- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f663e0: Use regular font-size in popovers by default
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f663e09b29dd166e846268468e4f088d05e3f85d https://github.com/galaxyproject/galaxy/commit/f663e09b29dd166e846268468e4f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Use regular font-size in popovers by default Commit: 9a6ae4d9d64f338a7069d736dd7b0026d02db865 https://github.com/galaxyproject/galaxy/commit/9a6ae4d9d64f338a7069d736dd7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- Use multistring for composite upload row template Commit: 73e027b8a6429e8882fb606f184a0108ae70daa5 https://github.com/galaxyproject/galaxy/commit/73e027b8a6429e8882fb606f184a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Use multistring for composite upload view template Commit: 4c0df7ef1ff4c39632c915de25ea37f861970566 https://github.com/galaxyproject/galaxy/commit/4c0df7ef1ff4c39632c915de25ea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js Log Message: ----------- Use multistring for collection upload view template Commit: 7e4a0518e59cdd11568b550440e549b6668808c7 https://github.com/galaxyproject/galaxy/commit/7e4a0518e59cdd11568b550440e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix font size handling in upload view Commit: ca4e5677db9044b993fe7ac552c1b0dbf5dd4e2c https://github.com/galaxyproject/galaxy/commit/ca4e5677db9044b993fe7ac552c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix footer styles in upload view Commit: bdc2584d1206a785b522c08e859a7b1fb3b70e29 https://github.com/galaxyproject/galaxy/commit/bdc2584d1206a785b522c08e859a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 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/entry/analysis/AnalysisRouter.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-preferences.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 R config/openid_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py A lib/galaxy/metadata/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py R lib/galaxy/openid/__init__.py R lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.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 lib/galaxy_ext/metadata/set_metadata.py M templates/user/index.mako M templates/user/login.mako R templates/user/openid_associate.mako R templates/user/openid_manage.mako M tox.ini Log Message: ----------- Merge branch 'dev' into upload_view_fixes Commit: bf27a7c99364d634182554c7126ad957c915203f https://github.com/galaxyproject/galaxy/commit/bf27a7c99364d634182554c7126a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: 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/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/scss/upload.scss Log Message: ----------- Use regular font size throughout uploader Commit: 43409ce5cb3e76648d31c4e4d09db260a28b6a69 https://github.com/galaxyproject/galaxy/commit/43409ce5cb3e76648d31c4e4d09d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix collection uploaders table header alignment Commit: 1cacdb76eb92927ed69b2ba0ae6af123a08fd685 https://github.com/galaxyproject/galaxy/commit/1cacdb76eb92927ed69b2ba0ae6a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Apply suggestions from code review Co-Authored-By: dannon <dannon.baker(a)gmail.com> Commit: 67136670cf96ab19ffee3e8096b7e3bb3ad000bc https://github.com/galaxyproject/galaxy/commit/67136670cf96ab19ffee3e8096b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Adjust info message padding for uploader, convert nav-tabs margin from fixed pixels to ems Commit: 7742bed9c9f3246da8ccc4fcf1f6084116643fe4 https://github.com/galaxyproject/galaxy/commit/7742bed9c9f3246da8ccc4fcf1f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Leave a block element in upload-top-info for consistent spacing. The other three tabs already start with info there. Commit: ce113af1fc86650401f95bcdb90fa0d6927d3a57 https://github.com/galaxyproject/galaxy/commit/ce113af1fc86650401f95bcdb90f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: 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/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Merge pull request #7232 from guerler/upload_view_fixes Use regular font-size and styling in uploader Compare: https://github.com/galaxyproject/galaxy/compare/40003111b3cc...ce113af1fc86 **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] 3040e9: Strip openid features from user controller
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3040e9f7a3cf7d761b3c258d377a8efb62341cc2 https://github.com/galaxyproject/galaxy/commit/3040e9f7a3cf7d761b3c258d377a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Strip openid features from user controller Commit: c9846391b2d4aa0e1e4f798a11c7258896c87705 https://github.com/galaxyproject/galaxy/commit/c9846391b2d4aa0e1e4f798a11c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R templates/user/openid_associate.mako R templates/user/openid_manage.mako Log Message: ----------- Remove openid related makos Commit: 260d2240134d6ea730ab22b9117fc290209c94e3 https://github.com/galaxyproject/galaxy/commit/260d2240134d6ea730ab22b9117f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 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: 62cc4e27e56f27ca5a293ca3f9f616623519fecc https://github.com/galaxyproject/galaxy/commit/62cc4e27e56f27ca5a293ca3f9f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M templates/user/login.mako Log Message: ----------- Remove openid feature from login form Commit: 73f75aeb11bd657819ce73f4509995a5c283418c https://github.com/galaxyproject/galaxy/commit/73f75aeb11bd657819ce73f45099… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M templates/user/index.mako Log Message: ----------- Remove openid feature from legacy toolshed preference view Commit: 4b678daab8c9c686ccc07a51d40062ba905dc87b https://github.com/galaxyproject/galaxy/commit/4b678daab8c9c686ccc07a51d400… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/app.py Log Message: ----------- Strip openid manager and providers from app Commit: 2f942eefb407b3449a90ef780181393041da7e6b https://github.com/galaxyproject/galaxy/commit/2f942eefb407b3449a90ef780181… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 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: 3fa2409de4355e7c1b88ef43cb540fb459b1923b https://github.com/galaxyproject/galaxy/commit/3fa2409de4355e7c1b88ef43cb54… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 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: 6fecb4a07aa079ed1a1430cf34562b53fda9d1ea https://github.com/galaxyproject/galaxy/commit/6fecb4a07aa079ed1a1430cf3456… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 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: bd3c37f06506066c96a1d939ce87627e4d4918c6 https://github.com/galaxyproject/galaxy/commit/bd3c37f06506066c96a1d939ce87… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 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: b9af75567c298944c026930892fd16ebbd9510ab https://github.com/galaxyproject/galaxy/commit/b9af75567c298944c026930892fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R lib/galaxy/openid/__init__.py R lib/galaxy/openid/providers.py Log Message: ----------- Remove openid service modules Commit: 8b9082ac19e43394f513f27dbf3ccf939c06c226 https://github.com/galaxyproject/galaxy/commit/8b9082ac19e43394f513f27dbf3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove