[galaxy-commits] [galaxyproject/galaxy] 9c49f5: Use API to initiate repository installation.

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c49f5720d1a25082d59187d70cc7980ea694ba4 https://github.com/galaxyproject/galaxy/commit/9c49f5720d1a25082d59187d70cc7... Author: Dave B <dave@bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Use API to initiate repository installation. Commit: 849cdab31b3f261d690f8479a87909ed60071941 https://github.com/galaxyproject/galaxy/commit/849cdab31b3f261d690f8479a8790... Author: Dave B <dave@bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Fix imminent import error in travis. Commit: 3f766f5d97a7614fce956bc166544b2834be234b https://github.com/galaxyproject/galaxy/commit/3f766f5d97a7614fce956bc166544... Author: Dave B <dave@bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Rename API endpoint. Correct url for API endpoint. Commit: cef6ad81f7ef41d01b85803a3639853722bd2b3e https://github.com/galaxyproject/galaxy/commit/cef6ad81f7ef41d01b85803a36398... Author: Dave B <dave@bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Typo. Commit: ea7ad2486add2357d59fac6c17b48c0bccb0c81d https://github.com/galaxyproject/galaxy/commit/ea7ad2486add2357d59fac6c17b48... Author: Dave B <dave@bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Additional cleanup. Commit: 6ce5ac58387a6dc38c0eae5c23f7440781d178a3 https://github.com/galaxyproject/galaxy/commit/6ce5ac58387a6dc38c0eae5c23f74... Author: Dave B <dave@bx.psu.edu> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add API endpoint to show installation status. This will return a dict of the repository, with the repository_dependencies element containing a list of dicts with the dependency chain descending from that repository. Commit: 992812eb860e58f0c19328bfc6db7ac3e4b26f28 https://github.com/galaxyproject/galaxy/commit/992812eb860e58f0c19328bfc6db7... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/categories.py A templates/admin/tool_shed_repository/browse_categories.mako Log Message: ----------- Load toolshed categories with API. Commit: 72e8f73858e5177432b51798cc0e229f81297826 https://github.com/galaxyproject/galaxy/commit/72e8f73858e5177432b51798cc0e2... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Update category API endpoint. Optionally show list of repositories in category. Commit: aff62e76c8c8a862166c7e0ac899b2c1a79fea86 https://github.com/galaxyproject/galaxy/commit/aff62e76c8c8a862166c7e0ac899b... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add API endpoint to check for updates to installed repositories. Commit: 2dca8f1812a7aaf9f20d3a8baa9f509e7ad8c15a https://github.com/galaxyproject/galaxy/commit/2dca8f1812a7aaf9f20d3a8baa9f5... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix the update check API method. Commit: a4bf833e219cc571fd87e6e154530449b44519f3 https://github.com/galaxyproject/galaxy/commit/a4bf833e219cc571fd87e6e154530... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako A templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add rudimentary mako files for the new interface. This is only for development purposes, until the UI designer fixes it. Commit: 83a9c6d440a630ea98b307ad67661c7f2314abef https://github.com/galaxyproject/galaxy/commit/83a9c6d440a630ea98b307ad67661... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add code to initiate repository installation. Commit: 6e58db947878f542ce51c78956e392afe1515a67 https://github.com/galaxyproject/galaxy/commit/6e58db947878f542ce51c78956e39... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Merge in changes from api_install branch. Commit: 099f8eb145cda5064ae587ba171cbd0713cbcaff https://github.com/galaxyproject/galaxy/commit/099f8eb145cda5064ae587ba171cb... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/util/common_util.py M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Functional installation of repository. Commit: 2a6712833223507700789440b63eaa6304cbacb5 https://github.com/galaxyproject/galaxy/commit/2a6712833223507700789440b63ea... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M client/GruntFile.js M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M 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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/unit/tools/test_actions.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: b55ac36a92f9d73406c986fb4b1c637d15065e4d https://github.com/galaxyproject/galaxy/commit/b55ac36a92f9d73406c986fb4b1c6... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Separate the decoupled and iframed toolshed installations. Commit: 271c8e97f7ddb849f6809a9d8b64a760e88e4efd https://github.com/galaxyproject/galaxy/commit/271c8e97f7ddb849f6809a9d8b64a... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako A templates/webapps/galaxy/admin/toolsheds.mako Log Message: ----------- Some refinements to the beta toolshed browsing. Commit: fb336b92b6b96f805efaf9bc51e8ab9829ebb8dc https://github.com/galaxyproject/galaxy/commit/fb336b92b6b96f805efaf9bc51e8a... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M .gitignore A Makefile M README.rst A client/.docker-build.sh A client/Dockerfile M client/README.md 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 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templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/history/share.mako A templates/webapps/galaxy/history/shared_grid.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/editor_generic_form.mako M templates/webapps/galaxy/workflow/editor_tool_form.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_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/casperjs/api-history-permission-tests.js R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py M test/casperjs/spaceghost.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/collection_type_source.xml A test/functional/tools/create_10.xml M test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml 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/functional/test_1460_data_managers.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_run_parameters.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: d91fff8f15fdf894b19c67a4328acf8c831c170e https://github.com/galaxyproject/galaxy/commit/d91fff8f15fdf894b19c67a4328ac... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add some styling, allow selecting revision to install. Commit: 9206e95144c645bd849043055d2ff5f2413d0144 https://github.com/galaxyproject/galaxy/commit/9206e95144c645bd849043055d2ff... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M lib/galaxy/app.py R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py A lib/galaxy/util/checkers.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/expressions.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/utils/uploadbox.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/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/qunit/test-app.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_evaluation.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 4fdfc0f47b430a68a90185ebdacd8aa120f60382 https://github.com/galaxyproject/galaxy/commit/4fdfc0f47b430a68a90185ebdacd8... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Update displayed metadata on changeset change. Commit: 7c357d1d56c98480b076bb7d80f9f1adde97e832 https://github.com/galaxyproject/galaxy/commit/7c357d1d56c98480b076bb7d80f9f... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/web/form_builder.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- More dynamic updating. - Repository dependencies reflect the selected changeset - So do tool dependencies - Tool panel select field shows/hides new tool panel section input field Commit: ba9493aed2ff1402097d9e383772e84dceb3f985 https://github.com/galaxyproject/galaxy/commit/ba9493aed2ff1402097d9e383772e... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/browse_category.mako Log Message: ----------- Fill in some gaps in the repository listing. Commit: e7072c0aa268d248872540cd56d1e4c054f1fa42 https://github.com/galaxyproject/galaxy/commit/e7072c0aa268d248872540cd56d1e... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/odict.py M lib/galaxy/util/xml_macros.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 68cecc6415054b84016f170c65c79a4460518d76 https://github.com/galaxyproject/galaxy/commit/68cecc6415054b84016f170c65c79... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix typo. Commit: bded6cdfd8f5283f0fc319df714687f374027c1f https://github.com/galaxyproject/galaxy/commit/bded6cdfd8f5283f0fc319df71468... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/admin/tool_shed_repository/browse_category.mako Log Message: ----------- Address travis' complaints. Commit: b5a8073d73c15455e89eecc48675cd2fc8bd0622 https://github.com/galaxyproject/galaxy/commit/b5a8073d73c15455e89eecc48675c... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Add endpoint for repositories in category, per Martin's suggestion. Commit: 86488d9c71e02a49e102e14acb0e8c1f68802989 https://github.com/galaxyproject/galaxy/commit/86488d9c71e02a49e102e14acb0e8... Author: Dave B <dave@bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- s/trans.app/self.app/g Commit: 78d50994bf1b2091cf0244d99a68356cd8fa34e0 https://github.com/galaxyproject/galaxy/commit/78d50994bf1b2091cf0244d99a683... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/visualizations/charts/templates/charts.mako M config/tool_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M 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lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/tool_util.py M run.sh M run_tests.sh M scripts/common_startup.sh M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/onload.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/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/admin/reload_tool.mako M templates/webapps/galaxy/galaxy.masthead.mako A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_routes.