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

[galaxyproject/galaxy] eab674: MacOS X fix for a test tool.
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eab674173c10ea62e781d19c17edfb4c2897b01a https://github.com/galaxyproject/galaxy/commit/eab674173c10ea62e781d19c17ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M test/functional/tools/collection_split_on_column.xml Log Message: ----------- MacOS X fix for a test tool. Commit: 709779b1dfe90c1936c2906a03988d5e820f25f4 https://github.com/galaxyproject/galaxy/commit/709779b1dfe90c1936c2906a0398… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M test/functional/tools/collection_split_on_column.xml Log Message: ----------- Merge pull request #4806 from jmchilton/awk_fix MacOS X fix for a test tool. Compare: https://github.com/galaxyproject/galaxy/compare/30ef7ef0683f...709779b1dfe9

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[galaxyproject/galaxy] 86929f: add augustus and snap datatypes
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 86929ff9f01201f0ef50429b96d4ab83a3887e8f https://github.com/galaxyproject/galaxy/commit/86929ff9f01201f0ef50429b96d4… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/annotation.py Log Message: ----------- add augustus and snap datatypes Commit: 8fa7cc8a1dcc1ced376912692aa0162ea133de12 https://github.com/galaxyproject/galaxy/commit/8fa7cc8a1dcc1ced376912692aa0… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- sniff snaphmm too Commit: deedb17caf66760855b4749771fa0e1655618dc0 https://github.com/galaxyproject/galaxy/commit/deedb17caf66760855b4749771fa… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/datatypes/annotation.py Log Message: ----------- edam terms Commit: 136925087e08eaef706e38b35299d1daa1ca2266 https://github.com/galaxyproject/galaxy/commit/136925087e08eaef706e38b35299… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/annotation.py Log Message: ----------- Merge pull request #4808 from abretaud/augsnaptypes [17.09] Add augustus and snap datatypes Compare: https://github.com/galaxyproject/galaxy/compare/b15f5a74957e...136925087e08

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[galaxyproject/galaxy] f31deb: Add babel loader.
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f31deb5286e5f649eb6eeefbfadc32ef0965f067 https://github.com/galaxyproject/galaxy/commit/f31deb5286e5f649eb6eeefbfadc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/package.json M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Add babel loader. Commit: c50b7b0f80f4331d4275b445cab45405bf65a5d2 https://github.com/galaxyproject/galaxy/commit/c50b7b0f80f4331d4275b445cab4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/GruntFile.js Log Message: ----------- webpack before uglify Commit: f3dbfa3669dbb9784538d74869b28430cd423cb6 https://github.com/galaxyproject/galaxy/commit/f3dbfa3669dbb9784538d74869b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/package.json M client/webpack.config.js Log Message: ----------- Use 'env' babel preset enabling all plugins Commit: 882901f51d4cb3b9b2fd342322d593ef95407e62 https://github.com/galaxyproject/galaxy/commit/882901f51d4cb3b9b2fd342322d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M Makefile M client/package.json M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Test npm scripts as an expansion point for potentially replacing grunt. Side benefit of being less hacky and allowing npm to use the correct grunt automatically. Commit: a24f91b431630bf5fe64b4a604a8dcb7ccd49f9e https://github.com/galaxyproject/galaxy/commit/a24f91b431630bf5fe64b4a604a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/GruntFile.js Log Message: ----------- Strip ancient and outdated comment. Commit: 31efa8af8ce553fd574b4ba7b4ffe654219ff7a8 https://github.com/galaxyproject/galaxy/commit/31efa8af8ce553fd574b4ba7b4ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/GruntFile.js R client/grunt-tasks/webpack.js M client/package.json Log Message: ----------- Pull webpack out of grunt, simplify. Commit: 21bc58b227c267626b4d3238bb0cdb97075b27f3 https://github.com/galaxyproject/galaxy/commit/21bc58b227c267626b4d3238bb0c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M Makefile M client/package.json Log Message: ----------- Webpack makefile targets, webpack-dev-watch npm script. Commit: efff669708f4cb8911a5340d63d77df809210473 https://github.com/galaxyproject/galaxy/commit/efff669708f4cb8911a5340d63d7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/package.json M client/webpack.config.js Log Message: ----------- Incremental work towards webpack 2 upgrade. amdi18n-loader is not working yet. Commit: e93eff35078d349ca5a3c2e285839f25d2168acb https://github.com/galaxyproject/galaxy/commit/e93eff35078d349ca5a3c2e28583… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M Makefile Log Message: ----------- Fix requirement for webpack Makefile task. Commit: cbb119c718889a893cbe82b43716a5b61a01e580 https://github.com/galaxyproject/galaxy/commit/cbb119c718889a893cbe82b43716… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/package.json M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Upgrade amdi18n-loader, fix webpack usage (loaders with webpack 2 no longer auto-append -loader) Commit: aae2cd352f8027e70fb62b6d6c9f4584b7d0a5c8 https://github.com/galaxyproject/galaxy/commit/aae2cd352f8027e70fb62b6d6c9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: A client/gulpfile.js M client/package.json M static/maps/galaxy.interactive_environments.js.map M 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static/maps/libs/jquery/jquery.cookie.js.map M static/maps/libs/jquery/jquery.dynatree.js.map M static/maps/libs/jquery/jquery.event.drag.js.map M static/maps/libs/jquery/jquery.event.drop.js.map M static/maps/libs/jquery/jquery.event.hover.js.map M static/maps/libs/jquery/jquery.form.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/jquery/jquery.mousewheel.js.map M static/maps/libs/jquery/jquery.rating.js.map M static/maps/libs/jquery/jquery.wymeditor.js.map M static/maps/libs/jquery/jstorage.js.map M static/maps/libs/jquery/jstree.js.map M static/maps/libs/jquery/select2.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/toastr.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/citation/citation-model.js.map M 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static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-li.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-base.js.map M 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static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/polyfills.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/editable-text.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M 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static/scripts/libs/common-libs.js M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery.sparklines.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/jquery/jquery-ui.js M static/scripts/libs/jquery/jquery.autocomplete.js M static/scripts/libs/jquery/jquery.cookie.js M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/libs/jquery/jquery.event.drag.js M static/scripts/libs/jquery/jquery.event.drop.js M static/scripts/libs/jquery/jquery.event.hover.js M static/scripts/libs/jquery/jquery.form.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/jquery/jquery.mousewheel.js M static/scripts/libs/jquery/jquery.rating.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/libs/jquery/jstorage.js M static/scripts/libs/jquery/jstree.js M static/scripts/libs/jquery/select2.js M static/scripts/libs/raven.js M static/scripts/libs/require.js R static/scripts/libs/showdown.js M static/scripts/libs/toastr.js M static/scripts/libs/underscore.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M 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static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js R static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tool-webhooks.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/change-password.js R static/scripts/mvc/user/extra-information.js R static/scripts/mvc/user/manage-user-information.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js R static/scripts/packed M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Minimal gulp task to run uglify, babel, sourcemaps. The new 'clean' approach also removed some cruft we had sitting in the static/scripts folder and were unintentionally shipping. Commit: b32f51a654211dde5d60565fe8dd12343f73fb32 https://github.com/galaxyproject/galaxy/commit/b32f51a654211dde5d60565fe8dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M templates/js-app.mako Log Message: ----------- Minor formatting js-app.mako Commit: 30e2b35fcb889912b7f1314b74c406da305e9df6 https://github.com/galaxyproject/galaxy/commit/30e2b35fcb889912b7f1314b74c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Exclude libs from webpack's babel processing Commit: 2b90e1e4a147bc9394b1c814ea12e967b0f0f0bf https://github.com/galaxyproject/galaxy/commit/2b90e1e4a147bc9394b1c814ea12… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/apps/history-panel.