- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 1f0ec9: Use a lock on cleanup, expire_tool and cache_tool
by Nicola Soranzo 04 Mar '19

04 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f0ec9424fd116a1f6896bf648d16a309f1e6847 https://github.com/galaxyproject/galaxy/commit/1f0ec9424fd116a1f6896bf648d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/tools/cache.py M test/unit/tools/test_toolbox.py Log Message: ----------- Use a lock on cleanup, expire_tool and cache_tool This should fix https://github.com/galaxyproject/galaxy/issues/7444. Commit: 2d7b3e32d300ba33b0dadd3b8ff1cbec6b98a9bb https://github.com/galaxyproject/galaxy/commit/2d7b3e32d300ba33b0dadd3b8ff1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/tools/cache.py M test/unit/tools/test_toolbox.py Log Message: ----------- Add debugging statements to ``ToolCache.cleanup()`` Commit: d3652f871a59e1dc9be40aaea693fb4219dbb48c https://github.com/galaxyproject/galaxy/commit/d3652f871a59e1dc9be40aaea693… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/tools/cache.py Log Message: ----------- Use lock also for ``ToolCache.reset_status()`` method Commit: 294c7b6eebfb02f947697111c82033b3ba68be04 https://github.com/galaxyproject/galaxy/commit/294c7b6eebfb02f947697111c820… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Use ``_try_until_no_errors`` also for ``test_tool_reload_when_macro_is_altered`` unit test Commit: 999c2c038e850a75d5fce0030bdcdbcf3bf0b13d https://github.com/galaxyproject/galaxy/commit/999c2c038e850a75d5fce0030bdc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Store toolbox in test_case._toolbox Apparently accessing double-underscore variables in threads leads to name-mangling issues, so effectively updating test_case.__toolbox wouldn't be reflected outside of the watcher thread. We previously used self.app.toolbox which circumenvented this issue. It is possible that `check_tool_errors` / `check_no_tool_errors` were accessing the old toolbox, unless the watching thread happened to fire between function definition and assert, and that's probably why increasing the number of trials had no effect. Commit: b84607728d7754347de94a1787f00e5a96cebde1 https://github.com/galaxyproject/galaxy/commit/b84607728d7754347de94a1787f0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Tear down started threads Commit: c1f8221b0bd9e8235a24d387990586b9dbbcb21c https://github.com/galaxyproject/galaxy/commit/c1f8221b0bd9e8235a24d3879905… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M test/unit/tools_support.py Log Message: ----------- Use ``with`` statement Commit: f9df69d5f2d58d86a4b0c834bb55e7debcec8707 https://github.com/galaxyproject/galaxy/commit/f9df69d5f2d58d86a4b0c834bb55… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/tools/cache.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #7446 from mvdbeek/fix_concurrent_add_remove Use a lock on cleanup, expire_tool and cache_tool Compare: https://github.com/galaxyproject/galaxy/compare/b76d5053fad7...f9df69d5f2d5

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[galaxyproject/galaxy] d08ce5: Fix doc for statsd conf for uwsgi
by Dannon 04 Mar '19

04 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d08ce52cce71214ed8812169f8051603b75626d3 https://github.com/galaxyproject/galaxy/commit/d08ce52cce71214ed8812169f805… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- Fix doc for statsd conf for uwsgi Commit: 3a220d02b9c3e6c1f178de9f579a248ff0993cfe https://github.com/galaxyproject/galaxy/commit/3a220d02b9c3e6c1f178de9f579a… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- typo Commit: ba2e0240fe4449dc8c6c19d40b69d3d1f1451c2f https://github.com/galaxyproject/galaxy/commit/ba2e0240fe4449dc8c6c19d40b69… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- add details on gxadmin Commit: 0156e61a585e9d8b431b4d5ec30269e247ff929a https://github.com/galaxyproject/galaxy/commit/0156e61a585e9d8b431b4d5ec302… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- remove reference to paster Commit: b76d5053fad7ecbc1141cf9d62ba55fcb547d9cf https://github.com/galaxyproject/galaxy/commit/b76d5053fad7ecbc1141cf9d62ba… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- Merge pull request #7453 from abretaud/patch-3 Fix doc for statsd conf for uwsgi? Compare: https://github.com/galaxyproject/galaxy/compare/4ec49c1197e4...b76d5053fad7

