February 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook]
by Martin Cech 11 Feb '19

11 Feb '19

Branch: refs/heads/max_client_body_size Home: https://github.com/galaxyproject/infrastructure-playbook

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[galaxyproject/usegalaxy-playbook] 38a244: limit nginx upload size for toolsheds server
by Martin Cech 11 Feb '19

11 Feb '19

Branch: refs/heads/martenson-patch-2 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 38a244ffeb8d61277113e89a69ae3636a21a4090 https://github.com/galaxyproject/usegalaxy-playbook/commit/38a244ffeb8d6127… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M env/common/group_vars/toolshedwebservers.yml Log Message: ----------- limit nginx upload size for toolsheds server should resolve galaxyproject/galaxy#2517, suggested by @natefoo

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[galaxyproject/infrastructure-playbook] 37b844: limit nginx upload size for toolsheds server
by Martin Cech 11 Feb '19

11 Feb '19

Branch: refs/heads/max_client_body_size Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 37b844caa6e5d75418cf462c956f276867c2d737 https://github.com/galaxyproject/infrastructure-playbook/commit/37b844caa6e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M env/galaxy/host_vars/radegast.galaxyproject.org/vars.yml Log Message: ----------- limit nginx upload size for toolsheds server should resolve https://github.com/galaxyproject/galaxy/issues/2517, suggested by @natefoo

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[galaxyproject/galaxy] 348b19: Update ``area`` issue/PR labels
by Martin Cech 11 Feb '19

11 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 348b190ecf70db5cb1297b423b71f92519aecd80 https://github.com/galaxyproject/galaxy/commit/348b190ecf70db5cb1297b423b71… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Update ``area`` issue/PR labels - Add some labels that were added on GitHub, but not here: - authentication - client-build - compliance - Rename `system` to `scripts`, since this was the original (I think) and `system` is too generic - Remove unused `roadmap`, we use GitHub `Projects` now Commit: 5b67fa7b7020b573f63616201421beb9b656b6c9 https://github.com/galaxyproject/galaxy/commit/5b67fa7b7020b573f63616201421… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Rename `authentication` to `auth` to include also authorization. Suggested by @martenson . Commit: 4b92f95e87b1af27bbb338e849f171176b320a89 https://github.com/galaxyproject/galaxy/commit/4b92f95e87b1af27bbb338e849f1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Merge pull request #7344 from nsoranzo/update_area_labels Update ``area`` issue/PR labels Compare: https://github.com/galaxyproject/galaxy/compare/f9f894d2e156...4b92f95e87b1

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[galaxyproject/galaxy] 7940bf: Remove ``ToolsController._rerun_tool()`` API method
by John Chilton 11 Feb '19

11 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7940bf3bd3193755363912398e0bb339ba9a0f9b https://github.com/galaxyproject/galaxy/commit/7940bf3bd3193755363912398e0b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/web/framework/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Remove ``ToolsController._rerun_tool()`` API method xref. https://github.com/galaxyproject/galaxy/pull/7333#issuecomment-461870147 Commit: f9f894d2e156c71406f2de5e79dd3e52ccb8c24a https://github.com/galaxyproject/galaxy/commit/f9f894d2e156c71406f2de5e79dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/web/framework/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #7345 from nsoranzo/remove_rerun_tool Remove ``ToolsController._rerun_tool()`` API method Compare: https://github.com/galaxyproject/galaxy/compare/8a16d68e76f7...f9f894d2e156

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[galaxyproject/galaxy] dbf8be: fix template broken in #7234
by John Chilton 09 Feb '19

09 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dbf8becac5bc43d867319f6b1ffd7b3269f623e5 https://github.com/galaxyproject/galaxy/commit/dbf8becac5bc43d867319f6b1ffd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix template broken in #7234 Commit: c5452fa87f6e068fabd9e3d280c63e7070bfb9a7 https://github.com/galaxyproject/galaxy/commit/c5452fa87f6e068fabd9e3d280c6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- remove tooltip from download button re add standard title to add datasets button Commit: 8a16d68e76f7642b546e9bd4c99105495c61b498 https://github.com/galaxyproject/galaxy/commit/8a16d68e76f7642b546e9bd4c991… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #7337 from martenson/fixlib ui fixes to datalibs Compare: https://github.com/galaxyproject/galaxy/compare/b227d1236280...8a16d68e76f7

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[galaxyproject/galaxy] 12789f: Fix ``test_import_metadata_regeneration`` API test
by John Chilton 09 Feb '19

