November 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 734c39: added global monitor for window.Galaxy
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 734c39d4f58cfc96c637d9121b88b14398a9c4b2 https://github.com/galaxyproject/galaxy/commit/734c39d4f58cfc96c637d9121b88… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M .gitignore A client/galaxy/jsconfig.json M client/galaxy/scripts/galaxy.js A client/galaxy/scripts/galaxy.monitor.js R client/galaxy/scripts/onload.js A client/galaxy/scripts/onload/index.js A client/galaxy/scripts/onload/loadConfig.js A client/galaxy/scripts/utils/installMonitor.js A client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/serverPath.js M client/webpack.config.js M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- added global monitor for window.Galaxy Commit: 0cdf78956f29abf53e9e2233a6545dc1fba71f5c https://github.com/galaxyproject/galaxy/commit/0cdf78956f29abf53e9e2233a654… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M client/galaxy/scripts/onload/loadConfig.js M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Corrected instructions, removed config function that is not used yet. Commit: 712aa6cb8742674777c4bc0ee36df9f361bfbeab https://github.com/galaxyproject/galaxy/commit/712aa6cb8742674777c4bc0ee36d… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Removed debugger statements Commit: 4c13d204c454203b17194c6174177de642c0a2ae https://github.com/galaxyproject/galaxy/commit/4c13d204c454203b17194c617417… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Corrected monitor value storage initialization Commit: ef5e01da82e532a819a343457ea31bf0cb16baa7 https://github.com/galaxyproject/galaxy/commit/ef5e01da82e532a819a343457ea3… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- White space awesomeness Commit: 3cf9dd85f4c20801807d0aef74b4628c26ca3f97 https://github.com/galaxyproject/galaxy/commit/3cf9dd85f4c20801807d0aef74b4… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M client/.babelrc M client/galaxy/scripts/polyfills.js M client/package.json M client/yarn.lock Log Message: ----------- Updating babel for proxy support with karma Commit: 04242c75034637f064173eca0c1e2f415343fe93 https://github.com/galaxyproject/galaxy/commit/04242c75034637f064173eca0c1e… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Renamed selenium utility function Commit: 66a7db94053763bfb1cc23ba5df1e537f0177219 https://github.com/galaxyproject/galaxy/commit/66a7db94053763bfb1cc23ba5df1… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M .gitignore M client/.babelrc R client/GruntFile.js A 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static/style/blue/warn_message_icon.png R static/style/blue/warn_small.png R static/style/blue/workflow_circle_drag.png R static/style/blue/workflow_circle_green.png R static/style/blue/workflow_circle_open.png R static/style/shared_images/data_running.gif R static/style/shared_images/error_large.png R static/style/shared_images/error_small.png R static/style/shared_images/info_large.png R static/style/shared_images/info_small.png R static/style/shared_images/ok_large.png R static/style/shared_images/ok_small.png R static/style/shared_images/wait_large.png R static/style/shared_images/wait_small.png R static/style/shared_images/warn_large.png R static/style/shared_images/warn_small.png M static/welcome.html.sample M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/repository/browse_repository.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako M test/base/driver_util.py M test/base/populators.py A test/integration/test_datatype_upload.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py Log Message: ----------- Merged dev Commit: 294cfbf6716dbac554da36f0c410276669c1dce9 https://github.com/galaxyproject/galaxy/commit/294cfbf6716dbac554da36f0c410… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Updated provide monitored proxy for Galaxy references Commit: d7d5e04f9276ba3c1cd9ef2c1a09ede1fc9f5ed0 https://github.com/galaxyproject/galaxy/commit/d7d5e04f9276ba3c1cd9ef2c1a09… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Changed toggle to installation toggle instead of logging toggle Commit: 5ffd438ebfef26c55b9b11da2f24abd6c2772b43 https://github.com/galaxyproject/galaxy/commit/5ffd438ebfef26c55b9b11da2f24… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/utils/installMonitor.js Log Message: ----------- Updated install console functions and instructions Commit: 11375a5692fe541e3df257f3ce2e36cd6f39a1f8 https://github.com/galaxyproject/galaxy/commit/11375a5692fe541e3df257f3ce2e… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/sample.test.js A client/galaxy/scripts/unitTestBundle.js M client/galaxy/style/scss/ui.scss R client/karma.config.