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

[galaxyproject/galaxy] 96d9d0: Better re-use of `tool` attribute
by GitHub 29 Mar '18

29 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 96d9d0e5a236eb3fc7cf6f6612d82915fa5790e8 https://github.com/galaxyproject/galaxy/commit/96d9d0e5a236eb3fc7cf6f6612d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Better re-use of `tool` attribute Commit: 4f870490f2d289b2921c422ff66e92ee5decb352 https://github.com/galaxyproject/galaxy/commit/4f870490f2d289b2921c422ff66e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Simplify get_datatype_by_extension() method Commit: 7e5a90cc1fd5de729e416dd249f92621f883cce8 https://github.com/galaxyproject/galaxy/commit/7e5a90cc1fd5de729e416dd249f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Use app.datatypes_registry in ValidationContext.from_app() Commit: d5baea1dfc1998bcba5a0083b6b94769455bc247 https://github.com/galaxyproject/galaxy/commit/d5baea1dfc1998bcba5a0083b6b9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Handle an empty datatypes_registry Also transform it to an object attribute for re-use. Commit: 2c4bf95c3c5416f381cd8aea210f66ffef43498d https://github.com/galaxyproject/galaxy/commit/2c4bf95c3c5416f381cd8aea210f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5806 from nsoranzo/release_18.01_ValidationContext_fixes [18.01] Use app.datatypes_registry in ValidationContext.from_app() Compare: https://github.com/galaxyproject/galaxy/compare/d53cbe3538f1...2c4bf95c3c54

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[galaxyproject/galaxy] 4d742c: Clarify make targets, update client/README
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 4d742c3b1316aa808201c5bf3faec2587c345590 https://github.com/galaxyproject/galaxy/commit/4d742c3b1316aa808201c5bf3fae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M Makefile M client/README.md Log Message: ----------- Clarify make targets, update client/README Commit: b960260a3449a23dc35a0f126de41c37276d8cfd https://github.com/galaxyproject/galaxy/commit/b960260a3449a23dc35a0f126de4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention the client README specifically in CONTRIBUTING, to make it more obvious. Commit: d61268cc6d58a5fbecc0399a7fe8087be45d4861 https://github.com/galaxyproject/galaxy/commit/d61268cc6d58a5fbecc0399a7fe8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Articles are important. Commit: cbd7cb3cbcc93ef9abd651fff0760a91b5624127 https://github.com/galaxyproject/galaxy/commit/cbd7cb3cbcc93ef9abd651fff076… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Reflow text Commit: 05584244a7a5fb8790c513d6e451ac629b2f2955 https://github.com/galaxyproject/galaxy/commit/05584244a7a5fb8790c513d6e451… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Drop old bitbucket/galaxy/galaxy-dist reference. Commit: 334aea3adc975793d215f1622efc892718ecad75 https://github.com/galaxyproject/galaxy/commit/334aea3adc975793d215f1622efc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Erase trello from Contributing. Commit: 7d394d243b7d041ab357a0279e4920ab4a03fe7b https://github.com/galaxyproject/galaxy/commit/7d394d243b7d041ab357a0279e49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M client/README.md Log Message: ----------- Proofreading - thanks @nsoranzo Commit: d53cbe3538f186da903726ac1d00630e94cfe894 https://github.com/galaxyproject/galaxy/commit/d53cbe3538f186da903726ac1d00… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md Log Message: ----------- Merge pull request #5800 from dannon/client_readme_clarifications [18.01] Client related readme/makefile clarifications Compare: https://github.com/galaxyproject/galaxy/compare/c6ae97edaef3...d53cbe3538f1

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[galaxyproject/usegalaxy-playbook] f6d161: Upgraded prokka to version 1.13
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f6d1619f1fc1e85d21d51edea8da5ef8c2bfa031 https://github.com/galaxyproject/usegalaxy-playbook/commit/f6d1619f1fc1e85d… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Upgraded prokka to version 1.13

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[galaxyproject/galaxy] 0a1ccd: Lock pysam to 0.14.1 in Pipfile.
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a1ccdba1275948e71cd4e2da86a182c2cb7a7eb https://github.com/galaxyproject/galaxy/commit/0a1ccdba1275948e71cd4e2da86a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- Lock pysam to 0.14.1 in Pipfile. Commit: a85b8a83cbfeb6aaba1b3e6d86f3ae737f369ed3 https://github.com/galaxyproject/galaxy/commit/a85b8a83cbfeb6aaba1b3e6d86f3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- Merge pull request #5798 from dannon/lock_pysam Lock pysam to 0.14.1 in Pipfile. Compare: https://github.com/galaxyproject/galaxy/compare/0ff93b0e537c...a85b8a83cbfe

