galaxy-commits February 2019

galaxy-commits@lists.galaxyproject.org

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152 discussions

[galaxyproject/galaxy] 203353: Fix HDF5 test assert docs
by Björn Grüning 19 Feb '19

19 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 203353597671ec7c3daa02791705ebb921fb28ad https://github.com/galaxyproject/galaxy/commit/203353597671ec7c3daa02791705… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix HDF5 test assert docs Alternative to https://github.com/galaxyproject/galaxy/pull/7382, fix documentation without giving up better validation one gets with actual types for assertion XML elements. Commit: 737bae8f9b920ec9bed43a2d25378b19ace12f58 https://github.com/galaxyproject/galaxy/commit/737bae8f9b920ec9bed43a2d2537… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Reword HDF5 attribute test docs Commit: 35529a05fb9210bd2f7fce3f91418cdf95cebb2f https://github.com/galaxyproject/galaxy/commit/35529a05fb9210bd2f7fce3f9141… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #7384 from jmchilton/fix_h5_assertion_docs [19.01] Fix HDF5 test assert docs Compare: https://github.com/galaxyproject/galaxy/compare/b67dc2ba24ec...35529a05fb92

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[galaxyproject/galaxy] 5ef4c3: Fix upload button style
by Martin Cech 18 Feb '19

18 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ef4c3b823469bff5fdb96943993a0bf0e9fbf94 https://github.com/galaxyproject/galaxy/commit/5ef4c3b823469bff5fdb96943993… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix upload button style Commit: 6b1b71425c68fae8dc51daec237b05a9ae4d4a6e https://github.com/galaxyproject/galaxy/commit/6b1b71425c68fae8dc51daec237b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Merge pull request #7381 from guerler/fix_upload Fix upload button style Compare: https://github.com/galaxyproject/galaxy/compare/8f30afc2db7c...6b1b71425c68

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[galaxyproject/galaxy] 73a5da: Remove unused legacy user manager index mako
by Dannon 18 Feb '19

18 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73a5da0bb32204e56acadefaf272380269bd5ab9 https://github.com/galaxyproject/galaxy/commit/73a5da0bb32204e56acadefaf272… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: R templates/user/index.mako Log Message: ----------- Remove unused legacy user manager index mako Commit: a7fc146bb80ee20b572f17b11b2e8487f620761d https://github.com/galaxyproject/galaxy/commit/a7fc146bb80ee20b572f17b11b2e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py R templates/user/logout.mako A templates/webapps/tool_shed/user/logout.mako Log Message: ----------- Handle logout redirect on client, move mako to toolshed Commit: 1d9fa2701e1947e85e8f8687caa688f35796974c https://github.com/galaxyproject/galaxy/commit/1d9fa2701e1947e85e8f8687caa6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Restore csrf check for login and registration Commit: 9c7b5c393b6cb251ec7c161ef6e9275fd6c56335 https://github.com/galaxyproject/galaxy/commit/9c7b5c393b6cb251ec7c161ef6e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix error message Commit: 5d8f6c623a93c49300e288b2caf5459333884c4b https://github.com/galaxyproject/galaxy/commit/5d8f6c623a93c49300e288b2caf5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Restore