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[galaxyproject/galaxy] 33a74c: Fix hotdata method access; this still needs a lot ...
by Dannon 04 Mar '19

04 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33a74cae2def618e9fe32d1a8b1355d00a39a525 https://github.com/galaxyproject/galaxy/commit/33a74cae2def618e9fe32d1a8b13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix hotdata method access; this still needs a lot of love/refactoring, but this makes it work again? Commit: a64a5cdc5e1ace5981452026c4aa2857fbfd729b https://github.com/galaxyproject/galaxy/commit/a64a5cdc5e1ace5981452026c4aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Prefer const, none of these are reassigned. Commit: 3c9f263c69c657f8a644fceb778a7ff36c888d0a https://github.com/galaxyproject/galaxy/commit/3c9f263c69c657f8a644fceb778a… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Restored hotData to computed, but removed unnecessary side-effects Commit: 205cdd0954ffdf34efc2c364ec1b62079e4a27d8 https://github.com/galaxyproject/galaxy/commit/205cdd0954ffdf34efc2c364ec1b… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Removed slice method on non-array property Commit: 569ea9ea36e15afcbd174b50ae2de79029c4bc0a https://github.com/galaxyproject/galaxy/commit/569ea9ea36e15afcbd174b50ae2d… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Removed commented code in RuleCollectionBuilder Commit: f729dab31312d1be5ef2226d533d4ad26fb25130 https://github.com/galaxyproject/galaxy/commit/f729dab31312d1be5ef2226d533d… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: R client/.babelrc M client/galaxy/scripts/bundleEntries.js A client/galaxy/scripts/components/Tags/GalaxyTags.test.js A client/galaxy/scripts/components/Tags/GalaxyTags.vue A client/galaxy/scripts/components/Tags/StandardTags.test.js A client/galaxy/scripts/components/Tags/StandardTags.vue A client/galaxy/scripts/components/Tags/autocomplete_tagging.scss A client/galaxy/scripts/components/Tags/index.js A client/galaxy/scripts/components/Tags/inits.js A client/galaxy/scripts/components/Tags/model.js A client/galaxy/scripts/components/Tags/model.test.js A client/galaxy/scripts/components/Tags/tagService.js A client/galaxy/scripts/components/Tags/tagService.test.js A client/galaxy/scripts/components/Tags/tagStyles.scss A client/galaxy/scripts/components/Tags/testData/autocompleteResponse.txt M client/galaxy/scripts/entry/analysis/AnalysisRouter.js M client/galaxy/scripts/mvc/grid/grid-view.js R client/galaxy/scripts/sample.test.js A client/galaxy/scripts/store/gridSearchStore.js A client/galaxy/scripts/store/index.js R client/galaxy/scripts/ui/autocom_tagging.js R client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/mountVueComponent.js A client/galaxy/scripts/utils/redirect.js M client/galaxy/scripts/viz/trackster.js R client/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/mixins.scss M client/karma/karma.config.mocha.js M client/karma/karma.config.qunit.js M client/karma/webpack.config.unittest.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/reports/framework/grids.py M templates/tagging_common.mako M templates/webapps/galaxy/workflow/editor.mako M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Tagging component Commit: f138022a163475e14347e9665facbaa3222efef9 https://github.com/galaxyproject/galaxy/commit/f138022a163475e14347e9665fac… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M client/karma/karma.config.mocha.js Log Message: ----------- Re-enable old mocha tests Commit: 2389b4dab241eade87fd60bd7792e3d38189c9aa https://github.com/galaxyproject/galaxy/commit/2389b4dab241eade87fd60bd7792… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M templates/tagging_common.mako Log Message: ----------- Removed unused import in tagging_common Commit: 787740561f19c90fa6b7032af6a7820eaee75187 https://github.com/galaxyproject/galaxy/commit/787740561f19c90fa6b7032af6a7… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M client/galaxy/scripts/layout/menu.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/library/library-dataset-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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M config/galaxy.yml.sample M config/tool_shed.yml.sample M cron/add_manual_builds.py M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/config.rst M doc/source/admin/galaxy_options.rst R doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.web.framework.rst M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/__init__.py M lib/galaxy/util/filelock.py M lib/galaxy/util/hash_util.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/workflow/modules.py M run_tests.sh M templates/user/logout.mako M templates/webapps/galaxy/workflow/display.mako M test/api/test_histories.py M test/api/test_workflows.py M test/functional/test_toolbox.py M test/unit/test_utils.py M tools/filters/sff_extract.py M tools/maf/maf_to_bed.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into tagging_component_3 Commit: 8a6b0a1cd260d2c91b4a4f8f689de5ae8d24e940 https://github.com/galaxyproject/galaxy/commit/8a6b0a1cd260d2c91b4a4f8f689d… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-02 (Sat, 02 Feb 2019) Changed paths: M client/galaxy/scripts/components/Tags/GalaxyTags.test.js M client/galaxy/scripts/components/Tags/GalaxyTags.vue M client/galaxy/scripts/components/Tags/StandardTags.test.js M client/galaxy/scripts/components/Tags/StandardTags.vue M client/galaxy/scripts/utils/mountVueComponent.js Log Message: ----------- Added localize filter and fixed optional hooks for GalaxyTags Commit: c33cd1665d3bfed2dd75086735a01b55f38d44bd https://github.com/galaxyproject/galaxy/commit/c33cd1665d3bfed2dd75086735a0… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/datatypes_conf.xml.sample M config/job_conf.xml.sample_advanced M doc/Makefile M doc/source/admin/apache.md M doc/source/admin/config_logging.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md M lib/galaxy/datatypes/sniff.