>git pull remote: Counting objects: 3704, done. remote: Compressing objects: 100% (327/327), done. remote: Total 3704 (delta 2363), reused 2156 (delta 2156), pack-reused 1221 Receiving objects: 100% (3704/3704), 7.52 MiB | 2.79 MiB/s, done. Resolving deltas: 100% (2964/2964), completed with 567 local objects. From https://github.com/galaxyproject/galaxy * branch HEAD -> FETCH_HEAD Updating 909a549..d15b103 Fast-forward client/galaxy/scripts/mvc/form/form-input.js | 176 ++-- client/galaxy/scripts/mvc/form/form-parameters.js | 4 +- .../galaxy/scripts/mvc/form/form-select-content.js | 347 ------ .../scripts/mvc/library/library-dataset-view.js | 99 ++- .../mvc/library/library-foldertoolbar-view.js | 566 +++++----- client/galaxy/scripts/mvc/ui/ui-select-content.js | 249 +++++ client/galaxy/scripts/mvc/ui/ui-select-default.js | 2 +- client/galaxy/scripts/utils/utils.js | 13 +- client/galaxy/scripts/viz/trackster/tracks.js | 2 +- client/galaxy/style/less/library.less | 13 + client/galaxy/style/less/ui.less | 20 +- config/datatypes_conf.xml.sample | 2 +- lib/galaxy/config.py | 1 - lib/galaxy/jobs/__init__.py | 11 +- lib/galaxy/model/__init__.py | 9 +- lib/galaxy/tools/__init__.py | 11 +- lib/galaxy/tools/execute.py | 1 + lib/galaxy/tools/parameters/__init__.py | 12 +- lib/galaxy/tools/parameters/basic.py | 6 +- lib/galaxy/tools/parameters/wrapped_json.py | 3 + lib/galaxy/util/__init__.py | 41 + lib/galaxy/web/framework/base.py | 1 + lib/galaxy/web/framework/middleware/statsd.py | 2 +- lib/galaxy/webapps/galaxy/api/datasets.py | 4 +- .../webapps/galaxy/api/tool_shed_repositories.py | 3 +- lib/galaxy/webapps/galaxy/controllers/admin.py | 8 +- .../webapps/galaxy/controllers/admin_toolshed.py | 30 +- lib/galaxy/webapps/galaxy/controllers/workflow.py | 3 +- lib/galaxy/webapps/tool_shed/config.py | 24 +- .../webapps/tool_shed/controllers/repository.py | 8 +- lib/galaxy/workflow/modules.py | 20 +- lib/galaxy/workflow/scheduling_manager.py | 1 + lib/tool_shed/capsule/capsule_manager.py | 3 +- lib/tool_shed/galaxy_install/dependency_display.py | 2 +- lib/tool_shed/galaxy_install/install_manager.py | 6 +- .../repository_dependency_manager.py | 8 +- .../tool_dependencies/recipe/tag_handler.py | 4 +- .../galaxy_install/tool_migration_manager.py | 2 +- .../galaxy_install/update_repository_manager.py | 3 +- lib/tool_shed/scripts/api/common.py | 5 +- .../deprecate_repositories_without_metadata.py | 4 +- lib/tool_shed/tool_shed_registry.py | 11 +- lib/tool_shed/util/common_util.py | 46 +- lib/tool_shed/util/readme_util.py | 4 +- lib/tool_shed/util/shed_util_common.py | 18 +- run_tests.sh | 138 +++- scripts/functional_tests.py | 614 ++--------- scripts/summarize_timings.py | 16 +- static/maps/mvc/form/form-input.js.map | 2 +- static/maps/mvc/form/form-parameters.js.map | 2 +- static/maps/mvc/form/form-select-content.js.map | 1 - .../maps/mvc/library/library-dataset-view.js.map | 2 +- .../mvc/library/library-foldertoolbar-view.js.map | 2 +- static/maps/mvc/ui/ui-select-content.js.map | 1 + static/maps/mvc/ui/ui-select-default.js.map | 2 +- static/maps/utils/utils.js.map | 2 +- static/maps/viz/trackster/tracks.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 22 +- static/scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 10 +- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/bundled/login.bundled.js | 2 +- static/scripts/bundled/login.bundled.js.map | 2 +- static/scripts/mvc/form/form-input.js | 2 +- static/scripts/mvc/form/form-parameters.js | 2 +- static/scripts/mvc/form/form-select-content.js | 2 - static/scripts/mvc/library/library-dataset-view.js | 2 +- .../mvc/library/library-foldertoolbar-view.js | 5 +- static/scripts/mvc/ui/ui-select-content.js | 2 + static/scripts/mvc/ui/ui-select-default.js | 2 +- static/scripts/utils/utils.js | 2 +- static/scripts/viz/trackster/tracks.js | 2 +- static/style/blue/base.css | 2 +- static/style/blue/library.css | 2 +- templates/base/base_panels.mako | 4 +- test/base/driver_util.py | 663 +++++++++++ test/base/twilltestcase.py | 3 +- test/functional/test_admin_features.py | 495 --------- test/functional/test_data_security.py | 206 ---- test/functional/test_dataset_features.py | 38 - test/functional/test_get_data.py | 635 ----------- test/functional/test_library_features.py | 621 ----------- test/functional/test_library_security.py | 585 ---------- test/functional/test_metadata_editing.py | 52 - test/functional/test_sample_tracking.py | 983 ----------------- test/functional/test_tags.py | 73 -- test/functional/test_ucsc_table_browser.py | 33 - test/functional/test_user_info.py | 237 ---- .../for_workflows/create_input_collection.xml | 40 + test/functional/tools/for_workflows/split.xml | 33 + test/functional/tools/samples_tool_conf.xml | 2 + test/functional/tools/upload_tool_conf.xml | 6 + test/functional/workflow.py | 2 +- .../__init__.py | 1 - .../base/test_db_util.py | 83 -- .../base/twilltestcase.py | 162 --- .../base/util.py | 1151 -------------------- .../functional/__init__.py | 1 - .../functional/test_install_repositories.py | 58 - .../repositories_with_tools/__init__.py | 1 - .../repositories_with_tools/functional_tests.py | 825 -------------- .../tool_dependency_definitions/__init__.py | 1 - .../functional_tests.py | 520 --------- test/manual/launch_and_run.sh | 78 ++ test/manual/workflow_job_conf.xml | 26 + test/manual/workflows_scaling.py | 98 ++- test/qunit/test-app.js | 4 + test/qunit/tests/form_tests.html | 11 + test/qunit/tests/form_tests.js | 53 + test/qunit/tests/ui_tests.js | 153 +++- test/tool_shed/functional_tests.py | 554 ++-------- test/unit/test_lazy_process.py | 10 +- 112 files changed, 2451 insertions(+), 8707 deletions(-) delete mode 100644 client/galaxy/scripts/mvc/form/form-select-content.js create mode 100644 client/galaxy/scripts/mvc/ui/ui-select-content.js delete mode 100644 static/maps/mvc/form/form-select-content.js.map create mode 100644 static/maps/mvc/ui/ui-select-content.js.map delete mode 100644 static/scripts/mvc/form/form-select-content.js create mode 100644 static/scripts/mvc/ui/ui-select-content.js create mode 100644 test/base/driver_util.py delete mode 100644 test/functional/test_admin_features.pypy delete mode 100644 test/functional/test_data_security.py delete mode 100644 test/functional/test_dataset_features.py delete mode 100644 test/functional/test_get_data.py delete mode 100644 test/functional/test_library_features.py delete mode 100644 test/functional/test_library_security.py delete mode 100644 test/functional/test_metadata_editing.py delete mode 100644 test/functional/test_sample_tracking.py delete mode 100644 test/functional/test_tags.py delete mode 100644 test/functional/test_ucsc_table_browser.py delete mode 100644 test/functional/test_user_info.py create mode 100644 test/functional/tools/for_workflows/create_input_collection.xml create mode 100644 test/functional/tools/for_workflows/split.xml create mode 100644 test/functional/tools/upload_tool_conf.xml delete mode 100644 test/install_and_test_tool_shed_repositories/__init__.py delete mode 100644 test/install_and_test_tool_shed_repositories/base/__init__.py delete mode 100644 test/install_and_test_tool_shed_repositories/base/test_db_util.py delete mode 100644 test/install_and_test_tool_shed_repositories/base/twilltestcase.py delete mode 100644 test/install_and_test_tool_shed_repositories/base/util.py delete mode 100644 test/install_and_test_tool_shed_repositories/functional/__init__.py delete mode 100644 test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py delete mode 100644 test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py delete mode 100644 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py delete mode 100644 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py delete mode 100644 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py create mode 100755 test/manual/launch_and_run.sh create mode 100644 test/manual/workflow_job_conf.xml reate mode 100644 test/qunit/tests/form_tests.html create mode 100644 test/qunit/tests/form_tests.js