logout csrf check Commit: d890ec28e7f62ee14c2a083bbd3d420e66a9450c https://github.com/galaxyproject/galaxy/commit/d890ec28e7f62ee14c2a083bbd3d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Move biostar logout handling to toolshed Commit: 2d44723787268f344bad377bc93094a9b5be66b5 https://github.com/galaxyproject/galaxy/commit/2d44723787268f344bad377bc930… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Accomodate csrf tokens in unit test Commit: af8ae86fbf4ebbcb03cddd9c14ffef622dd96736 https://github.com/galaxyproject/galaxy/commit/af8ae86fbf4ebbcb03cddd9c14ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Resolve csrf check for toolshed Commit: 71aba163b70340c8d5720b408f1479d6073b1da5 https://github.com/galaxyproject/galaxy/commit/71aba163b70340c8d5720b408f14… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Remove biostar logout helper Commit: 0866fe1ec8f938c05f79b02774f623c11e1c0c25 https://github.com/galaxyproject/galaxy/commit/0866fe1ec8f938c05f79b02774f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M .gitignore M Makefile M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/onload/initQueue.js M client/galaxy/scripts/ui/popupmenu.js M client/galaxy/style/scss/list-item.scss 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/project/issues.rst 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/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd R lib/galaxy/util/handlers.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/handlers.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/scheduling_manager.py M test/api/test_histories.py M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Merge branch 'dev' into remove_logout_mako Commit: ba3bc4d72f8ca6a126312918d708c82f211da31a https://github.com/galaxyproject/galaxy/commit/ba3bc4d72f8ca6a126312918d708… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Fix toolshed test cases Commit: 1793ad3c205a91151e68e2a5a8a770cd4a36be74 https://github.com/galaxyproject/galaxy/commit/1793ad3c205a91151e68e2a5a8a7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Fix order of session clearing after logout Commit: 3274aad17059fa6b64feebec3ca07ff675a179ad https://github.com/galaxyproject/galaxy/commit/3274aad17059fa6b64feebec3ca0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M test/selenium_tests/test_anon_history.py Log Message: ----------- Fix selenium test, navigate to analysis after logout Commit: 01634ceb5ec57c22722071c769cd373c068c8b16 https://github.com/galaxyproject/galaxy/commit/01634ceb5ec57c22722071c769cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Fix analysis route in masthead from login page Commit: 8f30afc2db7c122b259cc1cb7e0216fea66d1210 https://github.com/galaxyproject/galaxy/commit/8f30afc2db7c122b259cc1cb7e02… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue M client/galaxy/scripts/layout/menu.js M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py R templates/user/index.mako R templates/user/logout.mako A templates/webapps/tool_shed/user/logout.mako M test/selenium_tests/test_anon_history.py M test/shed_functional/base/twilltestcase.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #7329 from guerler/remove_logout_mako Remove logout mako, redirect to login page Compare: https://github.com/galaxyproject/galaxy/compare/9b73757d98e6...8f30afc2db7c