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/xml_util.py M scripts/check_python.py M templates/webapps/tool_shed/common/common.mako M test/api/test_workflows.py M test/galaxy_selenium/cli.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/workflows/test_modules.py M test/unit/workflows/workflow_support.py M tool-data/intermine_simple_display.loc.sample M tox.ini Log Message: ----------- Merge branch 'dev' into tagging_component_3 Commit: c89f6ef5764d26191ae4b30a2faef8c1776e65d9 https://github.com/galaxyproject/galaxy/commit/c89f6ef5764d26191ae4b30a2fae… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: A client/galaxy/scripts/components/Tags/GalaxyTags.usage.txt M client/galaxy/scripts/components/Tags/GalaxyTags.vue R client/galaxy/scripts/components/Tags/autocomplete_tagging.scss M client/galaxy/scripts/components/Tags/tagStyles.scss M client/galaxy/scripts/store/index.js M client/galaxy/scripts/viz/trackster.js A client/galaxy/style/scss/autocomplete_tagging.scss Log Message: ----------- Minor refinements of main galaxy tags component Commit: 410513e4e3fba93cb5634cc8a6d1d99366f129f8 https://github.com/galaxyproject/galaxy/commit/410513e4e3fba93cb5634cc8a6d1… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M client/galaxy/scripts/components/Tags/StandardTags.vue M templates/tagging_common.mako Log Message: ----------- Disabled editing for community tags display, fixed tag loading in mako, removed redundant component styles Commit: d6836c5998d0d63156fd9043cf3a714d8718aa27 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lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M scripts/common_startup.sh M templates/display_common.mako R templates/user/index.mako R templates/user/logout.mako R templates/user/register.mako M templates/webapps/tool_shed/user/login.mako A templates/webapps/tool_shed/user/logout.mako A templates/webapps/tool_shed/user/register.mako A test-data/groupby_out1.dat A test-data/groupby_out2.dat A test-data/groupby_out3.tabular A test-data/groupby_out4.tabular A test-data/matrix.cool M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_users.py M test/base/api.py M test/base/integration_util.py M test/functional/tools/output_filter.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_containerized_jobs.py M test/integration/test_job_recovery.py A test/integration/test_kubernetes_runner.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_registration.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_toolbox_filters.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/upload.py M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge branch 'dev' into tagging_component_3 Commit: 4af2bdeaef3d493b7c55f46445aeabff720b1b1e https://github.com/galaxyproject/galaxy/commit/4af2bdeaef3d493b7c55f46445ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M client/galaxy/scripts/components/Tags/GalaxyTags.test.js M client/galaxy/scripts/components/Tags/GalaxyTags.vue M client/galaxy/scripts/components/Tags/StandardTags.test.js M client/galaxy/scripts/components/Tags/StandardTags.vue M client/galaxy/scripts/components/Tags/model.js M client/galaxy/scripts/components/Tags/model.test.js M client/galaxy/scripts/components/Tags/tagService.js M client/galaxy/scripts/components/Tags/tagService.test.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/store/gridSearchStore.js M client/galaxy/scripts/utils/mountVueComponent.js M client/galaxy/scripts/utils/redirect.js Log Message: ----------- Client format. Commit: 8828fec5ee2aa9506a0475f33049255c48d02883 https://github.com/galaxyproject/galaxy/commit/8828fec5ee2aa9506a0475f33049… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M client/webpack.config.js Log Message: ----------- Drop vue resolver alias, use default package entrypoint. Commit: 4e2de8facb252214902aac70f60aaefca8309e78 https://github.com/galaxyproject/galaxy/commit/4e2de8facb252214902aac70f60a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M client/galaxy/scripts/bundleEntries.js M client/webpack.config.js Log Message: ----------- future-proof store alias used in old code Commit: 4ec49c1197e42fe2ac71a4d973955c26d3072452 https://github.com/galaxyproject/galaxy/commit/4ec49c1197e42fe2ac71a4d97395… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: R client/.babelrc M client/galaxy/scripts/bundleEntries.js A client/galaxy/scripts/components/Tags/GalaxyTags.test.js A client/galaxy/scripts/components/Tags/GalaxyTags.usage.txt A client/galaxy/scripts/components/Tags/GalaxyTags.vue A client/galaxy/scripts/components/Tags/StandardTags.test.js A client/galaxy/scripts/components/Tags/StandardTags.vue A client/galaxy/scripts/components/Tags/index.js A client/galaxy/scripts/components/Tags/inits.js A client/galaxy/scripts/components/Tags/model.js A client/galaxy/scripts/components/Tags/model.test.js A client/galaxy/scripts/components/Tags/tagService.js A client/galaxy/scripts/components/Tags/tagService.test.js A client/galaxy/scripts/components/Tags/testData/autocompleteResponse.txt M client/galaxy/scripts/entry/analysis/AnalysisRouter.js M client/galaxy/scripts/mvc/grid/grid-view.js R client/galaxy/scripts/sample.test.js A client/galaxy/scripts/store/gridSearchStore.js A client/galaxy/scripts/store/index.js R client/galaxy/scripts/ui/autocom_tagging.js R client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/mountVueComponent.js A client/galaxy/scripts/utils/redirect.js M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/mixins.scss M client/karma/karma.config.mocha.js M client/karma/karma.config.qunit.js M client/karma/webpack.config.unittest.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/reports/framework/grids.py M templates/tagging_common.mako M templates/webapps/galaxy/workflow/editor.mako M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #7270 from Nerdinacan/tagging_component_3 Tagging component Compare: https://github.com/galaxyproject/galaxy/compare/d3c51d6d29cd...4ec49c1197e4