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: cc8175be8ff5c9affd3eb3051739e0ec9071760b https://github.com/galaxyproject/galaxy/commit/cc8175be8ff5c9affd3eb3051739e... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/bower.json M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/onload.js M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/galaxy.ini.sample A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/onload.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 A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/onload.js A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako A test/api/test_tours.py M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_parameter_parsing.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 1c6cffd2926d0201d1c3935e228bdab9ca6f426a https://github.com/galaxyproject/galaxy/commit/1c6cffd2926d0201d1c3935e228bd... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Implemented selecting or creating a tool panel section. Cleaned up UI a little. Commit: a337118d6bea1623410561c5a164713af4fae38c https://github.com/galaxyproject/galaxy/commit/a337118d6bea1623410561c5a1647... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Revert per Eric's suggestion. Commit: 25c339a2324f13656a1fc3c112d70849fef235ed https://github.com/galaxyproject/galaxy/commit/25c339a2324f13656a1fc3c112d70... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- One more change to revert. Commit: 3840a6290d048195c3d6fc2748ccefbc96b72b13 https://github.com/galaxyproject/galaxy/commit/3840a6290d048195c3d6fc2748cce... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/project/issues.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-template.js M static/style/blue/base.css M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 6d649c1ec3a537bb383f7d25c0bd2a209f8dcb8d https://github.com/galaxyproject/galaxy/commit/6d649c1ec3a537bb383f7d25c0bd2... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M templates/admin/tool_shed_repository/initiate_repository_installation.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Un-break traditional repository installations. Commit: 8b29f3ad0d9d9e2c654bf51f56b3587d7158420e https://github.com/galaxyproject/galaxy/commit/8b29f3ad0d9d9e2c654bf51f56b35... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Fix failing tests in jenkins. Commit: d509e8f6028259b8ff055cc67873fcd573fd72de https://github.com/galaxyproject/galaxy/commit/d509e8f6028259b8ff055cc67873f... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Additional code and style cleanup. Commit: a156f1db1e28efad2a159caef0951261c50ad41f https://github.com/galaxyproject/galaxy/commit/a156f1db1e28efad2a159caef0951... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M .gitignore M .travis.yml M Makefile M lib/galaxy/tours/__init__.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/shed_util_common.py M templates/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: d51c7d2fd4afc9cb31ae34cd0274f03ee2d6a643 https://github.com/galaxyproject/galaxy/commit/d51c7d2fd4afc9cb31ae34cd0274f... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/list-collection-creator.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/history/history-view-edit.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/upload.less M config/galaxy.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.xml R config/plugins/interactive_environments/ipython/static/js/ipython.js R config/plugins/interactive_environments/ipython/templates/ipython.mako R config/plugins/interactive_environments/ipython/templates/notebook.ipynb M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml A config/plugins/tours/core.scratchbook.yaml M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/extract.py M lib/pulsar/client/amqp_exchange.py M requirements.txt M run.sh M run_tests.sh M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/mvc/collection/list-collection-creator.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/history/history-view-edit.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-settings.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/layout/menu.js M static/scripts/mvc/collection/list-collection-creator.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/history/history-view-edit.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako M test/api/helpers.py M test/api/test_tools.py M test/casperjs/casperjs_runner.py M test/casperjs/modules/user.js M test/functional/test_toolbox.py M test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: e2776530699e2ba4a6a4780dead63300a7575af3 https://github.com/galaxyproject/galaxy/commit/e2776530699e2ba4a6a4780dead63... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Enable selecting a tool panel section on a per-tool basis. Commit: 2483f7673a20997cf8ac764bf06e79f253f9b61c https://github.com/galaxyproject/galaxy/commit/2483f7673a20997cf8ac764bf06e7... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Do not attempt to update the tool panel section if it's not separately mapped. Commit: df722f9c7e192fcfe4fa693d5886d38ac4c3a6bc https://github.com/galaxyproject/galaxy/commit/df722f9c7e192fcfe4fa693d5886d... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample R config/plugins/visualizations/charts/static/build-app.js M lib/galaxy/config.py M lib/galaxy/web/framework/webapp.py M scripts/binary_compatibility.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-list.js.map 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/form/form-view.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/style/blue/base.css A test/qunit/tests/ui_tests.html A test/qunit/tests/ui_tests.js M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 6f72b05bd59708eb3b28b17a165f392f6640bf5a https://github.com/galaxyproject/galaxy/commit/6f72b05bd59708eb3b28b17a165f3... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/web/form_builder.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Some tweaks to the repository preview UI. Commit: a3a178a0d332626616e1854ad7829733ecca00e2 https://github.com/galaxyproject/galaxy/commit/a3a178a0d332626616e1854ad7829... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M 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client/grunt-tasks/style.js R client/grunt-tasks/templates.js A client/grunt-tasks/webpack.js M client/package.json M client/webpack.config.js M config/plugins/visualizations/scatterplot/Gruntfile.js M config/plugins/visualizations/scatterplot/package.json R config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/root.py R static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/dataset/states.js.map M static/maps/mvc/history/copy-dialog.js.map M 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static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/onload.js R static/scripts/templates/compiled/panel_section.js R static/scripts/templates/compiled/tool_form.js R static/scripts/templates/compiled/tool_link.js R static/scripts/templates/compiled/tool_search.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/show_params.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/docker/base/run_test_wrapper.sh A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 18bc2f39a3a71d4463f211ad4388eb275cff9f19 https://github.com/galaxyproject/galaxy/commit/18bc2f39a3a71d4463f211ad4388e... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/util/metadata_util.py M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Display repository dependencies. Commit: e6247d415c6c5af024e649a09a4d0475cf0ee1da https://github.com/galaxyproject/galaxy/commit/e6247d415c6c5af024e649a09a4d0... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/tour.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/interval.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/special_tools.py M lib/galaxy/webapps/galaxy/controllers/user.py M scripts/bootstrap_history.py M scripts/common_startup.sh R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css M test/api/test_workflows.py M test/api/workflows_format_2/converter.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 3d14626aeb276ecdd9b3f873ffae15d74f6a6b00 https://github.com/galaxyproject/galaxy/commit/3d14626aeb276ecdd9b3f873ffae1... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- Fix some travis errors. Commit: 8d2e17e6d7e276fb3d36f6d49429660d69b031f9 https://github.com/galaxyproject/galaxy/commit/8d2e17e6d7e276fb3d36f6d494296... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/tool_shed/util/metadata_util.py Log Message: ----------- Fix more travis errors. Commit: 5937e17c1ab40673904f1914211a6ba02c1f081d https://github.com/galaxyproject/galaxy/commit/5937e17c1ab40673904f1914211a6... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/tool_shed/util/metadata_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Code cleanup, fixing even more travis errors. Commit: 210d6e6b8e338a246237fde2bb6818b7d08bf065 https://github.com/galaxyproject/galaxy/commit/210d6e6b8e338a246237fde2bb681... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Minor cosmetic cleanup. Commit: aeba386436c3b6741fc3e610a239800149f7bb14 https://github.com/galaxyproject/galaxy/commit/aeba386436c3b6741fc3e610a2398... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: eff4462781c5b8c6c5c776abfee6ab2e3bd27c31 https://github.com/galaxyproject/galaxy/commit/eff4462781c5b8c6c5c776abfee6a... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Fix installation of selected repository. Commit: 02c15cbd2530989d454ebaedd3fb595332ac1fc5 https://github.com/galaxyproject/galaxy/commit/02c15cbd2530989d454ebaedd3fb5... Author: Dave B <dave@bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Remove unused methods and parameters. Commit: b9f9be49559635aec2b7a0690e9c3c58dc77da28 https://github.com/galaxyproject/galaxy/commit/b9f9be49559635aec2b7a0690e9c3... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: A .ci/first_startup.sh M .ci/flake8_blacklist.txt M .travis.yml M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.