- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 013a0c: This fixes display of the tour index names -- prev...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 013a0cbc5570341f9a47be7ac39feecb9ec86e33 https://github.com/galaxyproject/galaxy/commit/013a0cbc5570341f9a47be7ac39f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- This fixes display of the tour index names -- previously unnoticed since the id was displaying fine as the fallback. Commit: 3c99c546070c33498dce6ed4d7c592eb059ef748 https://github.com/galaxyproject/galaxy/commit/3c99c546070c33498dce6ed4d7c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Merge pull request #5900 from dannon/fix_tour_index_names This fixes display of the tour index names -- previously unnoticed since Compare: https://github.com/galaxyproject/galaxy/compare/04ad5cf47dd8...3c99c546070c

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[galaxyproject/galaxy] 3302b4: remove deprecated feature, deprecate method, link ...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3302b46775cdc76976a4bdc36353e014c6d5edbd https://github.com/galaxyproject/galaxy/commit/3302b46775cdc76976a4bdc36353… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- remove deprecated feature, deprecate method, link to preferred implementation Commit: 04ad5cf47dd8af5763af2b30465beeaf07692d49 https://github.com/galaxyproject/galaxy/commit/04ad5cf47dd8af5763af2b30465b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #5887 from martenson/remove-intid remove deprecated feature, deprecate method, link to preferred impl. Compare: https://github.com/galaxyproject/galaxy/compare/2829a1f1646b...04ad5cf47dd8

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[galaxyproject/galaxy] 8261a2: Make the startup scripts play just as nicely with ...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8261a2398a7981e77be056bae0e3c15f3a097a85 https://github.com/galaxyproject/galaxy/commit/8261a2398a7981e77be056bae0e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M create_db.sh M doc/source/admin/framework_dependencies.rst M extract_dataset_parts.sh M manage_db.sh M run_tests.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh Log Message: ----------- Make the startup scripts play just as nicely with Conda as they do with virtualenv. Commit: a88e19064a38415d867f4c118dd6938d8e368632 https://github.com/galaxyproject/galaxy/commit/a88e19064a38415d867f4c118dd6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M config/galaxy.yml.sample M scripts/get_uwsgi_args.py Log Message: ----------- Don't set uWSGI's virtualenv option when running from Conda Commit: b3eff87a1ba0ec0f07c69045f2b279cab8476a7b https://github.com/galaxyproject/galaxy/commit/b3eff87a1ba0ec0f07c69045f2b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh Log Message: ----------- Clean up and useability enhancements Commit: c5262e8971679bd431cb0238391f0ec7d5ba087e https://github.com/galaxyproject/galaxy/commit/c5262e8971679bd431cb0238391f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Look for both `base` and `root` conda envs Commit: 2829a1f1646b2ba85faf986b56799daccafb1060 https://github.com/galaxyproject/galaxy/commit/2829a1f1646b2ba85faf986b5679… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/galaxy.yml.sample M create_db.sh M doc/source/admin/framework_dependencies.rst M extract_dataset_parts.sh M lib/galaxy/dependencies/conda-file.sh M manage_db.sh M run_tests.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #5854 from natefoo/run-scripts-conda Improve startup interoperability with Conda Compare: https://github.com/galaxyproject/galaxy/compare/65d4aff437d0...2829a1f1646b

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[galaxyproject/galaxy] 7d7322: add link that explains quota management to quota i...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d73220c539f5803e5663c5d65218316a03bc375 https://github.com/galaxyproject/galaxy/commit/7d73220c539f5803e5663c5d6521… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js Log Message: ----------- add link that explains quota management to quota indicator Commit: 65d4aff437d03f5c1dae9f9fe4646426a1fe9e35 https://github.com/galaxyproject/galaxy/commit/65d4aff437d03f5c1dae9f9fe464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #5811 from martenson/quota-meter add link that explains quota management to quota indicator Compare: https://github.com/galaxyproject/galaxy/compare/1c433d7d041d...65d4aff437d0

