- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c9d039: Fix trackster toolbox filter for logged-in users
by Dannon 07 Feb '19

07 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9d039d54bd04bff9ecf5fb95843c1a3a53668c3 https://github.com/galaxyproject/galaxy/commit/c9d039d54bd04bff9ecf5fb95843… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Fix trackster toolbox filter for logged-in users Broken in commits 7a2f6cba32c5dd28d9a53329a6b3f71453cbd45d and f1ff62e82a620067a72f7705712afcc1e94ab72b Restore corresponding unit test. Commit: d19c30cc0a41baa1dbf2b95085c171cb86e38ece https://github.com/galaxyproject/galaxy/commit/d19c30cc0a41baa1dbf2b95085c1… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Merge pull request #7319 from nsoranzo/fix_trackster_toolbox_filter Fix trackster toolbox filter for logged-in users Compare: https://github.com/galaxyproject/galaxy/compare/0df943f5e3d0...d19c30cc0a41

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[galaxyproject/galaxy] 8acd07: Remove architecture slides
by John Chilton 07 Feb '19

07 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8acd07a50faf1b0f215d435e389a626237c22ca4 https://github.com/galaxyproject/galaxy/commit/8acd07a50faf1b0f215d435e389a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: R doc/source/slideshow/architecture/galaxy_architecture.md R doc/source/slideshow/architecture/images/backbone-model-view.svg R doc/source/slideshow/architecture/images/cluster_support.svg R doc/source/slideshow/architecture/images/data_managers.svg R doc/source/slideshow/architecture/images/docker-chart.png R doc/source/slideshow/architecture/images/family/team.png R doc/source/slideshow/architecture/images/galaxy_schema.png R doc/source/slideshow/architecture/images/hda.svg R doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg R doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt R doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg R doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt R doc/source/slideshow/architecture/images/jsload.png R doc/source/slideshow/architecture/images/libraries.svg R doc/source/slideshow/architecture/images/library_permissions.svg R doc/source/slideshow/architecture/images/objectstore.plantuml.svg R doc/source/slideshow/architecture/images/objectstore.plantuml.txt R doc/source/slideshow/architecture/images/objectstore_diagram.svg R doc/source/slideshow/architecture/images/plantuml_options.txt R doc/source/slideshow/architecture/images/sequence.json R doc/source/slideshow/architecture/images/server_client.plantuml.svg R doc/source/slideshow/architecture/images/server_client.plantuml.txt R doc/source/slideshow/architecture/images/server_client_old.plantuml.svg R doc/source/slideshow/architecture/images/server_client_old.plantuml.txt R doc/source/slideshow/architecture/images/sqla_arch_small.png R doc/source/slideshow/architecture/images/usegalaxy_webservers.svg R doc/source/slideshow/architecture/images/usegalaxyorg.svg R doc/source/slideshow/architecture/images/webapp.plantuml.svg R doc/source/slideshow/architecture/images/webapp.plantuml.txt R doc/source/slideshow/architecture/images/what-is-webpack.svg R doc/source/slideshow/architecture/images/workflow_definition.svg R doc/source/slideshow/architecture/images/workflow_run.svg R doc/source/slideshow/architecture/images/wsgi_app.svg R doc/source/slideshow/architecture/images/wsgi_request.svg R doc/source/slideshow/architecture/remark-latest.min.js R doc/source/slideshow/architecture/style.css Log Message: ----------- Remove architecture slides Now available at https://galaxyproject.github.io/training-material/topics/dev/tutorials/arch… Commit: e725f8423a68c5fb802cdbe27c17d30f01272c3c https://github.com/galaxyproject/galaxy/commit/e725f8423a68c5fb802cdbe27c17… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M doc/source/admin/apache.md M doc/source/admin/cluster.md M doc/source/admin/config.rst M doc/source/admin/jobs.md M doc/source/admin/nginx.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/conf.py M doc/source/releases/16.10.rst M doc/source/releases/17.09_announce.rst M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Disable auto toctree for Markdown docs. Doc syntax fixes recommonmark allows now to use the `.md` extension for cross referencing other documents, which also works on GitHub. Commit: e97634739dcb84985a14cedf4f483890c3c4d31c https://github.com/galaxyproject/galaxy/commit/e97634739dcb84985a14cedf4f48… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M .gitignore M Makefile M doc/Makefile R doc/fix_schema_rst.sh M doc/parse_gx_xsd.py M doc/source/conf.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt Log Message: ----------- Build tool XML schema docs using ``sphinx_markdown_tables`` instead of converting the Markdown to reStructuredText with pandoc. Fix the broken tables, but code inside tables is not coloured as in the rest of the document. Commit: 0df943f5e3d0229d5d355e842b15cf6cdc662914 https://github.com/galaxyproject/galaxy/commit/0df943f5e3d0229d5d355e842b15… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M .gitignore M Makefile M doc/Makefile R doc/fix_schema_rst.sh M doc/parse_gx_xsd.py M doc/source/admin/apache.md M doc/source/admin/cluster.md M doc/source/admin/config.rst M doc/source/admin/jobs.md M doc/source/admin/nginx.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/conf.py M doc/source/releases/16.10.rst M doc/source/releases/17.09_announce.rst R doc/source/slideshow/architecture/galaxy_architecture.md R doc/source/slideshow/architecture/images/backbone-model-view.svg R doc/source/slideshow/architecture/images/cluster_support.svg R doc/source/slideshow/architecture/images/data_managers.svg R doc/source/slideshow/architecture/images/docker-chart.png R doc/source/slideshow/architecture/images/family/team.png R doc/source/slideshow/architecture/images/galaxy_schema.png R doc/source/slideshow/architecture/images/hda.svg R doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg R doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt R doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg R doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt R doc/source/slideshow/architecture/images/jsload.png R doc/source/slideshow/architecture/images/libraries.svg R doc/source/slideshow/architecture/images/library_permissions.svg R doc/source/slideshow/architecture/images/objectstore.plantuml.svg R doc/source/slideshow/architecture/images/objectstore.plantuml.txt R doc/source/slideshow/architecture/images/objectstore_diagram.svg R doc/source/slideshow/architecture/images/plantuml_options.txt R doc/source/slideshow/architecture/images/sequence.json R doc/source/slideshow/architecture/images/server_client.plantuml.svg R doc/source/slideshow/architecture/images/server_client.plantuml.txt R doc/source/slideshow/architecture/images/server_client_old.plantuml.svg R doc/source/slideshow/architecture/images/server_client_old.plantuml.txt R doc/source/slideshow/architecture/images/sqla_arch_small.png R doc/source/slideshow/architecture/images/usegalaxy_webservers.svg R doc/source/slideshow/architecture/images/usegalaxyorg.svg R doc/source/slideshow/architecture/images/webapp.plantuml.svg R doc/source/slideshow/architecture/images/webapp.plantuml.txt R doc/source/slideshow/architecture/images/what-is-webpack.svg R doc/source/slideshow/architecture/images/workflow_definition.svg R doc/source/slideshow/architecture/images/workflow_run.svg R doc/source/slideshow/architecture/images/wsgi_app.svg R doc/source/slideshow/architecture/images/wsgi_request.svg R doc/source/slideshow/architecture/remark-latest.min.js R doc/source/slideshow/architecture/style.css M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #7313 from nsoranzo/doc_fixes Build tool XML schema docs using ``sphinx_markdown_tables`` Compare: https://github.com/galaxyproject/galaxy/compare/da4dbbac3f1c...0df943f5e3d0