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-section.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako M config/tool_conf.xml.sample M doc/source/admin/framework_dependencies.rst M doc/source/project/organization.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/none_like.py A lib/galaxy/util/ucsc.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/workflow_util.py M scripts/binary_compatibility.py M scripts/common_startup.sh R scripts/set_metadata.py R set_metadata.sh M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.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-section.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/upload/default/default-row.js.map M 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M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/onload.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/manage_repository.mako M templates/show_params.mako M templates/user/info.mako M templates/user/username.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test-data/3.bam M test/api/test_tools.py M test/base/twilltestcase.py M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/masthead_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M 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tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/linkToDavid.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py R tools/plotting/plot_filter.py R tools/plotting/plotter.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml M tools/stats/aggregate_scores_in_intervals.py R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Resolve merge conflict caused by other merge. Commit: 590115172fe6951ae1c5ac907b0ccc6143d680b2 https://github.com/galaxyproject/galaxy/commit/590115172fe6951ae1c5ac907b0cc... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/style/less/library.less M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-dataset-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: ed5894607dbe1d184d20135a1aa7ba5f9a362c23 https://github.com/galaxyproject/galaxy/commit/ed5894607dbe1d184d20135a1aa7b... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Remove duplicate method definition. Commit: 90d552b05f4727be124fae49767d3f4393e71fd0 https://github.com/galaxyproject/galaxy/commit/90d552b05f4727be124fae49767d3... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/util/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.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/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/tool_util.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge with dev branch. Commit: 7c64277299f576fe84dc1eda86771dc69968fd03 https://github.com/galaxyproject/galaxy/commit/7c64277299f576fe84dc1eda86771... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Somehow the resolution of the merge conflict didn't get committed. Commit: 9f239a011c2aee197a6539799ef568d65991426b https://github.com/galaxyproject/galaxy/commit/9f239a011c2aee197a6539799ef56... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove unused import. Commit: 5d1e86cfb21675b85248a9e58f3bfd3998643fe5 https://github.com/galaxyproject/galaxy/commit/5d1e86cfb21675b85248a9e58f3bf... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako Log Message: ----------- Add simple search functionality. Commit: dc7f048c4044bcb36582559526c15314461f608d https://github.com/galaxyproject/galaxy/commit/dc7f048c4044bcb36582559526c15... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 63d61b11f7bbd16f06bdcf770b987d798caa1680 https://github.com/galaxyproject/galaxy/commit/63d61b11f7bbd16f06bdcf770b987... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Do not load recursive metadata in the category browser. Commit: 6b5e1af81807d7d20942767cd3ebbe541379820b https://github.com/galaxyproject/galaxy/commit/6b5e1af81807d7d20942767cd3ebb... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M config/datatypes_conf.xml.sample M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py 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/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 7df463cdd88776a533aa06d9ae96f04e9bf0d58b https://github.com/galaxyproject/galaxy/commit/7df463cdd88776a533aa06d9ae96f... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Escape values of extra attributes for select fields. Commit: ad101ded626ee44b24d71884fb6fd257c58f1837 https://github.com/galaxyproject/galaxy/commit/ad101ded626ee44b24d71884fb6fd... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Apply modified version of fix from #1798. Commit: 4e3ad3c9845c8ee0546fbaaeb4a70b820ecece5b https://github.com/galaxyproject/galaxy/commit/4e3ad3c9845c8ee0546fbaaeb4a70... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- offer TS searching while browsing a category fix few usability issues Commit: 1b78b86a5ad64a8e91d2309d545a1a6b7ea33503 https://github.com/galaxyproject/galaxy/commit/1b78b86a5ad64a8e91d2309d545a1... Author: Dave B <dave@bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Merge pull request #3 from martenson/decouple-polish offer TS searching while browsing a category Commit: 3a5584ab1497d16a5c130641515b798a2c7794f5 https://github.com/galaxyproject/galaxy/commit/3a5584ab1497d16a5c130641515b7... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/grunt-tasks/style.js M client/package.json M config/galaxy.ini.sample M create_db.sh M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M manage_db.sh M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.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/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/empty_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml A test/functional/tools/validation_empty_dataset.xml M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_render.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: f44c3ae85ec195d6f59fa8eaf407d56bac4836a6 https://github.com/galaxyproject/galaxy/commit/f44c3ae85ec195d6f59fa8eaf407d... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Update javascript with Carl's suggestions. Commit: 2a91835da47badd9d2b32cbba0c308aa8907901e https://github.com/galaxyproject/galaxy/commit/2a91835da47badd9d2b32cbba0c30... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Do not display the valid tools section if there are none. Commit: 16b179f8a11ca81cc78498d2039ca088b00c0a95 https://github.com/galaxyproject/galaxy/commit/16b179f8a11ca81cc78498d2039ca... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/onload.js M config/tool_conf.xml.main M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M manage_tools.sh M run_reports.sh M run_tool_shed.sh M scripts/check_python.py M scripts/functional_tests.py M scripts/transfer.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/onload.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/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tours.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/onload.js M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: b8fc58523b7a1f324df8572a0293ae27dcfd08b4 https://github.com/galaxyproject/galaxy/commit/b8fc58523b7a1f324df8572a0293a... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: be2c51d882e0c5cab01bef1f500a61b7d48704cb https://github.com/galaxyproject/galaxy/commit/be2c51d882e0c5cab01bef1f500a6... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Return tools in metadata when repository has no dependencies. Commit: f60edb952a33ce05538fd10018d59c51dc5f656a https://github.com/galaxyproject/galaxy/commit/f60edb952a33ce05538fd10018d59... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M run_tool_shed.sh M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Show tool panel selector only when needed. Add the virtualenv to run_tool_shed.sh Commit: 96ca49b7d054b413fa2d939e9dcae470933f441e https://github.com/galaxyproject/galaxy/commit/96ca49b7d054b413fa2d939e9dcae... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init M doc/source/admin/framework_dependencies.rst M lib/galaxy/app.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/modules.py M lib/tool_shed/tool_shed_registry.py M run.sh M static/maps/layout/menu.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/display.mako M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: ef960a62f788c432b7891fbbf1f8762dfd3dc9e7 https://github.com/galaxyproject/galaxy/commit/ef960a62f788c432b7891fbbf1f87... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less 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lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/__init__.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/summarize_timings.py M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M 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static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M static/style/blue/library.css M templates/base/base_panels.mako M templates/webapps/galaxy/library/common/library_info.mako A test/base/driver_util.py M test/base/twilltestcase.py R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py M test/functional/test_toolbox.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py M test/functional/tools/collection_creates_list.xml A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py M test/qunit/test-app.js A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/test_lazy_process.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 3ad68fd68eb023e0a59d55e2489e896b6ce7aad7 https://github.com/galaxyproject/galaxy/commit/3ad68fd68eb023e0a59d55e2489e8... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M run_tool_shed.sh A templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/toolsheds.mako Log Message: ----------- Merge pull request #1392 from davebx/toolshed_decouple Use the API to install repositories instead of loading the toolshed in an iframe. Compare: https://github.com/galaxyproject/galaxy/compare/565f11f142de...3ad68fd68eb0