- galaxy-commits - lists.galaxyproject.org

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[galaxyproject/ansible-galaxy] 3a90b7: Fix typo in sample code (create_user)
by Helena Rasche 09 Feb '19

09 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 3a90b7f9404d6ef1d3b7d719783bd446a517d0a5 https://github.com/galaxyproject/ansible-galaxy/commit/3a90b7f9404d6ef1d3b7… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M README.md Log Message: ----------- Fix typo in sample code (create_user) Commit: 5230c2bb6b0c51701a7715e1a8e25066040cf8ff https://github.com/galaxyproject/ansible-galaxy/commit/5230c2bb6b0c51701a77… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M README.md M defaults/main.yml M tasks/client.yml Log Message: ----------- Add optional selection of client build type Building a client currently comes with 3 options for the type of build: development, production and production with source maps. The new client build task (see #52) defaults to the latter (production with source maps). While there are good arguments for including source maps with production code (useful for debugging, etc.), there should be an easy and documented way for opting out when needed. One such use case is size constraints (in my estimation, including source maps adds 35M). By the same token, offering an option for a dev build seems reasonable, especially considering that all three options are described in the Galaxy client documentaion. Commit: bdd33aa01b73d9fdfd17406ad5686550ca8d4bd8 https://github.com/galaxyproject/ansible-galaxy/commit/bdd33aa01b73d9fdfd17… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M README.md M defaults/main.yml Log Message: ----------- Change default value for client build to client-production-maps Commit: 3e9ff5520254bfe044995c29a1beada2acb2fe11 https://github.com/galaxyproject/ansible-galaxy/commit/3e9ff5520254bfe04499… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M README.md M defaults/main.yml M tasks/client.yml Log Message: ----------- Merge pull request #60 from ic4f/master (1) Fix typo in sample code; (2) Selection of client build type Compare: https://github.com/galaxyproject/ansible-galaxy/compare/971f7dd5b063...3e9f…

1 0

[galaxyproject/usegalaxy-playbook] c089d2: Fix missing sam/bam rename
by Nate Coraor 08 Feb '19

08 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c089d23463b3c3c592aeeaea1b897aafddb0c076 https://github.com/galaxyproject/usegalaxy-playbook/commit/c089d23463b3c3c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Fix missing sam/bam rename

1 0