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Correct initialization of CurrentHistoryView Commit: a8f81b2eabf17786be90186246ef0cb750ee84e4 https://github.com/galaxyproject/galaxy/commit/a8f81b2eabf17786be90186246ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Correct initialization of UserPreferences Commit: b77fb6f962f128ea184f06995e802bc3cd782661 https://github.com/galaxyproject/galaxy/commit/b77fb6f962f128ea184f06995e80… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/gulpfile.js Log Message: ----------- Prevent wiping out webpack bundles, fix scripts path exclusion. Commit: 71b1d3d1a64ef1cae23fd22b25839d097eca74fd https://github.com/galaxyproject/galaxy/commit/71b1d3d1a64ef1cae23fd22b2583… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: A client/.babelrc M client/webpack.config.js Log Message: ----------- Swap to a .babelrc instead of using inline configurations. Commit: 3374d21904f0293b7b16735210bbdbf842504be6 https://github.com/galaxyproject/galaxy/commit/3374d21904f0293b7b16735210bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Remove unnecessary (and invalid in strict mode) delete. Pop key out of payload separately. Commit: 07502bbfbcfe6d512fff61e7971e05b9bd8ff5e4 https://github.com/galaxyproject/galaxy/commit/07502bbfbcfe6d512fff61e7971e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M Makefile M client/gulpfile.js M client/package.json M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.js.map M static/maps/galaxy.library.js.map M static/maps/galaxy.pages.js.map M static/maps/i18n.js.map M static/maps/layout/generic-nav-view.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/modal.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/layout/scratchbook.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bbi/bigwig.js.map M static/maps/libs/bbi/jquery-ajax-native.js.map M static/maps/libs/bbi/jszlib.js.map M static/maps/libs/bbi/spans.js.map M static/maps/libs/bibtex.js.map M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/bootstrap.js.map M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery.sparklines.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/jquery/jquery-ui.js.map M static/maps/libs/jquery/jquery.autocomplete.js.map M static/maps/libs/jquery/jquery.cookie.js.map M static/maps/libs/jquery/jquery.dynatree.js.map M static/maps/libs/jquery/jquery.event.drag.js.map M static/maps/libs/jquery/jquery.event.drop.js.map M static/maps/libs/jquery/jquery.event.hover.js.map M static/maps/libs/jquery/jquery.form.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/jquery/jquery.mousewheel.js.map M static/maps/libs/jquery/jquery.rating.js.map M static/maps/libs/jquery/jquery.wymeditor.js.map M static/maps/libs/jquery/jstorage.js.map M static/maps/libs/jquery/jstree.js.map M static/maps/libs/jquery/select2.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/toastr.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/dataset/states.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-li.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/icon-button.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/polyfills.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/editable-text.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/scratchbook.js M static/scripts/libs/backbone.js M static/scripts/libs/bbi/bigwig.js M static/scripts/libs/bbi/jquery-ajax-native.js M static/scripts/libs/bbi/jszlib.js M static/scripts/libs/bbi/spans.js M static/scripts/libs/bibtex.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/bootstrap.js M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery.sparklines.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/jquery/jquery-ui.js M static/scripts/libs/jquery/jquery.autocomplete.js M static/scripts/libs/jquery/jquery.cookie.js M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/libs/jquery/jquery.event.drag.js M static/scripts/libs/jquery/jquery.event.drop.js M static/scripts/libs/jquery/jquery.event.hover.js M static/scripts/libs/jquery/jquery.form.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/jquery/jquery.mousewheel.js M static/scripts/libs/jquery/jquery.rating.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/libs/jquery/jstorage.js M static/scripts/libs/jquery/jstree.js M static/scripts/libs/jquery/select2.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/toastr.js M static/scripts/libs/underscore.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M 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static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M 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static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Babel transpiling for all gulped files. Commit: 7f1097f0fe1117410e4327f35eb9058400f887dd https://github.com/galaxyproject/galaxy/commit/7f1097f0fe1117410e4327f35eb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Correct for .. in usage in upload-view. Commit: 6789ae9af9bf2c7578c60db500e5886cbf827d78 https://github.com/galaxyproject/galaxy/commit/6789ae9af9bf2c7578c60db500e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/package.json Log Message: ----------- Preliminary jshint target. Commit: aa3b83f2fbdac31c175a50da407ee5c44e96e523 https://github.com/galaxyproject/galaxy/commit/aa3b83f2fbdac31c175a50da407e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Tours changes, es6 template strings. Commit: e231600441621f461efe1b14bcae7cafb1f09674 https://github.com/galaxyproject/galaxy/commit/e231600441621f461efe1b14bcae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/gulpfile.js M client/package.json Log Message: ----------- Separate clean as a prereq for scripts, enable watch mode Commit: 7d3d91fc555a6526d6708e4867cb2191399b7476 https://github.com/galaxyproject/galaxy/commit/7d3d91fc555a6526d6708e4867cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Strip old TODO about modals -- this is better left to the invoker. Commit: 15a80faf5dda3c4b95a40cd6a7e59f737d068c14 https://github.com/galaxyproject/galaxy/commit/15a80faf5dda3c4b95a40cd6a7e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Clean up tours.js Commit: f19ce179eb26a0c28655cdb63e0930839ac06e31 https://github.com/galaxyproject/galaxy/commit/f19ce179eb26a0c28655cdb63e09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Bundle cleaned up tours. Commit: 9ecb4e8761d508a2796cffec7732673fd754ad92 https://github.com/galaxyproject/galaxy/commit/9ecb4e8761d508a2796cffec7732… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M client/package.json M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Bump webpack to 2.4.1, hopefully fixes an entrypoint issue. Commit: bbe3980b8f922dff9f69becad0da666b6d38ef9c https://github.com/galaxyproject/galaxy/commit/bbe3980b8f922dff9f69becad0da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M client/gulpfile.js M static/maps/mvc/workflow/workflow-canvas.js.map M static/scripts/libs/backbone.js M static/scripts/libs/bbi/bigwig.js M static/scripts/libs/bbi/jquery-ajax-native.js M static/scripts/libs/bbi/jszlib.js M static/scripts/libs/bbi/spans.js M static/scripts/libs/bibtex.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/bootstrap.js M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery.sparklines.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/jquery/jquery-ui.js M static/scripts/libs/jquery/jquery.autocomplete.js M static/scripts/libs/jquery/jquery.cookie.js M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/libs/jquery/jquery.event.drag.js M static/scripts/libs/jquery/jquery.event.drop.js M static/scripts/libs/jquery/jquery.event.hover.js M static/scripts/libs/jquery/jquery.form.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/jquery/jquery.mousewheel.js M static/scripts/libs/jquery/jquery.rating.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/libs/jquery/jstorage.js M static/scripts/libs/jquery/jstree.js M static/scripts/libs/jquery/select2.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/toastr.js M static/scripts/libs/underscore.js M static/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Separate script and lib build logic -- we only want to babelify/sourcemap our own stuff. Commit: c0806a9996e99fd71446feb385089e17eb592161 https://github.com/galaxyproject/galaxy/commit/c0806a9996e99fd71446feb38508… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M client/gulpfile.js M client/package.json Log Message: ----------- Cache for script watching. Commit: 0df18b86eb79b7132ea32a9c9c37739a7e05b7c2 https://github.com/galaxyproject/galaxy/commit/0df18b86eb79b7132ea32a9c9c37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M Makefile Log Message: ----------- Update 'make client' to use gulp for supported tasks. Commit: f13097f623a9b796ae5ccc2cee57c3f59174f340 https://github.com/galaxyproject/galaxy/commit/f13097f623a9b796ae5ccc2cee57… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M Makefile M client/gulpfile.js M client/package.json Log Message: ----------- Consolidate and parallelize 'make client' actions. 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client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/citation/citation-view.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/collection-view.js M client/galaxy/scripts/mvc/dataset/data.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/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.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/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js A 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config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M 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M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/upload.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/filters/wc_gnu.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into es6 Commit: 0d2beb285074af4ef6a999fbfa049e7ca6eba06a https://github.com/galaxyproject/galaxy/commit/0d2beb285074af4ef6a999fbfa04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/router.