galaxy-commits January 2019

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] 8d9979: Fix data_source tools on python 3
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 8d99791afb6a699e987bd1e25aaea8582f7f7065 https://github.com/galaxyproject/galaxy/commit/8d99791afb6a699e987bd1e25aae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M tools/data_source/data_source.py Log Message: ----------- Fix data_source tools on python 3 Commit: 9467d0261cab5712d15dfcfa7ca5d7cdb765f631 https://github.com/galaxyproject/galaxy/commit/9467d0261cab5712d15dfcfa7ca5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M tools/data_source/data_source.py Log Message: ----------- Merge pull request #7236 from mvdbeek/data_source_fix [19.01] Fix data_source tools on python 3 Compare: https://github.com/galaxyproject/galaxy/compare/d2d87625f0a5...9467d0261cab **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] 7b14c3: Reduce duplicated code
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 7b14c3099876d5991ebdea85ff18c027de434be8 https://github.com/galaxyproject/galaxy/commit/7b14c3099876d5991ebdea85ff18… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Reduce duplicated code Commit: e92e978ca179870d586e08f16a0542b9dd499a2a https://github.com/galaxyproject/galaxy/commit/e92e978ca179870d586e08f16a05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Drop use of col1_startswith Contigs may start with whatever sequence you like. Luckily this isn't essential to the datatypes. Leaving data.col1_startswith in case toolshed datatypes import this. Commit: d2d87625f0a5989c40c40a8d50857efb5dc21c36 https://github.com/galaxyproject/galaxy/commit/d2d87625f0a5989c40c40a8d5085… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #7237 from mvdbeek/datatype_fixes [19.01] Interval datatype fixes Compare: https://github.com/galaxyproject/galaxy/compare/b0b5fb44d282...d2d87625f0a5 **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] 2aa8ed: fix tag_using_filenames not converted to bool
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 2aa8ed4efbcf1224d335593e9d64966b8b173bac https://github.com/galaxyproject/galaxy/commit/2aa8ed4efbcf1224d335593e9d64… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- fix tag_using_filenames not converted to bool Commit: 06aa30ffdca0fe092fa2d094aa23da34b10a1667 https://github.com/galaxyproject/galaxy/commit/06aa30ffdca0fe092fa2d094aa23… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/actions/library.py Log Message: ----------- disable tag_using_filenames by default (consistent with #5115) Commit: b0b5fb44d282b52391becdac1b190ebbd075168d https://github.com/galaxyproject/galaxy/commit/b0b5fb44d282b52391becdac1b19… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Merge pull request #7204 from abretaud/tag_fn [19.01] Data library: fix tag_using_filenames not properly converted to bool Compare: https://github.com/galaxyproject/galaxy/compare/ed6011755cf7...b0b5fb44d282 **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] 6ff846: Fix displaying tool help images on python 3
by GitHub 17 Jan '19

17 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 6ff84684bd577ea4610d63213cc090b86d983aa8 https://github.com/galaxyproject/galaxy/commit/6ff84684bd577ea4610d63213cc0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Fix displaying tool help images on python 3 Commit: 24f97f6917da606f8b9c1fc1fb4faef5c54f1933 https://github.com/galaxyproject/galaxy/commit/24f97f6917da606f8b9c1fc1fb4f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Open files in binary mode when sending data Commit: 7a9422600c76ad49515844d582bf6d5f507076e8 https://github.com/galaxyproject/galaxy/commit/7a9422600c76ad49515844d582bf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M test/api/test_galaxy_interactor.py Log Message: ----------- Fix ``GalaxyInteractorBackwardCompatTestCase.test_local_test_data_download`` API test Broken in commit bf851269c30996876c0614e7a5b57da495c44ac9 . Commit: ed6011755cf7cf5c7232bd43365dd01ab0b12af5 https://github.com/galaxyproject/galaxy/commit/ed6011755cf7cf5c7232bd43365d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/api/test_galaxy_interactor.py Log Message: ----------- Merge pull request #7228 from mvdbeek/fix_image_display_py3 [19.01] Fix displaying tool help images on python 3 Compare: https://github.com/galaxyproject/galaxy/compare/d460d218ad89...ed6011755cf7 **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] ab8ea1: Add error listener for input elements, utilize to ...