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json M client/yarn.lock M config/datatypes_conf.xml.sample M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/test/diamond.rma6 M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/tool_sheds.mako M templates/webapps/galaxy/admin/view_display_applications.mako M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into window_monitor Commit: 38e9225aff0997efe3b023cf28ec869faa09d161 https://github.com/galaxyproject/galaxy/commit/38e9225aff0997efe3b023cf28ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/jsconfig.json M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/sample.test.js M client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/mock.js Log Message: ----------- Client format Commit: 4405d15fea61b2610045ecfe4a6a1a0922142df8 https://github.com/galaxyproject/galaxy/commit/4405d15fea61b2610045ecfe4a6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M .gitignore A client/galaxy/jsconfig.json M client/galaxy/scripts/galaxy.js A client/galaxy/scripts/galaxy.monitor.js R client/galaxy/scripts/onload.js A client/galaxy/scripts/onload/index.js A client/galaxy/scripts/onload/loadConfig.js M client/galaxy/scripts/sample.test.js M client/galaxy/scripts/unitTestBundle.js A client/galaxy/scripts/utils/installMonitor.js A client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/serverPath.js M client/webpack.config.js M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge branch 'window_monitor' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e9f269393346...4405d15fea61 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/ansible-galaxy] afc7c3: Fix syntax error in sample code (under Requirement...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: afc7c33953fb4de4ab606997977bb7141150e08b https://github.com/galaxyproject/ansible-galaxy/commit/afc7c33953fb4de4ab60… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M README.md Log Message: ----------- Fix syntax error in sample code (under Requirements) Assignment vs. equality ('=' vs. '=='), see Jinja syntax. Commit: 1043f1c3931e185a2ba2b1ec367560885a1a7586 https://github.com/galaxyproject/ansible-galaxy/commit/1043f1c3931e185a2ba2… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M README.md Log Message: ----------- Merge pull request #40 from ic4f/master Fix syntax error in sample code (under Requirements) Compare: https://github.com/galaxyproject/ansible-galaxy/compare/1eed620a4a1f...1043… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] 2fe7e5: Test mutable config for DM upgrades
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2fe7e55082bccb39d0d7042d40dd2ee0067be2cc https://github.com/galaxyproject/usegalaxy-playbook/commit/2fe7e55082bccb39… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M env/test/files/galaxy/var/shed_data_manager_conf.xml Log Message: ----------- Test mutable config for DM upgrades Commit: fb1d9545e605f1527537071560f0cccafcba289e https://github.com/galaxyproject/usegalaxy-playbook/commit/fb1d9545e605f152… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M env/common/templates/supervisor/galaxy_handler.j2 M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Test and increase its handler shutdown timeout. Commit: 86c430efbc9db6a2577f58ca577858b8c71c7e5f https://github.com/galaxyproject/usegalaxy-playbook/commit/86c430efbc9db6a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml M env/testtoolshed/group_vars/toolshedservers/vars.yml M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Commit: 00c9258264550ee6d460bdc2f0d5c849f5bd3118 https://github.com/galaxyproject/usegalaxy-playbook/commit/00c9258264550ee6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/deafd85205f9...… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d898b6: Vue rewrite of admin data manager (local data): in...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d898b672adc6924395bbb8c282999e0183891b5a https://github.com/galaxyproject/galaxy/commit/d898b672adc6924395bbb8c28299… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Alert.vue A client/galaxy/scripts/components/admin/DataManager/DataManager.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/package.json M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- Vue rewrite of admin data manager (local data): index page * Added Alert component: Light bootstrap-vue b-alert wrapper. - Hides automatically when given message is empty. - Translates galaxy state keywords into bootstrap ones. * Added vue-router integration: Display (future) Data Manager Jobs and Job components inside router-views. - Added router-view component DataManagerView. * Rewrite (old mako, new json interface, new vue component) - Index page (index.mako, data_managers_list, DataManager) * Added Selenium test for DataManager component (index page) Commit: 747e998d40b82117c21b80e86a347c96ff86353b https://github.com/galaxyproject/galaxy/commit/747e998d40b82117c21b80e86a34… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/manage_data_manager.