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[galaxyproject/galaxy] 8833d1: add security announcement to the rn
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8833d1a8a49d7b6d4a9c849b0335d3260564b351 https://github.com/galaxyproject/galaxy/commit/8833d1a8a49d7b6d4a9c849b0335… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn Commit: e89290c33031d89365aa3ef3b6e4720d68390119 https://github.com/galaxyproject/galaxy/commit/e89290c33031d89365aa3ef3b6e4… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2018-03-18 (Sun, 18 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.rds A lib/galaxy/datatypes/test/test.sce A lib/galaxy/datatypes/test/test_error.rds Log Message: ----------- sniffers, test cases Commit: b0effc107af2bba7c0dfefbd7c5861a1597c9099 https://github.com/galaxyproject/galaxy/commit/b0effc107af2bba7c0dfefbd7c58… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix to class test Commit: ea993a8912b870de7780c68c003c5433badb469d https://github.com/galaxyproject/galaxy/commit/ea993a8912b870de7780c68c003c… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- rpy2 library for loading/testing R objects Commit: 1d2a0117199bc902896ca97cf5e5aa5b9b20b132 https://github.com/galaxyproject/galaxy/commit/1d2a0117199bc902896ca97cf5e5… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- linting fix Commit: a280211ca65ca88b3a7cd92d0d3c1d15b874d462 https://github.com/galaxyproject/galaxy/commit/a280211ca65ca88b3a7cd92d0d3c… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/galaxy into singlecellobject Commit: d31c05a67d40daa12fc3a2dbcdea35d1971d0e3d https://github.com/galaxyproject/galaxy/commit/d31c05a67d40daa12fc3a2dbcdea… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- removed sniffers, removed pinned, removed classes Commit: 695ed3ac68d9f690f649b7e57c1bdf4625cc20fe https://github.com/galaxyproject/galaxy/commit/695ed3ac68d9f690f649b7e57c1b… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: R lib/galaxy/datatypes/test/test.rds R lib/galaxy/datatypes/test/test.sce R lib/galaxy/datatypes/test/test_error.rds Log Message: ----------- removed test data Commit: d5cb6f636b19128ce64934fbae91a82e21d4c668 https://github.com/galaxyproject/galaxy/commit/d5cb6f636b19128ce64934fbae91… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2018-04-14 (Sat, 14 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- renamed type Commit: 8baea1f7c7551920bc2318b34247a29462a4e035 https://github.com/galaxyproject/galaxy/commit/8baea1f7c7551920bc2318b34247… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.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/legacy/grid/grid-view.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/collection-model.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-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.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/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.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-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-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js A client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js R client/galaxy/style/less/autocomplete_tagging.less R client/galaxy/style/less/base.less R client/galaxy/style/less/bootstrap.less R client/galaxy/style/less/bootstrap/alerts.less R client/galaxy/style/less/bootstrap/badges.less R client/galaxy/style/less/bootstrap/bootstrap.less R client/galaxy/style/less/bootstrap/breadcrumbs.less R client/galaxy/style/less/bootstrap/button-groups.less R client/galaxy/style/less/bootstrap/buttons.less R client/galaxy/style/less/bootstrap/carousel.less R 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static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/sharing_base.mako M templates/user/login.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py A test/base/data/rules_dsl_spec.yml M test/base/populators.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into singlecellobject Commit: 1c433d7d041d50d6e4c5bd886a606ff3af588d9f https://github.com/galaxyproject/galaxy/commit/1c433d7d041d50d6e4c5bd886a60… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5716 from mtekman/singlecellobject Add datatype(s): RDS object and SingleCellExperiment class Compare: https://github.com/galaxyproject/galaxy/compare/fe4bff1fb9d8...1c433d7d041d