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js A 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test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into es6 Commit: f56af9d9b35709f88987ed34f88a15e8a99a3149 https://github.com/galaxyproject/galaxy/commit/f56af9d9b35709f88987ed34f88a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/package-lock.json M client/package.json M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Webpack bump Commit: 8952516bc0e6ca04233937d4d57086b9def04397 https://github.com/galaxyproject/galaxy/commit/8952516bc0e6ca04233937d4d570… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/package-lock.json M client/package.json Log Message: ----------- Babel-loader update Commit: 3d08deee7bfe87e1d2d16169f9826564d5afdc3e https://github.com/galaxyproject/galaxy/commit/3d08deee7bfe87e1d2d16169f982… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/package-lock.json M client/package.json Log Message: ----------- amd18n-loader upgrade Commit: 84c461f40137f349e0ae7c0b2a8d2f6f26234f59 https://github.com/galaxyproject/galaxy/commit/84c461f40137f349e0ae7c0b2a8d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/package-lock.json M client/package.json Log Message: ----------- del upgrade Commit: e15c1b7a3e57d9d0e4c051002c7f23711ae10f53 https://github.com/galaxyproject/galaxy/commit/e15c1b7a3e57d9d0e4c051002c7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/package-lock.json M client/package.json Log Message: ----------- Add ajv manually to fix package mess with it not being installed correctly by dependency of webpack 3.5. 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static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js Log Message: ----------- gulp-uglify major version bump and rebuild Commit: 959506e853fa2677e9f33047f2e5cfa0c6edab37 https://github.com/galaxyproject/galaxy/commit/959506e853fa2677e9f33047f2e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/package-lock.json M client/package.json Log Message: ----------- One more webpack bump. Commit: 929ecc6ac45e351e410a86fec906fd839cf41f4d https://github.com/galaxyproject/galaxy/commit/929ecc6ac45e351e410a86fec906… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: R client/galaxy/scripts/apps/history-panel.js Log Message: ----------- Strip history-panel.js, was included due to bad merge. Commit: cee1710c61159e6080655afd69c925196638488d https://github.com/galaxyproject/galaxy/commit/cee1710c61159e6080655afd69c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: A client/yarn.lock Log Message: ----------- Add yarn.lock; now compatible with yarn installs. TODO implement this as the default. Commit: 18084224ad38392c1ce326df1df74e3bc478da3d https://github.com/galaxyproject/galaxy/commit/18084224ad38392c1ce326df1df7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M Makefile Log Message: ----------- Swap from npm to yarn for the js package manager. Commit: f78b569a1853ad03d1a96176dc401e0aa5a6bca3 https://github.com/galaxyproject/galaxy/commit/f78b569a1853ad03d1a96176dc40… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/package.json Log Message: ----------- Swap build scripts to yarn. Commit: c64d2d0d50449d8d30fa0f37f8aab0d14435d9fe https://github.com/galaxyproject/galaxy/commit/c64d2d0d50449d8d30fa0f37f8aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: R client/package-lock.json Log Message: ----------- Remove client/package-lock -- we'll be using yarn.lock moving forward. Commit: c68b5cabbd6b2cf20ba7bc9e941fba4dc2b75d05 https://github.com/galaxyproject/galaxy/commit/c68b5cabbd6b2cf20ba7bc9e941f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/GruntFile.js M client/grunt-tasks/style.js M client/package.json M client/yarn.lock Log Message: ----------- Remove grunt-check-modules -- yarn will handle this (all it did was npm ls and look at the return code) Commit: f953804f0da1bb9cbcd73793e1aa2e883bfb1fc7 https://github.com/galaxyproject/galaxy/commit/f953804f0da1bb9cbcd73793e1aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Explicitly including ajv was required due to npm handling of dependency-of-dependency w/ webpack3. Yarn handles this better, so we don't need it. Commit: d17f385076041b88c4dfb46bdb2fb2202484a4fa https://github.com/galaxyproject/galaxy/commit/d17f385076041b88c4dfb46bdb2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Revert unintentional change to workflow-forms Commit: b410bf3f3308c41ca2648bd404c9a6e766875d11 https://github.com/galaxyproject/galaxy/commit/b410bf3f3308c41ca2648bd404c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- One more fix to 3374d21904f0293b7b16735210bbdbf842504be6, thanks @guerler Commit: 394e4bd07708e1eae7e567974779d9637d12c77d https://github.com/galaxyproject/galaxy/commit/394e4bd07708e1eae7e567974779… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/bower.json M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Swap jquery from bower-installed to yarn, as a trial. Commit: 3e51c665e2e6d81abedf8edd0705f94cf1b26d9f https://github.com/galaxyproject/galaxy/commit/3e51c665e2e6d81abedf8edd0705… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: R client/galaxy/scripts/libs/jquery/jquery.js M client/package.json Log Message: ----------- Lib staging so we no longer have to ship prepacked copies. Commit: 9796d67927665dd9a3c185cf85babd23ded501d3 https://github.com/galaxyproject/galaxy/commit/9796d67927665dd9a3c185cf85ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M .gitignore Log Message: ----------- .gitignore bump to reflect no longer committing unpacked lib scripts to the repo (yarn/npm handle this now) Commit: 304569a54dbb3a95e6110713998f6c8b8db95da8 https://github.com/galaxyproject/galaxy/commit/304569a54dbb3a95e6110713998f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M client/bower.json M client/galaxy/scripts/libs/raven.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/scripts/libs/raven.js Log Message: ----------- Raven.js upgrade and swap to npm. Commit: 9b75f6677d576b34b51abb3dd159038f1536dbbb https://github.com/galaxyproject/galaxy/commit/9b75f6677d576b34b51abb3dd159… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: R client/galaxy/scripts/libs/raven.js Log Message: ----------- Remove raven.js from distributed pre-built libs. Commit: 71dbc84c992ba6fda3f67123878e464e6112ab93 https://github.com/galaxyproject/galaxy/commit/71dbc84c992ba6fda3f67123878e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M client/grunt-tasks/install-libs.js Log Message: ----------- Remove raven from old grunt task. Commit: 966c08754ec76a0be1c21ca87920b8ea7fcf108b https://github.com/galaxyproject/galaxy/commit/966c08754ec76a0be1c21ca87920… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/underscore.js M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Lock underscore w/ yarn, add to lib staging, remove from repo. Commit: f179c87a079fa545c75fb5f209fefc144caf797b https://github.com/galaxyproject/galaxy/commit/f179c87a079fa545c75fb5f209fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/grunt-tasks/install-libs.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/libs/jquery/jquery.migrate.js Log Message: ----------- Lock jqmigrate w/ yarn, minor version bump. Commit: 03a7a3dc86f262e3abf27ce502b3d35b50f1687a https://github.com/galaxyproject/galaxy/commit/03a7a3dc86f262e3abf27ce502b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: R client/galaxy/scripts/libs/jquery/jquery.migrate.js Log Message: ----------- Remove jquery.migrate from committed staged libs Commit: 2b85b148f8df2de39b2752ea0a3dbc2f2b7d97ac https://github.com/galaxyproject/galaxy/commit/2b85b148f8df2de39b2752ea0a3d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/backbone.js M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Lock backbone 1.3 w/ yarn, remove from committed staged libs. Commit: ea9dfc953cf6cf782ed3f2309bd0992067b219f8 https://github.com/galaxyproject/galaxy/commit/ea9dfc953cf6cf782ed3f2309bd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: R client/galaxy/scripts/libs/require.js M client/grunt-tasks/install-libs.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/scripts/libs/require.js Log Message: ----------- Lock requirejs w/ yarn, remove from committed staged libs. Minor version update. Commit: 7115a74f9a8b84b2e4519f25b7c69a1a467ac910 https://github.com/galaxyproject/galaxy/commit/7115a74f9a8b84b2e4519f25b7c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/d3.js M client/grunt-tasks/install-libs.js M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Lock d3.js w/ yarn, remove from committed staged libs. Commit: f779a17da226799b47e0549b02127bc785f81081 https://github.com/galaxyproject/galaxy/commit/f779a17da226799b47e0549b0212… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M client/galaxy/scripts/libs/bibtex.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/libs/bibtex.js M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Remove galaxy customizations in bibtex.js, monkeypatch it on load instead. Lock w/ yarn, etc. Commit: 293b36313a846d41e913a752ca167d6a16aeb041 https://github.com/galaxyproject/galaxy/commit/293b36313a846d41e913a752ca16… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: R client/galaxy/scripts/libs/bibtex.js Log Message: ----------- Remove bibtex from codebase. Commit: c6d7ed10680f73d1a9750509a7686fb4de2a0045 https://github.com/galaxyproject/galaxy/commit/c6d7ed10680f73d1a9750509a768… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.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/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.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-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.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.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M client/toolshed/scripts/mvc/groups/group-list-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M config/tool_conf.xml.main M config/tool_conf.xml.sample M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/__init__.py M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M 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test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/shed_functional/functional/test_1160_tool_help_images.py M test/shed_functional/functional/test_1170_prior_installation_required.py M test/shed_functional/functional/test_1180_circular_prior_installation_required.