galaxy-commits June 2016

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[galaxyproject/ansible-galaxy] 72ea23: Fix "bar config variables" warning
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/bare_config_vars Home: https://github.com/galaxyproject/ansible-galaxy Commit: 72ea23849e69903615369b88e11b0e6e6a5d70d3 https://github.com/galaxyproject/ansible-galaxy/commit/72ea23849e6990361536… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M tasks/static_setup.yml Log Message: ----------- Fix "bar config variables" warning

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[galaxyproject/galaxy] d98c89: Move metadata-related methods from shed_util_commo...
by GitHub 07 Jun '16

07 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d98c8965eb3433b9dbf26e9aa96a26818f8fc0fb https://github.com/galaxyproject/galaxy/commit/d98c8965eb3433b9dbf26e9aa96a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Move metadata-related methods from shed_util_common to metadata_util. Commit: 03102e5565319b7a38993fae934f7a27337adbd0 https://github.com/galaxyproject/galaxy/commit/03102e5565319b7a38993fae934f… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/grids/util.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correct travis errors and missing imports. Commit: 64f6a8bc7d09b61e7337e18011a7f852cea5c978 https://github.com/galaxyproject/galaxy/commit/64f6a8bc7d09b61e7337e18011a7… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py Log Message: ----------- Update method call. Commit: abb6176a4e1356595d33284a769245e63ece24d0 https://github.com/galaxyproject/galaxy/commit/abb6176a4e1356595d33284a7692… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0000_basic_repository_features.py Log Message: ----------- Fix category/repositories API endpoint. Add test. Commit: d78fd5f20c75a77b96d0dd9d54c477ad5ca9fe54 https://github.com/galaxyproject/galaxy/commit/d78fd5f20c75a77b96d0dd9d54c4… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M test/shed_functional/functional/test_0000_basic_repository_features.py Log Message: ----------- Placate Travis. Commit: acaedd470be1fbc53ac6f4cf8e6e7c109c9bcb29 https://github.com/galaxyproject/galaxy/commit/acaedd470be1fbc53ac6f4cf8e6e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-05 (Thu, 05 May 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/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.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/grids/repository_grids.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M test/shed_functional/functional/test_1000_install_basic_repository.py Log Message: ----------- Refactor out repository-related methods from shed_util_common. Commit: e1d9ce920d3272614b335002ed7d54d6dba2ffc1 https://github.com/galaxyproject/galaxy/commit/e1d9ce920d3272614b335002ed7d… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/installed_repository_manager.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/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Move more methods from shed_util_common to repository_util. Commit: 0400c172d6ba7f0fff2bd5a597b814eadf70500a https://github.com/galaxyproject/galaxy/commit/0400c172d6ba7f0fff2bd5a597b8… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py 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 lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.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/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_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/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/admin/tool_shed_repository/repair_repository.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Move a lot more things from shed_util_common to repository_util. Commit: 26396ffc82762edcaadb76eac31b1bdec675ba40 https://github.com/galaxyproject/galaxy/commit/26396ffc82762edcaadb76eac31b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Fix travis errors. Commit: 9f9e008d9f63d6fa19255a52122c6cf6e374058c https://github.com/galaxyproject/galaxy/commit/9f9e008d9f63d6fa19255a52122c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py Log Message: ----------- Remove another unused import. Commit: ac2fb6d745522d68b063226b622f25893052e1df https://github.com/galaxyproject/galaxy/commit/ac2fb6d745522d68b063226b622f… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M CONTRIBUTORS.md M Makefile M README.rst M client/README.md M client/bower.json M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/collection/collection-li.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/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M 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lib/galaxy/visualization/plugins/resource_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/framework/base.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.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_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.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/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy_ext/metadata/set_metadata.py M lib/galaxy_utils/sequence/fastq.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/installed_repository_manager.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/env_file_builder.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/galaxy_install/utility_containers/__init__.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py A scripts/api/filter_failed_datasets_from_collection.py M scripts/bootstrap_history.py M static/maps/libs/backbone.js.map M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/collection/collection-li.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/dataset/dataset-model.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-parameters.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/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/utils/metrics-logger.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/libs/backbone.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/libs/underscore.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.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.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/utils/metrics-logger.js M static/style/blue/base.css M templates/sharing_base.mako M templates/show_params.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/composite_output_expected_log 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/functional/tools/composite_output.xml M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/fakeserver.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/form_tests.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/workflow_editor_tests.js M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/test_objectstore.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into refactor_suc Commit: 8eb4f90be0e49b2ceda230a68ff3a888aaad1e9d https://github.com/galaxyproject/galaxy/commit/8eb4f90be0e49b2ceda230a68ff3… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Remove merge conflict aftereffects. Commit: 964779373e82b4096ffd4fe34acf9b9ce7161400 https://github.com/galaxyproject/galaxy/commit/964779373e82b4096ffd4fe34acf… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix another incorrectly resolved merge conflict. Commit: 9ee0d880db830c6a59ed9e9efffc2fce9aaf90c6 https://github.com/galaxyproject/galaxy/commit/9ee0d880db830c6a59ed9e9efffc… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Fix missing import and unused import. Commit: 172a4778c3a5fb54f8eec91a071b8f0a43bd2c3a https://github.com/galaxyproject/galaxy/commit/172a4778c3a5fb54f8eec91a071b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M test/shed_functional/functional/test_1000_install_basic_repository.py Log Message: ----------- Create categories in the right order. Commit: c0b5a2840bc954b199bb4cf0db4dafc81116df46 https://github.com/galaxyproject/galaxy/commit/c0b5a2840bc954b199bb4cf0db4d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/web/base/controllers/admin.py 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/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.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/metadata/installed_repository_metadata_manager.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/env_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/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/admin/tool_shed_repository/repair_repository.mako M templates/webapps/tool_shed/repository/common.mako M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_1000_install_basic_repository.py Log Message: ----------- Merge pull request #2269 from davebx/refactor_suc Move specific methods from shed_util_common.py to specific_util.py Compare: https://github.com/galaxyproject/galaxy/compare/e2f219335532...c0b5a2840bc9

