December 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 54b54b: UI, Users: when an first logging out, anon users m...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54b54b1f11a30bad0b2e15802c44b30e745ca4a6 https://github.com/galaxyproject/galaxy/commit/54b54b1f11a30bad0b2e15802c44… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- UI, Users: when an first logging out, anon users may not have a history when they're serialized, return 0 usage from the user serilializer when this is the case Commit: 0c8df84685c587322f6c3b83ea45c0b20819d3ab https://github.com/galaxyproject/galaxy/commit/0c8df84685c587322f6c3b83ea45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #1328 from carlfeberhard/fix.quotameter UI, Users: when an first logging out, anon users may not have a histo… Compare: https://github.com/galaxyproject/galaxy/compare/cf5d209e0f01...0c8df84685c5

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[galaxyproject/galaxy] 784274: UI, History: refactor the history copy dialog, use...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78427438adcb794af630ebb3b9b77b3628c2c5bb https://github.com/galaxyproject/galaxy/commit/78427438adcb794af630ebb3b9b7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/ui-modal.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/ui-modal.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/mvc/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/ui/ui-modal.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- UI, History: refactor the history copy dialog, use it from the options menu (instead of history/copy), pass ui-modal closing_callback a flag whether it was a cancellation or not Commit: e391fa4975800fd1d21e1e7d03183d146728f1c8 https://github.com/galaxyproject/galaxy/commit/e391fa4975800fd1d21e1e7d0318… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, History: allow copy dialog to have default of copy-all-datasets passed in as option; Replace import link with copy dialog in published histories Commit: 7187eddd2fdec95093c765b838814435c9f6b92d https://github.com/galaxyproject/galaxy/commit/7187eddd2fdec95093c765b83881… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M templates/display_base.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako Log Message: ----------- UI, published items: fix css bleeding of trackster.css into other published item displays Commit: 941109dda860325938960b93f66e50d314b67e4a https://github.com/galaxyproject/galaxy/commit/941109dda860325938960b93f66e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.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/mvc/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M templates/grid_base.mako M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, History: use copy dialog as import dialog in published history pages, refactor copy-dialog Commit: 253ca7ec4940188d11157448d73be09e762e65f8 https://github.com/galaxyproject/galaxy/commit/253ca7ec4940188d11157448d73b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/popup-menu.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/mvc/history/copy-dialog.js M static/scripts/mvc/ui/popup-menu.js M templates/webapps/galaxy/history/grid.mako Log Message: ----------- UI, History: insert/use copy dialog in the 'Saved Histories' grid Commit: 09cb673a9b13f6f9faae21b48c317e485afb8eb1 https://github.com/galaxyproject/galaxy/commit/09cb673a9b13f6f9faae21b48c31… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.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/mvc/history/copy-dialog.js M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako A templates/webapps/galaxy/history/shared_grid.mako Log Message: ----------- UI, History: use copy dialog for shared history popupmenus, use custom templates for both saved and shared history lists/grids. refactor custom grid code for insertion of copy dialog Commit: cb23e010d7750b533be7690e72c92500ddc8e2f1 https://github.com/galaxyproject/galaxy/commit/cb23e010d7750b533be7690e72c9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M static/maps/mvc/history/copy-dialog.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/history/copy-dialog.js M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, History: use copy dialog in history/view for import, minor fixes Commit: d72b913c1d25bf9e2ee2c9e7320bff4f52b366e3 https://github.com/galaxyproject/galaxy/commit/d72b913c1d25bf9e2ee2c9e7320b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/utils/ajax-queue.js M static/maps/utils/ajax-queue.js.map M static/scripts/utils/ajax-queue.js M templates/webapps/galaxy/history/shared_grid.mako Log Message: ----------- UI, History: hack multiple copy by API into the 'histories shared with me' mako grid Commit: 9e512f52465c158855c2a0750d8a7d794316940e https://github.com/galaxyproject/galaxy/commit/9e512f52465c158855c2a0750d8a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/model/__init__.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/tool/tools-form-base.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/history/copy-dialog.js M static/scripts/mvc/tool/tools-form-base.js M static/scripts/utils/ajax-queue.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, History: use copy dialog in the embedded histories in Pages, add autoClose option to copy dialog Commit: 324af9caeda230bfe35ce79cf3e6f84a3ca27ee5 https://github.com/galaxyproject/galaxy/commit/324af9caeda230bfe35ce79cf3e6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, History: remove copy and imp methods from controllers/history.py, remove history copy template Commit: 32be886f0f51103a648003997c7d06cd12ba08d9 https://github.com/galaxyproject/galaxy/commit/32be886f0f51103a648003997c7d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.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/history/copy-dialog.js Log Message: ----------- API, Histories: allow api/histories/create to be used as anon user; UI, Histories: minor fixes Commit: 84f3b72e1ad829e6f2f46049ff4af42f27429a5b https://github.com/galaxyproject/galaxy/commit/84f3b72e1ad829e6f2f46049ff4a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: A Makefile A client/.docker-build.sh A client/Dockerfile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/ui/ui-select-default.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-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M client/galaxy/style/less/ui.less M doc/source/dev/faq.rst M lib/galaxy/datatypes/text.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/ui/ui-select-default.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-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.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/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js M static/style/blue/base.css R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/base/interactor.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/functional/test_1460_data_managers.py M test/unit/managers/test_UserManager.py M test/unit/workflows/test_modules.py Log Message: ----------- (merge dev); Testing, histories: update tests to reflect allowing anon to create/copy histories via the API Commit: cf5d209e0f01b7fb13e06f013f2a3693f194ebb4 https://github.com/galaxyproject/galaxy/commit/cf5d209e0f01b7fb13e06f013f2a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/utils/ajax-queue.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/utils/ajax-queue.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/mvc/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/utils/ajax-queue.js M templates/display_base.mako M templates/grid_base.mako R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako A templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- Manual merge of #1303 to resolve build artifact conflicts. Compare: https://github.com/galaxyproject/galaxy/compare/d1fd23a2f4e5...cf5d209e0f01