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[galaxyproject/galaxy] 756f57: Remove unused keyword in resend email helper
by Nicola Soranzo 07 Feb '19

07 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 756f5788b03028c2a190c418c6afc64fedca8a4a https://github.com/galaxyproject/galaxy/commit/756f5788b03028c2a190c418c6af… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove unused keyword in resend email helper Commit: da4dbbac3f1c982a19365089d725a9e140c47f88 https://github.com/galaxyproject/galaxy/commit/da4dbbac3f1c982a19365089d725… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #7315 from guerler/remove_unavailable_key_word Remove unused keyword in resend email helper Compare: https://github.com/galaxyproject/galaxy/compare/a74376abec87...da4dbbac3f1c

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[galaxyproject/galaxy] 778aa3: Add registration routes to admin app
by Dannon 06 Feb '19

06 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 778aa301e344b2755714a318e7f4db8599b4444f https://github.com/galaxyproject/galaxy/commit/778aa301e344b2755714a318e7f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/apps/admin.js Log Message: ----------- Add registration routes to admin app Commit: 8b76d7e8075d2aa777e2e5af4585df4e0f672557 https://github.com/galaxyproject/galaxy/commit/8b76d7e8075d2aa777e2e5af4585… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: A client/galaxy/scripts/components/login/Index.vue Log Message: ----------- Add shared login/registration vue Commit: 63db28c853a19506f9dcc28e5f5ad7083418ad71 https://github.com/galaxyproject/galaxy/commit/63db28c853a19506f9dcc28e5f5a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: A client/galaxy/scripts/components/login/Register.vue Log Message: ----------- Add registration vue Commit: 68165da79f5e1cdcc59d8c53e2fea6ef6b7ab82b https://github.com/galaxyproject/galaxy/commit/68165da79f5e1cdcc59d8c53e2fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Adjust masthead to new registration route Commit: 9ed6b9dadb8b6aba796265e5c1dce0d3ff31c239 https://github.com/galaxyproject/galaxy/commit/9ed6b9dadb8b6aba796265e5c1dc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/managers/configuration.py Log Message: ----------- Add required configuration attributes to serializer Commit: 487fbdace397d9b3a8a487449e4f82e82f76b910 https://github.com/galaxyproject/galaxy/commit/487fbdace397d9b3a8a487449e4f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Add registration features to user manager Commit: e49d03a68d92cc1fa26d79c249e3e17fe903c06a https://github.com/galaxyproject/galaxy/commit/e49d03a68d92cc1fa26d79c249e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Augment admin controller Commit: 3a29c9b3f2020328bcab617db9090f68b1fae94d https://github.com/galaxyproject/galaxy/commit/3a29c9b3f2020328bcab617db909… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Use user managers registration feature in user controller Commit: f256dff7a39747e1f44c3848de0cd95f81b36893 https://github.com/galaxyproject/galaxy/commit/f256dff7a39747e1f44c3848de0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: R templates/user/register.mako A templates/webapps/tool_shed/user/register.mako Log Message: ----------- Move unused register mako to toolshed Commit: 323df2a81d33bd1eb6b626bc294c23a18b0bf1d8 https://github.com/galaxyproject/galaxy/commit/323df2a81d33bd1eb6b626bc294c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M templates/webapps/tool_shed/user/register.mako Log Message: ----------- Revise registration mako Commit: 63597b2faa3ef32d278ab88ab66ac49e91026c50 https://github.com/galaxyproject/galaxy/commit/63597b2faa3ef32d278ab88ab66a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/apps/login.js Log Message: ----------- Adjust login app Commit: 15fe780ba6dd3b3a26c7c9777e1fe19570662099 https://github.com/galaxyproject/galaxy/commit/15fe780ba6dd3b3a26c7c9777e1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Move legacy registration features to toolshed Commit: 0b0ec5b806e982cfce2db6bd5bbd327140e8f9c6 https://github.com/galaxyproject/galaxy/commit/0b0ec5b806e982cfce2db6bd5bbd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/user.py M templates/webapps/tool_shed/user/login.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Restore legacy toolshed login form styles Commit: 754b6a7e074349b5b5246177f90f1bba37211e5b https://github.com/galaxyproject/galaxy/commit/754b6a7e074349b5b5246177f90f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-08 (Sat, 08 Dec 2018) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_registration.py Log Message: ----------- Fix selenium tests Commit: fdc6557ab67e3621e3fa37bb5a19412d992b5069 https://github.com/galaxyproject/galaxy/commit/fdc6557ab67e3621e3fa37bb5a19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M .ci/jenkins/integration-py3/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .travis.yml M Makefile A client/.eslintignore A client/.eslintrc.js M client/README.md M client/galaxy/scripts/app/galaxy.js M client/galaxy/scripts/app/index.js M client/galaxy/scripts/app/monitor.js M client/galaxy/scripts/app/singleton.js R client/galaxy/scripts/apps/admin.js R client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/chart.js R client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/login.js R client/galaxy/scripts/apps/panels/admin-panel.js R client/galaxy/scripts/apps/panels/history-panel.js R client/galaxy/scripts/apps/panels/tool-panel.js A 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client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/components/admin/DataTypes.vue A client/galaxy/scripts/components/admin/DisplayApplications.vue A client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Password.vue A client/galaxy/scripts/entry/admin/AdminRouter.js A client/galaxy/scripts/entry/admin/index.js A client/galaxy/scripts/entry/analysis/AnalysisRouter.js A 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client/galaxy/scripts/mvc/grid/grid-model.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/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js R client/galaxy/scripts/mvc/job/job-params.js M 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test/integration/test_scripts.py A test/integration/test_workflow_sync.py M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_UserManager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py R tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/grouping.