openid check in dependencies Commit: f591999738d3e99c8f10abefd11c79515878cc98 https://github.com/galaxyproject/galaxy/commit/f591999738d3e99c8f10abefd11c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Strip openid from data model Commit: 4f0b1fbd79df9232cbde99d11d9089e323a37092 https://github.com/galaxyproject/galaxy/commit/4f0b1fbd79df9232cbde99d11d90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove unused imports Commit: 5426f3b5533417ba4fd6043dd6bdb6f81e8db678 https://github.com/galaxyproject/galaxy/commit/5426f3b5533417ba4fd6043dd6bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: A client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Add login vue component Commit: 92011492413a5ead7b8f1680d81096b28ae7e400 https://github.com/galaxyproject/galaxy/commit/92011492413a5ead7b8f1680d810… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: A client/galaxy/scripts/components/login/Password.vue Log Message: ----------- Add Password vue component Commit: ee465276d1d7537eca424302cb68f537c0832687 https://github.com/galaxyproject/galaxy/commit/ee465276d1d7537eca424302cb68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/apps/login.js Log Message: ----------- Revise login app to load vue components Commit: d78b5903388379f0642861b86731e08ba3e7c3b6 https://github.com/galaxyproject/galaxy/commit/d78b5903388379f0642861b86731… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Revise masthead routes Commit: a7ba7788a48af98febd890ddad6f84d033c7b15b https://github.com/galaxyproject/galaxy/commit/a7ba7788a48af98febd890ddad6f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- Remove unused parameter from auth manager Commit: 3065d7c5879d0831d4355f59613aea1c6266b9c0 https://github.com/galaxyproject/galaxy/commit/3065d7c5879d0831d4355f59613a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Move authentication logic to user manager Commit: 98a1dede27d3996b9450ae8c2f4bae23fab099ba https://github.com/galaxyproject/galaxy/commit/98a1dede27d3996b9450ae8c2f4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove CreatesUsersMixin from base controller Commit: 1bcb02da2071996de1637469b3b8df40379f9d65 https://github.com/galaxyproject/galaxy/commit/1bcb02da2071996de1637469b3b8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Reuse shared user manager features in user api Commit: a7bb8db3a966f87c2f472c3bc34768fe135cb6f1 https://github.com/galaxyproject/galaxy/commit/a7bb8db3a966f87c2f472c3bc347… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Revise user controller, user shared manager features Commit: 273e91a563bb74626e239490c6ce693408f59a87 https://github.com/galaxyproject/galaxy/commit/273e91a563bb74626e239490c6ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Align toolshed user controller Commit: 644d612083b94d7571c75792133585b26d7411bc https://github.com/galaxyproject/galaxy/commit/644d612083b94d7571c757921335… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/user/change_password.mako M templates/webapps/tool_shed/user/index.mako Log Message: ----------- Adjust toolshed makos Commit: 14912d72d00fb96c05786e82edcd6a23239d32a1 https://github.com/galaxyproject/galaxy/commit/14912d72d00fb96c05786e82edcd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R templates/user/login.mako R templates/user/reset_password.mako A templates/webapps/tool_shed/user/login.mako A templates/webapps/tool_shed/user/reset_password.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Move toolshed makos, adjust test cases Commit: 0ced7d393d05b011e101e25ff135956a4d45026f https://github.com/galaxyproject/galaxy/commit/0ced7d393d05b011e101e25ff135… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M test/unit/managers/test_HDAManager.py M test/unit/managers/test_UserManager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Add test cases for user manager Commit: 86b6786e0856ecb7c6e5618e5a5f5672a84e5960 https://github.com/galaxyproject/galaxy/commit/86b6786e0856ecb7c6e5618e5a5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R templates/user/index.mako Log Message: ----------- Remove unused user index mako Commit: 4e2192963879c61e65a450d8126878e1a951ed08 https://github.com/galaxyproject/galaxy/commit/4e2192963879c61e65a450d81268… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Remove openid use case from toolshed login controller Commit: f8db566f4e476eaf2a82d4277e4d18ba5d29f4b0 https://github.com/galaxyproject/galaxy/commit/f8db566f4e476eaf2a82d4277e4d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R templates/user/info.mako M templates/webapps/tool_shed/user/manage_info.mako Log Message: ----------- Remove user info mako Commit: b1ba31ea90f8239c03938c108045239a255702b0 https://github.com/galaxyproject/galaxy/commit/b1ba31ea90f8239c03938c108045… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Fix unit test case Commit: 29ceca884fbf50f4e5310404dfdaa4330979d0f8 https://github.com/galaxyproject/galaxy/commit/29ceca884fbf50f4e5310404dfda… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/components/login/Login.vue M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_login.py Log Message: ----------- Fix selenium login test case Commit: 06265ad536d4a4b0bfc85584e682a7279ef07730 https://github.com/galaxyproject/galaxy/commit/06265ad536d4a4b0bfc85584e682… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M .ci/jenkins/integration-py3/run_tests.sh M .ci/jenkins/integration/run_tests.sh M client/README.md 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/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/GalaxyLoader.vue A client/galaxy/scripts/components/Masthead/index.vue A client/galaxy/scripts/components/Masthead/initMasthead.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/DisplayApplications.vue A client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/components/login/Login.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/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.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery.custom.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.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/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.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/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/options-menu.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/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.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/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.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/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/user/user-preferences.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 client/galaxy/scripts/onload/globalInits/init_refresh_on_change.js A client/galaxy/scripts/onload/globalInits/onloadWebhooks.js A client/galaxy/scripts/onload/globalInits/panelManagement.js A client/galaxy/scripts/onload/globalInits/replace_big_select_inputs.js M client/galaxy/scripts/onload/index.js A client/galaxy/scripts/onload/initQueue.js M client/galaxy/scripts/onload/loadConfig.js A client/galaxy/scripts/onload/standardInit.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/popupmenu.js A client/galaxy/scripts/utils/genericConfig.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/viz_views.js M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/message.