by GitHub 17 Jan '19

17 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: ab8ea1ee40c2a7de3a7cc6e6aaafba95f451a6c6 https://github.com/galaxyproject/galaxy/commit/ab8ea1ee40c2a7de3a7cc6e6aaaf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add error listener for input elements, utilize to highlight numeric value range adjustments Commit: 48c2807e2ebecf7fd01bd56e102ccaaa25947a29 https://github.com/galaxyproject/galaxy/commit/48c2807e2ebecf7fd01bd56e102c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Fix name of error handler helper function Commit: d20c6f6d8c1cfdd677afa04ad70c10e11c7228f4 https://github.com/galaxyproject/galaxy/commit/d20c6f6d8c1cfdd677afa04ad70c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Remove unused default error message Commit: ef02c60f792a8aeadcaa58d8e0a4ac71d65aa42b https://github.com/galaxyproject/galaxy/commit/ef02c60f792a8aeadcaa58d8e0a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Move local slider helper variables into score/statement Commit: 8534ef5d5cef95bad2dbb882b8285a44deb0dca6 https://github.com/galaxyproject/galaxy/commit/8534ef5d5cef95bad2dbb882b828… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Move field error binding to input element wrapper Commit: 48811d4c0c79b5dfdba2e51471f71d9d9fa0b34e https://github.com/galaxyproject/galaxy/commit/48811d4c0c79b5dfdba2e51471f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Use listento caller to bind input element error listener Commit: 97651462212b2a08a18b67b9fe2d731732b3d1c3 https://github.com/galaxyproject/galaxy/commit/97651462212b2a08a18b67b9fe2d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to slider out-of-range error detection Commit: d460d218ad898242046c2422aa211fe6a4830462 https://github.com/galaxyproject/galaxy/commit/d460d218ad898242046c2422aa21… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #7229 from mvdbeek/backport_sliding_validator [19.01] Backport #7183 input element listener Compare: https://github.com/galaxyproject/galaxy/compare/7c13cdf00673...d460d218ad89 **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] c68cd2: Add error listener for input elements, utilize to ...
by GitHub 17 Jan '19

17 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c68cd231cbe52e0b51df6e530279dcd5ebb65f8d https://github.com/galaxyproject/galaxy/commit/c68cd231cbe52e0b51df6e530279… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add error listener for input elements, utilize to highlight numeric value range adjustments Commit: b72a6d5dffd2a0a8af7b4bdc28b308f3be2db407 https://github.com/galaxyproject/galaxy/commit/b72a6d5dffd2a0a8af7b4bdc28b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Fix name of error handler helper function Commit: caa50a8bed932291f00eb39ccefa2329665b17db https://github.com/galaxyproject/galaxy/commit/caa50a8bed932291f00eb39ccefa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Remove unused default error message Commit: 0939bfc64bf970ce8e816b4f9598a8e3e7b9de58 https://github.com/galaxyproject/galaxy/commit/0939bfc64bf970ce8e816b4f9598… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Move local slider helper variables into score/statement Commit: 5d5f7dbd95d620ac26a2a552e7e98c8e63194789 https://github.com/galaxyproject/galaxy/commit/5d5f7dbd95d620ac26a2a552e7e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Move field error binding to input element wrapper Commit: 2807f8f66af2ec1ddde6a4824cd958169f8aff03 https://github.com/galaxyproject/galaxy/commit/2807f8f66af2ec1ddde6a4824cd9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Use listento caller to bind input element error listener Commit: 0e6cf700fea90e2b4756f5787b8efd26ae994ce1 https://github.com/galaxyproject/galaxy/commit/0e6cf700fea90e2b4756f5787b8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to slider out-of-range error detection Commit: b8dc640dd13e67688b32cd0ba2edc59d19f16beb https://github.com/galaxyproject/galaxy/commit/b8dc640dd13e67688b32cd0ba2ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/scripts/app/index.js M client/galaxy/scripts/app/monitor.js M client/galaxy/scripts/app/singleton.js R client/galaxy/scripts/apps/admin.js R client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/chart.js R client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/login.js R client/galaxy/scripts/apps/panels/admin-panel.js R client/galaxy/scripts/apps/panels/history-panel.js R client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/bundleEntries.js A client/galaxy/scripts/components/Masthead/index.vue A client/galaxy/scripts/components/Masthead/initMasthead.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/ErrorStack.vue A client/galaxy/scripts/entry/admin/AdminRouter.js A client/galaxy/scripts/entry/admin/index.js A client/galaxy/scripts/entry/analysis/AnalysisRouter.js A client/galaxy/scripts/entry/analysis/index.js A client/galaxy/scripts/entry/generic.js A client/galaxy/scripts/entry/login/LoginPage.js A client/galaxy/scripts/entry/login/index.js A client/galaxy/scripts/entry/panels/admin-panel.js A client/galaxy/scripts/entry/panels/history-panel.js A client/galaxy/scripts/entry/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery.custom.