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py M 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test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/datatypes/test_data.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_datasets.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/jobs/test_runner_params.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_security_helper.py M test/unit/test_sqlite_utils.py M test/unit/test_topsort.py M test/unit/tools/filter_modules/filtermod.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_panel.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge latest upstream/dev Commit: 19125d39e3eca15eba3687dbf036b1a79cf4c177 https://github.com/galaxyproject/galaxy/commit/19125d39e3eca15eba3687dbf036… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M client/bower.json M client/grunt-tasks/install-libs.js Log Message: ----------- Remove (duplicate) custom bib2json references. Commit: 08e10b55a8bef9097196004c19a63dae711f714a https://github.com/galaxyproject/galaxy/commit/08e10b55a8bef9097196004c19a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M client/bower.json M client/galaxy/scripts/libs/jquery/jqtouch.js M client/grunt-tasks/install-libs.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/scripts/libs/jquery/jqtouch.js Log Message: ----------- jqtouch is now jqt, though it looks like we should just drop this instead. Commit: 324494b21b2ba63525e299e71e060df91253af19 https://github.com/galaxyproject/galaxy/commit/324494b21b2ba63525e299e71e06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: R client/galaxy/scripts/libs/jquery/jqtouch.js M client/gulpfile.js M client/package.json M client/yarn.lock R static/scripts/libs/jquery/jqtouch.js Log Message: ----------- We don't actually *use* jqtouch anywhere. Mobile controllers are defunct and redirect to root. Should we revisit this, I imagine we'll use a different technology. Commit: 6a0e9396d123c0a2f8fdae97ee3a536737ecaea1 https://github.com/galaxyproject/galaxy/commit/6a0e9396d123c0a2f8fdae97ee3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: R static/jqtouch/img/backButton.png R static/jqtouch/img/back_button.png R static/jqtouch/img/back_button_clicked.png R static/jqtouch/img/bg_row.gif R static/jqtouch/img/bg_row_select.gif R static/jqtouch/img/blueButton.png R static/jqtouch/img/button.png R static/jqtouch/img/button_clicked.png R static/jqtouch/img/cancel.png R static/jqtouch/img/chevron.png R static/jqtouch/img/chevron_select.png R static/jqtouch/img/grayButton.png R static/jqtouch/img/header.gif R static/jqtouch/img/listGroup.png R static/jqtouch/img/loading.gif R static/jqtouch/img/pinstripes.png R static/jqtouch/img/selection.png R static/jqtouch/img/thumb.png R static/jqtouch/img/toggle.png R static/jqtouch/img/toggleOn.png R static/jqtouch/img/toolButton.png R static/jqtouch/img/toolbar.gif R static/jqtouch/img/toolbar.png R static/jqtouch/img/whiteButton.png R static/jqtouch/jqtouch.css R static/maps/libs/jquery/jqtouch.js.map Log Message: ----------- Cleanup the rest of the jqtouch removal from static. Will remove mobile templates in a separate PR. Commit: 88a06e9e0ef1b13f9a3dd8be82b1176e2edd8403 https://github.com/galaxyproject/galaxy/commit/88a06e9e0ef1b13f9a3dd8be82b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/apps/panels/history-panel.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix history-panel.js (maybe a botched merge?), client now works. Commit: 44f2828b511254221adc092d57536b552822d9c8 https://github.com/galaxyproject/galaxy/commit/44f2828b511254221adc092d5753… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix jquery usage in workflows.js Commit: 005da343e22bf3b2fe916574a4e7550703ae6f91 https://github.com/galaxyproject/galaxy/commit/005da343e22bf3b2fe916574a4e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Fix creation of execute_button (previously would have no reference due the invalid syntax) Commit: 144d384c9b8663b342428411fefe34071ae5486c https://github.com/galaxyproject/galaxy/commit/144d384c9b8663b342428411fefe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M templates/base.mako Log Message: ----------- Remove unnessecary bootstrap-tour load; this happens correctly through the requires/bundles without the duplicate lib require. Commit: ff99fc917a1674b75cebd616887a43105e8ccd94 https://github.com/galaxyproject/galaxy/commit/ff99fc917a1674b75cebd616887a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Add expose-loader to step towards fixing some of the ancient global usage. Commit: 2071cf2366024b98259ddca5d2508d01b00c497f https://github.com/galaxyproject/galaxy/commit/2071cf2366024b98259ddca5d250… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M client/webpack.config.js M templates/display_base.mako Log Message: ----------- Move display jquery plugins to common, consolidating jquery loads. Commit: 6a6fe05abd7017253e3bffedfe2d99c7a97b8682 https://github.com/galaxyproject/galaxy/commit/6a6fe05abd7017253e3bffedfe2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M client/webpack.config.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M templates/base.mako M templates/base/base_panels.mako Log Message: ----------- Expose jquery, fix $ Commit: d1daca61b9ada64e24f53df2810118e0b5a9d87b https://github.com/galaxyproject/galaxy/commit/d1daca61b9ada64e24f53df28101… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M .travis.yml M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.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-dataset-view.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-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less R client/galaxy/style/less/iphone.less M client/galaxy/style/less/library.less A client/galaxy/style/less/theme/plain.less M client/grunt-tasks/style.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/error_report.yml.sample M config/galaxy.ini.sample A config/lmod_modules_mapping.yml.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M create_db.sh M doc/source/admin/special_topics/bug_reports.rst A doc/source/dev/finding_and_improving_slow_code.rst M extract_dataset_parts.sh M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bam_to_bai.xml R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/libraries.py A lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/requirements.py A lib/galaxy/tools/deps/resolvers/lmod.py A lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/base.py R lib/galaxy/webapps/galaxy/api/lda_datasets.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py R lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/xml_util.py M manage_db.sh M manage_tools.sh M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/layout/page.js.map M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css R static/style/blue/iphone.css M static/style/blue/library.css M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/dataset/copy_view.mako R templates/webapps/galaxy/mobile/dataset/detail.mako R templates/webapps/galaxy/mobile/dataset/peek.mako R templates/webapps/galaxy/mobile/form.mako R templates/webapps/galaxy/mobile/history/detail.mako R templates/webapps/galaxy/mobile/history/list.mako R templates/webapps/galaxy/mobile/index.mako R templates/webapps/galaxy/mobile/manage_library.mako R templates/webapps/galaxy/mobile/settings.mako M templates/webapps/galaxy/workflow/editor.mako A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml M test/functional/tools/metadata.xml M test/functional/tools/sample_datatypes_conf.xml A test/functional/twilltestcase.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py A test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py A test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_tool_deps.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml M tools/sr_assembly/velvetg.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into es6 Commit: 08eccf5550aae559d3595e51c2bba16f56a2dc8b https://github.com/galaxyproject/galaxy/commit/08eccf5550aae559d3595e51c2bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M templates/base.mako M templates/base/base_panels.mako Log Message: ----------- Unify and expose all the jqueries. Commit: 4d5f362c4d52abe205a75b6e3d33cb51862de7b7 https://github.com/galaxyproject/galaxy/commit/4d5f362c4d52abe205a75b6e3d33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Workflow view syntax fix. Commit: 392dfee0fbf0edf59aeb20a767b092268ba36d0f https://github.com/galaxyproject/galaxy/commit/392dfee0fbf0edf59aeb20a767b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M static/maps/mvc/workflow/workflow-manager.js.map M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Slight cleanup and a few definition fixes in workflow-manager. Commit: 0b3f5e9ab3d8b557f2d6121841402242e2f3faf1 https://github.com/galaxyproject/galaxy/commit/0b3f5e9ab3d8b557f2d612184140… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M static/maps/mvc/workflow/workflow-manager.js.map M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- One more explicit var fix in workflow-manager. Commit: be7bfc5ec22390b3665a031c656e6d7b52624e42 https://github.com/galaxyproject/galaxy/commit/be7bfc5ec22390b3665a031c656e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CITATION M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.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/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/upload.less M client/toolshed/scripts/mvc/groups/group-model.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/source/admin/reports.md M lib/galaxy/__init__.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py 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lib/galaxy/managers/jobs.