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[galaxyproject/galaxy] e505a4: Add the CSG Viewer visualization plugin
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e505a4f6123f119577955459cda1846b5f67f0b8 https://github.com/galaxyproject/galaxy/commit/e505a4f6123f119577955459cda1… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako Log Message: ----------- Add the CSG Viewer visualization plugin based on conversations here: https://github.com/galaxyproject/galaxy/issues/1191#issuecomment-162553926 Commit: 80bd59dd90722afb837c01a26b78eebe04dd277b https://github.com/galaxyproject/galaxy/commit/80bd59dd90722afb837c01a26b78… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.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-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.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-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.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/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/workflows_format_2/converter.py M test/docker/base/run_test_wrapper.sh M test/qunit/tests/workflow_editor_tests.js M test/unit/managers/test_UserManager.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 946438ceba25151706ba2ca62e5c488e358c4f55 https://github.com/galaxyproject/galaxy/commit/946438ceba25151706ba2ca62e5c… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh A Makefile A client/.docker-build.sh A client/Dockerfile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js R client/galaxy/scripts/mvc/tool/tools-form-base.js R client/galaxy/scripts/mvc/tool/tools-form-workflow.js R client/galaxy/scripts/mvc/tool/tools-form.js R client/galaxy/scripts/mvc/tool/tools-jobs.js R client/galaxy/scripts/mvc/tool/tools-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M config/reports.ini.sample M config/tool_shed.ini.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M doc/source/dev/faq.rst M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/text.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py A static/maps/galaxy-app-base.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.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-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tools-form-base.js.map R static/maps/mvc/tool/tools-form-workflow.js.map R static/maps/mvc/tool/tools-form.js.map R static/maps/mvc/tool/tools-jobs.js.map R static/maps/mvc/tool/tools-template.js.map M static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.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/mvc/citation/citation-model.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/paired-collection-creator.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js R static/scripts/mvc/history/history-panel.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tools-form-base.js R static/scripts/mvc/tool/tools-form-workflow.js R static/scripts/mvc/tool/tools-form.js R static/scripts/mvc/tool/tools-jobs.js R static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py M test/docker/base/Dockerfile M test/tool_shed/functional/test_1460_data_managers.py M test/unit/tools/test_tool_deps.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: d1fd23a2f4e5c5408f469ee5560f526833f5f682 https://github.com/galaxyproject/galaxy/commit/d1fd23a2f4e5c5408f469ee5560f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako Log Message: ----------- Merge pull request #1254 from gregvonkuster/dev Add the CSG Viewer visualization plugin Compare: https://github.com/galaxyproject/galaxy/compare/7b11ebc52e30...d1fd23a2f4e5