09 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 12789f4db7519835452bbd39acaa9237669426d7 https://github.com/galaxyproject/galaxy/commit/12789f4db7519835452bbd39acaa… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M test/api/test_histories.py Log Message: ----------- Fix ``test_import_metadata_regeneration`` API test Commit: b227d123628031af6f7522785f277468d218cc85 https://github.com/galaxyproject/galaxy/commit/b227d123628031af6f7522785f27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M test/api/test_histories.py Log Message: ----------- Merge pull request #7340 from nsoranzo/fix_test_import_metadata_regeneration Fix ``test_import_metadata_regeneration`` API test Compare: https://github.com/galaxyproject/galaxy/compare/572e91a52b67...b227d1236280

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[galaxyproject/galaxy] 9f501b: Add datatypes and sniffers for several directory-b...
by Björn Grüning 09 Feb '19

09 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 9f501bb2b0bfa5193cd908d5f43bdca9a4bc5a2d https://github.com/galaxyproject/galaxy/commit/9f501bb2b0bfa5193cd908d5f43b… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar Log Message: ----------- Add datatypes and sniffers for several directory-based mass spectrometry formats: Bruker BAF, Agilent/Bruker YEP, Bruker TDF, Agilent MassHunter, and Waters MassLynx Commit: 365ac400ae629b415b8ec11a364ec0e4465d1c7f https://github.com/galaxyproject/galaxy/commit/365ac400ae629b415b8ec11a364e… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix lint errors Commit: 413af14bb55d890ca053d08877cee98ab440008f https://github.com/galaxyproject/galaxy/commit/413af14bb55d890ca053d08877ce… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix lint errors Commit: d30852b286b9baba5cf6faffa389db8ec2837114 https://github.com/galaxyproject/galaxy/commit/d30852b286b9baba5cf6faffa389… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/some.wiff.tar Log Message: ----------- Add wiff.tar extension and sniffer Commit: dc303f004fc5254f6de14bc29084532d3db98912 https://github.com/galaxyproject/galaxy/commit/dc303f004fc5254f6de14bc29084… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Remove try/except in sniffers Add .d/.raw to file_ext Commit: f7322d85a317614de1a745da57d5e394b5eb8041 https://github.com/galaxyproject/galaxy/commit/f7322d85a317614de1a745da57d5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar A lib/galaxy/datatypes/test/some.wiff.tar Log Message: ----------- Merge pull request #7299 from chambm/feature/rawtar-datatypes Add datatypes and sniffers for tar archives of directory-based MS formats and WIFF/SCAN pairs Compare: https://github.com/galaxyproject/galaxy/compare/f0026962219e...f7322d85a317

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[galaxyproject/galaxy] f45dd3: Refactor galaxy.util.handlers -> galaxy.web.stack....
by Björn Grüning 09 Feb '19

09 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f45dd3ac05eba2e32b4fa78b6218f94d4ba3a8b5 https://github.com/galaxyproject/galaxy/commit/f45dd3ac05eba2e32b4fa78b6218… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py R lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/handlers.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Refactor galaxy.util.handlers -> galaxy.web.stack.handlers. Nothing in galaxy.util should import sqlalchemy stuff and this package does after #7129. Commit: 572e91a52b67c59d4180273754ef9efd28eaa032 https://github.com/galaxyproject/galaxy/commit/572e91a52b67c59d4180273754ef… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py R lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/handlers.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #7339 from jmchilton/refactor_handlers Refactor galaxy.util.handlers -> galaxy.web.stack.handlers. Compare: https://github.com/galaxyproject/galaxy/compare/0284ab391583...572e91a52b67

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[galaxyproject/galaxy] 67fed3: Moved initqueue to window to avoid CORS issue in t...
by Mason 09 Feb '19

09 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 67fed3524ffb437ad316e98d0740026e44abcd52 https://github.com/galaxyproject/galaxy/commit/67fed3524ffb437ad316e98d0740… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M client/galaxy/scripts/onload/initQueue.js Log Message: ----------- Moved initqueue to window to avoid CORS issue in toolshed iframe (issue 7335) Commit: d3af1a0eb853f2daa1fee3d45a815101537b5ee6 https://github.com/galaxyproject/galaxy/commit/d3af1a0eb853f2daa1fee3d45a81… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M client/galaxy/scripts/onload/initQueue.js Log Message: ----------- Preferred closure storage for initQueue Commit: 0284ab391583cc236f10726a58f6ffc8554c0b43 https://github.com/galaxyproject/galaxy/commit/0284ab391583cc236f10726a58f6… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M client/galaxy/scripts/onload/initQueue.js Log Message: ----------- Merge pull request #7338 from Nerdinacan/fix_cors_blocking_tts_7335 Fix CORS issue in legacy test tool frame installation Compare: https://github.com/galaxyproject/galaxy/compare/b6a97619b457...0284ab391583

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