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tox.ini Log Message: ----------- Merge branch 'dev' into registration_mako Commit: 4ef0575840c5bfff53fa4ad6fe582aa17eaca77d https://github.com/galaxyproject/galaxy/commit/4ef0575840c5bfff53fa4ad6fe58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Index.vue Log Message: ----------- Strip openid legacy from registration Commit: 142f8aa9c699e249740ff0f5b60aaaaf89e49537 https://github.com/galaxyproject/galaxy/commit/142f8aa9c699e249740ff0f5b60a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Index.vue Log Message: ----------- Remove unused axios import in login index vue Commit: 29fa76c74ff73cbc09107924160426470fbdb6c0 https://github.com/galaxyproject/galaxy/commit/29fa76c74ff73cbc091079241604… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Index.vue M client/galaxy/scripts/components/login/Register.vue Log Message: ----------- Fix access to galaxy root in registration vue Commit: e3edd7a6c194e6d09c0aa9bafe8f0e21d470c53d https://github.com/galaxyproject/galaxy/commit/e3edd7a6c194e6d09c0aa9bafe8f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Fix activation link submission order Commit: c906f84654977928051c9135bd628c0a1c518383 https://github.com/galaxyproject/galaxy/commit/c906f84654977928051c9135bd62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Allow users to register and login if initial activation email submission fails Commit: d8cc0336b2c5aba9552c417de2fc1845d459cfe2 https://github.com/galaxyproject/galaxy/commit/d8cc0336b2c5aba9552c417de2fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/actions/library.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M tools/data_source/data_source.py Log Message: ----------- Merge branch 'dev' into registration_mako Commit: 31d511b5269a2f848c600c702109b2d10fb3c7f3 https://github.com/galaxyproject/galaxy/commit/31d511b5269a2f848c600c702109… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M client/galaxy/scripts/components/RuleCollectionBuilder.vue 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/mvc/rules/rule-definitions.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/authentication.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/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-requirements.txt M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/filelock.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/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 test/api/test_histories.py M test/unit/test_utils.py M tools/filters/sff_extract.py Log Message: ----------- Merge branch 'dev' into registration_mako Commit: 4a155c7cbf2fdc2684237595764f013a2caac30c https://github.com/galaxyproject/galaxy/commit/4a155c7cbf2fdc2684237595764f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M test/selenium_tests/test_registration.py Log Message: ----------- Fix registration error message content Commit: a618905b7c626a8c0a42d1f4768844c1c9f7565c https://github.com/galaxyproject/galaxy/commit/a618905b7c626a8c0a42d1f47688… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M cron/add_manual_builds.py M doc/source/admin/cluster.md M lib/galaxy/actions/library.py 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/pulsar.py M lib/galaxy/managers/jobs.py M lib/galaxy/tools/imp_exp/__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/hash_util.py M lib/galaxy/webapps/galaxy/api/toolshed.py M scripts/check_python.py M templates/webapps/galaxy/workflow/display.mako M test/api/test_workflows.py M test/functional/test_toolbox.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 tools/maf/maf_to_bed.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into registration_mako Commit: 60d9592bcaddefbcd824933ac09d123994785a50 https://github.com/galaxyproject/galaxy/commit/60d9592bcaddefbcd824933ac09d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Index.vue M client/galaxy/scripts/components/login/Register.vue M client/galaxy/scripts/entry/admin/AdminRouter.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Client format sync. Commit: de886ef3c64d08338016d524fe8157b3651fb391 https://github.com/galaxyproject/galaxy/commit/de886ef3c64d08338016d524fe81… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Register.vue Log Message: ----------- Constrain registration form to match the login form's sizing (looks much better this way) Commit: 948ecfadf1236db0953c8b6926bff6e1d7537ccb https://github.com/galaxyproject/galaxy/commit/948ecfadf1236db0953c8b6926bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Index.vue M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue Log Message: ----------- Swap from tabs to a toggle with some ushering text. Commit: a960d0086b29ecc746247e2d77c74a375d8e4d0e https://github.com/galaxyproject/galaxy/commit/a960d0086b29ecc746247e2d77c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue Log Message: ----------- Fix link highlights in footer, slightly modify header for register card. Commit: f8d9dee591a9a1a2b5a203fa97bd0de4710c3ac6 https://github.com/galaxyproject/galaxy/commit/f8d9dee591a9a1a2b5a203fa97bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue Log Message: ----------- Since we're not using the router yet for swapping (we will, instead of toggling as was done here), use click.prevent. Commit: 9da2367a023e057c8f3ab3f9685fdcfcf93ec215 https://github.com/galaxyproject/galaxy/commit/9da2367a023e057c8f3ab3f9685f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Index.vue Log Message: ----------- Drop unused debug Commit: 5524805800ca4847a40b277d61daa8be7f784605 https://github.com/galaxyproject/galaxy/commit/5524805800ca4847a40b277d61da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix login/register selenium navigation targets. Commit: a74376abec87fb85200db674124842d788117208 https://github.com/galaxyproject/galaxy/commit/a74376abec87fb85200db6741248… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: A client/galaxy/scripts/components/login/Index.vue M client/galaxy/scripts/components/login/Login.vue A client/galaxy/scripts/components/login/Register.vue M client/galaxy/scripts/entry/admin/AdminRouter.js M client/galaxy/scripts/entry/login/index.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M lib/galaxy/managers/configuration.py M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py R templates/user/register.mako M templates/webapps/tool_shed/user/login.mako A templates/webapps/tool_shed/user/register.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_registration.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #6621 from guerler/registration_mako Replace registration mako with vue component Compare: https://github.com/galaxyproject/galaxy/compare/415444d31028...a74376abec87