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[galaxyproject/galaxy] edca79: Do not encode dict items that start with 'metadata...
by GitHub 07 Jun '16

07 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: edca79a0cf4d0e6afceb0f3b3894b6b3a169bd53 https://github.com/galaxyproject/galaxy/commit/edca79a0cf4d0e6afceb0f3b3894… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Do not encode dict items that start with 'metadata_' in return value of api/tools/create. Resolves #2423, #2137, and https://github.com/galaxyproject/tools-iuc/pull/770. However, this whole act of encoding by key.endswith('_id') is very messy. Commit: 42739c88c80d10742add92f2e3978ed65a295188 https://github.com/galaxyproject/galaxy/commit/42739c88c80d10742add92f2e397… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test for failing handling of BIOM1 metadata. Commit: 10a3f23de2f8d728780b7c1615e7d4c9afeaeeb2 https://github.com/galaxyproject/galaxy/commit/10a3f23de2f8d728780b7c1615e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2459 from blankenberg/metadata-id-fix [16.04] Do not encode dict items that start with 'metadata_' in return value of api/tools/create. Compare: https://github.com/galaxyproject/galaxy/compare/37a491599257...10a3f23de2f8

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[galaxyproject/infrastructure-playbook] 21ef33: Update nginx and common roles
by GitHub 07 Jun '16

07 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 21ef339f9467246cdcfef53ea3d363ba767db795 https://github.com/galaxyproject/infrastructure-playbook/commit/21ef339f946… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M common_roles M roles/galaxyprojectdotorg.nginx/README.md M roles/galaxyprojectdotorg.nginx/defaults/main.yml M roles/galaxyprojectdotorg.nginx/handlers/main.yml M roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info M roles/galaxyprojectdotorg.nginx/meta/main.yml M roles/galaxyprojectdotorg.nginx/tasks/apt.yml R roles/galaxyprojectdotorg.nginx/tasks/epel.yml M roles/galaxyprojectdotorg.nginx/tasks/main.yml A roles/galaxyprojectdotorg.nginx/tasks/pkgin.yml A roles/galaxyprojectdotorg.nginx/tasks/yum.yml A roles/galaxyprojectdotorg.nginx/templates/epel-nginx.conf.j2 A roles/galaxyprojectdotorg.nginx/templates/pkgin-nginx.conf.j2 A roles/galaxyprojectdotorg.nginx/templates/supervisord.conf.j2 A roles/galaxyprojectdotorg.nginx/vars/pkgin.yml Log Message: ----------- Update nginx and common roles Commit: c72d9b100b10740a4028a9a672085a0dbf395c63 https://github.com/galaxyproject/infrastructure-playbook/commit/c72d9b100b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M galaxyenv/host_vars/orval.galaxyproject.org.yml A galaxyenv/templates/nginx/bioarchive.j2 A galaxyenv/templates/nginx/depot.j2 A galaxyenv/templates/nginx/images.j2 A galaxyenv/templates/nginx/orval.j2 A galaxyenv/templates/nginx/sample-data.j2 A galaxyenv/templates/nginx/screencast.j2 A galaxyenv/templates/nginx/snpeff-data.j2 Log Message: ----------- Orval nginx stuff Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/6b30c2af50…