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M 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M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js R templates/admin/forms/create_form.mako R templates/admin/forms/edit_form_definition.mako R templates/admin/forms/grid.mako R templates/admin/forms/view_form_definition.mako R templates/admin/tool_shed_repository/browse_category.mako M templates/display_base.mako M templates/display_common.mako R templates/export_base.mako R templates/rss.mako R templates/webapps/galaxy/admin/toolsheds.mako R templates/webapps/galaxy/history/permissions.mako R templates/webapps/galaxy/history/rename.mako R templates/webapps/galaxy/page/create.mako R templates/webapps/galaxy/visualization/create.mako A test-data/selenium-test-notebook.ipynb M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py A test/api/test_tools_upload.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api.py M test/base/api_util.py A test/base/constants.py M test/base/driver_util.py M test/base/populators.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/twilltestcase.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml A test/integration/test_data_manager_table_reload.py M test/integration/test_resolvers.py M test/integration/test_upload_configuration_options.py A test/integration/tool_sheds_conf.xml M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py A test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py M test/selenium_tests/test_login.py A test/selenium_tests/test_navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py A test/unit/__init__.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_security_helper.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/workflow_support.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/joiner.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into es6 Commit: 16b5616acae0dee159b73519b506d6cf657b1254 https://github.com/galaxyproject/galaxy/commit/16b5616acae0dee159b73519b506… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix jquery definition and load order in galaxy.panels.mako. I cannot wait until this is all gone. Commit: 76676085cb0e8808a6f01de90c5540657ca21c83 https://github.com/galaxyproject/galaxy/commit/76676085cb0e8808a6f01de90c55… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- fix missing _l import in multi-panel Commit: 9385a37c4c7cd35b7270119555947a975a71ee94 https://github.com/galaxyproject/galaxy/commit/9385a37c4c7cd35b727011955594… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Reorder defines for multi-panel. Commit: 08f9700f26255d9a5ef64455ad83e3880f9af1a0 https://github.com/galaxyproject/galaxy/commit/08f9700f26255d9a5ef64455ad83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-06 (Fri, 06 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M static/maps/mvc/collection/base-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/base-creator.js Log Message: ----------- Fix 'this' scoping bug in base-creator. Commit: e671138e93c1ae3c3e402e839c4cf687c6ea285e https://github.com/galaxyproject/galaxy/commit/e671138e93c1ae3c3e402e839c4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-06 (Fri, 06 Oct 2017) Changed paths: M client/galaxy/scripts/utils/config.js M static/maps/utils/config.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/config.js Log Message: ----------- Fix trackster scoping issues causing a failed load. Commit: 56855b6f9429bbbac93fc118a4e41adc280063c2 https://github.com/galaxyproject/galaxy/commit/56855b6f9429bbbac93fc118a4e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M .ci/jenkins/selenium/Dockerfile M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/galaxy.ini M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh A client/galaxy/scripts/mvc/lazy/lazy-limited.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/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js A client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M lib/galaxy/config.py M lib/galaxy/datatypes/text.py M lib/galaxy/model/custom_types.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy_ext/metadata/set_metadata.py M run.sh M run_tests.sh M setup.cfg A static/maps/mvc/lazy/lazy-limited.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map A static/maps/mvc/upload/upload-extension.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js A static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M templates/sharing_base.mako A test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/galaxy_selenium/smart_components.py M test/integration/test_upload_configuration_options.py M test/qunit/tests/upload_dialog_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge upstream/dev. Commit: 43ca2681382f904f111597a2589058606659be07 https://github.com/galaxyproject/galaxy/commit/43ca2681382f904f111597a25890… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Swap default mode to 'Auto' in configs Commit: d9a810d35f82b3e144c379df7435ff355fd43e7f https://github.com/galaxyproject/galaxy/commit/d9a810d35f82b3e144c379df7435… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Use a different approach for getting default configs. Works, and allows flexible modes down the road. Commit: 9c0e52a53fcf899385bddde7d4aa882500f51b16 https://github.com/galaxyproject/galaxy/commit/9c0e52a53fcf899385bddde7d4aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/bower.json Log Message: ----------- jquery-migrate has been yarned. Commit: c55861151e14f4d7b04ee28d89f953ce61aca577 https://github.com/galaxyproject/galaxy/commit/c55861151e14f4d7b04ee28d89f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/package.json M client/yarn.lock M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/icon-button.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/utils/ajax-queue.js.map M static/maps/viz/circster.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/visualization.js.map M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/libs/raven.js Log Message: ----------- Start segmenting dependencies/devDependencies. Commit: 14f4182f102a99bd8f16e9602bc50d6d0b071280 https://github.com/galaxyproject/galaxy/commit/14f4182f102a99bd8f16e9602bc5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/yarn.lock Log Message: ----------- Webpack upgrade. Commit: 5cce6d2c26caf15f4302e127c9120aaca1bc9fb9 https://github.com/galaxyproject/galaxy/commit/5cce6d2c26caf15f4302e127c912… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M config/error_report.yml.sample M lib/galaxy/dataset_collections/type_description.py A lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M static/maps/mvc/upload/default/default-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/default/default-view.js M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into es6 Commit: 503bdd15a6c11f311d8a2a06b7674c118a864d26 https://github.com/galaxyproject/galaxy/commit/503bdd15a6c11f311d8a2a06b767… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/package.json M client/yarn.lock M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/libs/jquery/jquery.js Log Message: ----------- Jquery incremental major version bump (to 2.x) Commit: fe6da5162b26ab1c833eb7de0dcfbf33f56e5484 https://github.com/galaxyproject/galaxy/commit/fe6da5162b26ab1c833eb7de0dcf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/bower.json M client/galaxy/scripts/libs/jquery/jquery.mousewheel.js M client/grunt-tasks/install-libs.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/libs/jquery/jquery.mousewheel.js Log Message: ----------- De-bowerify jquery-mousewheel. Commit: e731d8585cf8da569d7acb5d377258b6e66adbf7 https://github.com/galaxyproject/galaxy/commit/e731d8585cf8da569d7acb5d3772… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js Log Message: ----------- Remove staged mousewheel from tracking. Commit: d9427829891308b3e564bd8015e1c072204c3980 https://github.com/galaxyproject/galaxy/commit/d9427829891308b3e564bd8015e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/bower.json M client/galaxy/scripts/libs/jquery/jquery.cookie.js M client/grunt-tasks/install-libs.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/scripts/libs/jquery/jquery.cookie.js Log Message: ----------- Debowerify jquery.cookie Commit: 9edf3564476ed21db6582d0626cf0a4deac6e71a https://github.com/galaxyproject/galaxy/commit/9edf3564476ed21db6582d0626cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: R client/galaxy/scripts/libs/jquery/jquery.cookie.js Log Message: ----------- Remove jquery.cookie from staged libs. Commit: 9e876c322aa1a19a840e63cabc965ca2a2ddc3b3 https://github.com/galaxyproject/galaxy/commit/9e876c322aa1a19a840e63cabc96… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/bower.json Log Message: ----------- Remove inaccurate resolutions (newer jquery, anyway). Commit: 9678ebcc86d95a37ef5a081154ea35db1ceefa4f https://github.com/galaxyproject/galaxy/commit/9678ebcc86d95a37ef5a081154ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/jquery.complexify.js M client/grunt-tasks/install-libs.