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

[galaxyproject/usegalaxy-playbook] 4480e3: Re-enable sentry on test
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4480e3199496563ddcf31c1aa2e88a5031700fc5 https://github.com/galaxyproject/usegalaxy-playbook/commit/4480e3199496563d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Re-enable sentry on test Commit: aa74d76efb826314c541203138e512eb523590a6 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa74d76efb826314… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Merge pull request #76 from galaxyproject/test_reenable_sentry Re-enable sentry on test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a7b84fe15f7e...…

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[galaxyproject/usegalaxy-playbook] a7b84f: Update Test
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a7b84fe15f7ed8743880602e824d4ac157c36b98 https://github.com/galaxyproject/usegalaxy-playbook/commit/a7b84fe15f7ed874… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 1fedf7: add maintenance.sh to simplify setting up a cleanu...
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1fedf7e680ef287e81e7a55b668b74a0aefc5d77 https://github.com/galaxyproject/galaxy/commit/1fedf7e680ef287e81e7a55b668b… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: A scripts/common_startup_variables.sh A scripts/maintenance.sh Log Message: ----------- add maintenance.sh to simplify setting up a cleanup cron job or run the cleanup scripts in general Commit: b372c3b4b9e339b8c4f81ae88e57fc4a37731769 https://github.com/galaxyproject/galaxy/commit/b372c3b4b9e339b8c4f81ae88e57… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M scripts/maintenance.sh Log Message: ----------- fix location of cleanup_datasets.py if executed outside of the root Commit: 33bd54079be7b7c27afa1ce8a1ff80d2cacfb0d3 https://github.com/galaxyproject/galaxy/commit/33bd54079be7b7c27afa1ce8a1ff… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: A scripts/common_startup_variables.sh A scripts/maintenance.sh Log Message: ----------- Merge pull request #4916 from scholtalbers/add_maintenance_script Add maintenance script.. Compare: https://github.com/galaxyproject/galaxy/compare/c8a7b7b07cad...33bd54079be7

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[galaxyproject/galaxy] 1a43ef: Work around (temporarily) wrong getsize() output
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a43ef5b83d7378faa653451ebc38a54725a7481 https://github.com/galaxyproject/galaxy/commit/1a43ef5b83d7378faa653451ebc3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Work around (temporarily) wrong getsize() output I'm not sure how/why this happens, but this can be reproduced by copying a file to a location in one process, while checking the size in another process: Run this to copy a file indefinitely: ``` import os import shutil open('test').write("foo") while True: shutil.copy('test', 'test.file') os.remove('test.file') ``` In the same directory run this ``` import os count = 0 wrong_size = False while True: try: size = os.path.getsize('test.file') if size == 0: wrong_size = True wrong_count = count elif wrong_size and os.path.getsize('test.file') != 0: # We have seen the wrong size being reported, but now it's correct again print("Got wrong file size at %dnd try, was fixed in %dnd try" % (wrong_count, count)) break except Exception: pass count += 1 ``` It'll (probably) fail like this: ``` Got wrong file size at 0nd try, was fixed in 1nd try ``` or more often: ``` Got wrong file size at 31nd try, was fixed in 32nd try ``` This seems to be fixed when running os.path.getsize() another time, so we simply do that here. Commit: 16344a62d3a8f30f4c468b552ce49ca989a1f0b7 https://github.com/galaxyproject/galaxy/commit/16344a62d3a8f30f4c468b552ce4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Alternative fix for missing metadata on datasets that report output size 0 Commit: 161467513b3f911cde15b890c404ed373f4571f4 https://github.com/galaxyproject/galaxy/commit/161467513b3f911cde15b890c404… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Use a for loop when checking size in object store and adjust `empty()` to use the new code. Thanks @nsoranzo. Commit: c8a7b7b07cad174b0d8ed142be9fa3ec4a6ed997 https://github.com/galaxyproject/galaxy/commit/c8a7b7b07cad174b0d8ed142be9f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #5335 from mvdbeek/no_check_data Work around (temporarily) wrong getsize() output Compare: https://github.com/galaxyproject/galaxy/compare/4993249ab6b9...c8a7b7b07cad