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[galaxyproject/galaxy] bf5414: Use es6 literal for library toolbar header, use ic...
by Martin Cech 06 Feb '19

06 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf5414d7e037e37de3c5df87649e3ebef0f2a21f https://github.com/galaxyproject/galaxy/commit/bf5414d7e037e37de3c5df87649e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- Use es6 literal for library toolbar header, use icon buttons, left align Commit: 8702d671a8250fb67d49a76ae72b4a50e675bc43 https://github.com/galaxyproject/galaxy/commit/8702d671a8250fb67d49a76ae72b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- Use es6 for library folder template, align toolbar appearance with library list view Commit: 3caa59634a22850d0b12ae7556d5bc52e58b11f3 https://github.com/galaxyproject/galaxy/commit/3caa59634a22850d0b12ae7556d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revise history export button Commit: b44f8475806f0379fa8a0d4443bd94262da6e24d https://github.com/galaxyproject/galaxy/commit/b44f8475806f0379fa8a0d4443bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: A client/galaxy/scripts/components/login/Login.vue A client/galaxy/scripts/components/login/Password.vue R client/galaxy/scripts/entry/login/LoginPage.js M client/galaxy/scripts/entry/login/index.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/upload.scss M config/job_conf.xml.sample_advanced M lib/galaxy/actions/library.py M lib/galaxy/auth/__init__.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh R templates/user/info.mako R templates/user/login.mako R templates/user/reset_password.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/user/change_password.mako M templates/webapps/tool_shed/user/index.mako A templates/webapps/tool_shed/user/login.mako M templates/webapps/tool_shed/user/manage_info.mako A templates/webapps/tool_shed/user/reset_password.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_login.py M test/shed_functional/base/twilltestcase.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_UserManager.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/data_source.py Log Message: ----------- Merge branch 'dev' into library_fix Commit: b5ec33230fffb964d7fbf12ff47b96dddf617a02 https://github.com/galaxyproject/galaxy/commit/b5ec33230fffb964d7fbf12ff47b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-30 (Wed, 30 Jan 2019) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M client/galaxy/scripts/components/RuleCollectionBuilder.vue 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/mvc/rules/rule-definitions.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M config/galaxy.yml.sample M config/tool_shed.yml.sample 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/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-requirements.txt M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/filelock.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/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 test/api/test_histories.py M test/unit/test_utils.py M tools/filters/sff_extract.py Log Message: ----------- Merge branch 'dev' into library_fix Commit: 88724a2d9cd1e3081d0e6c2e5010f63c092dfe36 https://github.com/galaxyproject/galaxy/commit/88724a2d9cd1e3081d0e6c2e5010… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M cron/add_manual_builds.py M lib/galaxy/actions/library.py 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/pulsar.py M lib/galaxy/managers/jobs.py M lib/galaxy/tools/imp_exp/__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/hash_util.py M lib/galaxy/webapps/galaxy/api/toolshed.py M scripts/check_python.py M templates/webapps/galaxy/workflow/display.mako M test/api/test_workflows.py M test/functional/test_toolbox.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 tools/maf/maf_to_bed.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into library_fix Commit: 415444d31028ad650967cd100862c1a3262818c8 https://github.com/galaxyproject/galaxy/commit/415444d31028ad650967cd100862… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- Merge pull request #7234 from guerler/library_fix Use es6 literal for library toolbar header, use icon buttons, left align Compare: https://github.com/galaxyproject/galaxy/compare/2ec2933e0ebb...415444d31028

