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

[galaxyproject/galaxy] e3435e: Remove backbone thumbnail element
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e3435eb23d62815f5a08aca7dbaf68991b05ab60 https://github.com/galaxyproject/galaxy/commit/e3435eb23d62815f5a08aca7dbaf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Remove backbone thumbnail element Commit: 03702d0a61733682cd80ee3d4849cd094c00d0d1 https://github.com/galaxyproject/galaxy/commit/03702d0a61733682cd80ee3d4849… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove unused thumbnail styles Commit: 0b1d804cf675fb47f4132363f32b27680becbdf8 https://github.com/galaxyproject/galaxy/commit/0b1d804cf675fb47f4132363f32b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6587 from guerler/remove_bb_thumbnail Remove backbone version of thumbnail element Compare: https://github.com/galaxyproject/galaxy/compare/0ea1430136c5...0b1d804cf675 **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] 1d0f51: Fix upload file selector value resetting
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d0f51a05e5e5fb73940d7dae284bf9c00a4054c https://github.com/galaxyproject/galaxy/commit/1d0f51a05e5e5fb73940d7dae284… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: f992980d458edeebc0501ac036c2ee5c6fba7989 https://github.com/galaxyproject/galaxy/commit/f992980d458edeebc0501ac036c2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6573 from guerler/fix_upload_naming [18.05] Fix upload file selector value resetting Commit: ec60327f983ced46fa2a8489c359100960b72d5b https://github.com/galaxyproject/galaxy/commit/ec60327f983ced46fa2a8489c359… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Client rebuild to include uploadbox value fix in release branch. Commit: d7398672a1a3432ae11b0c41b291e45e77bbd183 https://github.com/galaxyproject/galaxy/commit/d7398672a1a3432ae11b0c41b291… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6574 from dannon/release_18.05 [18.05] Client rebuild to include uploadbox value fix in release branch. Commit: 2f87087ba2a88d71d539f888401d79167997a4ea https://github.com/galaxyproject/galaxy/commit/2f87087ba2a88d71d539f888401d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Use object store to check for existence of extra_files_path This should fix https://github.com/galaxyproject/galaxy/issues/6585 Commit: 1ddaf4a64d6307fd477653d3bba7353a30e88eb2 https://github.com/galaxyproject/galaxy/commit/1ddaf4a64d6307fd477653d3bba7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #6588 from mvdbeek/extra_path_nested_object_store_issue [18.05] Use object store to check for existence of extra_files_path Commit: 0ea1430136c51c5558f17e4a051e8d1a58009fd3 https://github.com/galaxyproject/galaxy/commit/0ea1430136c51c5558f17e4a051e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9910ea47d9b3...0ea1430136c5 **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] 2f8708: Use object store to check for existence of extra_f...
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2f87087ba2a88d71d539f888401d79167997a4ea https://github.com/galaxyproject/galaxy/commit/2f87087ba2a88d71d539f888401d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Use object store to check for existence of extra_files_path This should fix https://github.com/galaxyproject/galaxy/issues/6585 Commit: 1ddaf4a64d6307fd477653d3bba7353a30e88eb2 https://github.com/galaxyproject/galaxy/commit/1ddaf4a64d6307fd477653d3bba7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #6588 from mvdbeek/extra_path_nested_object_store_issue [18.05] Use object store to check for existence of extra_files_path Compare: https://github.com/galaxyproject/galaxy/compare/d7398672a1a3...1ddaf4a64d63 **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] 4d1ce0: Cancel jobs when exiting test_history decorator.
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d1ce0f431d337a45964eee3aa3813be1f4e41c6 https://github.com/galaxyproject/galaxy/commit/4d1ce0f431d337a45964eee3aa38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Cancel jobs when exiting test_history decorator. Should reduce the probability of a test interferring with other tests. Commit: 136255c0ad7a2aca6584f4c1fa3d10ea5e4a632e https://github.com/galaxyproject/galaxy/commit/136255c0ad7a2aca6584f4c1fa3d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M run_tests.sh M test/base/populators.py Log Message: ----------- Allow test_history context to annotate whether new histories are needed by test. Usually tests should have new histories but we should still capture this information so we can target tests are particular histories for debugging interactively and so we could potentially reduce the number of new histories created when testing remote Galaxies (there have been complaints about this in the past). Commit: 36e1d6cfce946b46f5904af3cc924cb0f21970ee https://github.com/galaxyproject/galaxy/commit/36e1d6cfce946b46f5904af3cc92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/api/test_tools.py M test/base/populators.py Log Message: ----------- More use of test_history contextmanager in test_tools. Commit: 9910ea47d9b353fe61fc510469a0599210009a25 https://github.com/galaxyproject/galaxy/commit/9910ea47d9b353fe61fc510469a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh M test/api/test_tools.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #6586 from jmchilton/toward_test_history_cleaning Smarter Test Histories (Part I) Compare: https://github.com/galaxyproject/galaxy/compare/5d85c32da243...9910ea47d9b3 **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] 38e581: Redirect unindentifed routes in admin panel
by GitHub 08 Aug '18