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[galaxyproject/galaxy] 148c11: Adjust interface to basic.py.
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 148c11f403674d133bb0301ce2fc01ef108c38bd https://github.com/galaxyproject/galaxy/commit/148c11f403674d133bb0301ce2fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Adjust interface to basic.py. Commit: 9f68003438cac76a223e84756b0584d7530df239 https://github.com/galaxyproject/galaxy/commit/9f68003438cac76a223e84756b05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise checking for workflow parameters in tooling code. - Use verbose and higher level abstractions. - Tighten up checks (use re.match instead of search when appropriate, replace startwith.("$") with more robust regex matches). Commit: 7687ed7fad52ef69002a2f985fcf682999068f00 https://github.com/galaxyproject/galaxy/commit/7687ed7fad52ef69002a2f985fcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Tighten workflow parameter check. a440813e37941d050ac503a0898dcf00c5f1b4fe always skipped validation of text/int/float values if they looked like they were workflow parameters. This restricts that check to just occurring when coming from the workflow editor tool form. Commit: fafa72dde200b05954d038902e317c8fe0d302bd https://github.com/galaxyproject/galaxy/commit/fafa72dde200b05954d038902e31… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Slightly tighten up relaxed validation of workflow paramters. Don't allow mid-parameter placement of values for integers, floats, etc... (e.g. 10${param}). This is enforced other places as well. Commit: 9dad7f76c41845e23d07a8583950d41e4b60b3cf https://github.com/galaxyproject/galaxy/commit/9dad7f76c41845e23d07a8583950… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix another instance of using _allow_workflow_parameters_in_context. As recommended by @nsoranzo. Commit: 7b11ebc52e30e6613e1b94c6db0db6bda70a5255 https://github.com/galaxyproject/galaxy/commit/7b11ebc52e30e6613e1b94c6db0d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1319 from jmchilton/workflow_validation_2 More tightening up of parameter validation during workflow stuff. Compare: https://github.com/galaxyproject/galaxy/compare/d5cddaf7cc4f...7b11ebc52e30

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[galaxyproject/usegalaxy-playbook] aa5b1b: Remove trello card creator. Redirect to GH issues...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa5b1bc855fadaa8121ee98b3d00e9d1b73c7305 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa5b1bc855fadaa8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: R app_infrastructure.yml M common/inventory R roles/trello_card_creator/handlers/main.yml R roles/trello_card_creator/tasks/main.yml R roles/trello_card_creator/templates/trello_card_creator.ini.j2 M templates/nginx/galaxyproject.j2 Log Message: ----------- Remove trello card creator. Redirect to GH issues.