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- Vue rewrite of admin data manager (local data): manager page * Rewrite (old mako, new json interface, new vue component) - Manager page (manage_data_manager.mako, jobs_list, DataManagerJobs) * Added Selenium test for DataManagerJobs component (manager page) Commit: 13b8098259c9fc7a53b2db51a07b530b1d748b76 https://github.com/galaxyproject/galaxy/commit/13b8098259c9fc7a53b2db51a07b… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/view_job.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- Vue rewrite of admin data manager (local data): view job page * Rewrite (old mako, new json interface, new vue component) - View job page (view_job.mako, job_info, DataManagerJob) * Added Selenium test for DataManagerJob component (view job page) Commit: 126c432bcf52279aea7ff952e771b0f4eefe012b https://github.com/galaxyproject/galaxy/commit/126c432bcf52279aea7ff952e771… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/main-tools-py3/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M .gitignore M client/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/scratchbook.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/form/form-input.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/form/form-wrapper.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M 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templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflow_fixtures.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_stock_tours.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py A test/unit/test_compression_util.py M test/unit/test_galaxy_mapping.py A test/unit/test_utils.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' Commit: 2ef1aeef3c986938a3cd48e42758329e29792860 https://github.com/galaxyproject/galaxy/commit/2ef1aeef3c986938a3cd48e42758… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue Log Message: ----------- DataManager: delay rendering until server data is ready Commit: 8db26fe522f9cab6d29d3b03f41975b5354bcef3 https://github.com/galaxyproject/galaxy/commit/8db26fe522f9cab6d29d3b03f419… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue Log Message: ----------- DataManagerJobs: delay rendering until server data is ready Commit: d3b43da3f518a8d221f8ba71883ad97a95f610f9 https://github.com/galaxyproject/galaxy/commit/d3b43da3f518a8d221f8ba71883a… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue Log Message: ----------- DataManagerJob: delay rendering until server data is ready Commit: 8b7d203ec8ffe685ff56479d79243536f27d0252 https://github.com/galaxyproject/galaxy/commit/8b7d203ec8ffe685ff56479d7924… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue Log Message: ----------- DataManager: check for empty server data Commit: 3af83f4254a284e50e3a30ce6ed81dea82b2eabc https://github.com/galaxyproject/galaxy/commit/3af83f4254a284e50e3a30ce6ed8… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py Log Message: ----------- DataManagerJobs: check for empty server data Fix jobs_list redirect in case data manager is non-existent with empty server response containing an error message and status. Commit: 877feae8bacd7104add9b31632843c7d3cbd2a39 https://github.com/galaxyproject/galaxy/commit/877feae8bacd7104add9b3163284… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- DataManagerJob: check for empty server data & refactoring * DataManagerJob - Check for empty server data & refactoring - Fix and numerate data-card ids * job_info - Fix error log in job_info. - Fix redirect in case job is non-existent with empty server response containing an error message and status. * Extend DataManagerJob test Commit: 53a505eaef3e8d91689ecfeb3b785928c54a8e42 https://github.com/galaxyproject/galaxy/commit/53a505eaef3e8d91689ecfeb3b78… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/manage_data_table.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py Log Message: ----------- Vue rewrite of admin data manager (local data): manage data table * Rewrite (old mako, new json interface, new vue component) - Manage data table page (manage_data_table.mako, tool_data_table_info, DataManagerTable) * Added Selenium test for DataManagerTable component (Manage data table page) Commit: 6d2a755614239149193d87e8cb695c963c17dc71 https://github.com/galaxyproject/galaxy/commit/6d2a755614239149193d87e8cb69… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/README.md A 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templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako M test/api/test_tools.py A test/base/ssh_util.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py M test/unit/test_remote_shell.py Log Message: ----------- Merge branch 'dev' into admin.data.manager.vue.steps Commit: 31b484492260f554020ed8eed1d1a20cd98089ef https://github.com/galaxyproject/galaxy/commit/31b484492260f554020ed8eed1d1… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/data_manager.py Log Message: ----------- Fix linting error by removing unused import markupsafe escape Commit: 8789713b9584c8ee58692b4dc02a282f32484502 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static/style/shared_images/wait_small.png R static/style/shared_images/warn_large.png R static/style/shared_images/warn_small.png M static/welcome.html.sample M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/message.