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/onload/defaultAppFactory.js A client/galaxy/scripts/onload/defaultConfigs.js A client/galaxy/scripts/onload/getRootFromIndexLink.js A client/galaxy/scripts/onload/globalInits/iframesAreTerrible.js A client/galaxy/scripts/onload/globalInits/index.js A client/galaxy/scripts/onload/globalInits/initModals.js A client/galaxy/scripts/onload/globalInits/initSentry.js A client/galaxy/scripts/onload/globalInits/initTooltips.js A client/galaxy/scripts/onload/globalInits/initTours.js A 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client/gulpfile.js M client/karma/karma.config.qunit.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/webhooks/demo/tour_generator/script.js M config/plugins/webhooks/demo/tour_generator/tour_generator.js M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/version.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M run_tests.sh M templates/admin/tool_shed_repository/common.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/message.mako M templates/no_access.mako M templates/refresh_frames.mako M templates/slug_editing_js.mako M templates/tagging_common.mako M templates/user/info.mako M templates/user/login.mako M templates/user/logout.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/display.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/page/wymiframe.mako M templates/webapps/galaxy/root/redirect.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/browse_repository.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako A test/api/test_galaxy_interactor.py M test/api/test_histories.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py M tools/filters/uniq.xml Log Message: ----------- Merge branch 'dev' into highlight_floating Commit: f2ccea2ded16f9f547c6ee351cbe330aa299c273 https://github.com/galaxyproject/galaxy/commit/f2ccea2ded16f9f547c6ee351cbe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #7183 from guerler/highlight_floating Add error listener for input elements Compare: https://github.com/galaxyproject/galaxy/compare/9d6e85da8b12...f2ccea2ded16 **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] 76f818: Strip openid features from user controller
by GitHub 16 Jan '19

16 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76f818b0c5142b65e42318856d428e1a1ce0ff00 https://github.com/galaxyproject/galaxy/commit/76f818b0c5142b65e42318856d42… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Strip openid features from user controller Commit: a30f3b2e2376f112ca94340ef15aa95a010c6626 https://github.com/galaxyproject/galaxy/commit/a30f3b2e2376f112ca94340ef15a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: R templates/user/openid_associate.mako R templates/user/openid_manage.mako Log Message: ----------- Remove openid related makos Commit: 6796c187acd8f8705d78a43d7ffb9936967cbec6 https://github.com/galaxyproject/galaxy/commit/6796c187acd8f8705d78a43d7ffb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove openid access links from preferences Commit: d9098324ee26e18c5f1e5da32ccee851f167cc9b https://github.com/galaxyproject/galaxy/commit/d9098324ee26e18c5f1e5da32cce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M templates/user/login.mako Log Message: ----------- Remove openid feature from login form Commit: a48e445abb0f337d5bc18c31a14f22a550719986 https://github.com/galaxyproject/galaxy/commit/a48e445abb0f337d5bc18c31a14f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M templates/user/index.mako Log Message: ----------- Remove openid feature from legacy toolshed preference view Commit: bf38a74e71fc68d6794f7c33c462c8468c648520 https://github.com/galaxyproject/galaxy/commit/bf38a74e71fc68d6794f7c33c462… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/app.py Log Message: ----------- Strip openid manager and providers from app Commit: bb67f5e6167ccaf8e39b07ce2abcee05a205a3ae https://github.com/galaxyproject/galaxy/commit/bb67f5e6167ccaf8e39b07ce2abc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: R config/openid_conf.xml.sample M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Remove openid options from config schema Commit: 79445c51c966d3e2fd7e3fa5b5a2f1c6e2bd5e4c https://github.com/galaxyproject/galaxy/commit/79445c51c966d3e2fd7e3fa5b5a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/app.py Log Message: ----------- Remove openid from schema and controller endpoints Commit: a19abdb73b88a941cfe3c90648ba2de532581d0b https://github.com/galaxyproject/galaxy/commit/a19abdb73b88a941cfe3c90648ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: R lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Remove openid manager and routes Commit: ca8fc817683949b8b003cc12c80dd143a16760c1 https://github.com/galaxyproject/galaxy/commit/ca8fc817683949b8b003cc12c80d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Remove openid settings from config and toolshed Commit: df31cb1ad6f1018575f2f241e0afd7ea9cffeb1d https://github.com/galaxyproject/galaxy/commit/df31cb1ad6f1018575f2f241e0af… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: R lib/galaxy/openid/__init__.py R lib/galaxy/openid/providers.py Log Message: ----------- Remove openid service modules Commit: f31d61b71c739c03e5068bff188a56f175a18297 https://github.com/galaxyproject/galaxy/commit/f31d61b71c739c03e5068bff188a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove openid check in dependencies Commit: 0a23204b888b958aa59c198f620bbc1383a8e9b4 https://github.com/galaxyproject/galaxy/commit/0a23204b888b958aa59c198f620b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Strip openid from data model Commit: eba5214e95347c306d3211261106877675e77179 https://github.com/galaxyproject/galaxy/commit/eba5214e95347c306d3211261106… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove unused imports Commit: 9d6e85da8b12e02504b8706d977a27d522bced54 https://github.com/galaxyproject/galaxy/commit/9d6e85da8b12e02504b8706d977a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/entry/analysis/AnalysisRouter.js M client/galaxy/scripts/mvc/user/user-preferences.js R config/openid_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py R lib/galaxy/openid/__init__.py R lib/galaxy/openid/providers.py R lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M templates/user/index.mako M templates/user/login.mako R templates/user/openid_associate.mako R templates/user/openid_manage.mako Log Message: ----------- Merge remote-tracking branch 'guerler/remove_openid' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f8b87d988c96...9d6e85da8b12 **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] a9ed02: Add eslint, start setting up targets. Needs exclu...
by GitHub 16 Jan '19

16 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9ed02de64637748c43fd7744a47d09b80d01327 https://github.com/galaxyproject/galaxy/commit/a9ed02de64637748c43fd7744a47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: A client/.eslintrc.js M client/package.json M client/yarn.lock Log Message: ----------- Add eslint, start setting up targets. Needs exclusions, rule tweaking, and a ton of quick error resolution. Commit: 5811e7268256fc3364ad2e08388f82c42132ecc7 https://github.com/galaxyproject/galaxy/commit/5811e7268256fc3364ad2e08388f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/scss/base.scss Log Message: ----------- Sync formatting. Commit: e5691776396a7b7d8a993e23ebf670960dc6284e https://github.com/galaxyproject/galaxy/commit/e5691776396a7b7d8a993e23ebf6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/package.json A client/prettier.config.js M client/yarn.lock Log Message: ----------- Upgrade prettier, simplify config/exclusion, haven't run it yet. Commit: 49eecece5b8398ec6552e32d1448bb1a51370223 https://github.com/galaxyproject/galaxy/commit/49eecece5b8398ec6552e32d1448… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Avoid empty catch/log error. Commit: 89d3fc3c54ddf3bf09896b8d20c3d43dc0d70df1 https://github.com/galaxyproject/galaxy/commit/89d3fc3c54ddf3bf09896b8d20c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Fix most import errors in scripts/mvc Commit: 86dd5f63b448d4e8a514ceca92d5745bf6350ad8 https://github.com/galaxyproject/galaxy/commit/86dd5f63b448d4e8a514ceca92d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js Log Message: ----------- Relocate search function; should be refactored... Commit: b8e56700dbe55fe13b865122a9ac83d107306483 https://github.com/galaxyproject/galaxy/commit/b8e56700dbe55fe13b865122a9ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Fix no-useless-escape errors. Commit: 9cc5a01b94caf4644442fb8081da6da408850a19 https://github.com/galaxyproject/galaxy/commit/9cc5a01b94caf4644442fb8081da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/job-dag.js Log Message: ----------- Fix Graph reference in job-dag. Commit: 9174cb4b1df890a29d8341ad2705184b9becbb5d https://github.com/galaxyproject/galaxy/commit/9174cb4b1df890a29d8341ad2705… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-genomespace.js Log Message: ----------- Fix genomespace tool reference to config/errorcallback Commit: 02ccffb6801924b6f1d4dc6302e686bde28ef1ac https://github.com/galaxyproject/galaxy/commit/02ccffb6801924b6f1d4dc6302e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Fix reference to galaxy_main frame Commit: 8c94cdf91518a21b79793b73473fe3937b4016e8 https://github.com/galaxyproject/galaxy/commit/8c94cdf91518a21b79793b73473f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js Log Message: ----------- Drop unreachable code in colorpicker Commit: 8220705766dc3e23ddfbac45d887f82f8c36c85e https://github.com/galaxyproject/galaxy/commit/8220705766dc3e23ddfbac45d887… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js Log Message: ----------- Fix color picker template (was missing a trailing div before, see previous commit), also fix inner definition of hex. Commit: f0205d4103b1a49466e58061a066852c360a51ea https://github.com/galaxyproject/galaxy/commit/f0205d4103b1a49466e58061a066… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js Log Message: ----------- Fix noop catches, one final import in mvc. Commit: 56731df0f7ac43c6eaffe0c3a73ff685017973f6 https://github.com/galaxyproject/galaxy/commit/56731df0f7ac43c6eaffe0c3a73f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix no-redeclares in scripts/mvc Commit: f410a461bbd5b43ac855ebd2de666fa5d9113c83 https://github.com/galaxyproject/galaxy/commit/f410a461bbd5b43ac855ebd2de66… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/.eslintrc.js Log Message: ----------- Drop prettier plugin from eslint; we'll just run this -- no point in duplicating that check. Also set up a few rules that we can enable after the cleanup. Commit: 0a8edbb0643a00c1aabf643c6883fecff66e431f https://github.com/galaxyproject/galaxy/commit/0a8edbb0643a00c1aabf643c6883… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Fix bug in collection moodel toString -- this was always literally Commit: e69d540a8f28c5715822d432912d5c00d0c0ca81 https://github.com/galaxyproject/galaxy/commit/e69d540a8f28c5715822d432912d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: R client/galaxy/scripts/mvc/job/job-params.js Log Message: ----------- Remove inadvertently(?) added job-params file, looks to never have been used (and is mostly commented out code) Commit: 8004fad3e6614e24572d09648e40a88ece77b674 https://github.com/galaxyproject/galaxy/commit/8004fad3e6614e24572d09648e40… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Drop unused getGalaxyInstance in library-foldertoolbar -- these vars are templated in elsewhere, not pulled from the context. Commit: 639c9cecc0cef3a2da332f57ac8f7c63d44ee75d https://github.com/galaxyproject/galaxy/commit/639c9cecc0cef3a2da332f57ac8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Fix final no-unused-vars for scripts/mvc Commit: 653452de56339c16017601fb5f5823bbe46771e8 https://github.com/galaxyproject/galaxy/commit/653452de56339c16017601fb5f58… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/viz/phyloviz.js Log Message: ----------- Drop /* global blah */ directives, correctly supply sources for $, Galaxy, and more. Left out test dir and google analytics references. Commit: d30b7dfbe0aba80b7d14446f208a395f2f1e7a61 https://github.com/galaxyproject/galaxy/commit/d30b7dfbe0aba80b7d14446f208a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js Log Message: ----------- Standardize backbone and underscore imports. Commit: 140d53f56477feeac1368cd662e4e13e4f8b0dcd https://github.com/galaxyproject/galaxy/commit/140d53f56477feeac1368cd662e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: A client/.eslintignore M client/.eslintrc.js M client/package.json Log Message: ----------- Enable vue linting and include verything but galaxy/scripts/libs Commit: 62a65c448266ffae47ec72da087861bdbe14d433 https://github.com/galaxyproject/galaxy/commit/62a65c448266ffae47ec72da0878… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Fix most of the non-vue-specific linting issues in components Commit: 6e1f1eca44c93be02972896d44d69793f154b948 https://github.com/galaxyproject/galaxy/commit/6e1f1eca44c93be02972896d44d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/.eslintignore Log Message: ----------- Add tests, legacy, nls to eslintignore for now. Commit: 8e465b36b7c747c3a5dc336339bccd2111ec0aea https://github.com/galaxyproject/galaxy/commit/8e465b36b7c747c3a5dc336339bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/.eslintignore Log Message: ----------- Ignore .test.js files Commit: 3256849f683109c4831e36e5c30465d5d56858cb https://github.com/galaxyproject/galaxy/commit/3256849f683109c4831e36e5c304… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/.eslintignore Log Message: ----------- Ignore scripts/toolshed in linting -- we're dropping all this (I think?) from the repo. Commit: ac0d027b2517e1fb2011ba75fb5879a6b682963e https://github.com/galaxyproject/galaxy/commit/ac0d027b2517e1fb2011ba75fb58… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/natural-sort.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Cleanup in galaxy/scripts/utils Commit: aede1ab2befaf89a9c002fca69d8310b7ad7f130 https://github.com/galaxyproject/galaxy/commit/aede1ab2befaf89a9c002fca69d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/.eslintignore M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- Add scripts/toolshed back to eslint; go ahead and fix the straightforward import issues Commit: 756ff01a5328c53dac7aafe90c77506de516cd9e https://github.com/galaxyproject/galaxy/commit/756ff01a5328c53dac7aafe90c77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/util.