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[galaxyproject/usegalaxy-playbook] c52ccb: Update interactive_environments role
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c52ccbe9d8525be4f9e97dce03a879e2b2b30b25 https://github.com/galaxyproject/usegalaxy-playbook/commit/c52ccbe9d8525be4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M roles/galaxyprojectdotorg.interactive_environments/README.md M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml Log Message: ----------- Update interactive_environments role Commit: b3c4a0b0ec0d965eee356d333d0cd18feace8408 https://github.com/galaxyproject/usegalaxy-playbook/commit/b3c4a0b0ec0d965e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M templates/supervisor/toolshed.conf.j2 Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Commit: 3edc4c9d17ff2467937943b5c180d9d87985018f https://github.com/galaxyproject/usegalaxy-playbook/commit/3edc4c9d17ff2467… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 15facabe5f7c0dbc6c80ae093a56fc837ee5bacd https://github.com/galaxyproject/usegalaxy-playbook/commit/15facabe5f7c0dbc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Resource changes for Anton Commit: ffa181b7f4f422cf0a01e8fc9b1534fc15431cf7 https://github.com/galaxyproject/usegalaxy-playbook/commit/ffa181b7f4f422cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Mutable configs on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b4841230c39d...…

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[galaxyproject/galaxy] 74be6f: Fix for creating workflow outputs on initial workf...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74be6f54cd1868f663dc89609c90a28c0db8214f https://github.com/galaxyproject/galaxy/commit/74be6f54cd1868f663dc89609c90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix for creating workflow outputs on initial workflow upload. Commit: d5cddaf7cc4fa734cb738521167e854393e5d380 https://github.com/galaxyproject/galaxy/commit/d5cddaf7cc4fa734cb738521167e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1330 from jmchilton/failing_test Fix for creating workflow outputs on initial workflow upload. Compare: https://github.com/galaxyproject/galaxy/compare/bb0c1366f723...d5cddaf7cc4f

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[galaxyproject/galaxy] b3e3b3: Update Kombu and AMQP wheels to fix problems with ...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3e3b359aec1bce3d7ee4a23289d96318f5b0af3 https://github.com/galaxyproject/galaxy/commit/b3e3b359aec1bce3d7ee4a23289d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Update Kombu and AMQP wheels to fix problems with El Capitan's System Integrity Protection Commit: bb0c1366f723b8236872d05da4c553a53d1aedc7 https://github.com/galaxyproject/galaxy/commit/bb0c1366f723b8236872d05da4c5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1327 from natefoo/kombu-el-cap-wheels Update Kombu and AMQP wheels to fix problems with El Capitan's System Integrity Protection Compare: https://github.com/galaxyproject/galaxy/compare/86632afdd3b7...bb0c1366f723

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[galaxyproject/galaxy] 31f174: Add enhancements to the Galaxy repository install ...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 31f174a4254e5cc4c85747a76c3908b0170cf358 https://github.com/galaxyproject/galaxy/commit/31f174a4254e5cc4c85747a76c39… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: a23e644a9cd7ab64f0fa56314ae5ec2b5a768f7a https://github.com/galaxyproject/galaxy/commit/a23e644a9cd7ab64f0fa56314ae5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1329 from martenson/release_15.10 [15.10] Add enhancements to the Galaxy repository install process Compare: https://github.com/galaxyproject/galaxy/compare/c48965ffcc5d...a23e644a9cd7

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[galaxyproject/galaxy] f95300: Fix typo causing the option "Link files instead of...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: f953005f72310279fe69a0deb0b9adef973bf6da https://github.com/galaxyproject/galaxy/commit/f953005f72310279fe69a0deb0b9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Fix typo causing the option "Link files instead of copying" to be ignored. When uploading folders with the new data library interface. Commit: c48965ffcc5d35877f00dcf1941317cf23c3d4f4 https://github.com/galaxyproject/galaxy/commit/c48965ffcc5d35877f00dcf19413… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1326 from nsoranzo/release_15.10_link_data_only [15.10] Fix typo causing the option "Link files instead of copying" to be ignored. Compare: https://github.com/galaxyproject/galaxy/compare/989f961fb635...c48965ffcc5d

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