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/tool_sheds.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/repository/browse_repository.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako A test-data/MTBLS6.zip M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/driver_util.py M test/base/populators.py M test/base/workflow_fixtures.py M test/functional/tools/output_filter.xml A test/functional/tools/remove_value.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/__init__.py M test/galaxy_selenium/navigation.yml A test/integration/test_datatype_upload.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into admin.data.manager.vue.steps Commit: 91df3971be62419620c3cd08b0c9162ec6989856 https://github.com/galaxyproject/galaxy/commit/91df3971be62419620c3cd08b0c9… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-11-03 (Sat, 03 Nov 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- DataManagerRouter, DataManager, DataManagerJobs: Fix routing problem * Forward path following the data manager url to DataManagerRouter * encode id in DataManager and DataManagerJobs Commit: 45d0f161c92c6fdac103ca3eecec421ac3fa3db3 https://github.com/galaxyproject/galaxy/commit/45d0f161c92c6fdac103ca3eecec… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-11-03 (Sat, 03 Nov 2018) Changed paths: M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1460_data_managers.py Log Message: ----------- Fix functional test case test_1460_data_managers Commit: 4b3606f1acd57064c3b4a2da6842a58d5d634a9b https://github.com/galaxyproject/galaxy/commit/4b3606f1acd57064c3b4a2da6842… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue Log Message: ----------- Target top with rerun to avoid nested Galaxy. Commit: e9f269393346175c2d88dd6e190d3d00547ef3c6 https://github.com/galaxyproject/galaxy/commit/e9f269393346175c2d88dd6e190d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Alert.vue A client/galaxy/scripts/components/admin/DataManager/DataManager.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/package.json M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/index.mako R templates/webapps/galaxy/data_manager/manage_data_manager.mako R templates/webapps/galaxy/data_manager/manage_data_table.mako R templates/webapps/galaxy/data_manager/view_job.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1460_data_managers.py Log Message: ----------- Merge pull request #6729 from scrathat/admin.data.manager.vue.steps Vue rewrite of admin data manager (local data) in steps Compare: https://github.com/galaxyproject/galaxy/compare/a53de291fefd...e9f269393346 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] e8a64a: Split qunit and mocha tests, clean up karma config...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8a64a862212af970690fcd1969ac8f5ebaaf407 https://github.com/galaxyproject/galaxy/commit/e8a64a862212af970690fcd1969a… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: A client/galaxy/scripts/apps/sample.test.js A client/galaxy/scripts/unitTestBundle.js A client/karma.config.base.js R client/karma.config.js A client/karma.config.mocha.js A client/karma.config.qunit.js M client/package.json A client/webpack.config.test.js M client/yarn.lock Log Message: ----------- Split qunit and mocha tests, clean up karma configs Commit: 1490b6ae839bd704af45b7a415ba70d7fc013df3 https://github.com/galaxyproject/galaxy/commit/1490b6ae839bd704af45b7a415ba… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M client/galaxy/style/scss/ui.scss M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Merge branch 'dev' into karma_chromeheadless Commit: b52b2d8c4817295f9dad56a057fe9d5a095d3a37 https://github.com/galaxyproject/galaxy/commit/b52b2d8c4817295f9dad56a057fe… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py M templates/webapps/galaxy/admin/tool_sheds.mako M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into karma_chromeheadless Commit: 2cc0417530cb33dfa43cb0c0d64f2f807d5396d5 https://github.com/galaxyproject/galaxy/commit/2cc0417530cb33dfa43cb0c0d64f… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M .travis.yml M client/karma.config.base.js Log Message: ----------- Added chrome to qunit build, tried no sandbox flag on chrome Commit: b637c7575a6cdd17960b57e803cabcaa9fe5972c https://github.com/galaxyproject/galaxy/commit/b637c7575a6cdd17960b57e803ca… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M Makefile M client/karma.config.base.js M client/package.json Log Message: ----------- Modified test script calls Commit: 31d3c97e757fd9e9206c815d7b0c9b9d22d0d7a8 