1 0

[galaxyproject/galaxy] 63f674: Add routes for workflow import view, apply consist...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63f674c26d371569a3aaf8887a53f97e8707f951 https://github.com/galaxyproject/galaxy/commit/63f674c26d371569a3aaf8887a53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add routes for workflow import view, apply consistent routes Commit: 962811b586e7e2cbf4213fbeff914aac0c66a755 https://github.com/galaxyproject/galaxy/commit/962811b586e7e2cbf4213fbeff91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: A client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Add vue component for workflow import form Commit: 20ce0e42d9ef5a26539de08e1749eb1617e2960a https://github.com/galaxyproject/galaxy/commit/20ce0e42d9ef5a26539de08e1749… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove legacy view Commit: e55f8c5f56fceae6d3ec2e53a019c43407b4dba3 https://github.com/galaxyproject/galaxy/commit/e55f8c5f56fceae6d3ec2e53a019… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add import workflow from file option to api endpoint Commit: f086080c65e98ed60794fae6e4f7e552d5c9c42c https://github.com/galaxyproject/galaxy/commit/f086080c65e98ed60794fae6e4f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused controller endpoint, and disabled legacy option Commit: 68af8c9e780417a4e34de1ca349b1e5ace7c8e58 https://github.com/galaxyproject/galaxy/commit/68af8c9e780417a4e34de1ca349b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unnecessary check Commit: 5173d6f222c684d132c05684aae3b6e0c47b6e0c https://github.com/galaxyproject/galaxy/commit/5173d6f222c684d132c05684aae3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore broken installed_repository_file option Commit: b6ee0a53ec5c116e2aacb4f9e8f47868ba76bb51 https://github.com/galaxyproject/galaxy/commit/b6ee0a53ec5c116e2aacb4f9e8f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unnecessary spacing and unused variable Commit: 8a51d02ce641184bdb9da51eb6017004cfdfd777 https://github.com/galaxyproject/galaxy/commit/8a51d02ce641184bdb9da51eb601… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix library usage, and parameter naming Fix file reading caller Avoid using bare except Fix file parameter name Add missing library Commit: e5a564ef17990ba4b7c6db6381ef8fb98cd5bab9 https://github.com/galaxyproject/galaxy/commit/e5a564ef17990ba4b7c6db6381ef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add additional checks for installed repository handler, open files using with-block Commit: 6a57ba8d28fb2f7c95850411118adb9e17c23c72 https://github.com/galaxyproject/galaxy/commit/6a57ba8d28fb2f7c95850411118a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Use archive_source and not url Commit: 51e32b6beaabe35fbd8a1cbaf38200d46ce33e3f https://github.com/galaxyproject/galaxy/commit/51e32b6beaabe35fbd8a1cbaf382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix error message Commit: 4c483a884a0948f86ca47e4b32494fc40e6764b8 https://github.com/galaxyproject/galaxy/commit/4c483a884a0948f86ca47e4b3249… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/components/WorkflowImport.vue M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Show warning if import was successful but has errors Commit: 12096d2a9fa4a7d177b419e0a7c7bbff9d1af982 https://github.com/galaxyproject/galaxy/commit/12096d2a9fa4a7d177b419e0a7c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix spacing in import block Commit: 3f34055e8ae3dccdaf8d235662b3e82591959bbd https://github.com/galaxyproject/galaxy/commit/3f34055e8ae3dccdaf8d235662b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Attempt to fix selenium tests Fix lint Commit: 368691624bc408bdad2383f04e6fb5c266e2ff4a https://github.com/galaxyproject/galaxy/commit/368691624bc408bdad2383f04e6f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'exact_version_handling' into workflow_import Commit: 3a3c796fcf154e94d910f24e6e40b59afa999265 https://github.com/galaxyproject/galaxy/commit/3a3c796fcf154e94d910f24e6e40… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix failing tests Commit: 8ba207de7199c66090f9526e451b8095751790d8 https://github.com/galaxyproject/galaxy/commit/8ba207de7199c66090f9526e451b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore error handling variation Commit: 2fa340842cca7b46da121743153f5d31afe16eea https://github.com/galaxyproject/galaxy/commit/2fa340842cca7b46da121743153f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove api flag check from workflow manager Commit: 8d5c1d08d8e3eb8a459343b2b4f4e4376407ea5d https://github.com/galaxyproject/galaxy/commit/8d5c1d08d8e3eb8a459343b2b4f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add source to workflow name Commit: 75c2c4f2494be66a459aece8e1707a6024e36e61 https://github.com/galaxyproject/galaxy/commit/75c2c4f2494be66a459aece8e170… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix import from myexperiment service Commit: 2cb4d52d4dbb1b3a74a5bcf01205cfa6cb3181f1 https://github.com/galaxyproject/galaxy/commit/2cb4d52d4dbb1b3a74a5bcf01205… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix default parameters for 3rd party workflow import controller Commit: fbd9d81409df888cd99c4d3f05875721b4505baf https://github.com/galaxyproject/galaxy/commit/fbd9d81409df888cd99c4d3f0587… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused variable Commit: ffe9c3bd294c55b4c4576dcc5187a3593d1bf9a1 https://github.com/galaxyproject/galaxy/commit/ffe9c3bd294c55b4c4576dcc5187… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused source identifier Commit: fe4bff1fb9d84c057b40f04a9285ca5ca4dfb5fc https://github.com/galaxyproject/galaxy/commit/fe4bff1fb9d84c057b40f04a9285… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #5804 from guerler/workflow_import Use vue and api to handle workflow imports Compare: https://github.com/galaxyproject/galaxy/compare/679083c935c1...fe4bff1fb9d8