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/jquery.complexify.js A static/scripts/libs/jquery/jquery.complexify.js Log Message: ----------- De-bowerify complexify; use the same location/naming schema for where jquery.complexify is stored. Update libs bundle. Commit: 73ce0821a094a68e5806bf87c05ac3d1d4b751c6 https://github.com/galaxyproject/galaxy/commit/73ce0821a094a68e5806bf87c05a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/gulpfile.js Log Message: ----------- Trim less than useful logging, use the callback to bail on error. Commit: 1ab8f4cdae937fb3beca1582090066a2ece3a173 https://github.com/galaxyproject/galaxy/commit/1ab8f4cdae937fb3beca15820900… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/gulpfile.js Log Message: ----------- Slightly more information in staging failure message. Commit: c4c15e323cf67ddb4c86a715d72b78d58478a8fc https://github.com/galaxyproject/galaxy/commit/c4c15e323cf67ddb4c86a715d72b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js.map M test/qunit/test-common.js R test/qunit/test-libs/sinon-1.17.3.js A test/qunit/test-libs/sinon-1.17.7.js Log Message: ----------- Upgrade sinon to the latest (still legacy) version, fix jquery animation tests handling. Commit: 6ac5de9ec690539a983aa257f512264ae10e3abf https://github.com/galaxyproject/galaxy/commit/6ac5de9ec690539a983aa257f512… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M test/qunit/test-common.js Log Message: ----------- Strip testing cruft from qunit/test-common.js Commit: 66b89f83ad99af79ddf1dde4f4283bc31fee1316 https://github.com/galaxyproject/galaxy/commit/66b89f83ad99af79ddf1dde4f428… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: 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-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/ui.less M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into es6 Commit: 1e9601d209fca0943fe8bfc8c6081a601879d61a https://github.com/galaxyproject/galaxy/commit/1e9601d209fca0943fe8bfc8c608… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/base.mako Log Message: ----------- Typo fix Commit: 34749b0440f5326e7c823bbc469d5d439225b7c7 https://github.com/galaxyproject/galaxy/commit/34749b0440f5326e7c823bbc469d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M Makefile Log Message: ----------- All libs moving forward are installed by yarn, this endpoint is not to be used. Commit: 70ef3895549fcb75069f362aac66bd4999130a8a https://github.com/galaxyproject/galaxy/commit/70ef3895549fcb75069f362aac66… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M Makefile Log Message: ----------- Trim client make targets Commit: 731a9a6d3e7ad2e12d902ba3b5537aa232a777e1 https://github.com/galaxyproject/galaxy/commit/731a9a6d3e7ad2e12d902ba3b553… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M Makefile Log Message: ----------- Client-develop -> client-watch, style is built into build and has a package.json target if anyone really needs it. Commit: 1486ee3730e10f2e98d29092ea41cd46ce236b40 https://github.com/galaxyproject/galaxy/commit/1486ee3730e10f2e98d29092ea41… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/router.js M static/scripts/mvc/dataset/dataset-li-edit.js M templates/show_params.mako Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into es6 Commit: deb282c7b421e785917e753b70cd0fd14afadcbf https://github.com/galaxyproject/galaxy/commit/deb282c7b421e785917e753b70cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M client/webpack.config.js Log Message: ----------- webpack config formatting Commit: 5f64b0b5243a024c9c175c4d69b20dd8b8332683 https://github.com/galaxyproject/galaxy/commit/5f64b0b5243a024c9c175c4d69b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M client/webpack.config.js Log Message: ----------- More reorg; separate vars. Commit: 5e3187405abd4792c87e9fcce5f363077eef542f https://github.com/galaxyproject/galaxy/commit/5e3187405abd4792c87e9fcce5f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Bundle toastr in common libs Commit: f0bf0226584d6d97bf2031b87eb2011f697aac87 https://github.com/galaxyproject/galaxy/commit/f0bf0226584d6d97bf2031b87eb2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M Makefile Log Message: ----------- Client-watch does depend on node-deps Commit: 926cf3ef05bd88893c8940be248f615899b5cdd7 https://github.com/galaxyproject/galaxy/commit/926cf3ef05bd88893c8940be248f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M client/package.json Log Message: ----------- Prior to watching, make sure libs are staged. Commit: 9c9cd098947cec37b589408c426b0e13eb77f60c https://github.com/galaxyproject/galaxy/commit/9c9cd098947cec37b589408c426b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M templates/js-app.mako Log Message: ----------- For js-app, also configure window jquery (supporting unbundled access, things like webhooks, etc.) Commit: 4df90df0d15ccafe69a78f87be8e42aab55049cb https://github.com/galaxyproject/galaxy/commit/4df90df0d15ccafe69a78f87be8e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M Makefile Log Message: ----------- Force yarn to check-files. This is fast, anyway, and prevents confusion when switching between branches and having differing (sometimes missing) node_modules like gulp, etc. Commit: 258675edfa418a1adc259bd8629f9a85ae55fbd5 https://github.com/galaxyproject/galaxy/commit/258675edfa418a1adc259bd8629f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M client/package.json Log Message: ----------- Make package scripts more concise. Commit: 5707e95d4800f01c81fda64d02f069d7d41e23fb https://github.com/galaxyproject/galaxy/commit/5707e95d4800f01c81fda64d02f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Update webpack config, rebuild charts. Commit: f6b2e1b92ca52c0a0df25ab2ddfc0a418d4fa281 https://github.com/galaxyproject/galaxy/commit/f6b2e1b92ca52c0a0df25ab2ddfc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M Makefile M client/package.json M config/plugins/visualizations/charts/static/repository/build/registry.js.map Log Message: ----------- Roll charts building into package scripts, simplify makefile. Commit: 23db8e7109a7b94eaa0345c38e3b3d81a0baace8 https://github.com/galaxyproject/galaxy/commit/23db8e7109a7b94eaa0345c38e3b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M Makefile Log Message: ----------- Remove Makefile cruft; we'll never want to execute webpack directly from here. Commit: ca48aa93ab10e8bcde4303fd3fc9a69e5ff6faf0 https://github.com/galaxyproject/galaxy/commit/ca48aa93ab10e8bcde4303fd3fc9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/README.md Log Message: ----------- Client README updates. Commit: 2af5dfad6ae5291134f84beed35610953264c89e https://github.com/galaxyproject/galaxy/commit/2af5dfad6ae5291134f84beed356… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/README.md M client/package.json Log Message: ----------- Add build-toolshed target to package scripts. Commit: 078b431cdc917011a100ccc0739dece1c691a943 https://github.com/galaxyproject/galaxy/commit/078b431cdc917011a100ccc0739d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M Makefile Log Message: ----------- Remove another target from the Makefile, shepherding people into fewer entrypoints for client build. Commit: ebb8977a7815e3f646f35bc9d208f3ce812b5efb https://github.com/galaxyproject/galaxy/commit/ebb8977a7815e3f646f35bc9d208… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/README.md Log Message: ----------- More minor client readme tweaks. Commit: ace6cd719b9c7845a3a00e0656d687b5c98931aa https://github.com/galaxyproject/galaxy/commit/ace6cd719b9c7845a3a00e0656d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/README.md Log Message: ----------- makefile/Makefile Commit: a9a81d1f0d3138029526de22d023615f99af386c https://github.com/galaxyproject/galaxy/commit/a9a81d1f0d3138029526de22d023… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/py3_sources.txt M contrib/galaxy_config_merger.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/s3.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/__init__.py M lib/galaxy/util/jstree.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/mimeparse.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/library_upload_dir.py M scripts/api/workflow_import.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/extract_toolbox_sections.py M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_tools.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/update_shed_config_path.py A test/functional/tools/empty_datasets.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/filters/bed_to_gff_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into es6 Commit: 4309c5467f3f4f94c6511d7e6e76c508bf9fb462 https://github.com/galaxyproject/galaxy/commit/4309c5467f3f4f94c6511d7e6e76… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/README.md M client/package.json Log Message: ----------- Style and watch-style naming changes for package scripts. Commit: 3e509bd5fb14ac47ba5fac296966ac77e76ff71c https://github.com/galaxyproject/galaxy/commit/3e509bd5fb14ac47ba5fac296966… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/package.json Log Message: ----------- Include style-watch in 'watch' overhead task. 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static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/icon-button.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-extension.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/de/locale.js.map M static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/polyfills.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/editable-text.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js R static/scripts/analysis.js R static/scripts/app.js R static/scripts/app/analysis.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M 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static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M 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static/scripts/mvc/toolshed/shed-category-view.js M static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/shed-repo-details-view.js R static/scripts/mvc/toolshed/shed-repo-list-view.js R static/scripts/mvc/toolshed/sheds-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/change-password.js R static/scripts/mvc/user/extra-information.js R static/scripts/mvc/user/manage-user-information.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js R static/scripts/packed M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako M test/qunit/test-common.js R test/qunit/test-libs/sinon-1.17.3.js A test/qunit/test-libs/sinon-1.17.7.js Log Message: ----------- Merge pull request #4435 from dannon/es6 Galaxy client tooling overhaul, ES6 Compare: https://github.com/galaxyproject/galaxy/compare/5aa624c45a50...30ef7ef0683f

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[galaxyproject/infrastructure-playbook] 532ec3: Add Galaxy memory limiting via systemd + cgroups.