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[galaxyproject/galaxy] b59d76: Fix emoji tags
by Martin Cech 06 Feb '19

06 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: b59d76eb4a928af8866275cb91afd583a82fee99 https://github.com/galaxyproject/galaxy/commit/b59d76eb4a928af8866275cb91af… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix emoji tags Commit: dd917099ba43b3d9638c16623ca45bc13edfc9c5 https://github.com/galaxyproject/galaxy/commit/dd917099ba43b3d9638c16623ca4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Only block the single category of C characters that is problematic Co-Authored-By: erasche <hxr(a)hx42.org> Commit: e3f1234b2c1359e4d5353ba0e0b56834a964bb28 https://github.com/galaxyproject/galaxy/commit/e3f1234b2c1359e4d5353ba0e0b5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #7310 from erasche/fix-emoji-tags [19.01] Fix emoji tags Compare: https://github.com/galaxyproject/galaxy/compare/c4fbe94bcfee...e3f1234b2c13

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[galaxyproject/usegalaxy-playbook] bfebbc: Add Multiple Alignments section to Test
by Nate Coraor 06 Feb '19

06 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfebbc2bd1d0f9b1e0ca106cec230e8309ba8e9e https://github.com/galaxyproject/usegalaxy-playbook/commit/bfebbc2bd1d0f9b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Add Multiple Alignments section to Test

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[galaxyproject/usegalaxy-playbook] eb6c83: More tool panel updates for Test
by Nate Coraor 06 Feb '19

06 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: eb6c83fe74dff0260dbb0c3e21275561f1002bb8 https://github.com/galaxyproject/usegalaxy-playbook/commit/eb6c83fe74dff026… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- More tool panel updates for Test Commit: 9dc7fbf15dc7db0f832e9f7749fe7f06f5b1419b https://github.com/galaxyproject/usegalaxy-playbook/commit/9dc7fbf15dc7db0f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/main/files/galaxy/config/tool_conf.xml M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- (Untested) tool panel updates for Main Commit: d994112d73f2846edf8d5d04b475b189ede439cc https://github.com/galaxyproject/usegalaxy-playbook/commit/d994112d73f2846e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M env/test/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Rearrange Test tool panel again Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/9aad46a8b713...…

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[galaxyproject/galaxy] 9258b2: Define doctype method on XMLParser target
by Nicola Soranzo 06 Feb '19

06 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9258b28e7d2c5cdec497f723b7b124619546d52b https://github.com/galaxyproject/galaxy/commit/9258b28e7d2c5cdec497f723b7b1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Define doctype method on XMLParser target That should silence some Deprecation Warnings. Commit: 28240d83536abac75288f4fb79b981a6cc6a83f1 https://github.com/galaxyproject/galaxy/commit/28240d83536abac75288f4fb79b9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Remove deprecated U mode option Commit: 6c8a523d59c9783ed6d444a5dad8340837cc1ebe https://github.com/galaxyproject/galaxy/commit/6c8a523d59c9783ed6d444a5dad8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py Log Message: ----------- Replace more instances of 'U' mode Commit: 2ec2933e0ebbe4e33a27e8d855f9f0fc771c6ff5 https://github.com/galaxyproject/galaxy/commit/2ec2933e0ebbe4e33a27e8d855f9… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #7303 from mvdbeek/xml_parser_deprecation_warning Define doctype method on XMLParser target Compare: https://github.com/galaxyproject/galaxy/compare/3b49be59a12c...2ec2933e0ebb

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[galaxyproject/usegalaxy-playbook] 9aad46: Combine BCF Tools in to VCF Manipulation
by Nate Coraor 05 Feb '19

05 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9aad46a8b71363490f403fc10380586af2500eb7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9aad46a8b7136349… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Combine BCF Tools in to VCF Manipulation

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[galaxyproject/usegalaxy-playbook] 612d51: Use CVMFS path in Test shed_tool_conf.xml
by Nate Coraor 05 Feb '19

05 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 612d5183bfd439084157666bd277faede17dbfe9 https://github.com/galaxyproject/usegalaxy-playbook/commit/612d5183bfd43908… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Use CVMFS path in Test shed_tool_conf.xml Commit: 7ef7bbc7d3e5e8475eb8737a2187d460fe0d959b https://github.com/galaxyproject/usegalaxy-playbook/commit/7ef7bbc7d3e5e847… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Point Main migrated_tools_conf.xml and shed_tool_conf.xml at actual CVMFS paths instead of symlinks to CVMFS. Commit: bd4b0ddfb0293fcf3bee3b7636680ec0d4e34a79 https://github.com/galaxyproject/usegalaxy-playbook/commit/bd4b0ddfb0293fcf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/17c556e0caec...…

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[galaxyproject/usegalaxy-playbook] 17c556: update Test
by Martin Cech 05 Feb '19

05 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 17c556e0caec30b6994cd035070e0b3bf7f7ce2d https://github.com/galaxyproject/usegalaxy-playbook/commit/17c556e0caec30b6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update Test