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[galaxyproject/galaxy] fc546c: allow admins to set any role for library datasets ...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc546cb1abd2060eea159cc1198e09b55fbaaf41 https://github.com/galaxyproject/galaxy/commit/fc546cb1abd2060eea159cc1198e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- allow admins to set any role for library datasets permissions this bug led to a funny problem where admins couldn't add themselves Commit: 51c05d7a28926a1257fb0b9b82d16f0a5b9d7ab2 https://github.com/galaxyproject/galaxy/commit/51c05d7a28926a1257fb0b9b82d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- modify checks that will never be true Commit: 7f9fcf99e403194558f5eb7a3f5545ee25a91c65 https://github.com/galaxyproject/galaxy/commit/7f9fcf99e403194558f5eb7a3f55… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- refactor the lib dataset update permissions process to mirror the library's Commit: 679083c935c10013dc4a24f9f2a8ead77651c567 https://github.com/galaxyproject/galaxy/commit/679083c935c10013dc4a24f9f2a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #5899 from martenson/fix-admin-datalib-perms Fix admin datalib dataset perms Compare: https://github.com/galaxyproject/galaxy/compare/921fde4b8cdc...679083c935c1

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[galaxyproject/galaxy] bf4f43: Rough implentation of the DockerAPIInterface.
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf4f43d96a4cf3bdf090d82822a688677600e3f2 https://github.com/galaxyproject/galaxy/commit/bf4f43d96a4cf3bdf090d82822a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Rough implentation of the DockerAPIInterface. Commit: 2e9c25da28535c268467e9dc5dc982b067ed14bc https://github.com/galaxyproject/galaxy/commit/2e9c25da28535c268467e9dc5dc9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Create a general method for handling galaxy.containers param -> docker-py param mapping. Plus some cleanup. Commit: b7531593697175ad9c8f110e9943c9086c779ae4 https://github.com/galaxyproject/galaxy/commit/b7531593697175ad9c8f110e9943… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Corrections to Docker spec handling Commit: ac9fce9a3c5e6995bafa5fbac602c2b2a4ccb003 https://github.com/galaxyproject/galaxy/commit/ac9fce9a3c5e6995bafa5fbac602… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- WIP Docker Swarm API interface Commit: 0bba56d106dbeedfac2c67226a749bf6354df4e2 https://github.com/galaxyproject/galaxy/commit/0bba56d106dbeedfac2c67226a74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Docker API TLS support Commit: 26d265e0107143a62e7799ecf51ea85ac698696c https://github.com/galaxyproject/galaxy/commit/26d265e0107143a62e7799ecf51e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Docker service fixes Commit: c8ab4fae4db13b106dcd1dbc4f109cc66c305d8a https://github.com/galaxyproject/galaxy/commit/c8ab4fae4db13b106dcd1dbc4f10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Enable setting defaults for docker API data structures. Commit: 360e43095a5036c8cedd452a5809160780f361a8 https://github.com/galaxyproject/galaxy/commit/360e43095a5036c8cedd452a5809… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Docker swarm interface for the API Commit: 0e357ca73729f67f27a31b83a7df6c5c74c43c99 https://github.com/galaxyproject/galaxy/commit/0e357ca73729f67f27a31b83a7df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Lint fixes Commit: 2794a650f5cd885f684d79e5124e349ccdf09879 https://github.com/galaxyproject/galaxy/commit/2794a650f5cd885f684d79e5124e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Fixes for swarm manager. Commit: 806703a5e2ac679bcac496bb9acd36a9b248ce48 