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[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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[galaxyproject/galaxy] 3d3738: Fix dataset discovery for YAML/dictified tools.
by GitHub 29 Dec '18

29 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3d373827b3b1d59dd166ad6db1b95dedcb256004 https://github.com/galaxyproject/galaxy/commit/3d373827b3b1d59dd166ad6db1b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Fix dataset discovery for YAML/dictified tools. Commit: 4c741ef00ef0fcde5af1b2e270acc0f0f2f407ec https://github.com/galaxyproject/galaxy/commit/4c741ef00ef0fcde5af1b2e270ac… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-12-29 (Sat, 29 Dec 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #7152 from jmchilton/fix_yaml_discovery Fix dataset discovery for YAML/dictified tools. Compare: https://github.com/galaxyproject/galaxy/compare/7b911c6fcd4b...4c741ef00ef0 **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] 647479: Fix for parsing collection outputs for YAML/dictif...
by GitHub 29 Dec '18

29 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 647479f40ae1c5e4c1569b173c7cc0ae8c029c93 https://github.com/galaxyproject/galaxy/commit/647479f40ae1c5e4c1569b173c7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M lib/galaxy/tools/parser/yaml.py A test/functional/tools/collection_creates_pair_y.yml M test/unit/tools/test_parsing.py Log Message: ----------- Fix for parsing collection outputs for YAML/dictified tools. Commit: 7b911c6fcd4b6fca661275afee13c247b766c169 https://github.com/galaxyproject/galaxy/commit/7b911c6fcd4b6fca661275afee13… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-12-29 (Sat, 29 Dec 2018) Changed paths: M lib/galaxy/tools/parser/yaml.py A test/functional/tools/collection_creates_pair_y.yml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #7153 from jmchilton/fix_output_collection_yaml Fix for parsing collection outputs for YAML/dictified tools. Compare: https://github.com/galaxyproject/galaxy/compare/471d54c27af2...7b911c6fcd4b **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] 234d3e: Remove redundant Task code.
by GitHub 27 Dec '18

27 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 234d3ee8a6c4979aeeea4bbd9a07d875c379f0be https://github.com/galaxyproject/galaxy/commit/234d3ee8a6c4979aeeea4bbd9a07… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Remove redundant Task code. get_job is overridden in Task, that should be sufficient I suspect. Commit: 47d8fedfa4d4b84ef47fcebd2b0f5536b919c353 https://github.com/galaxyproject/galaxy/commit/47d8fedfa4d4b84ef47fcebd2b0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Reuse get_param_dict in job wrapper. There is a comment to this, listen to the smart comment and then delete. Commit: 471d54c27af26699be234155585bc488b5d16f65 https://github.com/galaxyproject/galaxy/commit/471d54c27af26699be234155585b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-27 (Thu, 27 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #7155 from jmchilton/reuse_get_params Small de-duplication cleanups to galaxy.jobs Compare: https://github.com/galaxyproject/galaxy/compare/26c950f56911...471d54c27af2 **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] 356d94: Allow pulsar jobs to be resubmitted on connection ...
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 356d949199359a974a96d531db0dc39d97007df6 https://github.com/galaxyproject/galaxy/commit/356d949199359a974a96d531db0d… Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Allow pulsar jobs to be resubmitted on connection failures Commit: 263d10ca1c7577f3138df83f19468c1c20b85ea0 https://github.com/galaxyproject/galaxy/commit/263d10ca1c7577f3138df83f1946… Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: A test/integration/resubmission_pulsar_job_conf.xml M test/integration/test_job_resubmission.py Log Message: ----------- Added test for pulsar resubmission Commit: 2632c071cdf1f6f49c30d243eea4931ee6fcaab2 https://github.com/galaxyproject/galaxy/commit/2632c071cdf1f6f49c30d243eea4… Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py Log Message: ----------- Added referrer parameter for dynamic destinations + test Commit: cd119d641ad59a9da008875b5c32f20127bcbd65 https://github.com/galaxyproject/galaxy/commit/cd119d641ad59a9da008875b5c32… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/README.md M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/layout/menu.js 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-edit-attributes.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/history/options-menu.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/utils.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_resource_params_conf.xml.sample M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/tool_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M config/workflow_schedulers_conf.xml.sample M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/scaling.md M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py 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 lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/grt/export.py M scripts/grt/grt.yml.sample M templates/admin/tool_shed_repository/manage_repository.mako M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/functional/tools/for_workflows/head.xml 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/integration/test_dockerized_jobs.py A test/integration/test_workflow_sync.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py R tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/grouping.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into pulsar_resubmit Commit: 0727f17ade3bb964a260907860a7ab0aee39a4b3 https://github.com/galaxyproject/galaxy/commit/0727f17ade3bb964a260907860a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py M test/integration/resubmission_pulsar_job_conf.xml Log Message: ----------- Fixes for Pulsar error handling. More uniform error hanlding to fix test. Simplify test case of resubmission to test just jobs resubmit properly (no need to test Pulsar-to-Pulsar resubmission in particular here I don't think, maybe as a second test - but not a first?). Commit: abf98be7833f1df15ad292b453f5b79899e8412f https://github.com/galaxyproject/galaxy/commit/abf98be7833f1df15ad292b453f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- lint fix Commit: 26c950f569111ccd61621849c0fc7aecbf70e76b https://github.com/galaxyproject/galaxy/commit/26c950f569111ccd61621849c0fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/pulsar.py A test/integration/resubmission_pulsar_job_conf.xml M test/integration/test_job_resubmission.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py Log Message: ----------- Merge pull request #7053 from nuwang/pulsar_resubmit Added resubmit handlers on Pulsar connection failures Compare: https://github.com/galaxyproject/galaxy/compare/e4e2d9c09a45...26c950f56911 **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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