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[galaxyproject/galaxy] 4df1de: Map over multiple=true in workflow run
by Martin Cech 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4df1de38ba390ee6513bc85fbb0643e6e152bd25 https://github.com/galaxyproject/galaxy/commit/4df1de38ba390ee6513bc85fbb06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Map over multiple=true in workflow run There is some unfortunate divergence between the mapping over code in tool runs vs workflow runs. Without this patch a list:list input to a multiple="true" data input would get fully reduced in workflow, while tool runs would just reduce the inner collection (and I think that's the correct behavior). Commit: cf68cbe907729283a8a359d9a8dbcb0013ebcee5 https://github.com/galaxyproject/galaxy/commit/cf68cbe907729283a8a359d9a8db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Verify that list:list will be reduced to list in multi data input Commit: a36b56e6940cf8e406ebca90114e2a9974e50e0d https://github.com/galaxyproject/galaxy/commit/a36b56e6940cf8e406ebca90114e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Drop redundant wait for history wait_for_invocation_and_jobs does that already, thx @nsoranzo. Commit: c4fbe94bcfeef2acc5edf516a625578c7578feff https://github.com/galaxyproject/galaxy/commit/c4fbe94bcfeef2acc5edf516a625… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #7302 from mvdbeek/dont_reduce_list_list_in_multi_data_input_workflow_step [19.01] Don't reduce list:list in multi data input workflow step Commit: 3b49be59a12cf886040e894d3b1b1e644ff7cfa4 https://github.com/galaxyproject/galaxy/commit/3b49be59a12cf886040e894d3b1b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e4d798cecdcb...3b49be59a12c

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[galaxyproject/galaxy] 9aed42: Determine collection_type for all workflow steps
by Dannon 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9aed429a359d0fdf3933417aae89e81e6981c8f2 https://github.com/galaxyproject/galaxy/commit/9aed429a359d0fdf3933417aae89… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Determine collection_type for all workflow steps Commit: 6a4307609d90264b45104ae017e1056d055e7170 https://github.com/galaxyproject/galaxy/commit/6a4307609d90264b45104ae017e1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Unit test resolve_collection_type Commit: 65583ba4034302e02c87bf2db8c84fb7b83c0dee https://github.com/galaxyproject/galaxy/commit/65583ba4034302e02c87bf2db8c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Don't fail if tool is not installed Commit: ef50e872973710774cf62fc5eb3b7a761e503259 https://github.com/galaxyproject/galaxy/commit/ef50e872973710774cf62fc5eb3b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Only fill collection_type for subworkflows, the top level stuff is managed by the client Commit: 5ac0802dd71236801ed0709f9b6df4014a60f850 https://github.com/galaxyproject/galaxy/commit/5ac0802dd71236801ed0709f9b6d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Don't display subworkflow inputs as workflow_outputs Commit: c5726c33b27756c1b5768f654b59935265160341 https://github.com/galaxyproject/galaxy/commit/c5726c33b27756c1b5768f654b59… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/workflow/modules.py Log Message: ----------- Add input collection_type when including subworkflow Commit: 667f8aa761df88d48f1c00dd7fd98bb764e0032d https://github.com/galaxyproject/galaxy/commit/667f8aa761df88d48f1c00dd7fd9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py M test/unit/workflows/workflow_support.py Log Message: ----------- Only add collection_type if collection_type has been specified We don't force the collection_type to be set in any way. We might want to think about defaulting to list if not specified, but that's not for now. Commit: e4d798cecdcb819c2f5ef4ee6caf8aa64b53faba https://github.com/galaxyproject/galaxy/commit/e4d798cecdcb819c2f5ef4ee6caf… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #7254 from mvdbeek/subworkflow_connectivity Determine collection_type for all workflow steps Compare: https://github.com/galaxyproject/galaxy/compare/0fba7f30c13c...e4d798cecdcb

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[galaxyproject/usegalaxy-playbook] a08bd2: Tool panel fixes for Assembly/Annotation/Mapping
by Nate Coraor 05 Feb '19

05 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a08bd26ccd758142c11070c90cab0dc42b512c32 https://github.com/galaxyproject/usegalaxy-playbook/commit/a08bd26ccd758142… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Tool panel fixes for Assembly/Annotation/Mapping Commit: 991d4f38a48e34e5ce4299cef2beb554b29cc32f https://github.com/galaxyproject/usegalaxy-playbook/commit/991d4f38a48e34e5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test usegalaxy.* toolbox sync Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/cce48a7764ed...…

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[galaxyproject/galaxy] 4df1de: Map over multiple=true in workflow run
by Nicola Soranzo 05 Feb '19

05 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 4df1de38ba390ee6513bc85fbb0643e6e152bd25 https://github.com/galaxyproject/galaxy/commit/4df1de38ba390ee6513bc85fbb06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Map over multiple=true in workflow run There is some unfortunate divergence between the mapping over code in tool runs vs workflow runs. Without this patch a list:list input to a multiple="true" data input would get fully reduced in workflow, while tool runs would just reduce the inner collection (and I think that's the correct behavior). Commit: cf68cbe907729283a8a359d9a8dbcb0013ebcee5 https://github.com/galaxyproject/galaxy/commit/cf68cbe907729283a8a359d9a8db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Verify that list:list will be reduced to list in multi data input Commit: a36b56e6940cf8e406ebca90114e2a9974e50e0d https://github.com/galaxyproject/galaxy/commit/a36b56e6940cf8e406ebca90114e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Drop redundant wait for history wait_for_invocation_and_jobs does that already, thx @nsoranzo. Commit: c4fbe94bcfeef2acc5edf516a625578c7578feff https://github.com/galaxyproject/galaxy/commit/c4fbe94bcfeef2acc5edf516a625… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #7302 from mvdbeek/dont_reduce_list_list_in_multi_data_input_workflow_step [19.01] Don't reduce list:list in multi data input workflow step Compare: https://github.com/galaxyproject/galaxy/compare/526bebbb2817...c4fbe94bcfee