https://github.com/galaxyproject/galaxy/commit/806703a5e2ac679bcac496bb9acd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Move DockerVolume to containers lib model and fix bugs. Commit: 9cd589508d260a8e04191701aa86e98548e97def https://github.com/galaxyproject/galaxy/commit/9cd589508d260a8e04191701aa86… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/util/__init__.py Log Message: ----------- More detailed swarm manager state logging Commit: 605a156d618b352c0755af0b3e6e9e0922c126f8 https://github.com/galaxyproject/galaxy/commit/605a156d618b352c0755af0b3e6e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Attempt to handle "phantom" docker tasks Commit: 0d90235b1c5e6742bc65f270c5ac0e19b48ee1d0 https://github.com/galaxyproject/galaxy/commit/0d90235b1c5e6742bc65f270c5ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Fix lint/unit test errors Commit: 9de17e248feb2fa39e3a026727df75a5f42b7c59 https://github.com/galaxyproject/galaxy/commit/9de17e248feb2fa39e3a026727df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Add some error handling to the Docker API interface Commit: 507fed9e3c2e2ea6a7fc9938400c7642701bc3ad https://github.com/galaxyproject/galaxy/commit/507fed9e3c2e2ea6a7fc9938400c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Fix lint error Commit: 10e0314e8fe8d378fdeb97bfa0b3466e95e35f07 https://github.com/galaxyproject/galaxy/commit/10e0314e8fe8d378fdeb97bfa0b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/util/json.py Log Message: ----------- Move json format function to galaxy.util.json Commit: 8369d88295554639926ad5ddac445a20e449a0e4 https://github.com/galaxyproject/galaxy/commit/8369d88295554639926ad5ddac44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional docker dependency for containers interface Commit: 5537ce1fa748422a27aea062165095cfba07c754 https://github.com/galaxyproject/galaxy/commit/5537ce1fa748422a27aea0621650… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py Log Message: ----------- Handle the case where a node claims a task exists but the tasks/services API disagrees Commit: 559fb9df9ba0379b975aaa2b5df7ac963c18f037 https://github.com/galaxyproject/galaxy/commit/559fb9df9ba0379b975aaa2b5df7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Allow docker client callers to pass in a test function that the client wrapper will call on certain types of expected failures. If the function returns a truthy value, it is returned instead. This is useful for state-altering changes where the request may have succeeded but the response failed. Commit: 9db3d23eaca5ce7270a9480038acd52f52951298 https://github.com/galaxyproject/galaxy/commit/9db3d23eaca5ce7270a9480038ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py Log Message: ----------- Use consistent whitespace in containers lib classes Commit: c42d642233d962fc513c1039771acb00718d7348 https://github.com/galaxyproject/galaxy/commit/c42d642233d962fc513c1039771a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Containers: - Improve documentation of docker API param mapping - Improve sample containers config file - Fix constraints - A couple other minor bug/logging fixes Commit: b205956b3882a4b1dbc0529742ba8f5aafddafe5 https://github.com/galaxyproject/galaxy/commit/b205956b3882a4b1dbc0529742ba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Docker: Don't retry 4xx errors indefinitely. Possibly need to do this for more APIErrors. Commit: 9e2ada9a008addbfbcf1d764d80d216dca6978a0 https://github.com/galaxyproject/galaxy/commit/9e2ada9a008addbfbcf1d764d80d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Infinite loop retry is probably bad. This should help with surviving transient