject/galaxy/commit/d385be993a4939f5741c54296a04… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue Log Message: ----------- Fix consistency of parameter naming to in error stack component Commit: 65419bd3763dcfc78d92808a6a323ed10ee014ef https://github.com/galaxyproject/galaxy/commit/65419bd3763dcfc78d92808a6a32… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/ErrorStack.vue M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/tool_errors.mako Log Message: ----------- Merge pull request #7124 from guerler/admin_error_log Adds a vue component to display tool errors in the admin panel Compare: https://github.com/galaxyproject/galaxy/compare/a8944f5a039a...65419bd3763d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c8b6fa: Fix connected value handling in workflow editor
by GitHub 02 Jan '19

02 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8b6fa0ead77a707d839a8e03c286fcefedb7d52 https://github.com/galaxyproject/galaxy/commit/c8b6fa0ead77a707d839a8e03c28… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-23 (Sun, 23 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Fix connected value handling in workflow editor Commit: fd205ebfbe25f9ba8f19da20ae2e2a20b0cd600a https://github.com/galaxyproject/galaxy/commit/fd205ebfbe25f9ba8f19da20ae2e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-23 (Sun, 23 Dec 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Remove pointer from inactive collapsible title Commit: f0b88169334f695e957029357d759cb841df2499 https://github.com/galaxyproject/galaxy/commit/f0b88169334f695e957029357d75… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-23 (Sun, 23 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Fix tooltip update for collapsible and connected input parameters in workflow editor Commit: 04623376d76db8086625a4d0fa4cbd9549fbae99 https://github.com/galaxyproject/galaxy/commit/04623376d76db8086625a4d0fa4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-23 (Sun, 23 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Fix logic for collapsible options Commit: bbe86fb2cc9a01dbc53995ec823b1f3a9ca4c460 https://github.com/galaxyproject/galaxy/commit/bbe86fb2cc9a01dbc53995ec823b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-23 (Sun, 23 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Fix type in form input wrapper related to connected modules Commit: 0f8db20c8e12bbb35804a911ae0dd7b1bfa4f55c https://github.com/galaxyproject/galaxy/commit/0f8db20c8e12bbb35804a911ae0d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-23 (Sun, 23 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Remove show call to connected/collapsible tooltip, not required for refresh Commit: 460c0ac014016837f4d64f3f46f5cec79ca37f24 https://github.com/galaxyproject/galaxy/commit/460c0ac014016837f4d64f3f46f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-23 (Sun, 23 Dec 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Remove fixed width from parameter option icons Commit: 1dad09fc92c0d14479d6c58a36c28e46971aaf5c https://github.com/galaxyproject/galaxy/commit/1dad09fc92c0d14479d6c58a36c2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-23 (Sun, 23 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Add connected check directly to associated value Commit: a8944f5a039aee937b1d31855a4f00d2e84a1c64 https://github.com/galaxyproject/galaxy/commit/a8944f5a039aee937b1d31855a4f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/scss/ui.scss Log Message: ----------- Merge pull request #7150 from guerler/connected_value Follow-up on handling connectable and collapsible parameters in workflows Compare: https://github.com/galaxyproject/galaxy/compare/e87e1561e336...a8944f5a039a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 0d28c6: Allow anonymous downloading of test-data files
by GitHub 02 Jan '19

02 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0d28c65c3d1ce504850a3ba94b99099abb68cd92 https://github.com/galaxyproject/galaxy/commit/0d28c65c3d1ce504850a3ba94b99… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-31 (Mon, 31 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py Log Message: ----------- Allow anonymous downloading of test-data files Commit: 6791f3b99905ac0db0a8e2c23f38a4bce8b1d3c8 https://github.com/galaxyproject/galaxy/commit/6791f3b99905ac0db0a8e2c23f38… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-31 (Mon, 31 Dec 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Also allow downloading test-data directories This is (apparently ...) used by tools that create/test directories in the extra_files_path. Commit: e30ff62b0e1069d4316e15660d130df87e6c6217 https://github.com/galaxyproject/galaxy/commit/e30ff62b0e1069d4316e15660d13… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-31 (Mon, 31 Dec 2018) Changed paths: M lib/galaxy/util/streamball.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Move stream_archive to galaxy.util.streamball Commit: 5490a6db7c5fa5db431c64b51998f923110106a6 https://github.com/galaxyproject/galaxy/commit/5490a6db7c5fa5db431c64b51998… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-31 (Mon, 31 Dec 2018) Changed paths: M test/functional/tools/composite_output_tests.xml Log Message: ----------- Add `extra_files type="directory"` test Commit: 95f866d77c4adbe2055b28f37808b709658a9903 https://github.com/galaxyproject/galaxy/commit/95f866d77c4adbe2055b28f37808… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-31 (Mon, 31 Dec 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Make type="directory" remote compatible We download an archive containing the specified directory for tests. Commit: f1acff02ded73df1014316f276b7e89d9decec37 https://github.com/galaxyproject/galaxy/commit/f1acff02ded73df1014316f276b7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-31 (Mon, 31 Dec 2018) Changed paths: M test/functional/tools/composite_output_tests.xml Log Message: ----------- Quote remaining parametera Commit: 4877bfafa6cd5b8af419c9dad0615bcd39e9559e https://github.com/galaxyproject/galaxy/commit/4877bfafa6cd5b8af419c9dad061… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-01 (Tue, 01 Jan 2019) Changed paths: M test/api/test_tools.py Log Message: ----------- Test that test-data paths outside of test-data folder cannot be downloaded Commit: e87e1561e336bb187ac5e40f55a107614bc38686 https://github.com/galaxyproject/galaxy/commit/e87e1561e336bb187ac5e40f55a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/streamball.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/functional/tools/composite_output_tests.xml Log Message: ----------- Merge pull request #7160 from mvdbeek/unprivileged_remote_tool_tests Unprivileged remote tool tests Compare: https://github.com/galaxyproject/galaxy/compare/6869883309bb...e87e1561e336 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 0eb96a: doc: added missing docs for new UNIVA runner
by GitHub 02 Jan '19

02 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0eb96a63f59f3def6e82df045357e61d2e4e6196 https://github.com/galaxyproject/galaxy/commit/0eb96a63f59f3def6e82df045357… Author: M Bernt <m.bernt(a)ufz.de> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- doc: added missing docs for new UNIVA runner Commit: 6869883309bbef76d36b62d388c604e989734cc6 https://github.com/galaxyproject/galaxy/commit/6869883309bbef76d36b62d388c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #7161 from bernt-matthias/topic/univa-doc doc: added missing docs for new UNIVA runner Compare: https://github.com/galaxyproject/galaxy/compare/9c08b416dbdb...6869883309bb **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d3cdf4: Add to_dict() to ObjectStores.
by GitHub 01 Jan '19

01 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3cdf43563c1f3eacfae7cb5f887589a81f2acc6 https://github.com/galaxyproject/galaxy/commit/d3cdf43563c1f3eacfae7cb5f887… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3.py M test/unit/test_objectstore.py Log Message: ----------- Add to_dict() to ObjectStores. Dictify an object store configuration back to its to config_dict description. Commit: 9c08b416dbdbac16106f7dbd5b7eaf805d2ec996 https://github.com/galaxyproject/galaxy/commit/9c08b416dbdbac16106f7dbd5b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-01 (Tue, 01 Jan 2019) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3.py M test/unit/test_objectstore.py Log Message: ----------- Merge pull request #7110 from jmchilton/os_to_dict Add to_dict() to ObjectStores. Compare: https://github.com/galaxyproject/galaxy/compare/4c741ef00ef0...9c08b416dbdb **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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