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[galaxyproject/galaxy] 45a962: Update proxy dependencies -- mine wouldn't build a...
by Martin Cech 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45a962a8a8930ad6706372e4d770a23cd1ee777c https://github.com/galaxyproject/galaxy/commit/45a962a8a8930ad6706372e4d770… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Update proxy dependencies -- mine wouldn't build anymore with an older version of sqlite3. I'm hoping the versions I've updated to are backwards compatible in terms of compilation (seem to be in terms of functionality -- it's working for me), but I'd appreciate someone else checking. Commit: 0fba7f30c13c38f28ada0eb90fc1fd7816704a4d https://github.com/galaxyproject/galaxy/commit/0fba7f30c13c38f28ada0eb90fc1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #7208 from dannon/update_ie_proxy Update IE proxy dependencies Compare: https://github.com/galaxyproject/galaxy/compare/03463f4b0598...0fba7f30c13c

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[galaxyproject/galaxy] 37a9f2: Update logging config docs:
by Nicola Soranzo 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 37a9f2bcea99ea55f7b36b94aa481558702ca897 https://github.com/galaxyproject/galaxy/commit/37a9f2bcea99ea55f7b36b94aa48… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M doc/Makefile M doc/source/admin/config_logging.rst Log Message: ----------- Update logging config docs: - The example for split file logging was invalid (referenced the nonexistent "generic" formatter) - Switch YAML dicts from 4- to 2-space indent to match the indentation style in galaxy.yml.sample - Document setting the message format with the YAML config - Reword a few things to hopefully be a bit clearer Commit: 79672df45221e4417d2c363bb262c19a2eb48b1f https://github.com/galaxyproject/galaxy/commit/79672df45221e4417d2c363bb262… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M config/job_conf.xml.sample_advanced M doc/source/admin/scaling.md Log Message: ----------- Update documentation for handler assignment method configurability and remove some legacy stuff. Commit: e9773f17335bea2d9106aa364d29f1f53454c883 https://github.com/galaxyproject/galaxy/commit/e9773f17335bea2d9106aa364d29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M doc/source/admin/config_logging.rst Log Message: ----------- Minor spello Commit: 35c60489e8d52a47e82ae4462dfd7af5ced26f2b https://github.com/galaxyproject/galaxy/commit/35c60489e8d52a47e82ae4462dfd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Fixed link to proxy_package_layout in proxy docs Commit: bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479 https://github.com/galaxyproject/galaxy/commit/bdc6243a78b0fcf1e0d0a89670ec… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Darker tool form in workflow editor Commit: 038d1a1d83fac689e0d00f85cb59057bfe79bfcc https://github.com/galaxyproject/galaxy/commit/038d1a1d83fac689e0d00f85cb59… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Revert "Darker tool form in workflow editor" This reverts commit bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479. Commit: 9a133e91f84d31e0c4e39c36301a368d66c48508 https://github.com/galaxyproject/galaxy/commit/9a133e91f84d31e0c4e39c36301a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Remove spurious characters Co-Authored-By: natefoo <nate(a)bx.psu.edu> Commit: 74fcf12fa0968ef448fecb3f0ff9bd4736f91cd2 https://github.com/galaxyproject/galaxy/commit/74fcf12fa0968ef448fecb3f0ff9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Incorporate suggestions from @nsoranzo Commit: 49cbad5debb649013e142134b3b4ad8361125914 https://github.com/galaxyproject/galaxy/commit/49cbad5debb649013e142134b3b4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-02 (Sat, 02 Feb 2019) Changed paths: 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 Log Message: ----------- Merge pull request #7191 from natefoo/admin-docs-19.01 [19.01] Properly document handler assignment method configuration and fix logging configuration docs Commit: 428c6632f0196ebd45a42d1c61776ac3402e985f https://github.com/galaxyproject/galaxy/commit/428c6632f0196ebd45a42d1c6177… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Remove errant space in intermine_simple_display.loc.sample Commit: 526bebbb2817376b4c4e131890d75d1ea76b0e85 https://github.com/galaxyproject/galaxy/commit/526bebbb2817376b4c4e131890d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Merge pull request #7298 from blankenberg/intermine-loc-fix-19.01 [19.01] Remove errant space in intermine_simple_display.loc.sample Commit: 03463f4b0598df5619def5230de3fb758b4090ba https://github.com/galaxyproject/galaxy/commit/03463f4b0598df5619def5230de3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: 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 tool-data/intermine_simple_display.loc.sample Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f84a29b9545d...03463f4b0598