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M 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/container_resolvers_conf.xml.sample 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 A config/plugins/visualizations/aequatus/README.md A config/plugins/visualizations/aequatus/config/aequatus.xml A config/plugins/visualizations/aequatus/static/aequatus-vis/LICENSE A config/plugins/visualizations/aequatus/static/aequatus-vis/README.md A config/plugins/visualizations/aequatus/static/aequatus-vis/_config.yml A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/cigarUtils.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/d3_tree.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawCIGARs.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGene.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGeneExonOnly.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/geneView.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/init.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery-ui-1.12.1.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery.svg.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-3.3.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-migrate-1.4.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-ui-1.12.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.cookie.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.svg.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/newick.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/scriptaculous/prototype.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/util.js A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/fontawesome.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/solid.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/FontAwesome.otf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff2 A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/style.css A config/plugins/visualizations/aequatus/static/scripts/controls.js A config/plugins/visualizations/aequatus/static/scripts/popup.js A config/plugins/visualizations/aequatus/static/scripts/readSQLite.js A config/plugins/visualizations/aequatus/static/scripts/sql.js A config/plugins/visualizations/aequatus/static/scripts/worker.js A config/plugins/visualizations/aequatus/static/scripts/worker.sql.js A config/plugins/visualizations/aequatus/static/styles/aequatus.css A config/plugins/visualizations/aequatus/templates/aequatus.mako 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 config/tool_conf.xml.sample M config/tool_shed.yml.sample M config/workflow_resource_params_conf.xml.sample M config/workflow_schedulers_conf.xml.sample M doc/source/admin/cluster.md 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 doc/source/dev/build_a_job_runner.rst M lib/galaxy/app.py M lib/galaxy/authnz/managers.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/command_factory.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/rule_helper.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/__init__.py A lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py 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/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/yaml.py 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/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/util/streamball.py M lib/galaxy/version.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/cloud.py A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.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/webapps/tool_shed/config_schema.yml M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/repository_util.py M run_tests.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample R templates/admin/tool_errors.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.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/logout.mako R templates/webapps/galaxy/admin/view_display_applications.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/base_panels.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 M templates/webapps/tool_shed/user/login.mako A test/api/test_galaxy_interactor.py M test/api/test_histories.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/integration_util.py M test/base/populators.py M test/base/workflow_fixtures.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh R test/docker/base/start_mysql.sh A test/functional/tools/collection_creates_pair_y.yml M test/functional/tools/composite_output_tests.xml M test/functional/tools/for_workflows/head.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/multi_output.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 A test/integration/handler_template_job_conf.xml A test/integration/resubmission_pulsar_job_conf.xml A test/integration/singularity_job_conf.xml A test/integration/test_containerized_jobs.py R test/integration/test_dockerized_jobs.py A test/integration/test_handler_assignment_methods.py M test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/integration/test_scripts.py A test/integration/test_workflow_sync.py M test/selenium_tests/test_admin_app.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 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_mapper.py M test/unit/jobs/test_rules/10_site.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_collect_primary_datasets.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_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/uniq.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 branch 'dev' into remove_openid_login_mako Commit: 6bd675e0396166e92bc305b0b04ae9d1403461c5 https://github.com/galaxyproject/galaxy/commit/6bd675e0396166e92bc305b0b04a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: R client/galaxy/scripts/apps/login.js Log Message: ----------- Remove previous login.js file Commit: 6ae064d903a366088715d31de5f49cabc15acd2d https://github.com/galaxyproject/galaxy/commit/6ae064d903a366088715d31de5f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Password.vue M client/galaxy/scripts/entry/login/index.js Log Message: ----------- Load galaxy instance in password vue component Commit: a38eec9c063f17aa189d7509507264f9205b62f1 https://github.com/galaxyproject/galaxy/commit/a38eec9c063f17aa189d75095072… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Password.vue Log Message: ----------- Use urlroot and galaxy instance in password component Commit: 26ffce5fa1c6944001af6edec58acfb0dd011d4c https://github.com/galaxyproject/galaxy/commit/26ffce5fa1c6944001af6edec58a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Password.vue Log Message: ----------- Fix galaxy instance access in password vue Commit: f5f5f432ad18cbef1c221d7661ec3c5e39ed39c6 https://github.com/galaxyproject/galaxy/commit/f5f5f432ad18cbef1c221d7661ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Fix error message for password token validation Commit: 9926bbfb0e4e9be29803addb51b3f2c57477d2a7 https://github.com/galaxyproject/galaxy/commit/9926bbfb0e4e9be29803addb51b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py Log Message: ----------- Add host to password reset email Commit: e264c48399202a3e7a30672a24a3e1a741d2fed0 https://github.com/galaxyproject/galaxy/commit/e264c48399202a3e7a30672a24a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/scripts/entry/login/index.js Log Message: ----------- Remove legacy mako-based login variation Commit: 75435cb8f974e82b240d6365f0b6dc112e97dc21 