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Cleanup in galaxy/scripts/viz, lints cleanly with one exception that I do not understand. Commit: 9316659b12b13f827d0ca24c75a1fd85075c6135 https://github.com/galaxyproject/galaxy/commit/9316659b12b13f827d0ca24c75a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/popupmenu.js M client/galaxy/scripts/ui/scroll-panel.js Log Message: ----------- Cleanup in galaxy/scripts/ui, lints cleanly now. Commit: be943ef6331ee7c469cdd423c764e8b2107e581a https://github.com/galaxyproject/galaxy/commit/be943ef6331ee7c469cdd423c764… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js Log Message: ----------- Document global usage and nonstandard bundling for galaxy.interactive_environments Commit: 441e5bb93b6be6571959613aacd5f9434168ffde https://github.com/galaxyproject/galaxy/commit/441e5bb93b6be6571959613aacd5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/app/galaxy.js M client/galaxy/scripts/entry/admin/index.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/unitTestBundle.js Log Message: ----------- Fix final standalone file linting issues. Component-specific issues remain. Commit: 86d728ab98128b6995db3c354229a5dd2dd14b00 https://github.com/galaxyproject/galaxy/commit/86d728ab98128b6995db3c354229… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/Alert.vue M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/Masthead/index.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/components/admin/DisplayApplications.vue M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Run updated and now successfully passing Prettier. Commit: 917fc8702f1a6d8d8403c924b90ad2186429b9e1 https://github.com/galaxyproject/galaxy/commit/917fc8702f1a6d8d8403c924b90a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/app/galaxy.js Log Message: ----------- This is way too chatty to log Commit: 08b4bc2ae9dbcc78561f72517047ea2e9aa71a38 https://github.com/galaxyproject/galaxy/commit/08b4bc2ae9dbcc78561f72517047… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/utils/localization.js Log Message: ----------- next-line is more reliable... prettier broke the disable-line comment that was previously here Commit: c3cf826565464ad58ef9c65e99d83cd8fe9bc916 https://github.com/galaxyproject/galaxy/commit/c3cf826565464ad58ef9c65e99d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Drop one more unnecessary escape, this time in Sharing.vue Commit: 1c1c37c23ccd4619317d49ece3543e34e5ab06ab https://github.com/galaxyproject/galaxy/commit/1c1c37c23ccd4619317d49ece354… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Drop modalTitle (display is busted and it's unused/redundant, so I think this was unintentional -- also lacks a default value for the computed prop) Commit: 44b020e852ac34ec1102c511cf5c482109ca1674 https://github.com/galaxyproject/galaxy/commit/44b020e852ac34ec1102c511cf5c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/package.json Log Message: ----------- With eslintignore in the right spot, we don't need to specify this path. Commit: 07334d5adb74c5d654b3eb45a34e79da8ea7939b https://github.com/galaxyproject/galaxy/commit/07334d5adb74c5d654b3eb45a34e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue Log Message: ----------- Drop unnecessary key, after reading more about how v-for key indexes are used. Commit: f349e5f56e06f84ecc948b348528629e82e749b4 https://github.com/galaxyproject/galaxy/commit/f349e5f56e06f84ecc948b348528… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue Log Message: ----------- We'll want to look at each usage of these and document them as skippable or (likely) use an appropriate index for iteration. Commit: f576cd5494233cfbcc9d4d51ced02014049449a8 https://github.com/galaxyproject/galaxy/commit/f576cd5494233cfbcc9d4d51ced0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Use appropriate keys for plugin list iteration. Commit: 3b9857d7b7de716077eaa20ca2468aa41a7d932b https://github.com/galaxyproject/galaxy/commit/3b9857d7b7de716077eaa20ca246… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Address require-v-for-key as appropriate, either documenting a skip for simple iteration or indexing for keyed objects Commit: 2924f1fda1554416bfa81258874aef52329c971b https://github.com/galaxyproject/galaxy/commit/2924f1fda1554416bfa81258874a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/BaseGrid.vue Log Message: ----------- Fix remaining straightforward-ish linting issues. Two remaining errors -- a side effect in RuleBuilder's hotData and the trackster filter issue. Commit: 875dab36edb5dee20e563d847b2e9bd7b7258cc0 https://github.com/galaxyproject/galaxy/commit/875dab36edb5dee20e563d847b2e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Run