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[galaxyproject/galaxy] 1b13bf: Log the pid of the first uWSGI process
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b13bfa48e1b3e805a46feec55a3c698ce1fa524 https://github.com/galaxyproject/galaxy/commit/1b13bfa48e1b3e805a46feec55a3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log the pid of the first uWSGI process So it is the same that gets written to file when using the `--pidfile` option of `uwsgi`. Commit: c6ae97edaef3a146955731aefe510887f4c8b6d0 https://github.com/galaxyproject/galaxy/commit/c6ae97edaef3a146955731aefe51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge pull request #5774 from nsoranzo/release_18.01_fix_pid [18.01] Log the pid of the first uWSGI process Commit: 0ff93b0e537c4717111a833aeb6d33e63b41d2f6 https://github.com/galaxyproject/galaxy/commit/0ff93b0e537c4717111a833aeb6d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/70128b5d69c0...0ff93b0e537c

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[galaxyproject/galaxy] 1b13bf: Log the pid of the first uWSGI process
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 1b13bfa48e1b3e805a46feec55a3c698ce1fa524 https://github.com/galaxyproject/galaxy/commit/1b13bfa48e1b3e805a46feec55a3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log the pid of the first uWSGI process So it is the same that gets written to file when using the `--pidfile` option of `uwsgi`. Commit: c6ae97edaef3a146955731aefe510887f4c8b6d0 https://github.com/galaxyproject/galaxy/commit/c6ae97edaef3a146955731aefe51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge pull request #5774 from nsoranzo/release_18.01_fix_pid [18.01] Log the pid of the first uWSGI process Compare: https://github.com/galaxyproject/galaxy/compare/d6be56256fcb...c6ae97edaef3

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[galaxyproject/galaxy] 528201: Add delayed column attribute to grid helper
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 528201e56ac651087fba38d20803ecce320050aa https://github.com/galaxyproject/galaxy/commit/528201e56ac651087fba38d20803… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Add delayed column attribute to grid helper Commit: db1b8bc64b35265faa04268ad382c86067a214bc https://github.com/galaxyproject/galaxy/commit/db1b8bc64b35265faa04268ad382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Use delayed flag for history grid Commit: 70128b5d69c0c7aef8c6cdfdbd2f84cbeac4f8f5 https://github.com/galaxyproject/galaxy/commit/70128b5d69c0c7aef8c6cdfdbd2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5789 from guerler/add_delay_handler Add delay attribute to grid handler Compare: https://github.com/galaxyproject/galaxy/compare/16291826d2b1...70128b5d69c0

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[galaxyproject/galaxy] 4ae322: Fix history link to visualizations view
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ae3222e10d6367c2d43b60e138fe9298903b2f3 https://github.com/galaxyproject/galaxy/commit/4ae3222e10d6367c2d43b60e138f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix history link to visualizations view Commit: 16291826d2b1852a0823c259d2ce4dcf086b936a https://github.com/galaxyproject/galaxy/commit/16291826d2b1852a0823c259d2ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #5799 from guerler/fix_viz_list Fix history link to visualizations view Compare: https://github.com/galaxyproject/galaxy/compare/fa69c7507ba6...16291826d2b1

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[galaxyproject/galaxy] b4a30b: Revise uwsgi defaults and display.
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4a30bcd824f5bbb6e68717b508dd522ab640f26 https://github.com/galaxyproject/galaxy/commit/b4a30bcd824f5bbb6e68717b508d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Revise uwsgi defaults and display. In https://github.com/galaxyproject/galaxy/issues/1530 we realized that buffer-size needs to be increased for Galaxy requests. Also mention thunder-lock since that should frequently be enabled - https://github.com/galaxyproject/ansible-galaxy-extras/pull/195. Commit: fa69c7507ba623a378aac517b11087d843f07067 https://github.com/galaxyproject/galaxy/commit/fa69c7507ba623a378aac517b110… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #5743 from jmchilton/uwsg-buffer-size Revise uwsgi defaults and display. Compare: https://github.com/galaxyproject/galaxy/compare/449e25200b20...fa69c7507ba6

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[galaxyproject/galaxy] 04a901: [18.01] Fix SQL query for "workflows shared with m...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 04a901771b59d1fcf8070cd4c4de1f464e304e55 https://github.com/galaxyproject/galaxy/commit/04a901771b59d1fcf8070cd4c4de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Before and after queries here: https://gist.github.com/jmchilton/dc57bca60178341d9ce0f6cf6d4bd36f You can see that before the joined load of the stored workflow wasn't being registered by SQLalchemy properly and so it was joining that table twice - once using the proper index and another time just walking the whole table. The filter and order by were being applied to the unconditional version - kind of like saying give me all the workflows and the right workflows and I will check all the workflows to see if this one is deleted instead of just the subset of workflows that are actually being shared with the target user. Commit: d6be56256fcbee53509dc867d863819621ef1d08 https://github.com/galaxyproject/galaxy/commit/d6be56256fcbee53509dc867d863… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5782 from jmchilton/fix_1801 [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Commit: 449e25200b2099ddbd253ee7f528ee69e997c2aa https://github.com/galaxyproject/galaxy/commit/449e25200b2099ddbd253ee7f528… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2558d2780109...449e25200b20

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