https://github.com/galaxyproject/galaxy/commit/75435cb8f974e82b240d6365f0b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Password.vue Log Message: ----------- Move alert message in password component to the top Commit: a276e5befebf65fa5633a2f28c49424b260be38f https://github.com/galaxyproject/galaxy/commit/a276e5befebf65fa5633a2f28c49… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Restore login redirects to galaxy resources Commit: 905a7d0aa5461efd9e23929606fedbfdf8cac5a4 https://github.com/galaxyproject/galaxy/commit/905a7d0aa5461efd9e23929606fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M test/unit/managers/test_UserManager.py Log Message: ----------- Fix message content test in user manager test case Commit: bad54ea5dbc9dd08c11bfa2cd3462d391f65346f https://github.com/galaxyproject/galaxy/commit/bad54ea5dbc9dd08c11bfa2cd346… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix url for in unit login test case Commit: 70dacdd4d2706e46c22a04bbf0f7986b684f57ef https://github.com/galaxyproject/galaxy/commit/70dacdd4d2706e46c22a04bbf0f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/entry/login/index.js Log Message: ----------- Remove unused imports in login/index.js Commit: 0ad0de987dae7bb6b34ffa9c9a4fa4e13e413469 https://github.com/galaxyproject/galaxy/commit/0ad0de987dae7bb6b34ffa9c9a4f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Password.vue M client/galaxy/scripts/entry/login/index.js Log Message: ----------- Minor formatting tweaks (prettier update) Commit: 40003111b3cc28a7eba0994767ecf50d49f80363 https://github.com/galaxyproject/galaxy/commit/40003111b3cc28a7eba0994767ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: A client/galaxy/scripts/components/login/Login.vue A client/galaxy/scripts/components/login/Password.vue R client/galaxy/scripts/entry/login/LoginPage.js M client/galaxy/scripts/entry/login/index.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/auth/__init__.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py R templates/user/info.mako R templates/user/login.mako R templates/user/reset_password.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/user/change_password.mako M templates/webapps/tool_shed/user/index.mako A templates/webapps/tool_shed/user/login.mako M templates/webapps/tool_shed/user/manage_info.mako A templates/webapps/tool_shed/user/reset_password.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_login.py M test/shed_functional/base/twilltestcase.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_UserManager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'remove_openid_login_mako' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4044704f131d...40003111b3cc **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] bad8cf: Verify .venv's node version is in line with what w...
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bad8cffdbca2afbd2e5653041326abdfde3673bd https://github.com/galaxyproject/galaxy/commit/bad8cffdbca2afbd2e5653041326… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Verify .venv's node version is in line with what we've specified as being locked, rather than just checking if node exists. Commit: 4044704f131d713372c4db7a8e10064a91ce20fa https://github.com/galaxyproject/galaxy/commit/4044704f131d713372c4db7a8e10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7220 from dannon/node-version-upgrades Verify/update .venv's node version Compare: https://github.com/galaxyproject/galaxy/compare/91fc612af677...4044704f131d **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] 54aecb: Properly deal with missing tools in subworkflows
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 54aecb3f31812c86d370034cf557537780efbcdf https://github.com/galaxyproject/galaxy/commit/54aecb3f31812c86d370034cf557… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Properly deal with missing tools in subworkflows If a subworkflow is missing tools the entire parent workflow couldn't be loaded into the editor, because we raised an exception. This is now only logged as an error. On the user side we now prevent running and saving such workflows by actually implementing the `get_errors` method for the SubWorkflowModule class. This should fix https://github.com/galaxyproject/galaxy/issues/7140. Commit: b1b1d848d35816cfa344aeb687c78c7a0c93e66f https://github.com/galaxyproject/galaxy/commit/b1b1d848d35816cfa344aeb687c7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix loading subworkflows Commit: 6f861dec7e897bbc06b2cffbb33b2fdd9e6ac11a https://github.com/galaxyproject/galaxy/commit/6f861dec7e897bbc06b2cffbb33b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/exceptions/__init__.py Log Message: ----------- Overridde __init__ for ToolMissingException Commit: 889c1026c0893636b4fc6375443408c0ec2b4a8a https://github.com/galaxyproject/galaxy/commit/889c1026c0893636b4fc63754434… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7227 from mvdbeek/fix_workflow_loading_saving [18.09] Properly deal with missing tools in workflows Compare: https://github.com/galaxyproject/galaxy/compare/105a1d8a61ef...889c1026c089 **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] 42be5b: Add galaxycloudrunner as a conditional dependency.
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 42be5b61f2bf67a579cc1841630328e6244003fe https://github.com/galaxyproject/galaxy/commit/42be5b61f2bf67a579cc18416303… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add galaxycloudrunner as a conditional dependency. Commit: c14c358ce23ae90b2e51c01802296d0a987e0295 https://github.com/galaxyproject/galaxy/commit/c14c358ce23ae90b2e51c0180229… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Rename dynamic_destination_plugins to job_rule_modules Commit: e822f95fcbc4768d145858d7841c935aeed36cf9 https://github.com/galaxyproject/galaxy/commit/e822f95fcbc4768d145858d7841c… Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Added galaxycloudrunner config example and pipfile dependency Commit: 76ac19839911cfebf4ef8facf2f364f8a509cb1a https://github.com/galaxyproject/galaxy/commit/76ac19839911cfebf4ef8facf2f3… Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com> Date: 2019-01-17 (Thu, 17 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/entry/analysis/AnalysisRouter.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-preferences.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 R config/openid_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py A lib/galaxy/metadata/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py R lib/galaxy/openid/__init__.py R lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.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 lib/galaxy_ext/metadata/set_metadata.py M templates/user/index.mako M templates/user/login.mako R templates/user/openid_associate.mako R templates/user/openid_manage.mako M tox.ini Log Message: ----------- Merge pull request #2 from dannon/conditional_galaxycloudrunner Conditional galaxycloudrunner Commit: 91fc612af67725beb31830624d448e2c1a74bd20 https://github.com/galaxyproject/galaxy/commit/91fc612af67725beb31830624d44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #7226 from nuwang/add_galaxy_cloud_runner Added galaxy cloud runner Compare: https://github.com/galaxyproject/galaxy/compare/f2ccea2ded16...91fc612af677 **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] 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.