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[galaxyproject/galaxy] 3f7528: Allow connecting nested collections to multiple=tr...
by John Chilton 04 Mar '19

04 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f752864aeecb0f64b5d64b00933d817cc5ae721 https://github.com/galaxyproject/galaxy/commit/3f752864aeecb0f64b5d64b00933… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Allow connecting nested collections to multiple=true inputs in workflow editor Commit: 38219a2499af233edea95b3b7430ed359c9a752e https://github.com/galaxyproject/galaxy/commit/38219a2499af233edea95b3b7430… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Only decrement output termninal map over Otherwise collection connections into multiple="true" inputs would be destroyed by the `destroyIfInvalid` check. Commit: ebd6c5cead38b257dab45a8990304d66ba695778 https://github.com/galaxyproject/galaxy/commit/ebd6c5cead38b257dab45a899030… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Don't allow connection to paired input, fix qunit test Commit: 6c22f13e3ad7773337f84e72ab21d295f934ee9e https://github.com/galaxyproject/galaxy/commit/6c22f13e3ad7773337f84e72ab21… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix qunit test Commit: d3c51d6d29cd0605c21d96006d40cb5c889b235e https://github.com/galaxyproject/galaxy/commit/d3c51d6d29cd0605c21d96006d40… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #7435 from mvdbeek/multiple_true_nesting_wf_editor Allow connecting nested collections to multiple=true inputs in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/050f9b662c8e...d3c51d6d29cd

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[galaxyproject/galaxy] bf8dbd: Slim down testing image
by Martin Cech 04 Mar '19