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[galaxyproject/galaxy] c0dca7: Respect `section=False` parameter in `BaseToolBoxT...
by Marius van den Beek 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0dca7a44cd12492ec34ad9c7cf2a7aa5ab0d116 https://github.com/galaxyproject/galaxy/commit/c0dca7a44cd12492ec34ad9c7cf2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Respect `section=False` parameter in `BaseToolBoxTestCase._setup_two_versions_in_config()` Broken in commit fd1c34b4c9fec55286c3d33e2802062ef393de82 Commit: 87d4904189e42b9263bea70a321bf80ae4549a93 https://github.com/galaxyproject/galaxy/commit/87d4904189e42b9263bea70a321b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Remove spurious quote Commit: ab03de44e86a376a4c7d98dad9b683992327aa32 https://github.com/galaxyproject/galaxy/commit/ab03de44e86a376a4c7d98dad9b6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Do not remove tools from other installed revisions when uninstalling TS repo Multiple installed revisions of a repository can provide the same version of a tool, e.g. for the repository https://toolshed.g2.bx.psu.edu/view/nilesh/rseqc only one tool out of 22 has a different version in revision 57 with respect to revision 56. In this case, when uninstalling one repository, the tools with the same guid were removed also from the other repository revisions in the `shed_tool_conf` file. This can be prevented by checking also the tool path. Commit: f84a29b9545d544d8d1bbe0a433f3e8dd647cbaf https://github.com/galaxyproject/galaxy/commit/f84a29b9545d544d8d1bbe0a433f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M templates/webapps/tool_shed/common/common.mako M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #7300 from nsoranzo/toolshed_fixes Do not remove tools from other installed revisions when uninstalling TS repo Compare: https://github.com/galaxyproject/galaxy/compare/71b01b1be3f7...f84a29b9545d

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[galaxyproject/usegalaxy-playbook] cce48a: usegalaxy.* integration updates for Test
by Nate Coraor 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cce48a7764ed202c79dd9e0407a7e7eeb2d3c3c1 https://github.com/galaxyproject/usegalaxy-playbook/commit/cce48a7764ed202c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/test/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- usegalaxy.* integration updates for Test

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[galaxyproject/usegalaxy-playbook] eacbc7: Test tool_conf.xml changes for usegalaxy.* integra...
by Nate Coraor 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: eacbc7190e92f0055b11c856eda6a0b6c9c402b9 https://github.com/galaxyproject/usegalaxy-playbook/commit/eacbc7190e92f005… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Test tool_conf.xml changes for usegalaxy.* integration Commit: e233c920e97a6b756db9951bf058d6ac4ee39bcd https://github.com/galaxyproject/usegalaxy-playbook/commit/e233c920e97a6b75… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Partial Test mutable config fixes for usegalaxy.* integration Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4aeeb45287d2...…

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[galaxyproject/galaxy] 428c66: Remove errant space in intermine_simple_display.lo...
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 428c6632f0196ebd45a42d1c61776ac3402e985f https://github.com/galaxyproject/galaxy/commit/428c6632f0196ebd45a42d1c6177… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Remove errant space in intermine_simple_display.loc.sample Commit: 526bebbb2817376b4c4e131890d75d1ea76b0e85 https://github.com/galaxyproject/galaxy/commit/526bebbb2817376b4c4e131890d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Merge pull request #7298 from blankenberg/intermine-loc-fix-19.01 [19.01] Remove errant space in intermine_simple_display.loc.sample Compare: https://github.com/galaxyproject/galaxy/compare/49cbad5debb6...526bebbb2817

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[galaxyproject/galaxy] 7dd921: Add longer pauses for some selenium tests, mark as...
by Aysam Guerler 04 Feb '19

04 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7dd9213fd874a4bf12d0eee86f03c48dd467a6f2 https://github.com/galaxyproject/galaxy/commit/7dd9213fd874a4bf12d0eee86f03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_custom_builds.py Log Message: ----------- Add longer pauses for some selenium tests, mark as slow renders for easier tracking down and fixing. Commit: d59352224c8f41ba8a1a9219b2bafa24e1a1f142 https://github.com/galaxyproject/galaxy/commit/d59352224c8f41ba8a1a9219b2ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/driver_factory.py Log Message: ----------- Set chrome to run headlessly -- todo configure via env var or switch Commit: 78c66f260c4bad5b2d632919fe14307602c8fb4e https://github.com/galaxyproject/galaxy/commit/78c66f260c4bad5b2d632919fe14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Wait for logout redirect. Commit: 9e879b731f27d7b17161c83a60ef559aa529ec63 https://github.com/galaxyproject/galaxy/commit/9e879b731f27d7b17161c83a60ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_custom_builds.py Log Message: ----------- Drop now unused slowrender Commit: 817a8469b69e37c48e72a081a75d5c734e636624 https://github.com/galaxyproject/galaxy/commit/817a8469b69e37c48e72a081a75d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M test/galaxy_selenium/cli.py M test/galaxy_selenium/driver_factory.py M test/selenium_tests/framework.py Log Message: ----------- Tie chrome native headless mode into existing HEADLESS logic, functioning with or without pyvirtualdisplay. Commit: 71b01b1be3f70f239fe9114b43eeef87fd9801d9 https://github.com/galaxyproject/galaxy/commit/71b01b1be3f70f239fe9114b43ee… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: 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 Log Message: ----------- Merge pull request #7287 from dannon/slow_selenium_tests Fix remaining selenium tests and add headless testing option. Compare: https://github.com/galaxyproject/galaxy/compare/645031578d31...71b01b1be3f7

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[galaxyproject/usegalaxy-playbook] 4aeeb4: update TTS
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4aeeb45287d27fc2e4cf19ccfae7e2d31ecc8e77 https://github.com/galaxyproject/usegalaxy-playbook/commit/4aeeb45287d27fc2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update TTS

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[galaxyproject/usegalaxy-playbook] 6f0e88: update MTS
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f0e88a96ebb95fceecc50ba7e93fd4ad02bc0fe https://github.com/galaxyproject/usegalaxy-playbook/commit/6f0e88a96ebb95fc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update MTS

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