08 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38e5816b06d0804324dfe2a9c642859d990cfdb9 https://github.com/galaxyproject/galaxy/commit/38e5816b06d0804324dfe2a9c642… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-28 (Sat, 28 Jul 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Redirect unindentifed routes in admin panel Fix Commit: af755a098061f8db55db5ecc398c3410f180f9e1 https://github.com/galaxyproject/galaxy/commit/af755a098061f8db55db5ecc398c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Minor import cleanup, formatting. Commit: 4072d68e0d6d182a4249df143ab4fcba3e8f35cf https://github.com/galaxyproject/galaxy/commit/4072d68e0d6d182a4249df143ab4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js Log Message: ----------- Redirect without using backbone Commit: 5d85c32da24396a4853d09cf5fccb12481f1ccee https://github.com/galaxyproject/galaxy/commit/5d85c32da24396a4853d09cf5fcc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Merge pull request #6551 from guerler/fix_admin_routes Redirect unidentified routes in admin panel Compare: https://github.com/galaxyproject/galaxy/compare/75e50d3fdd98...5d85c32da243 **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] c2246d: Fix last consistently failing Selenium test.
by GitHub 08 Aug '18

08 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2246d8b8a17fdf126aefb5f6b53eb680bb58848 https://github.com/galaxyproject/galaxy/commit/c2246d8b8a17fdf126aefb5f6b53… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/base/rules_test_data.py Log Message: ----------- Fix last consistently failing Selenium test. Commit: 75e50d3fdd98a75cc0c109616293608bdab5eac3 https://github.com/galaxyproject/galaxy/commit/75e50d3fdd98a75cc0c109616293… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/base/rules_test_data.py Log Message: ----------- Merge pull request #6578 from jmchilton/selenium_fixes_44 Fix last consistently failing Selenium test. Compare: https://github.com/galaxyproject/galaxy/compare/a7e159dd8b8c...75e50d3fdd98 **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] ec6032: Client rebuild to include uploadbox value fix in r...
by GitHub 08 Aug '18

08 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ec60327f983ced46fa2a8489c359100960b72d5b https://github.com/galaxyproject/galaxy/commit/ec60327f983ced46fa2a8489c359… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Client rebuild to include uploadbox value fix in release branch. Commit: d7398672a1a3432ae11b0c41b291e45e77bbd183 https://github.com/galaxyproject/galaxy/commit/d7398672a1a3432ae11b0c41b291… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6574 from dannon/release_18.05 [18.05] Client rebuild to include uploadbox value fix in release branch. Compare: https://github.com/galaxyproject/galaxy/compare/f992980d458e...d7398672a1a3 **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] 4f3cd8: Typo and wording fixes for dependency resolvers do...
by GitHub 07 Aug '18

07 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f3cd889f1cb2371519cabbc975dfffee6ec9b71 https://github.com/galaxyproject/galaxy/commit/4f3cd889f1cb2371519cabbc975d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Typo and wording fixes for dependency resolvers docs Commit: a7e159dd8b8c584772defb6becb56f5450172dad https://github.com/galaxyproject/galaxy/commit/a7e159dd8b8c584772defb6becb5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge pull request #6575 from afgane/dev Typo and wording fixes for dependency resolvers docs Compare: https://github.com/galaxyproject/galaxy/compare/55436c38008c...a7e159dd8b8c **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] 1d0f51: Fix upload file selector value resetting
by GitHub 07 Aug '18