errors. Commit: ca7b3fd59355df39304d37972f46940e88f1a975 https://github.com/galaxyproject/galaxy/commit/ca7b3fd59355df39304d37972f46… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Fix tests due to missing name in mock module Commit: 91a25d0a08b969c9d6b7161fae6f34eff1c66f59 https://github.com/galaxyproject/galaxy/commit/91a25d0a08b969c9d6b7161fae6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker.py Log Message: ----------- Support manager failover for Docker Swarm mode Commit: 5127fd29570171f55d41e7458a5e2d7cec9a9837 https://github.com/galaxyproject/galaxy/commit/5127fd29570171f55d41e7458a5e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Swarm manager: log services that do not have tasks on any node. Commit: e651b34156a3af022bac250464d92ca6394c3d85 https://github.com/galaxyproject/galaxy/commit/e651b34156a3af022bac250464d9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py A scripts/docker_swarm_manager.py Log Message: ----------- Remove swarm manager from lib Commit: d3038f859a03ad4b29eb6143ea9d88f915cfaac2 https://github.com/galaxyproject/galaxy/commit/d3038f859a03ad4b29eb6143ea9d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Load containers interface on app load if enable_beta_containers_interface is set. Commit: 860aaf8241759f915501dba221a49b80a18a4e3e https://github.com/galaxyproject/galaxy/commit/860aaf8241759f915501dba221a4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Fix docker interface failover by making the docker.APIClient wrapper use class vars, since we only ever want callers to use one APIClient. Commit: 564f7ecafe61d0c890cb9cde58640ce221935067 https://github.com/galaxyproject/galaxy/commit/564f7ecafe61d0c890cb9cde5864… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M scripts/docker_swarm_manager.py Log Message: ----------- Make the swarm manager recover on uncaught exceptions. It should do a better job of catching them in the application, but this is good enough for the moment. Commit: feb3e9ddf039e56f972149e7338138fb662745b4 https://github.com/galaxyproject/galaxy/commit/feb3e9ddf039e56f972149e73381… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix lint error Commit: 921fde4b8cdce2ab32846ba473846f1388b0592a https://github.com/galaxyproject/galaxy/commit/921fde4b8cdce2ab32846ba47384… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/app.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/util/__init__.py M lib/galaxy/util/json.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py A scripts/docker_swarm_manager.py Log Message: ----------- Merge pull request #5861 from natefoo/containers-docker-lib Implement the API version of the Docker containers interface Compare: https://github.com/galaxyproject/galaxy/compare/881dc3601823...921fde4b8cdc

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[galaxyproject/infrastructure-playbook] dd951a: Block a specific pervasive spam message
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dd951a455bd8adada7a7d7246a33614239853ed5 https://github.com/galaxyproject/infrastructure-playbook/commit/dd951a455bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/galaxy/inventory M roles/postfix/templates/local.cf.j2 Log Message: ----------- Block a specific pervasive spam message

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[galaxyproject/usegalaxy-playbook] 2e8637: Replaced sbtas_se with btman
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2e8637f67c843a5c23eb0f98aaadaf7461c26396 https://github.com/galaxyproject/usegalaxy-playbook/commit/2e8637f67c843a5c… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Replaced sbtas_se with btman

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