https://github.com/galaxyproject/galaxy/commit/31d3c97e757fd9e9206c815d7b0c… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/karma.config.qunit.js Log Message: ----------- Remove one failing test just to check build Commit: e92ce870928700917d69e9c3d939087d6d48eb56 https://github.com/galaxyproject/galaxy/commit/e92ce870928700917d69e9c3d939… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/qunit/test.js M client/karma.config.qunit.js Log Message: ----------- Removed bad test just to test build Commit: b06957e90619b3b7c4cf1f7b989ae32242b55f83 https://github.com/galaxyproject/galaxy/commit/b06957e90619b3b7c4cf1f7b989a… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/karma.config.mocha.js Log Message: ----------- Added existing mocha tests back Commit: a7a73bcfcd32de2b89a6cd4119ba64db8be045ef https://github.com/galaxyproject/galaxy/commit/a7a73bcfcd32de2b89a6cd4119ba… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/karma.config.base.js M client/karma.config.mocha.js M client/karma.config.qunit.js M client/package.json A client/webpack.config.qunit.js R client/webpack.config.test.js A client/webpack.config.unittest.js M client/yarn.lock Log Message: ----------- Documented differences bretween different webpack configs, used cleaner tool and ignore-loader for true unit-tests Commit: c2f71c3a3ec31fd6af7479db9ae13f8b0975d584 https://github.com/galaxyproject/galaxy/commit/c2f71c3a3ec31fd6af7479db9ae1… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/webpack.config.qunit.js Log Message: ----------- Added missing settings on special qunit webpack config Commit: 19b2fdd73ba82d0eb3ae38141134915d8a745827 https://github.com/galaxyproject/galaxy/commit/19b2fdd73ba82d0eb3ae38141134… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-03 (Sat, 03 Nov 2018) Changed paths: R client/galaxy/scripts/apps/sample.test.js A client/galaxy/scripts/sample.test.js R client/karma.config.base.js R client/karma.config.mocha.js R client/karma.config.qunit.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json R client/webpack.config.qunit.js R client/webpack.config.unittest.js Log Message: ----------- Reorganized config scripts, fleshed out comments and instructions Commit: a53de291fefd34ca9fcdf1a03bacd9739f768edf https://github.com/galaxyproject/galaxy/commit/a53de291fefd34ca9fcdf1a03bac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/sample.test.js A client/galaxy/scripts/unitTestBundle.js R client/karma.config.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json M client/yarn.lock Log Message: ----------- Merge pull request #6959 from Nerdinacan/karma_chromeheadless Switch from PhantomJS to Chrome Headless for unit tests Compare: https://github.com/galaxyproject/galaxy/compare/c3dc2392ce1a...a53de291fefd **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 69b447: Allow deferring 'to_ext' extension to the server, ...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 69b447169fb96048ea492a1d99d653585571c15b https://github.com/galaxyproject/galaxy/commit/69b447169fb96048ea492a1d99d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M lib/galaxy/datatypes/data.py Log Message: ----------- Allow deferring 'to_ext' extension to the server, implement for collections. Commit: 3be8d66d71bcdb3eccde2d1a37731442ed1aa63a https://github.com/galaxyproject/galaxy/commit/3be8d66d71bcdb3eccde2d1a3773… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Remove unncecessary implementations of display_data These were not updated to use `_download_filename`, and so this fixes the download name for collection elements to include the element identifier. Note that the Data class should handle composite data just fine. Commit: f8b160535c5f9363e85c6c1d041b69ce5c3e9cc2 https://github.com/galaxyproject/galaxy/commit/f8b160535c5f9363e85c6c1d041b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Some minor fixes for the blast datatype The signature for Data.display_data wasn't quite correct, and the description of display_data was also a little misleading. Commit: 61bda3d11a1d608ac8e1a731faf144ff989affc9 https://github.com/galaxyproject/galaxy/commit/61bda3d11a1d608ac8e1a731faf1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Merge pull request #6960 from dannon/collection_ext_dl [18.09] Allow deferring 'to_ext' extension to the server Compare: https://github.com/galaxyproject/galaxy/compare/2deb302ae7be...61bda3d11a1d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 717605: added test
