galaxy-commits February 2019

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] 68a66f: update h5py dependency
by John Chilton 07 Feb '19

07 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 68a66f462e007fdbcf8e966fc5cc1a7ea06a8527 https://github.com/galaxyproject/galaxy/commit/68a66f462e007fdbcf8e966fc5cc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- update h5py dependency Commit: d79514b823371c36c12dcbb6aef25a4490cd50ca https://github.com/galaxyproject/galaxy/commit/d79514b823371c36c12dcbb6aef2… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/__init__.py Log Message: ----------- allow assertions on binary inputs Commit: e37036af04ac34dd7c865f5f11ccaa0ee4e17e9a https://github.com/galaxyproject/galaxy/commit/e37036af04ac34dd7c865f5f11cc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A lib/galaxy/tools/verify/asserts/hdf5.py Log Message: ----------- add hdf5 assert tests Commit: db2987b2b21fefad9feb2af0bd4f93b7d490361f https://github.com/galaxyproject/galaxy/commit/db2987b2b21fefad9feb2af0bd4f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A test/functional/tools/validation_hdf5.xml Log Message: ----------- add test tool for new assertions Commit: d4420b75662b7667d430f78be67b09e69037a77b https://github.com/galaxyproject/galaxy/commit/d4420b75662b7667d430f78be67b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- register new test tool Commit: a00fd508b758fc73aeb537ca98156fff1c7ac14d https://github.com/galaxyproject/galaxy/commit/a00fd508b758fc73aeb537ca9815… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- adopt XSD for new syntax Commit: cb13e56e6bd00a932e9594241fe043f845d4f815 https://github.com/galaxyproject/galaxy/commit/cb13e56e6bd00a932e9594241fe0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A test-data/matrix.cool Log Message: ----------- add test-data for new hdf5 based tool test Commit: e9f40f2f95a611f0fab6d81bb225cf409b86f353 https://github.com/galaxyproject/galaxy/commit/e9f40f2f95a611f0fab6d81bb225… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py Log Message: ----------- fix pep8 Commit: 2a97f726cc86d44610738d04755622e8e4b8342a https://github.com/galaxyproject/galaxy/commit/2a97f726cc86d44610738d047556… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- Tweaks to hdf5 testing. - This is in galaxy-lib so h5py import should probably be conditional. - Namespace very generic test functions a bit by adding h5 into the names. - Stricter validation of XSD (the other assertions don't have this but that is problematic on their part), I'm not sure if the docs will render unevenly now though - we may want to revisit that and do this for all the assertions. Commit: 3d4ff4fc372bc6b44b384af944b548915427fda4 https://github.com/galaxyproject/galaxy/commit/3d4ff4fc372bc6b44b384af944b5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #41 from jmchilton/hdf5_tests Tweaks to hdf5 testing. Commit: d36cf51f6b63407fd96e49918fe6092d993275a9 https://github.com/galaxyproject/galaxy/commit/d36cf51f6b63407fd96e49918fe6… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- change "name" to "key" Commit: 8f7263a1dcce4a2d3e5c251e4253dece2998e61d https://github.com/galaxyproject/galaxy/commit/8f7263a1dcce4a2d3e5c251e4253… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #7301 from bgruening/hdf5_tests Add new test syntax specific for HDF5 files Compare: https://github.com/galaxyproject/galaxy/compare/e3f1234b2c13...8f7263a1dcce

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[galaxyproject/galaxy] ab8ab1: Trim whitespace.
by Nicola Soranzo 07 Feb '19

07 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab8ab10be77e243025fefb185dce6945914ed7a2 https://github.com/galaxyproject/galaxy/commit/ab8ab10be77e243025fefb185dce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Trim whitespace. Commit: 321caf78e4fac8859d2a0b308cff25763d7ba1ef https://github.com/galaxyproject/galaxy/commit/321caf78e4fac8859d2a0b308cff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/ui/popupmenu.js Log Message: ----------- Fix popupmenu creation. Commit: 69a6d1aabaf242b0748a3205695364c9740a7cda https://github.com/galaxyproject/galaxy/commit/69a6d1aabaf242b0748a32056953… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: 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. Commit: e0cfaa452e2cfb06b6560e6285ca499b0eabda57 https://github.com/galaxyproject/galaxy/commit/e0cfaa452e2cfb06b6560e6285ca… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/ui/popupmenu.js Log Message: ----------- Merge pull request #7318 from dannon/fix_popupmenu_creation Fix popupmenu creation Compare: https://github.com/galaxyproject/galaxy/compare/d19c30cc0a41...e0cfaa452e2c

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[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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lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/repository_util.py M run_tests.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M static/welcome.html.sample R templates/admin/tool_errors.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/message.mako M templates/no_access.mako M templates/refresh_frames.mako M templates/slug_editing_js.mako M templates/tagging_common.mako A templates/user/index.mako M templates/user/logout.mako R templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/base_panels.mako M 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test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh R test/docker/base/start_mysql.sh A test/functional/tools/collection_creates_pair_y.yml M test/functional/tools/composite_output_tests.xml M test/functional/tools/for_workflows/head.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/multi_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml A test/integration/handler_template_job_conf.xml A test/integration/resubmission_pulsar_job_conf.xml A test/integration/singularity_job_conf.xml A test/integration/test_containerized_jobs.py R test/integration/test_dockerized_jobs.py A test/integration/test_handler_assignment_methods.py M test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M 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

1 0

[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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