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[galaxyproject/galaxy] b97c79: Filter missing inputs when processing data
by GitHub 07 Jun '16

07 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: b97c7964457010318b4639e57ca01fd6185269f2 https://github.com/galaxyproject/galaxy/commit/b97c7964457010318b4639e57ca0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Filter missing inputs when processing data Commit: 37a491599257c4045ad9e45ae53d12b9d97be418 https://github.com/galaxyproject/galaxy/commit/37a491599257c4045ad9e45ae53d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2458 from guerler/fix_process_data [16.04] Filter missing inputs when processing data Compare: https://github.com/galaxyproject/galaxy/compare/58f3f5c7dd4c...37a491599257

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[galaxyproject/usegalaxy-playbook] 6aaca4: Updated slide rotation - RepeatExplorer replaced w...
by GitHub 06 Jun '16

06 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6aaca420ef70315fc1bb5b2c333ea7c1c0e7dc09 https://github.com/galaxyproject/usegalaxy-playbook/commit/6aaca420ef70315f… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: A files/galaxy/common/static/welcome_img/ErasmusGalaxy.png A files/galaxy/common/static/welcome_img/GCC2016CUBloominton.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation - RepeatExplorer replaced with ErasmusMC, and GCC slide update.

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[galaxyproject/usegalaxy-playbook] 874057: Changes for updating Main in CVMFS
by GitHub 06 Jun '16

06 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 87405741c28d32c3f7e81fa309dfe7b3d7cde564 https://github.com/galaxyproject/usegalaxy-playbook/commit/87405741c28d32c3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M production/inventory Log Message: ----------- Changes for updating Main in CVMFS Commit: 078d41f74dbb22fc1aedb98f2e34e15cdd7e0f21 https://github.com/galaxyproject/usegalaxy-playbook/commit/078d41f74dbb22fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: A production/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/bdda45d00af9...…

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[galaxyproject/usegalaxy-playbook] bdda45: Missed a play for the no-update tag
by GitHub 06 Jun '16

06 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bdda45d00af93d4bba0ad88874a6feef0f784867 https://github.com/galaxyproject/usegalaxy-playbook/commit/bdda45d00af93d4b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M galaxy.yml Log Message: ----------- Missed a play for the no-update tag

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[galaxyproject/usegalaxy-playbook] 076284: Add a no-update tag so failures can be retried aft...
by GitHub 06 Jun '16

06 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 076284df7df813cccf0f9478f5d48abcbd2eccc0 https://github.com/galaxyproject/usegalaxy-playbook/commit/076284df7df813cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M galaxy.yml Log Message: ----------- Add a no-update tag so failures can be retried after the stratum 0 has been updated.

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[galaxyproject/usegalaxy-playbook] 38e681: Update Test
by GitHub 06 Jun '16

06 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 38e68197257a31dd2e67e129ea06bec4e902c8e7 https://github.com/galaxyproject/usegalaxy-playbook/commit/38e68197257a31dd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test Commit: 2a3a6cd8010f0fffab98dd9d21e2de22789cf818 https://github.com/galaxyproject/usegalaxy-playbook/commit/2a3a6cd8010f0fff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M galaxy.yml M stage/group_vars/all.yml Log Message: ----------- Do those things I told myself to do on Friday Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ade5239f76c5...…

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