1 0

[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.

1 0

[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.

1 0

[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.

1 0

[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.

1 0

[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 client/galaxy/scripts/onload/globalInits/init_refresh_on_change.js A client/galaxy/scripts/onload/globalInits/onloadWebhooks.js A client/galaxy/scripts/onload/globalInits/panelManagement.js A client/galaxy/scripts/onload/globalInits/replace_big_select_inputs.js M client/galaxy/scripts/onload/index.js A client/galaxy/scripts/onload/initQueue.js M client/galaxy/scripts/onload/loadConfig.js A client/galaxy/scripts/onload/standardInit.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/popupmenu.js A client/galaxy/scripts/utils/genericConfig.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/viz/viz_views.js M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/message.scss M 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.

1 0

[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.

1 0

[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.

1 0

[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.

1 0

[galaxyproject/galaxy] 3fa43d: Swap to normal event bindings for multipanel drop....
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 3fa43dfecea37a5f56e3675afad0bd65d3196f56 https://github.com/galaxyproject/galaxy/commit/3fa43dfecea37a5f56e3675afad0… 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-view-edit.js Log Message: ----------- Swap to normal event bindings for multipanel drop. get(0) isn't great, but we'll overhaul this more in the future. Commit: 7c13cdf006733182b4bfb07ced24df729600e670 https://github.com/galaxyproject/galaxy/commit/7c13cdf006733182b4bfb07ced24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #7218 from dannon/fix_multipanel_drop [19.01] Swap to normal event bindings for multipanel drag/drop. Compare: https://github.com/galaxyproject/galaxy/compare/af21a8fa58fc...7c13cdf00673 **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] 1befc3: Update ``use_interactive`` default in docs
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1befc3881067b9b2178dce2a77a6fee7e50a8d79 https://github.com/galaxyproject/galaxy/commit/1befc3881067b9b2178dce2a77a6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: 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/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Update ``use_interactive`` default in docs This was never enabled by default in the code, but it was explicitly set to True in `config/galaxy.ini.sample` . Since we moved to `galaxy.yml.sample`, this has defaulted to False in practice. Commit: 1887e9f54a1c1fde6962ae7a47f956337854c71d https://github.com/galaxyproject/galaxy/commit/1887e9f54a1c1fde6962ae7a47f9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: 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/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 pull request #7221 from nsoranzo/use_interactive_docs Update ``use_interactive`` default in docs Compare: https://github.com/galaxyproject/galaxy/compare/9ada3b4d6e4c...1887e9f54a1c **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] ac74d1: Lock pygments back to same version as -dev depenen...
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac74d1b589b1ad62f93393a8f98f1850e92c63f1 https://github.com/galaxyproject/galaxy/commit/ac74d1b589b1ad62f93393a8f98f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Lock pygments back to same version as -dev depenency, avoiding conflicting uninstall/reinstall on startup. Commit: dc4d4fbacf8f82a70e96ddfcc73669438b855690 https://github.com/galaxyproject/galaxy/commit/dc4d4fbacf8f82a70e96ddfcc736… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- lower conditional req's; pypi is case insensitive and this matches the other requirements files for easier grepping Commit: 8ff1a6a1b7a3f59bd7ffcba45a3813742af64199 https://github.com/galaxyproject/galaxy/commit/8ff1a6a1b7a3f59bd7ffcba45a38… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- drop pygments conditional requirements and rely on it being a weberror dep, since we never use it directly Commit: 9ada3b4d6e4c4da26a05c23bd3a70c5fe42049c5 https://github.com/galaxyproject/galaxy/commit/9ada3b4d6e4c4da26a05c23bd3a7… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #7219 from dannon/update-and-lock-pygments Drop conditional pygmentz requirement (autoinstalled as necessary), minor formatting in conditional-reqs Compare: https://github.com/galaxyproject/galaxy/compare/72459797a610...9ada3b4d6e4c **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] c96092: Allow passing test_history in verify_tool func
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c960924e892c44d91436a618bd8169a60ef74142 https://github.com/galaxyproject/galaxy/commit/c960924e892c44d91436a618bd81… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Allow passing test_history in verify_tool func Commit: 4b920afba2e0b2ad24bbe00511a51297e60a2f06 https://github.com/galaxyproject/galaxy/commit/4b920afba2e0b2ad24bbe00511a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py A test/api/test_galaxy_interactor.py Log Message: ----------- Make interactor changes backwards compatible Commit: 338020f2a5203afad239e3a1b6e0becf7edad22b https://github.com/galaxyproject/galaxy/commit/338020f2a5203afad239e3a1b6e0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Fix error in view_tool_metadata (https://sentry.galaxyproject.org/sentry/toolshed/issues/294272/) Commit: 141c2a1ef37ae29b4c6e481337c6efd3a41fcd1d https://github.com/galaxyproject/galaxy/commit/141c2a1ef37ae29b4c6e481337c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Fix indentation Broken in commit cf2645f9a658c5e122fea0309bf73a1f64590c39 . Commit: 72bb23fc2df3e00d55e59259d4a995e5ad939eb8 https://github.com/galaxyproject/galaxy/commit/72bb23fc2df3e00d55e59259d4a9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py A test/api/test_galaxy_interactor.py Log Message: ----------- Merge pull request #7199 from mvdbeek/backport_interactor_improvements [19.01] Backport #7167 - interactor improvements Commit: 105a1d8a61ef6ec79992017d2cff3a18decab113 https://github.com/galaxyproject/galaxy/commit/105a1d8a61ef6ec79992017d2cff… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Merge pull request #7201 from mvdbeek/fix_view_metadata_error [18.09] Fix error in view_tool_metadata Commit: af21a8fa58fcd6945786cc307a5a258775854fe5 https://github.com/galaxyproject/galaxy/commit/af21a8fa58fcd6945786cc307a5a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 72459797a610774d45758e66fb579b19f9e4ffd8 https://github.com/galaxyproject/galaxy/commit/72459797a610774d45758e66fb57… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/107f67495713...72459797a610 **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] ea6d26: Remove fixed color from ui styles
