[galaxyproject/galaxy] 458766: Add run workflow tool form
Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 458766b00f05a2d46c834d461e59201796ff0358 https://github.com/galaxyproject/galaxy/commit/458766b00f05a2d46c834d461e592... Author: guerler <aysam.guerler@gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.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 M client/galaxy/scripts/mvc/tools.js R client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/tools/tools-form-workflow.js R client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-template.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-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/app/app-analysis.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 M static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.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-slider.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/app/app-analysis.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 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 M static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Add run workflow tool form Move styles to css Improve handling of numeric workflow parameters Commit: 9f7dff740f0133d6ba66abe067fb2edeb7a6b705 https://github.com/galaxyproject/galaxy/commit/9f7dff740f0133d6ba66abe067fb2... Author: guerler <aysam.guerler@gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Revise is_workflow setting Commit: 0770d8d988b20e36c2178d906bd05c6471018edf https://github.com/galaxyproject/galaxy/commit/0770d8d988b20e36c2178d906bd05... Author: guerler <aysam.guerler@gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Revise workflow mode flag handling Fix comment Commit: 28715a5bca299933c69859559d5b88b381b6c998 https://github.com/galaxyproject/galaxy/commit/28715a5bca299933c69859559d5b8... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css Log Message: ----------- Add runtime modification switch Commit: 2f31a3cbcd087f26caa9b8754920a6dddb924b30 https://github.com/galaxyproject/galaxy/commit/2f31a3cbcd087f26caa9b8754920a... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Cleanup collapsible handling Commit: 3017c61f380c8caa722ff04d11e2e3d37ca56b1c https://github.com/galaxyproject/galaxy/commit/3017c61f380c8caa722ff04d11e2e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix step order Commit: 98e738d6f0cb2faae1c304a889baaa66b10df953 https://github.com/galaxyproject/galaxy/commit/98e738d6f0cb2faae1c304a889baa... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Show pja info inside form portlet Improve readability Commit: aa90e346dd4e10850482e38c7331864bef50f007 https://github.com/galaxyproject/galaxy/commit/aa90e346dd4e10850482e38c73318... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.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-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/form/form-view.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-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/mvc/form/form-view.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-workflow.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise form base Fix style Commit: a8a4480d5c7e92e0f121eefd66357f5504c4cb26 https://github.com/galaxyproject/galaxy/commit/a8a4480d5c7e92e0f121eefd66357... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less 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 lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.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 M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/form/form-input.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 M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix dataset matching Commit: ac79cf191c0a0588cdaf45b5075a2494bf097f57 https://github.com/galaxyproject/galaxy/commit/ac79cf191c0a0588cdaf45b5075a2... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js M static/style/blue/base.css Log Message: ----------- Fix style naming Commit: 4dc134d43bfa415cf3d1b77475dc0d4a3efb05b1 https://github.com/galaxyproject/galaxy/commit/4dc134d43bfa415cf3d1b77475dc0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M .gitignore M README.rst M client/GruntFile.js A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/modal.js A 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M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.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/actions/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M 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static/style/blue/embed_item.css R static/style/blue/galaxy.frame.masthead.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/user/logout.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/base/twilltestcase.py M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml A test/functional/tools/collection_type_source.xml A test/functional/tools/create_10.xml A test/functional/tools/maxseconds.xml A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_loader.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 8e5b8016c6684e2364ba14b9061b0d5a2d218eb1 https://github.com/galaxyproject/galaxy/commit/8e5b8016c6684e2364ba14b9061b0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: R client/galaxy/scripts/mvc/app/app-analysis.js R static/maps/mvc/app/app-analysis.js.map Log Message: ----------- Remove files Commit: 7e5069baff533ba61fef3f8f6fc46ecab565a9c6 https://github.com/galaxyproject/galaxy/commit/7e5069baff533ba61fef3f8f6fc46... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: 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 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 R static/maps/mvc/tools/tools-form-base.js.map 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 R static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Remove files Commit: 0f9cb1478f81d512d4232b42cf490b8022b3a420 https://github.com/galaxyproject/galaxy/commit/0f9cb1478f81d512d4232b42cf490... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M static/style/blue/base.css Log Message: ----------- Repack files Commit: e29f7155c479365ede4a69513e729fa1bc67c369 https://github.com/galaxyproject/galaxy/commit/e29f7155c479365ede4a69513e729... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: R static/maps/mvc/tools.js.map R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/tools.js Log Message: ----------- Remove files Commit: 6820b29d3b867b452205c275f274449fb55c8119 https://github.com/galaxyproject/galaxy/commit/6820b29d3b867b452205c275f2744... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/datatypes/constructive_solid_geometry.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M test/api/helpers.py M test/functional/tools/maxseconds.xml Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: ab651fa89c0e24d637daa8bd5716b3932532c6a3 https://github.com/galaxyproject/galaxy/commit/ab651fa89c0e24d637daa8bd5716b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.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/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/utils/utils.js Log Message: ----------- Fix url, lint and packing Catch missing history, fix failing api test Commit: 00452e1b8aecd3ed2fc4c06262f451c9efafa1c6 https://github.com/galaxyproject/galaxy/commit/00452e1b8aecd3ed2fc4c06262f45... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add more specific error message for workflow parameters Commit: a951d34c703a239ac00c780025a9657bc7101b0b https://github.com/galaxyproject/galaxy/commit/a951d34c703a239ac00c780025a96... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M lib/galaxy/managers/configuration.py 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: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 8c6d530a661842a56fbb8800856237582701fc56 https://github.com/galaxyproject/galaxy/commit/8c6d530a661842a56fbb880085623... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 485e8ef8f22330bce5a402c5b4bb0182ce5b180c https://github.com/galaxyproject/galaxy/commit/485e8ef8f22330bce5a402c5b4bb0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.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/form/form-section.js Log Message: ----------- Add fallback for missing section and repeat title Commit: 2b63427e965837eb29df54e5918cf8f84004f534 https://github.com/galaxyproject/galaxy/commit/2b63427e965837eb29df54e5918cf... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Handle late validated dataset references Commit: 636e9900ba5e82c37a26fee84f56872c9413bd1b https://github.com/galaxyproject/galaxy/commit/636e9900ba5e82c37a26fee84f568... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Improve handling of unspecified workflow editor values Commit: 9a4c8343701c676ccf996cbbaa864f12135bac5b https://github.com/galaxyproject/galaxy/commit/9a4c8343701c676ccf996cbbaa864... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-drilldown.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/ui/ui-drilldown.js M static/style/blue/base.css Log Message: ----------- Use fa icons for drill down expansion Commit: c61a5529b4c788580d2c3615c7dab2386a9b8e4e https://github.com/galaxyproject/galaxy/commit/c61a5529b4c788580d2c3615c7dab... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-14 (Mon, 14 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/base-mvc.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/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 config/dependency_resolvers_conf.xml.sample 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/text.py 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/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.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/reports/config.py M lib/galaxy/webapps/tool_shed/config.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/migrate/check.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/collection/list-of-pairs-collection-creator.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/collection/list-of-pairs-collection-creator.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/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/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: b8d7cf035df49f2fda9291b91eadf59fd48bfdd0 https://github.com/galaxyproject/galaxy/commit/b8d7cf035df49f2fda9291b91eadf... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Add config setting, disable by default Commit: 42edfca679f204aa7e69a6c3df6dc14c8118e22c https://github.com/galaxyproject/galaxy/commit/42edfca679f204aa7e69a6c3df6dc... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/tools/__init__.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Repack, refix section validation Commit: 10fff14ce5ba6952f21da10c81a31ceda397a666 https://github.com/galaxyproject/galaxy/commit/10fff14ce5ba6952f21da10c81a31... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix missing wf parameter issue in classic form Commit: 57bc4660cf4e21ebe8b73035095e021e4f298680 https://github.com/galaxyproject/galaxy/commit/57bc4660cf4e21ebe8b73035095e0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix workflow parameter validation Commit: 3108ba5c01ded7b0209685f57ab231c2cfe92938 https://github.com/galaxyproject/galaxy/commit/3108ba5c01ded7b0209685f57ab23... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Ensure that text fields only display text Commit: a440813e37941d050ac503a0898dcf00c5f1b4fe https://github.com/galaxyproject/galaxy/commit/a440813e37941d050ac503a0898dc... Author: guerler <aysam.guerler@gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add workflow_mode flag to validation Commit: e838b03300964615bc2144ceeb9ba785cf5f7a7d https://github.com/galaxyproject/galaxy/commit/e838b03300964615bc2144ceeb9ba... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.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-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/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 lib/galaxy/tools/__init__.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/webapps/galaxy/api/workflows.py A static/maps/galaxy-app-base.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-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/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 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-slider.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1249 from guerler/run_workflow_form_004 Run workflow form Compare: https://github.com/galaxyproject/galaxy/compare/0fce226b96f9...e838b0330096
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