prettier after rebase Commit: f95cff627bd64c6dba446128617e94037132d2e7 https://github.com/galaxyproject/galaxy/commit/f95cff627bd64c6dba446128617e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M Makefile M tox.ini Log Message: ----------- Attempt to add eslint to travis. Commit: 6a4297a9fc4320fdfcda59385ad6fc6a2cb546da https://github.com/galaxyproject/galaxy/commit/6a4297a9fc4320fdfcda59385ad6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Tox works, add eslint to travis.yml Commit: 7b97bd3e1b97d02be8288bae0767ebbcde2c188e https://github.com/galaxyproject/galaxy/commit/7b97bd3e1b97d02be8288bae0767… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Test specifying node version in travis config Commit: 588e2d7460c74a103a8075a93fdfe6aab4d71ad5 https://github.com/galaxyproject/galaxy/commit/588e2d7460c74a103a8075a93fdf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Test building without tox Commit: 61774f5126c9eab5e3fe42e3b1cde1d12e5bf1b0 https://github.com/galaxyproject/galaxy/commit/61774f5126c9eab5e3fe42e3b1cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M .travis.yml M Makefile M tox.ini Log Message: ----------- re-enable full matrix, overhaul qunit/lint implementations. Commit: b8347c0fb1729500002dfa272758ac62d8f2c3d0 https://github.com/galaxyproject/galaxy/commit/b8347c0fb1729500002dfa272758… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Test adding a qunit js env Commit: 19af921845050d708a1bcc56882fa77cd2a1dc1e https://github.com/galaxyproject/galaxy/commit/19af921845050d708a1bcc56882f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- DRop js primary env, use specific defs in matrix Commit: 4986f62a8d14601c1eafb584a766e99180ca7577 https://github.com/galaxyproject/galaxy/commit/4986f62a8d14601c1eafb584a766… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- qunit actually needs a build, because of base.css... (we should really fix this, should not be required) Commit: 2025eab2184750611338600a1f22828b15847707 https://github.com/galaxyproject/galaxy/commit/2025eab2184750611338600a1f22… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Use 'name' in the travis build matrix instead of env for javascript jobs Commit: 9ddcba91be81fcb7265c6fd449d4dc2a2825d647 https://github.com/galaxyproject/galaxy/commit/9ddcba91be81fcb7265c6fd449d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M Makefile Log Message: ----------- Drop internal client-test-* makefile targets Commit: b50e87ff2888ecac672740b0f68216ab8245736b https://github.com/galaxyproject/galaxy/commit/b50e87ff2888ecac672740b0f682… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Better names for js travis jobs Commit: 92323e05d64f6d50caa6ca57f6061ba387d77017 https://github.com/galaxyproject/galaxy/commit/92323e05d64f6d50caa6ca57f606… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/viz/trackster/filters.js Log Message: ----------- Document eslint exception, create issue for trackster filter/group functionality not working. Commit: a482c5ce4cd70b208f07e79eb0f5c08ec1e67292 https://github.com/galaxyproject/galaxy/commit/a482c5ce4cd70b208f07e79eb0f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Swap hotData() from a computed property to a method, since it has side effects. see https://github.com/vuejs/eslint-plugin-vue/blob/master/docs/rules/no-side-e… and https://vuejs.org/v2/guide/computed.html#Computed-Caching-vs-Methods Commit: 8cd8a03284e710d7b8bedc2244c13087941dfa89 https://github.com/galaxyproject/galaxy/commit/8cd8a03284e710d7b8bedc2244c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/components/Sharing.vue M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into eslint, resolving conflict in "Sharing.vue" Commit: f8b87d988c965a04806adf7ff9dccf3a41f52d86 https://github.com/galaxyproject/galaxy/commit/f8b87d988c965a04806adf7ff9dc… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M .travis.yml M Makefile A client/.eslintignore A client/.eslintrc.js M client/galaxy/scripts/app/galaxy.js M client/galaxy/scripts/components/Alert.vue M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/Masthead/index.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/components/admin/DisplayApplications.vue M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/entry/admin/index.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js R client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/popupmenu.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/natural-sort.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M client/package.json A client/prettier.config.js M client/yarn.lock M tox.ini Log Message: ----------- Merge pull request #7202 from dannon/eslint Eslint Compare: https://github.com/galaxyproject/galaxy/compare/10c2f9cbc286...f8b87d988c96 **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] 8570db: Abstraction for different metadata collection stra...