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[galaxyproject/galaxy] 3ae7aa: introduce ability to favorite a tool
by Martin Cech 18 Feb '19

18 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3ae7aa2b23e71ca9e3295e9304b65389d13bc4f5 https://github.com/galaxyproject/galaxy/commit/3ae7aa2b23e71ca9e3295e9304b6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- introduce ability to favorite a tool Commit: a39b2d2e3e6e237c2478f24b29c002ece8fb1dab https://github.com/galaxyproject/galaxy/commit/a39b2d2e3e6e237c2478f24b29c0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- refactor and enhance the API to be generic favorite endpoint Commit: bbf0879c5a3cb4f026346d3b16f6abbbcb107747 https://github.com/galaxyproject/galaxy/commit/bbf0879c5a3cb4f026346d3b16f6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- refactor the favorite API to use DELETE method for removal Commit: 04908cefd6de34a698b91f2ab520b89576aa88bf https://github.com/galaxyproject/galaxy/commit/04908cefd6de34a698b91f2ab520… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M test/api/test_users.py M test/base/api.py Log Message: ----------- add basic API tests for favoriting and fix errors caught by the tests Commit: a76b11f62529956606ee9edaf6cd6c56a5e4589b https://github.com/galaxyproject/galaxy/commit/a76b11f62529956606ee9edaf6cd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- refactor the global Galaxy access and buttonIcon for toolfavs Commit: 7d37c186af50c652530ac6d2aa49733ada84d05d https://github.com/galaxyproject/galaxy/commit/7d37c186af50c652530ac6d2aa49… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- stringify the favorites before adding to the app state this is consistent with how everythong else in that object is treated Commit: 7a1af318b1182da8f59282cdd6a7d57d1520103c https://github.com/galaxyproject/galaxy/commit/7a1af318b1182da8f59282cdd6a7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- remove logging Commit: 4a245a6f464ebb9cdba134539272ba5179d6f910 https://github.com/galaxyproject/galaxy/commit/4a245a6f464ebb9cdba134539272… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- add functionality to show only favorited tools using the special search terms Commit: 38d9914f83a314dc53f88b3ad236ffd6c2ac16c6 https://github.com/galaxyproject/galaxy/commit/38d9914f83a314dc53f88b3ad236… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- formalize the reserved search words Commit: 2c11362c7570e6e60ed3cf0fab60a4dde861bdf1 https://github.com/galaxyproject/galaxy/commit/2c11362c7570e6e60ed3cf0fab60… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M test/api/test_tools.py M test/api/test_users.py Log Message: ----------- add tests, add handling of cornercases Commit: c63b675448c4bda47651309f68c3bce6f6e09b8f https://github.com/galaxyproject/galaxy/commit/c63b675448c4bda47651309f68c3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M test/api/test_users.py Log Message: ----------- remove comments Commit: 8023f2ef64c9dd4b69b8881d550ab94f48ae0ead https://github.com/galaxyproject/galaxy/commit/8023f2ef64c9dd4b69b8881d550a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-model.js M test/api/test_users.py Log Message: ----------- refactor user preferences to handle serialization tweak tool favoriting Commit: 86b6e9eeba1e974ea226b69f283c4016b16f30fc https://github.com/galaxyproject/galaxy/commit/86b6e9eeba1e974ea226b69f283c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-model.js Log Message: ----------- improve consistency when handling stringified data Commit: 67e53de5ca4c080df952384644b78b159b283b7d https://github.com/galaxyproject/galaxy/commit/67e53de5ca4c080df952384644b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/entry/panels/tool-panel.js Log Message: ----------- add favorite button to the tool panel Commit: 247ba6fa42e20ec2155e7883c89fa6bb5b931840 https://github.com/galaxyproject/galaxy/commit/247ba6fa42e20ec2155e7883c89f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M test/api/test_users.py Log Message: ----------- fix missing import Commit: f21b688e7fc70e6bea5c6765e5323d8cca0d596c https://github.com/galaxyproject/galaxy/commit/f21b688e7fc70e6bea5c6765e532… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/entry/panels/tool-panel.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Resolve button style conflicts in panel header Commit: 34676772a54e4a0783ef3c917812ac81312e2a3a https://github.com/galaxyproject/galaxy/commit/34676772a54e4a0783ef3c917812… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- check client-local user preferences before making api call Commit: febf54b9f7e36f35fb10a160f78da63c5b63af4d https://github.com/galaxyproject/galaxy/commit/febf54b9f7e36f35fb10a160f78d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/entry/panels/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- reduce reserved word conflict probability Commit: a82c405d62fb37b92f5718ca1f94fbe292e64313 https://github.com/galaxyproject/galaxy/commit/a82c405d62fb37b92f5718ca1f94… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M test/api/test_users.py Log Message: ----------- fix the test after updating the reserved word to include # Commit: 5fae26db3c79898bb24f582c2e8caee913a0a4a3 https://github.com/galaxyproject/galaxy/commit/5fae26db3c79898bb24f582c2e8c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/entry/panels/tool-panel.js Log Message: ----------- explicitly import jquery Commit: 26f8e0edc9ff3632a28f24f0b168b82829bbbc8e https://github.com/galaxyproject/galaxy/commit/26f8e0edc9ff3632a28f24f0b168… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- add accidentally removed method due to a bad merge Commit: 9b73757d98e68772050da02e53af564451189321 https://github.com/galaxyproject/galaxy/commit/9b73757d98e68772050da02e53af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M client/galaxy/scripts/entry/panels/tool-panel.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/upload.scss M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/api/test_users.py M test/base/api.py Log Message: ----------- Merge pull request #7209 from martenson/toolfavs introduce the ability to favorite tools Compare: https://github.com/galaxyproject/galaxy/compare/8c207ab17e8a...9b73757d98e6

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[galaxyproject/galaxy] 8ffa95: Possible fix for fasta file never getting filesize
by John Chilton 18 Feb '19