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea6d26923fd03b8d4aeea2beafe56519210faefc https://github.com/galaxyproject/galaxy/commit/ea6d26923fd03b8d4aeea2beafe5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Remove fixed color from ui styles Commit: 2a3bd642f58c32ae6a763f6b4fa1fc1c2985e9db https://github.com/galaxyproject/galaxy/commit/2a3bd642f58c32ae6a763f6b4fa1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Use panel background for upload button initial background Commit: 8cabc95a4a48b1bdfbd5618d96497c6d45ee4092 https://github.com/galaxyproject/galaxy/commit/8cabc95a4a48b1bdfbd5618d9649… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Use default text color for upload paste field Commit: 55b22bee08fefaec45c7046e96679f830d3a0f03 https://github.com/galaxyproject/galaxy/commit/55b22bee08fefaec45c7046e9667… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/frame.scss Log Message: ----------- Use theme colors for scratchbook Commit: 535c2ae5fbdaec72957075f4a6d6a5890d7526de https://github.com/galaxyproject/galaxy/commit/535c2ae5fbdaec72957075f4a6d6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/charts.scss Log Message: ----------- Use panel button color in charts Commit: d5539a4472f5b82afb4f1ce2478a32bef9327c7b https://github.com/galaxyproject/galaxy/commit/d5539a4472f5b82afb4f1ce2478a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Replace a subset of fixed color in base styles Commit: 63fe99662870834baa00bedc6c7bc8f462fe343f https://github.com/galaxyproject/galaxy/commit/63fe99662870834baa00bedc6c7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Replace footer text color Commit: 76a0bea2627774e93985df5a50cfd95575372f9b https://github.com/galaxyproject/galaxy/commit/76a0bea2627774e93985df5a50cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove custom tool title style variation Commit: 58926ae2fe81fdc60237c1800e5662b696b472da https://github.com/galaxyproject/galaxy/commit/58926ae2fe81fdc60237c1800e56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Remove unused styles, reuse existing colors in base styles Commit: 17aa51cb85a084e57d99ca70c208bca2dc8079af https://github.com/galaxyproject/galaxy/commit/17aa51cb85a084e57d99ca70c208… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Introduce brand color parameters, leave actual ui colors unchanged Commit: f1ca1a92156531bf0b269de12f3c87cfc7e722b8 https://github.com/galaxyproject/galaxy/commit/f1ca1a92156531bf0b269de12f3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Replace with actual color values Commit: f806e7b4f1c60d826c8604a725d52a5c78cf2e78 https://github.com/galaxyproject/galaxy/commit/f806e7b4f1c60d826c8604a725d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/tour.scss Log Message: ----------- Consolidate base colors Commit: d8801ecd595142166fa41afbdfa18fa622fb4915 https://github.com/galaxyproject/galaxy/commit/d8801ecd595142166fa41afbdfa1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Replace fixed masthead toggle color Commit: 3bce850b05599622eb876c51be8504f7d9c69134 https://github.com/galaxyproject/galaxy/commit/3bce850b05599622eb876c51be85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Remove duplicate border color Commit: 8cce43838bda9b56a7448ccf1d37e18571ae442f https://github.com/galaxyproject/galaxy/commit/8cce43838bda9b56a7448ccf1d37… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Consolidate panel related footer color, remove duplicates Commit: 85713f4d4dbc15f6e6a04b55929b64f2d368774c https://github.com/galaxyproject/galaxy/commit/85713f4d4dbc15f6e6a04b55929b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Fix table accent color Commit: 2e4f5fb52fc48c6be921582805194d1ba9f9fc35 https://github.com/galaxyproject/galaxy/commit/2e4f5fb52fc48c6be92158280519… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Fix unused colors Commit: daf601e8342e2fabe05f9b45ed4a3f71b7bd22ee https://github.com/galaxyproject/galaxy/commit/daf601e8342e2fabe05f9b45ed4a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Remove unused input style specs Commit: 9d0d1231efd16c95ae1da0e90338349002172444 https://github.com/galaxyproject/galaxy/commit/9d0d1231efd16c95ae1da0e90338… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Resolve background panel portlet contrast Commit: 5a36b9dd2cc2091bf278ace6ee78e551a3e87089 https://github.com/galaxyproject/galaxy/commit/5a36b9dd2cc2091bf278ace6ee78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M static/welcome.html.sample Log Message: ----------- Remove rounded borders from welcome box Commit: 2d9ccf5e9fdae128938827447781a50b73795ffc https://github.com/galaxyproject/galaxy/commit/2d9ccf5e9fdae128938827447781… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/ui/search-input.scss Log Message: ----------- Fix tool search icon position Commit: e6cd79bd424e3f8126d1ef5fe7bc29b720b000e1 https://github.com/galaxyproject/galaxy/commit/e6cd79bd424e3f8126d1ef5fe7bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/tour.scss Log Message: ----------- Consolidate base color Commit: b998553b3afa9c5a88e70ffc908b0d3283336b45 https://github.com/galaxyproject/galaxy/commit/b998553b3afa9c5a88e70ffc908b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Consolidate text and border colors Fix Commit: b6271da34db8156ffd189ebd313f4dd2f5b45cda https://github.com/galaxyproject/galaxy/commit/b6271da34db8156ffd189ebd313f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/style/scss/base.scss Log Message: ----------- Fix grid search field style Commit: f30989343a5435cd59a68d3108e5ff1659022223 https://github.com/galaxyproject/galaxy/commit/f30989343a5435cd59a68d3108e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Fix alert text level, fix search field background Commit: 34de1db38acdd699c764a3ce5bb2fab03382bc13 https://github.com/galaxyproject/galaxy/commit/34de1db38acdd699c764a3ce5bb2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-12 (Sat, 12 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Fix running status brightness Commit: 258975879b95f95afeb138350747d3e1d7a9e421 https://github.com/galaxyproject/galaxy/commit/258975879b95f95afeb138350747… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M client/galaxy/scripts/qunit/tests/form_tests.js Log Message: ----------- Fix color related test case Commit: 107f67495713ea71dd97e9f83656f4ded8dccc9f https://github.com/galaxyproject/galaxy/commit/107f67495713ea71dd97e9f83656… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/tour.