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 532ec3cb60e962e34992ba75d908c58fedd27d67 https://github.com/galaxyproject/infrastructure-playbook/commit/532ec3cb60e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: A roles/systemd/handlers/main.yml A roles/systemd/tasks/main.yml A roles/systemd/templates/resource_controls.conf.j2 M taccenv/group_vars/maingalaxyservers/vars.yml M taccenv/group_vars/testgalaxyservers/vars.yml M taccenv/playbook.yml Log Message: ----------- Add Galaxy memory limiting via systemd + cgroups.

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[galaxyproject/galaxy] e4518f: Rebase hardening commits from dev
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: e4518ff3e3d628f2cd47ea48217da6352ef11e30 https://github.com/galaxyproject/galaxy/commit/e4518ff3e3d628f2cd47ea48217d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Rebase hardening commits from dev Commit: b5ded00eb50181f17b3c003e1b7c895098b85d25 https://github.com/galaxyproject/galaxy/commit/b5ded00eb50181f17b3c003e1b7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 545d5556588dfe28c8a9857333366ba62dbcd2fd https://github.com/galaxyproject/galaxy/commit/545d5556588dfe28c8a985733336… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Fix additional uses of subprocess shell=True Commit: 2f79351e3cdb1fe9705f00590038b11cba4b428e https://github.com/galaxyproject/galaxy/commit/2f79351e3cdb1fe9705f00590038… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Rebase script integrity check improvements (#4720) from dev Commit: 9fa9d42c5093ddd8f70193cc6a07ae0af0394f8c https://github.com/galaxyproject/galaxy/commit/9fa9d42c5093ddd8f70193cc6a07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/proxy/__init__.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix backport issues Commit: f925ffe4b743d080585bc6d151dc8ca98cc4f171 https://github.com/galaxyproject/galaxy/commit/f925ffe4b743d080585bc6d151dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4801 from natefoo/backport-hardening-16.07 [16.07] Various bits of hardening from #4604 Commit: e60f324b66676cc5020aa74bfa011f886eaeca68 https://github.com/galaxyproject/galaxy/commit/e60f324b66676cc5020aa74bfa01… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into backport-hardening-16.10 Commit: ef268027191b526b8c8dfe69c3d8352c0412ce1d https://github.com/galaxyproject/galaxy/commit/ef268027191b526b8c8dfe69c3d8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- Hardening backport differences from dev present in 16.10 but not 16.07 Commit: d70713d07a3c4d98b71df9247bbd8644ab6b2b40 https://github.com/galaxyproject/galaxy/commit/d70713d07a3c4d98b71df9247bbd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: fe9839bf7ca720061548ff3bcebdc79062e7adf5 https://github.com/galaxyproject/galaxy/commit/fe9839bf7ca720061548ff3bcebd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: 36b974c90514332c6cb732f9c376a66767100944 https://github.com/galaxyproject/galaxy/commit/36b974c90514332c6cb732f9c376… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 3bb5d825c13ae2dbd366f24dc316bcdaa7171eb9 https://github.com/galaxyproject/galaxy/commit/3bb5d825c13ae2dbd366f24dc316… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Ignore I201 errors in 16.10 Commit: 8d573db729a92344ad9115b7657ace07a4718a21 https://github.com/galaxyproject/galaxy/commit/8d573db729a92344ad9115b7657a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 6d8f8ecb466ae75ca7d586496512cb70206a08f6 https://github.com/galaxyproject/galaxy/commit/6d8f8ecb466ae75ca7d586496512… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Add missing backport of hardening to scripts/grt.py Commit: b04aafa8e871f4d2f3bf7a636ccf0ef432fda875 https://github.com/galaxyproject/galaxy/commit/b04aafa8e871f4d2f3bf7a636ccf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M .travis.yml M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M setup.cfg M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py M tox.ini Log Message: ----------- Merge pull request #4804 from natefoo/backport-hardening-16.10 [16.10] Various bits of hardening from #4604 Commit: 139ba7c13e38a98a090a91167e0538f259baa7c2 https://github.com/galaxyproject/galaxy/commit/139ba7c13e38a98a090a91167e05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 03087e5ee77701e410e7d9336a74cedf3206e3f3 https://github.com/galaxyproject/galaxy/commit/03087e5ee77701e410e7d9336a74… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Rebase hardening commits from dev Commit: f9213b16f5bb26b2b7176d50602d852ea4e08562 https://github.com/galaxyproject/galaxy/commit/f9213b16f5bb26b2b7176d50602d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 7ad6182ef4952480354e4737b72c062fc75be93e https://github.com/galaxyproject/galaxy/commit/7ad6182ef4952480354e4737b72c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Fix additional uses of subprocess shell=True Commit: b13f5d7f943106cf27670c7153e6c8967a749bcf https://github.com/galaxyproject/galaxy/commit/b13f5d7f943106cf27670c7153e6… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Rebase script integrity check improvements (#4720) from dev Commit: 24c8a26852aecdcc5d8d23300e551f282b90c628 https://github.com/galaxyproject/galaxy/commit/24c8a26852aecdcc5d8d23300e55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Fix backport issues Commit: 9955c4d24bff197b01f2ff6227fdfb06224d9ab9 https://github.com/galaxyproject/galaxy/commit/9955c4d24bff197b01f2ff6227fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Ignore I201 errors in 16.10 Commit: 950f92627176068609fc5191c72f681e3e16fb22 https://github.com/galaxyproject/galaxy/commit/950f92627176068609fc5191c72f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Add missing backport of hardening to scripts/grt.py Commit: d8ee1a9a8d42f1287262a25fa282799d44d4f583 https://github.com/galaxyproject/galaxy/commit/d8ee1a9a8d42f1287262a25fa282… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Revert ignoring I201 from 16.10 in 17.01 Commit: 25fc0982b75243e9c95a5312b56359f83bc72e87 https://github.com/galaxyproject/galaxy/commit/25fc0982b75243e9c95a5312b563… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Log Message: ----------- Merge branch 'release_16.10' into backport-hardening-17.01 Commit: 54d3994131f28963a1c3c4beccaf029a121d15b1 https://github.com/galaxyproject/galaxy/commit/54d3994131f28963a1c3c4beccaf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4807 from natefoo/backport-hardening-17.01 [17.01] Various bits of hardening from #4604 Commit: 66820a46eba8f8adc0a573a8c2727e28e0de23e8 https://github.com/galaxyproject/galaxy/commit/66820a46eba8f8adc0a573a8c272… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Backport of hardening fixes to 17.05 Commit: 9241c9e3dbf67bb3f55fa89181c80a13e5466e0e https://github.com/galaxyproject/galaxy/commit/9241c9e3dbf67bb3f55fa89181c8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into backport-hardening-17.05 Commit: ef203a69e95facee788086fc507b062528cbb638 https://github.com/galaxyproject/galaxy/commit/ef203a69e95facee788086fc507b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4816 from natefoo/backport-hardening-17.05 [17.05] Various bits of hardening from #4604 Compare: https://github.com/galaxyproject/galaxy/compare/a474822f3cbe...ef203a69e95f

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[galaxyproject/galaxy] c96e99: Force absolute import in much of galaxy.util
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: c96e9945a613a27f4826baf3c0e61edda2dfa0bb https://github.com/galaxyproject/galaxy/commit/c96e9945a613a27f4826baf3c0e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py Log Message: ----------- Force absolute import in much of galaxy.util Commit: b15f5a74957ec154e7cd501f0a65936d11206aa0 https://github.com/galaxyproject/galaxy/commit/b15f5a74957ec154e7cd501f0a65… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py Log Message: ----------- Merge pull request #4817 from dannon/backport_abs_import [17.09] Backport abs-import changes from util. Compare: https://github.com/galaxyproject/galaxy/compare/7906a946f110...b15f5a74957e

1 0

[galaxyproject/galaxy] 60b5ab: fix TDT's dependency
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 60b5abfa3e85502631fc922b231f51f63b118234 https://github.com/galaxyproject/galaxy/commit/60b5abfa3e85502631fc922b231f… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- fix TDT's dependency Commit: 7906a946f110ef8f55524121e3addb320982979c https://github.com/galaxyproject/galaxy/commit/7906a946f110ef8f55524121e3ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Merge pull request #4815 from anatskiy/release_17.09_tdt_fix Fix TDT's dependency Compare: https://github.com/galaxyproject/galaxy/compare/ebdadb68ad7c...7906a946f110

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[galaxyproject/galaxy] 3879f3: You're a depedencies.