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 717605af96bcb5fb9a5193295c9941d0d4632a93 https://github.com/galaxyproject/galaxy/commit/717605af96bcb5fb9a5193295c99… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M test/functional/tools/output_filter.xml Log Message: ----------- added test Commit: 20cecd2a68527015d8b98a430367b8fcdf9a364d https://github.com/galaxyproject/galaxy/commit/20cecd2a68527015d8b98a430367… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- galaxy test needs to count data sets and collection outputs Commit: 4e098c5d5291209f4760010ff8bebd919ba19479 https://github.com/galaxyproject/galaxy/commit/4e098c5d5291209f4760010ff8be… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- tests: add parameter to output_filter Commit: 9b42032098edaae076f5f88c48f135d8035a9ad6 https://github.com/galaxyproject/galaxy/commit/9b42032098edaae076f5f88c48f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fill in default state for test_optional_workflow_output Commit: 2deb302ae7be93924a8bdcaff17a43caa0b5e3b4 https://github.com/galaxyproject/galaxy/commit/2deb302ae7be93924a8bdcaff17a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/api/test_workflows.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge pull request #6951 from bernt-matthias/topic/test-colouts-backport [18.09] Backport: tests need to count data sets and collections Compare: https://github.com/galaxyproject/galaxy/compare/3d91738a697f...2deb302ae7be **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d4b6bf: Test for parameter replacement of GUI-style normal...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d4b6bf28b5c834dc82591761a98a1aeefc0ed412 https://github.com/galaxyproject/galaxy/commit/d4b6bf28b5c834dc82591761a98a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test for parameter replacement of GUI-style normalized parameters. Commit: 06aea92eb8614faa06afdeaeffe91565e1390774 https://github.com/galaxyproject/galaxy/commit/06aea92eb8614faa06afdeaeffe9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- cleaner test test_run_subworkflow_runtime_parameters Commit: c3dc2392ce1a3c9ca91369caf63fa0b6008820d2 https://github.com/galaxyproject/galaxy/commit/c3dc2392ce1a3c9ca91369caf63f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #6954 from jmchilton/workflow_tests_2 Small API Workflow Test Improvements. Compare: https://github.com/galaxyproject/galaxy/compare/c1e4b0111a70...c3dc2392ce1a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b1fe6f: Refactor collection mapping workflows toward indep...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1fe6fee9373f025341e25b248ffa003a10213b3 https://github.com/galaxyproject/galaxy/commit/b1fe6fee9373f025341e25b248ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Refactor collection mapping workflows toward independence from tools. Refactor get_data_inputs into get_all_inputs and use the resulting dictionaries to reason about if collection mapping should occur during invocation of tools. Using these dictionaries instead of explicit tool input objects should allow reuse within other module types since they may produce the same interface. Commit: c1e4b0111a70e3bae63791f60a44e6b14b259a5c https://github.com/galaxyproject/galaxy/commit/c1e4b0111a70e3bae63791f60a44… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #6911 from jmchilton/workflow_mapping_refactor Refactor collection mapping workflows toward independence from tools. Compare: https://github.com/galaxyproject/galaxy/compare/a3f213e3c531...c1e4b0111a70 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 0beac8: rma: add RMA6 data type (MEGAN6 read-match archive...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0beac8fdf4835271ccafefd6a50f928afa055c2c https://github.com/galaxyproject/galaxy/commit/0beac8fdf4835271ccafefd6a50f… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.rma Log Message: ----------- rma: add RMA6 data type (MEGAN6 read-match archive) Commit: dcae06624a7561d082a7630917d095925795d30e https://github.com/galaxyproject/galaxy/commit/dcae06624a7561d082a7630917d0… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- rma: RMA->RMA6 Commit: 09de6fe4961adcfe09f8701989ac37b8f8df1930 https://github.com/galaxyproject/galaxy/commit/09de6fe4961adcfe09f8701989ac… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- rma: fix test Commit: ee0038a01f8ddd9f8b99d0612497fc6681a14acc https://github.com/galaxyproject/galaxy/commit/ee0038a01f8ddd9f8b99d0612497… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- rma: extension rma6 for consistency Commit: 562b10b7efc93c5ab15bd3a3d5918f32491d934d https://github.com/galaxyproject/galaxy/commit/562b10b7efc93c5ab15bd3a3d591… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/test/diamond.rma A lib/galaxy/datatypes/test/diamond.rma6 Log Message: ----------- rma: renamed test data to rma6 Commit: a3f213e3c5319bd8125e4856e0094fd3cd7ef737 https://github.com/galaxyproject/galaxy/commit/a3f213e3c5319bd8125e4856e009… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.rma6 Log Message: ----------- Merge pull request #6962 from bernt-matthias/topic/rma add RMA6 data type (MEGAN6 read-match archive) Compare: https://github.com/galaxyproject/galaxy/compare/0ede377925c4...a3f213e3c531 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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