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/ui/search-input.scss M client/galaxy/style/scss/upload.scss M static/welcome.html.sample M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #7203 from guerler/color_handling Replace custom UI colors with equivalent theme colors, consolidate color handling Compare: https://github.com/galaxyproject/galaxy/compare/e42dcfab2a93...107f67495713 **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] d5dea3: Pin pysam to 0.15.2 . Update all dependencies
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5dea33a86a79334b831776529956105c173673b https://github.com/galaxyproject/galaxy/commit/d5dea33a86a79334b83177652995… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: 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 Log Message: ----------- Pin pysam to 0.15.2 . Update all dependencies with `make update-dependencies` using pipenv 2018.11.26 . Commit: ce5895f585878a8952e8cda7df952027b2c48c11 https://github.com/galaxyproject/galaxy/commit/ce5895f585878a8952e8cda7df95… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M doc/source/conf.py Log Message: ----------- Update recommonmark configuration in Sphinx See https://github.com/rtfd/recommonmark/pull/113 Commit: 4bb6f18b30d850019230cd4e347b574ac0593052 https://github.com/galaxyproject/galaxy/commit/4bb6f18b30d850019230cd4e347b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M doc/source/conf.py Log Message: ----------- Do not build rst files starting with '_' Commit: 46b3539a35c09fc3d8d2d9b2a7ec7fefbc53c95e https://github.com/galaxyproject/galaxy/commit/46b3539a35c09fc3d8d2d9b2a7ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/dev/index.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/18.01.rst Log Message: ----------- Fix doc bugs Use proper cross-referencing with `:doc:`. Commit: 891576627515febaa749981fbb7e0aa850df495a https://github.com/galaxyproject/galaxy/commit/891576627515febaa749981fbb7e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M doc/source/conf.py Log Message: ----------- Do not exclude releases docs when using ``GALAXY_DOCS_SKIP_SOURCE`` They are quite fast to build. Commit: 1f3eec2879e356a671a2280b3589e938c391c668 https://github.com/galaxyproject/galaxy/commit/1f3eec2879e356a671a2280b3589… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 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: b23a2a44d99c9d68def546bda3bbf0d7059c8f95 https://github.com/galaxyproject/galaxy/commit/b23a2a44d99c9d68def546bda3bb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix ``UnicodeDecodeError`` exception under Python3 Fix the following exception reported in the startup logs: ``` galaxy.webhooks ERROR 2019-01-15 11:31:18,095 'ascii' codec can't decode byte 0xef in position 8291: ordinal not in range(128) Traceback (most recent call last): File "/galaxy/lib/galaxy/webhooks/__init__.py", line 62, in load_webhooks self.load_webhook_from_config(directory, config_file_path) File "/galaxy/lib/galaxy/webhooks/__init__.py", line 96, in load_webhook_from_config webhook.script = file.read() File "/galaxy_venv3/lib/python3.5/encodings/ascii.py", line 26, in decode return codecs.ascii_decode(input, self.errors)[0] UnicodeDecodeError: 'ascii' codec can't decode byte 0xef in position 8291: ordinal not in range(128) ``` Also rename variables from `file` (Python2 standard library function and class) to `fh`. Commit: f70d24afb5ed151237d7c7e0491b5db9337fdefc https://github.com/galaxyproject/galaxy/commit/f70d24afb5ed151237d7c7e0491b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M test/api/test_histories.py Log Message: ----------- Python3: open 2 files in binary mode Fix `HistoriesApiTestCase.test_import_metadata_regeneration()` API test introduced in commit 38f7aded0b11f4c75f2265ba95ed674e8d655e7d . See: https://jenkins.galaxyproject.org/job/docker-api-py3/193/testReport/junit/t… Commit: e42dcfab2a930e8d736b021ff69cb3428a77663e https://github.com/galaxyproject/galaxy/commit/e42dcfab2a930e8d736b021ff69c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/conf.py M doc/source/dev/index.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/18.01.rst 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/web/framework/base.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webhooks/__init__.py M test/api/test_galaxy_interactor.py M test/api/test_histories.py Log Message: ----------- Merge pull request #7215 from nsoranzo/recommonmark_0.5.0 Dependency update and doc fixes Compare: https://github.com/galaxyproject/galaxy/compare/c6a681fa8bb2...e42dcfab2a93 **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] cbe875: Fix global non-sense in setup_external_metadata?
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cbe87540dea874a8148e08e8d91d5a2e72c02529 https://github.com/galaxyproject/galaxy/commit/cbe87540dea874a8148e08e8d91d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix global non-sense in setup_external_metadata? Commit: c6a681fa8bb212f4274ea436cf4b53fe0d3c9c1f https://github.com/galaxyproject/galaxy/commit/c6a681fa8bb212f4274ea436cf4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Merge pull request #7213 from jmchilton/metadata_globals_bad Fix global var badness in setup_external_metadata? Compare: https://github.com/galaxyproject/galaxy/compare/f954dc45fe94...c6a681fa8bb2 **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] 0a2049: Re-add a `py27-first-startup` Travis job on osx
by GitHub 14 Jan '19