04 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf8dbdade3b009d7bd0822b657374b992342a466 https://github.com/galaxyproject/galaxy/commit/bf8dbdade3b009d7bd0822b65737… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Slim down testing image Commit: d9ac24a9828daa00120da3014634c38a34e1934b https://github.com/galaxyproject/galaxy/commit/d9ac24a9828daa00120da3014634… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Don't install slurm, it isn't used in any test Commit: 3bed43fb841a371ab350406dc8b01dd5ce55dad8 https://github.com/galaxyproject/galaxy/commit/3bed43fb841a371ab350406dc8b0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Don't add compiler-stack (will still come in ansible), use prebuilt singularity Commit: a0fd6438d99d55a5337fc5fbdf2a8629b2779c4b https://github.com/galaxyproject/galaxy/commit/a0fd6438d99d55a5337fc5fbdf2a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M test/docker/base/ansible_vars.yml Log Message: ----------- Directlyy setup virtualenv in /galaxy_venv, saves 700MB Commit: c357d303fe57a685cf57895bac9070828c81bbec https://github.com/galaxyproject/galaxy/commit/c357d303fe57a685cf57895bac90… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M run_tests.sh Log Message: ----------- Test from new image Commit: 087070c72ce212cadedbd3dc5b2b2ae823b980c6 https://github.com/galaxyproject/galaxy/commit/087070c72ce212cadedbd3dc5b2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Still need python3-dev for uwsgi Commit: 0455eb4f665dca2f9ba4d7129f31aeb2f2dbf579 https://github.com/galaxyproject/galaxy/commit/0455eb4f665dca2f9ba4d7129f31… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M run_tests.sh Log Message: ----------- Use newer image Commit: b0f3d921492870310ec50d240f5af397cca9b8d0 https://github.com/galaxyproject/galaxy/commit/b0f3d921492870310ec50d240f5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M test/base/integration_util.py M test/integration/test_containerized_jobs.py Log Message: ----------- Don't use skip_unless_docker decorator This is handled in setupClass. Also drop unused skip_unless_singularity. Commit: d5f3efbf08b07bdc2891c7b1c713f6ba2abe7c6e https://github.com/galaxyproject/galaxy/commit/d5f3efbf08b07bdc2891c7b1c713… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M run_tests.sh Log Message: ----------- Use new image from galaxy namespace Commit: 050f9b662c8e92e1a4c2386cb68145e2fc451aa1 https://github.com/galaxyproject/galaxy/commit/050f9b662c8e92e1a4c2386cb681… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M run_tests.sh M test/base/integration_util.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/integration/test_containerized_jobs.py Log Message: ----------- Merge pull request #7439 from mvdbeek/new_testing_image New testing image Compare: https://github.com/galaxyproject/galaxy/compare/cb8c60168363...050f9b662c8e

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[galaxyproject/galaxy] 90c29f: Allow configuring user preferences location
by Nicola Soranzo 04 Mar '19

04 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90c29fcaee81b11e15d3781e5a9a7bd2a75a8186 https://github.com/galaxyproject/galaxy/commit/90c29fcaee81b11e15d3781e5a9a… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow configuring user preferences location Commit: 9fad329e3fa2d14314d8e608257e9c0bc1497f6b https://github.com/galaxyproject/galaxy/commit/9fad329e3fa2d14314d8e608257e… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Load at boot time and not runtime Commit: 2362f77a084a9e17c051730a6ed78fded20df1fa https://github.com/galaxyproject/galaxy/commit/2362f77a084a9e17c051730a6ed7… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/config.py Log Message: ----------- Remove default per @martenson suggestion Commit: 43a68a30ca1df4b1358bfad9014c18921958db07 https://github.com/galaxyproject/galaxy/commit/43a68a30ca1df4b1358bfad9014c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/config.py Log Message: ----------- Update lib/galaxy/config.py Co-Authored-By: erasche <hxr(a)hx42.org> Commit: c2d4645e213446cee21dd37063f4dc2df52ea462 https://github.com/galaxyproject/galaxy/commit/c2d4645e213446cee21dd37063f4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/config.py Log Message: ----------- fix import ordering Commit: c533aa49f8ad9aaa569b2ffeaf8e666fd92c103f https://github.com/galaxyproject/galaxy/commit/c533aa49f8ad9aaa569b2ffeaf8e… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Correct help per @nsoranzo request Commit: fa559f49a85968da3f775f0adbfe9d64aafb3195 https://github.com/galaxyproject/galaxy/commit/fa559f49a85968da3f775f0adbfe… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'user-prefs-location' of github.com:erasche/galaxy into user-prefs-location Commit: cb8c60168363479a8b3d976d828674aa5c0ff4dd https://github.com/galaxyproject/galaxy/commit/cb8c60168363479a8b3d976d8286… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7428 from erasche/user-prefs-location Allow configuration location of user preferences extra configuration Compare: https://github.com/galaxyproject/galaxy/compare/a5ff4eabc09a...cb8c60168363