18 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ffa95d738ffed9d18e490c6356d572852cd4728 https://github.com/galaxyproject/galaxy/commit/8ffa95d738ffed9d18e490c6356d… Author: Slugger70 <slugger70(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Possible fix for fasta file never getting filesize Commit: 8c207ab17e8a5100ac505a535fe17a55eca306a0 https://github.com/galaxyproject/galaxy/commit/8c207ab17e8a5100ac505a535fe1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #7374 from Slugger70/dtd_fix Possible fix for fasta file never getting filesize Compare: https://github.com/galaxyproject/galaxy/compare/dbf11ad13950...8c207ab17e8a

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[galaxyproject/galaxy] c21e07: Do not default to DEV_WHEELS=1 if no Git is found
by John Chilton 16 Feb '19

16 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c21e07e1a05830ad5ee8e05c0f87dbee8e9e4559 https://github.com/galaxyproject/galaxy/commit/c21e07e1a05830ad5ee8e05c0f87… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Do not default to DEV_WHEELS=1 if no Git is found If there is no Git repo in a Galaxy install, DEV_WHEELS will not be turned on by default. If they are needed, use the --dev-wheels flag. (Current behavior: common_startup.sh will turn on the DEV_WHEELS option if no git repo is found, making the assumption that it is dealing with a dev install. Thus, dev dependencies are installed whenever there's no Git repo, including the use case when Galaxy was downloaded as a tarball - when they may or may not be desired. There is no option to override this behavior without editing the script.) Commit: dbf11ad139500d0acb785b376776a11e0b122967 https://github.com/galaxyproject/galaxy/commit/dbf11ad139500d0acb785b376776… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-16 (Sat, 16 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7371 from ic4f/dev Do not default to DEV_WHEELS=1 if no Git is found Compare: https://github.com/galaxyproject/galaxy/compare/61d12b739f2e...dbf11ad13950

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[galaxyproject/galaxy] f790af: Reduce comment spam in history import/export.
by Martin Cech 15 Feb '19

15 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f790aff9a1af60e775d5811ffcfba2e21850d51c https://github.com/galaxyproject/galaxy/commit/f790aff9a1af60e775d5811ffcfb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Reduce comment spam in history import/export. This stuff keeps getting in the way when rebasing and fixing a bunch of small and big issues. Commit: 61d12b739f2e859262903eaf92885fa10dc15307 https://github.com/galaxyproject/galaxy/commit/61d12b739f2e859262903eaf9288… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #7370 from jmchilton/export_simp_4 Reduce comment spam in history import/export. Compare: https://github.com/galaxyproject/galaxy/compare/503c2cc82148...61d12b739f2e

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[galaxyproject/galaxy] 3e7193: Remove another unused variables from history export.
by Martin Cech 15 Feb '19

15 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e7193599c45e37bdfe88b221b443bfbd650a27f https://github.com/galaxyproject/galaxy/commit/3e7193599c45e37bdfe88b221b44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M test/unit/tools/test_history_imp_exp.py Log Message: ----------- Remove another unused variables from history export. Commit: 503c2cc8214808dfdca18f823d530ce880a84959 https://github.com/galaxyproject/galaxy/commit/503c2cc8214808dfdca18f823d53… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M test/unit/tools/test_history_imp_exp.py Log Message: ----------- Merge pull request #7366 from jmchilton/imp_exp_simple Remove another unused variables from history export. Compare: https://github.com/galaxyproject/galaxy/compare/945c317db849...503c2cc82148

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[galaxyproject/galaxy] 08ed41: Fix oidc login redirection to work with new login ...
by John Chilton 15 Feb '19

