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
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
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
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