07 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 1d0f51a05e5e5fb73940d7dae284bf9c00a4054c https://github.com/galaxyproject/galaxy/commit/1d0f51a05e5e5fb73940d7dae284… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: f992980d458edeebc0501ac036c2ee5c6fba7989 https://github.com/galaxyproject/galaxy/commit/f992980d458edeebc0501ac036c2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6573 from guerler/fix_upload_naming [18.05] Fix upload file selector value resetting Compare: https://github.com/galaxyproject/galaxy/compare/ea085b07a0ef...f992980d458e **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] fa3a23: WIP: add a SelectTagParameter
by GitHub 07 Aug '18

07 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa3a2371e1b2873456a3034874036d9b8cadd01c https://github.com/galaxyproject/galaxy/commit/fa3a2371e1b2873456a303487403… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py Log Message: ----------- WIP: add a SelectTagParameter Commit: 4afbdbab31791101578be08acc3526e04c1835d6 https://github.com/galaxyproject/galaxy/commit/4afbdbab31791101578be08acc35… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py Log Message: ----------- Fix unit tests Commit: 04b0cfcc1388de18aeb93a39fa44451009bbd67f https://github.com/galaxyproject/galaxy/commit/04b0cfcc1388de18aeb93a39fa44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Make `get_datasets_for_group` case insensitive to tag Commit: 45b2b7f434fc1bd1e646c72c6024bacc482a8b8e https://github.com/galaxyproject/galaxy/commit/45b2b7f434fc1bd1e646c72c6024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml 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-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue A client/galaxy/scripts/components/Sharing.vue A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/communication-server-view.js A client/galaxy/scripts/layout/data.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/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.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/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-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-contents.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M 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config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js M config/plugins/webhooks/demo/search/script.js M config/plugins/webhooks/demo/tour_generator/__init__.py M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.yml.sample M config/user_preferences_extra_conf.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M create_db.sh M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml A display_applications/intermine/intermine_simple.xml M doc/parse_gx_xsd.py M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/nginx.md M doc/source/admin/reports_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/conf.py A doc/source/conf.versioning.py M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/project/organization.rst A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M extract_dataset_parts.sh M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.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/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M 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tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into select_tag_parameter Commit: d417e9b239309707274011d4199b8f827fcc0f6d https://github.com/galaxyproject/galaxy/commit/d417e9b239309707274011d4199b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Flush out collection tag parameters a bit. - Switch select_tag to group_tag as a parameter name - since it is restricted to group_tags and we don't call data parameters select_data. - Add minimal XSD documentation for this new parameter type. - Add example tools - for single and multiple tags. - Add API tests for these tools and the tag handling. Commit: e5c532298d5db34da04d8f046ebe44abddbbaa64 https://github.com/galaxyproject/galaxy/commit/e5c532298d5db34da04d8f046ebe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Make tag order stable when using group_tag parameters. Commit: 6677e7b91385d027989613bdc621108da76e8425 https://github.com/galaxyproject/galaxy/commit/6677e7b91385d027989613bdc621… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix failing import/export test for group_tag changes. Commit: 5a914b9fa71ff2c00d7ba1a7c1dc3ccbb8437eae https://github.com/galaxyproject/galaxy/commit/5a914b9fa71ff2c00d7ba1a7c1dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Keep all user-selected tags, including duplicates Commit: 95e8a3491280cc26d435bebc1cf03488d7db3b88 https://github.com/galaxyproject/galaxy/commit/95e8a3491280cc26d435bebc1cf0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Correct copy-pasted docstring Commit: 55436c38008c3d1b261b7d9dfc728cc968bd6622 https://github.com/galaxyproject/galaxy/commit/55436c38008c3d1b261b7d9dfc72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #5457 from mvdbeek/select_tag_parameter Allow selecting subset of collection by group tag Compare: https://github.com/galaxyproject/galaxy/compare/d1423b6e18cb...55436c38008c **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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