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[galaxyproject/galaxy] c2c73f: Fix shallow clone on CircleCI for PRs
by Martin Cech 04 Mar '19

04 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2c73f624d6af5cc8d27d57dbdc14636f7eaa8a2 https://github.com/galaxyproject/galaxy/commit/c2c73f624d6af5cc8d27d57dbdc1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M .circleci/config.yml Log Message: ----------- Fix shallow clone on CircleCI for PRs Commit: a5ff4eabc09a3ede79aae138de21c0cf4c70e943 https://github.com/galaxyproject/galaxy/commit/a5ff4eabc09a3ede79aae138de21… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M .circleci/config.yml Log Message: ----------- Merge pull request #7451 from nsoranzo/fix_circleci_PRs Fix shallow clone on CircleCI for PRs Compare: https://github.com/galaxyproject/galaxy/compare/d359c70a0ed5...a5ff4eabc09a

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[galaxyproject/ansible-galaxy] d07ef3: forgot another check mode
by Helena Rasche 04 Mar '19

04 Mar '19

Branch: refs/heads/check-mode Home: https://github.com/galaxyproject/ansible-galaxy Commit: d07ef3bae57904cde204551256d34aca0105925c https://github.com/galaxyproject/ansible-galaxy/commit/d07ef3bae57904cde204… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M tasks/dependencies.yml Log Message: ----------- forgot another check mode

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[galaxyproject/galaxy] 338aae: Restore get_filename to galaxy.tools.verify:verify()
by John Chilton 03 Mar '19

03 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 338aae53f2ce2c0ddb4df9b259a24737efd07f3f https://github.com/galaxyproject/galaxy/commit/338aae53f2ce2c0ddb4df9b259a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Restore get_filename to galaxy.tools.verify:verify() Commit: d359c70a0ed533c43a75106ab4a448fa69d85c15 https://github.com/galaxyproject/galaxy/commit/d359c70a0ed533c43a75106ab4a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #7452 from jmchilton/restore_verify_getfilename Restore get_filename to galaxy.tools.verify:verify() Compare: https://github.com/galaxyproject/galaxy/compare/7017d92d1063...d359c70a0ed5

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[galaxyproject/galaxy] 5142d0: Fix loading workflows with steps without default l...
by Nicola Soranzo 03 Mar '19

03 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5142d0df0732faaf5983d4bb2c025a89e93f5964 https://github.com/galaxyproject/galaxy/commit/5142d0df0732faaf5983d4bb2c02… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix loading workflows with steps without default label Prior to https://github.com/galaxyproject/galaxy/pull/7422 we'd call str(default_label), so if `default_label` was None we'd get 'None'. Fixes part of https://github.com/galaxyproject/galaxy/issues/7447 Commit: bc8cf37d09b66efaa994735e994d69998ee34695 https://github.com/galaxyproject/galaxy/commit/bc8cf37d09b66efaa994735e994d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Remove broken tool_submission_burst Commit: d96034062af9fc358b1c4f3964f0492d4000b3b8 https://github.com/galaxyproject/galaxy/commit/d96034062af9fc358b1c4f3964f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- fix lint Commit: 6c80ca50a44d75a675a08c466cbd78726cc64b90 https://github.com/galaxyproject/galaxy/commit/6c80ca50a44d75a675a08c466cbd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7449 from mvdbeek/remove_broken_tool_submission_burst [18.09] Remove broken tool_submission_burst Commit: 996d7c9a60f037ca1e0120c201e74d2072c29d8d https://github.com/galaxyproject/galaxy/commit/996d7c9a60f037ca1e0120c201e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #7448 from mvdbeek/fix_when_default_label_is_none [18.09] Fix loading workflows with steps without default label Commit: 91e49acf374fe60b5c8a4dae2fbb448cc626019d https://github.com/galaxyproject/galaxy/commit/91e49acf374fe60b5c8a4dae2fbb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 7017d92d1063b70906951541ce248f5eefe05907 https://github.com/galaxyproject/galaxy/commit/7017d92d1063b70906951541ce24… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d04b32d0ac58...7017d92d1063

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