15 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08ed4189a5979f8936b6a4938765e3dcdf4eb759 https://github.com/galaxyproject/galaxy/commit/08ed4189a5979f8936b6a4938765… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Fix oidc login redirection to work with new login component (which simply redirects on successful login, as done here) Commit: 5c5197e84120551b551164f6b73eea2df260a157 https://github.com/galaxyproject/galaxy/commit/5c5197e84120551b551164f6b73e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix oidc file/backends default location parsing/handling. Commit: 6c9a765b83009869e09e7b7abc39efe5a9d5e843 https://github.com/galaxyproject/galaxy/commit/6c9a765b83009869e09e7b7abc39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Simple google via oidc login button. Commit: 646fbd63a37a2ab4b9f70541d1109a97e1e66bf9 https://github.com/galaxyproject/galaxy/commit/646fbd63a37a2ab4b9f70541d110… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/layout/menu.js Log Message: ----------- ODIC tweaks. Google only for now, needs to consume API Commit: a0536889e6a3191fdc87fe0d46cb2cf896971534 https://github.com/galaxyproject/galaxy/commit/a0536889e6a3191fdc87fe0d46cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M .gitignore M Makefile 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/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.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 client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/job_conf.xml.sample_advanced 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/config_logging.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/datatypes/sniff.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/compression_utils.py M lib/galaxy/web/proxy/js/package.json 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 M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/xml_util.py R templates/user/register.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/user/login.mako A templates/webapps/tool_shed/user/register.mako M test/api/test_workflows.py M test/galaxy_selenium/cli.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_registration.py M test/shed_functional/base/twilltestcase.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/workflows/test_modules.py M test/unit/workflows/workflow_support.py M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fix_oidc_login_redirect Commit: 9551272a8439c434974734a45e47d1debc8bd92a https://github.com/galaxyproject/galaxy/commit/9551272a8439c434974734a45e47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue Log Message: ----------- Cleanup. Commit: 08f1fc1c2346fb58d8f724d3a915e85665bc20d9 https://github.com/galaxyproject/galaxy/commit/08f1fc1c2346fb58d8f724d3a915… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Standardize to lowercase link for google authnz login endpoint Commit: ff31f09b9ec06e3674d2f5ca677da6fcaf6d5037 https://github.com/galaxyproject/galaxy/commit/ff31f09b9ec06e3674d2f5ca677d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Drop stray debug Commit: 370a8ce03e91729493d01aea48cc9ecb6632fc0c https://github.com/galaxyproject/galaxy/commit/370a8ce03e91729493d01aea48cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- JSApp refactoring; set up authnz controller to be able to serve a full client on the auth callback. Commit: ba39f2cc86a770822aaa3d43ae1eaceea1ce5471 https://github.com/galaxyproject/galaxy/commit/ba39f2cc86a770822aaa3d43ae1e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Fix documented route for non-api authnz controller. Commit: 78c94660ca9505099f2d90842c4f185e4d1ac008 https://github.com/galaxyproject/galaxy/commit/78c94660ca9505099f2d90842c4f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Drop cruft from refactoring. Commit: 945c317db8499ad143dc1165f9e993cad864e8c4 https://github.com/galaxyproject/galaxy/commit/945c317db8499ad143dc1165f9e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Register.vue M lib/galaxy/config.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #7347 from dannon/fix_oidc_login_redirect Overhaul OIDC login handling Compare: https://github.com/galaxyproject/galaxy/compare/11bbcfa87d01...945c317db849

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[galaxyproject/galaxy] 76aa7d: Remove unused variables in history export.
by Nicola Soranzo 15 Feb '19

15 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76aa7d9c5faea119b409d3d2889dbbe1afb52e8b https://github.com/galaxyproject/galaxy/commit/76aa7d9c5faea119b409d3d2889d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Remove unused variables in history export. Commit: 15ab8a321b9fff4530decec51d536eeda01506d4 https://github.com/galaxyproject/galaxy/commit/15ab8a321b9fff4530decec51d53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M test/unit/tools/test_history_imp_exp.py Log Message: ----------- Drop includes_deleted_datasets, includes_hidden_datasets from test HISTORY_ATTRS Commit: 11bbcfa87d014f80f10153a2fcca7a4f15951cf8 https://github.com/galaxyproject/galaxy/commit/11bbcfa87d014f80f10153a2fcca… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M test/unit/tools/test_history_imp_exp.py Log Message: ----------- Merge pull request #7363 from jmchilton/remove_unused_variables_in_export Remove unused exported variables in history export. Compare: https://github.com/galaxyproject/galaxy/compare/c1a6a2a48f4c...11bbcfa87d01

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galaxy-commits February 2019