Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ada33d06be9ab789a7aaee2d4366e25dbd98ce0 https://github.com/galaxyproject/galaxy/commit/4ada33d06be9ab789a7aaee2d4366... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: 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 Log Message: ----------- prevent TS from creating sessions for repo status checks this had to be done: - enable Routes middleware - redirect in the middleware before the request reaches the app - properly forward the contents of the query string - move the controller method to the API namespace and properly decorate - provide the ability to not hexlify the response (so we can dump it in future Galaxy release) I hope that this work will allow easier transition from controllers to APIs and also smoother deprecation of API endpoints. Commit: c311c4a3c82d7d114075c400fe638bb0ab0a4a6e https://github.com/galaxyproject/galaxy/commit/c311c4a3c82d7d114075c400fe638... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- reorder middleware imports, explicitly store and pass routes mapper Commit: 682a28de67c3f1ccd0900067e19299deac640cfe https://github.com/galaxyproject/galaxy/commit/682a28de67c3f1ccd0900067e1929... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- amke endpoint name more RESTful Commit: b41f500a9fb88c43dd8ed99178a101512db4d209 https://github.com/galaxyproject/galaxy/commit/b41f500a9fb88c43dd8ed99178a10... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' into sessionless_controller_using_redirect Commit: fb1703587b9170712aeafe09ab8068c7c981b47b https://github.com/galaxyproject/galaxy/commit/fb1703587b9170712aeafe09ab806... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Commit: 674f5989e4bf5abb1af8afe6477e6c2294ed7977 https://github.com/galaxyproject/galaxy/commit/674f5989e4bf5abb1af8afe6477e6... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py Log Message: ----------- make routes.middleware less chatty, and reorder import Commit: f957f80854411cbd29326805bf696338c0725ecb https://github.com/galaxyproject/galaxy/commit/f957f80854411cbd29326805bf696... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- be python3 compatible, thanks EagleEyes Commit: 4d5851ae715e5f7bec6d5013f06001f527219f13 https://github.com/galaxyproject/galaxy/commit/4d5851ae715e5f7bec6d5013f0600... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/repositories.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/tool_shed/api/common.py M setup.cfg M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.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/scratchbook.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js R static/style/blue/tool_menu.css M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Commit: 62ca1312d6dbc56795f34f646ed59fb01955ddb3 https://github.com/galaxyproject/galaxy/commit/62ca1312d6dbc56795f34f646ed59... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/shed_functional/functional/test_0310_hg_api_features.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Conflicts: lib/galaxy/webapps/tool_shed/buildapp.py Commit: 123ceeb34ac1858fcc333d332bb2ae4e671d6c72 https://github.com/galaxyproject/galaxy/commit/123ceeb34ac1858fcc333d332bb2a... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/first_startup.sh M Makefile M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample A doc/source/dev/build_a_job_runner.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/managers/datasets.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M run.sh M scripts/common_startup.sh M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.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/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/unit/tools/test_tool_deps.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Commit: 85aec3bc119b1e8f450c3eff2da1414c53447cca https://github.com/galaxyproject/galaxy/commit/85aec3bc119b1e8f450c3eff2da14... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/library.less M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/update_repository_manager.py M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Commit: 0dd74d164fc32b186ccca334a0e97c8ae1fae6fa https://github.com/galaxyproject/galaxy/commit/0dd74d164fc32b186ccca334a0e97... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- create own mapper for middleware redirects Commit: 3fd7ba3e8eb46caca843e85f9066cdf24f5d203d https://github.com/galaxyproject/galaxy/commit/3fd7ba3e8eb46caca843e85f9066c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- fix pep8 Commit: 000e7ea7c9a8c7e069f3ca92c548e38110905003 https://github.com/galaxyproject/galaxy/commit/000e7ea7c9a8c7e069f3ca92c548e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Merge pull request #2732 from martenson/sessionless_controller_using_redirect prevent TS from creating sessions for repo status checks Compare: https://github.com/galaxyproject/galaxy/compare/5cc3613ff555...000e7ea7c9a8