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3879f33d39fc8b4bc15c665bb227f9b0fa30783c https://github.com/galaxyproject/galaxy/commit/3879f33d39fc8b4bc15c665bb227… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- You're a depedencies. Commit: 5aa624c45a502f1a152a49c1609f63a1c4c501b9 https://github.com/galaxyproject/galaxy/commit/5aa624c45a502f1a152a49c1609f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #4814 from blankenberg/depedencies Typo: depedencies. Compare: https://github.com/galaxyproject/galaxy/compare/24e0c3d5978c...5aa624c45a50

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[galaxyproject/galaxy] e4518f: Rebase hardening commits from dev
by GitHub 16 Oct '17

16 Oct '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: e4518ff3e3d628f2cd47ea48217da6352ef11e30 https://github.com/galaxyproject/galaxy/commit/e4518ff3e3d628f2cd47ea48217d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Rebase hardening commits from dev Commit: b5ded00eb50181f17b3c003e1b7c895098b85d25 https://github.com/galaxyproject/galaxy/commit/b5ded00eb50181f17b3c003e1b7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 545d5556588dfe28c8a9857333366ba62dbcd2fd https://github.com/galaxyproject/galaxy/commit/545d5556588dfe28c8a985733336… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Fix additional uses of subprocess shell=True Commit: 2f79351e3cdb1fe9705f00590038b11cba4b428e https://github.com/galaxyproject/galaxy/commit/2f79351e3cdb1fe9705f00590038… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Rebase script integrity check improvements (#4720) from dev Commit: 9fa9d42c5093ddd8f70193cc6a07ae0af0394f8c https://github.com/galaxyproject/galaxy/commit/9fa9d42c5093ddd8f70193cc6a07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/proxy/__init__.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix backport issues Commit: f925ffe4b743d080585bc6d151dc8ca98cc4f171 https://github.com/galaxyproject/galaxy/commit/f925ffe4b743d080585bc6d151dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4801 from natefoo/backport-hardening-16.07 [16.07] Various bits of hardening from #4604 Commit: e60f324b66676cc5020aa74bfa011f886eaeca68 https://github.com/galaxyproject/galaxy/commit/e60f324b66676cc5020aa74bfa01… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into backport-hardening-16.10 Commit: ef268027191b526b8c8dfe69c3d8352c0412ce1d https://github.com/galaxyproject/galaxy/commit/ef268027191b526b8c8dfe69c3d8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- Hardening backport differences from dev present in 16.10 but not 16.07 Commit: d70713d07a3c4d98b71df9247bbd8644ab6b2b40 https://github.com/galaxyproject/galaxy/commit/d70713d07a3c4d98b71df9247bbd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: fe9839bf7ca720061548ff3bcebdc79062e7adf5 https://github.com/galaxyproject/galaxy/commit/fe9839bf7ca720061548ff3bcebd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: 36b974c90514332c6cb732f9c376a66767100944 https://github.com/galaxyproject/galaxy/commit/36b974c90514332c6cb732f9c376… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 3bb5d825c13ae2dbd366f24dc316bcdaa7171eb9 https://github.com/galaxyproject/galaxy/commit/3bb5d825c13ae2dbd366f24dc316… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Ignore I201 errors in 16.10 Commit: 8d573db729a92344ad9115b7657ace07a4718a21 https://github.com/galaxyproject/galaxy/commit/8d573db729a92344ad9115b7657a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 6d8f8ecb466ae75ca7d586496512cb70206a08f6 https://github.com/galaxyproject/galaxy/commit/6d8f8ecb466ae75ca7d586496512… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Add missing backport of hardening to scripts/grt.py Commit: b04aafa8e871f4d2f3bf7a636ccf0ef432fda875 https://github.com/galaxyproject/galaxy/commit/b04aafa8e871f4d2f3bf7a636ccf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M .travis.yml M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M setup.cfg M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py M tox.ini Log Message: ----------- Merge pull request #4804 from natefoo/backport-hardening-16.10 [16.10] Various bits of hardening from #4604 Commit: 139ba7c13e38a98a090a91167e0538f259baa7c2 https://github.com/galaxyproject/galaxy/commit/139ba7c13e38a98a090a91167e05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 03087e5ee77701e410e7d9336a74cedf3206e3f3 https://github.com/galaxyproject/galaxy/commit/03087e5ee77701e410e7d9336a74… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Rebase hardening commits from dev Commit: f9213b16f5bb26b2b7176d50602d852ea4e08562 https://github.com/galaxyproject/galaxy/commit/f9213b16f5bb26b2b7176d50602d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 7ad6182ef4952480354e4737b72c062fc75be93e https://github.com/galaxyproject/galaxy/commit/7ad6182ef4952480354e4737b72c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Fix additional uses of subprocess shell=True Commit: b13f5d7f943106cf27670c7153e6c8967a749bcf https://github.com/galaxyproject/galaxy/commit/b13f5d7f943106cf27670c7153e6… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Rebase script integrity check improvements (#4720) from dev Commit: 24c8a26852aecdcc5d8d23300e551f282b90c628 https://github.com/galaxyproject/galaxy/commit/24c8a26852aecdcc5d8d23300e55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Fix backport issues Commit: 9955c4d24bff197b01f2ff6227fdfb06224d9ab9 https://github.com/galaxyproject/galaxy/commit/9955c4d24bff197b01f2ff6227fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Ignore I201 errors in 16.10 Commit: 950f92627176068609fc5191c72f681e3e16fb22 https://github.com/galaxyproject/galaxy/commit/950f92627176068609fc5191c72f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Add missing backport of hardening to scripts/grt.py Commit: d8ee1a9a8d42f1287262a25fa282799d44d4f583 https://github.com/galaxyproject/galaxy/commit/d8ee1a9a8d42f1287262a25fa282… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Revert ignoring I201 from 16.10 in 17.01 Commit: 25fc0982b75243e9c95a5312b56359f83bc72e87 https://github.com/galaxyproject/galaxy/commit/25fc0982b75243e9c95a5312b563… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Log Message: ----------- Merge branch 'release_16.10' into backport-hardening-17.01 Commit: 54d3994131f28963a1c3c4beccaf029a121d15b1 https://github.com/galaxyproject/galaxy/commit/54d3994131f28963a1c3c4beccaf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4807 from natefoo/backport-hardening-17.01 [17.01] Various bits of hardening from #4604 Compare: https://github.com/galaxyproject/galaxy/compare/f64b7fcfb124...54d3994131f2

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[galaxyproject/galaxy] b95640: Fix Python3 compatibility and import order for 21 ...
by GitHub 16 Oct '17

16 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b956406c4d14a3410e8d80f7c6acda674e297830 https://github.com/galaxyproject/galaxy/commit/b956406c4d14a3410e8d80f7c6ac… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/util/jstree.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/mimeparse.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/common.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/deprecate_repositories_without_metadata.py Log Message: ----------- Fix Python3 compatibility and import order for 21 files Commit: f39019e898f7fd67f80894c8fe680934525827f9 https://github.com/galaxyproject/galaxy/commit/f39019e898f7fd67f80894c8fe68… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add doctests for unicodify() Commit: 255d3daf50a957299171858fdea9f5622ec6173e https://github.com/galaxyproject/galaxy/commit/255d3daf50a957299171858fdea9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: R .ci/flake8_py3_wrapper.sh M tox.ini Log Message: ----------- Extend Python3 flake8 linting to whole codebase Keep .ci/py3_sources.txt as list of manually ported files. Commit: 24e0c3d5978c8dac5a0c1e0cd034b739cad61fac https://github.com/galaxyproject/galaxy/commit/24e0c3d5978c8dac5a0c1e0cd034… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/py3_sources.txt M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/jstree.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/mimeparse.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/common.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M tox.ini Log Message: ----------- Merge pull request #4811 from nsoranzo/python3 Extend Python3 flake8 linting to whole codebase Compare: https://github.com/galaxyproject/galaxy/compare/f4d45549cf9e...24e0c3d5978c

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