by GitHub 16 Jan '19

16 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8570db46fd5cf9669315376041e80bc733255025 https://github.com/galaxyproject/galaxy/commit/8570db46fd5cf9669315376041e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/datatypes/metadata.py M lib/galaxy/jobs/__init__.py A lib/galaxy/metadata/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Abstraction for different metadata collection strategies. Commit: 0aa7474bce58f3e5778330dc7abab3bd222e65ff https://github.com/galaxyproject/galaxy/commit/0aa7474bce58f3e5778330dc7aba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/metadata/__init__.py M lib/galaxy/tools/__init__.py Log Message: ----------- Simplify metadata strategy interface - load_metadata entry point. Eliminates two methods from the "public interface" for this strategy and replaces them with one that exposes much less of what I'd consider to be internals of what is going on. Commit: 31dd08dde248a3446f8dbf769221158f96f04580 https://github.com/galaxyproject/galaxy/commit/31dd08dde248a3446f8dbf769221… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/metadata/__init__.py Log Message: ----------- Simplify metadata strategy - make method "private". Commit: 6f449107e4fcb180feda9854188939dea67dd270 https://github.com/galaxyproject/galaxy/commit/6f449107e4fcb180feda98541889… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/metadata/__init__.py Log Message: ----------- Formalize interface for metadata strategy. Commit: ecd6a9c054c8b203be2bc5a3799975b9a8579b94 https://github.com/galaxyproject/galaxy/commit/ecd6a9c054c8b203be2bc5a37999… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/metadata/__init__.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Refactor metadata strategy interface to consume dict of outputs. Exposing output names to the generation strategy should allow a more grok-able alternative metadata collection strategy to be implemented with simple output name keys and such. Commit: d2b7e8af32f60548b06abde87211bc24c3f07aa8 https://github.com/galaxyproject/galaxy/commit/d2b7e8af32f60548b06abde87211… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Refactor set_metadata.py to simplify provided metadata access. Commit: 8bcda83aad15200dd6e72988ef65bf256ac5c18b https://github.com/galaxyproject/galaxy/commit/8bcda83aad15200dd6e72988ef65… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Bug fix for reading metadata and extension from galaxy.json in set_metadata.py. Commit: 10c2f9cbc286477550e708d65bcd1381857dca15 https://github.com/galaxyproject/galaxy/commit/10c2f9cbc286477550e708d65bcd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M lib/galaxy/datatypes/metadata.py M lib/galaxy/jobs/__init__.py A lib/galaxy/metadata/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #7158 from jmchilton/refactor_metadata Cleanup, test, and fix metadata collection code. Compare: https://github.com/galaxyproject/galaxy/compare/74c70ee1d542...10c2f9cbc286 **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.

1 0

[galaxyproject/galaxy] 2d2a51: Fix spacing between checkbox and buttons in histor...
by GitHub 16 Jan '19

16 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2d2a51db167434450fc7b2a3b6c938e4338e1925 https://github.com/galaxyproject/galaxy/commit/2d2a51db167434450fc7b2a3b6c9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Fix spacing between checkbox and buttons in history sharing view Commit: 74c70ee1d542a6d6f669d1120850d9a564446e51 https://github.com/galaxyproject/galaxy/commit/74c70ee1d542a6d6f669d1120850… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Merge pull request #7222 from guerler/fix_spacing_check Fix spacing between checkbox and buttons in history sharing view Compare: https://github.com/galaxyproject/galaxy/compare/1887e9f54a1c...74c70ee1d542 **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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