14 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a20498c67e5d9075a5566d2c8abf3073c611341 https://github.com/galaxyproject/galaxy/commit/0a20498c67e5d9075a5566d2c8ab… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Re-add a `py27-first-startup` Travis job on osx Commit: f954dc45fe94706f2ea04accc9fc92bcbcea892f https://github.com/galaxyproject/galaxy/commit/f954dc45fe94706f2ea04accc9fc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #7207 from nsoranzo/readd_travis_osx Re-add a `py27-first-startup` Travis job on osx Compare: https://github.com/galaxyproject/galaxy/compare/b58bed1eefd4...f954dc45fe94 **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] d91a66: Remove collect_outputs_from option.
by GitHub 07 Jan '19

07 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d91a666d5cc3cb84fac4051e8869e887728cccf8 https://github.com/galaxyproject/galaxy/commit/d91a666d5cc3cb84fac4051e8869… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/functional/tools/multi_output.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Remove collect_outputs_from option. And just disable dynamic discovery of outputs from new_file_path for legacy profile tools. This is part of an ongoing effort to kill new_file_path and simplify output discovery. This option was added by @natefoo 10 years ago and he switched main to disable new_file_path discovery and noone ever complained. So lets just do this for all Galaxies - if main hasn't run tools that require this functionality in a decade - I very much doubt any Galaxies require this. Commit: 681225bc9cb0f25c5e717658f37a4302c1c4166a https://github.com/galaxyproject/galaxy/commit/681225bc9cb0f25c5e717658f37a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/functional/tools/multi_output.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #7144 from jmchilton/remove_collect_outputs_from Remove collect_outputs_from option. Compare: https://github.com/galaxyproject/galaxy/compare/03b363a1ef92...681225bc9cb0 **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]
by GitHub 07 Jan '19

07 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy **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