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[galaxyproject/galaxy] 7af638: Disable galaxy tour 'path' navigation -- this styl...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7af6381e24c8bcd8efc5c56491eaa02571ba8f17 https://github.com/galaxyproject/galaxy/commit/7af6381e24c8bcd8efc5c56491ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Disable galaxy tour 'path' navigation -- this style of tour nav behaves very poorly with Galaxy and it's pretty easy to get a tour completely *stuck* in reload loops from the user experience, forcing manual cache cleaning or the like to make Galaxy usable again. Commit: 4993249ab6b995026ad1db2ba22eb3014ee0e7c2 https://github.com/galaxyproject/galaxy/commit/4993249ab6b995026ad1db2ba22e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Merge pull request #5340 from dannon/tour_path_tweak Disable galaxy tour 'path' navigation Compare: https://github.com/galaxyproject/galaxy/compare/7659efc68c92...4993249ab6b9

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[galaxyproject/galaxy] c1debb: Refactor galaxy.ini.sample config comments toward ...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1debb7c63d9b61d7391bb8abbf474d6272be662 https://github.com/galaxyproject/galaxy/commit/c1debb7c63d9b61d7391bb8abbf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Refactor galaxy.ini.sample config comments toward per-option docs. Commit: 025f92bb73c7347536bf23f2adcff833c3c7284c https://github.com/galaxyproject/galaxy/commit/025f92bb73c7347536bf23f2adcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Random fix for tool filters. Commit: cd30a3424f3e564f3729b083e6abbd642c0122fa https://github.com/galaxyproject/galaxy/commit/cd30a3424f3e564f3729b083e6ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/config.py Log Message: ----------- Don't read global configuration for reports - it doesn't use it. Commit: 6dd0684be3f8825676a7854b6f36faf874f03176 https://github.com/galaxyproject/galaxy/commit/6dd0684be3f8825676a7854b6f36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix ignoring ".sample" in newish path module. Required to correctly detect the extension of sample configuration files. Commit: 4a2a7e79459f65f1686c8814ca1a4a59bf829be5 https://github.com/galaxyproject/galaxy/commit/4a2a7e79459f65f1686c8814ca1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - allow printing comment header on sample description files. Generated from the desc field in the app schema. Commit: 87ace980d73ba7130dd29015145a09bd10f6dd68 https://github.com/galaxyproject/galaxy/commit/87ace980d73ba7130dd29015145a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - fix sample file generation for large default values. The various messages in the Galaxy config were being split across lines and generating invalid YAML. Commit: 146dfd21143774d5451b4417eb223d73cdc23573 https://github.com/galaxyproject/galaxy/commit/146dfd21143774d5451b4417eb22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - hack uWSGI section of sample file generation. Because uWSGI seems really bad at parsing fairly simple, entirely valid YAML. Commit: 72466136d148848b560827ac5b34945d308216ed https://github.com/galaxyproject/galaxy/commit/72466136d148848b560827ac5b34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - improve default value formatting in RST. Commit: 1b58157d003db7a663aa102994aea2873e2f7a7b https://github.com/galaxyproject/galaxy/commit/1b58157d003db7a663aa102994ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - fix to generate YAML booleans in RST docs. The new default - might as well use that representation. Commit: 0ae21925b7c08c82a8daf4887e78ca66b06f38e9 https://github.com/galaxyproject/galaxy/commit/0ae21925b7c08c82a8daf4887e78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A tmp_config_convert/convert.py Log Message: ----------- convert_yaml - script to convert galaxy.ini.sample to config_schema.yml. Commit: 44341ba5c1ca11bf94eb97c9644d3ac11f1b0268 https://github.com/galaxyproject/galaxy/commit/44341ba5c1ca11bf94eb97c9644d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A tmp_config_convert/galaxy.ini.sample Log Message: ----------- convert_yaml - setup copy of galaxy.ini.sample for conversion to work on. Commit: 3703f05c33b702bf4c27e14619bb6965f1d4e38f https://github.com/galaxyproject/galaxy/commit/3703f05c33b702bf4c27e14619bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M tmp_config_convert/galaxy.ini.sample Log Message: ----------- convert_yaml - cleanup noise in conversion's copy of galaxy.ini.sample before conversion. Commit: f058370a98fa84f3b7bdf5286c4e16cd3b811947 https://github.com/galaxyproject/galaxy/commit/f058370a98fa84f3b7bdf5286c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- convert_yaml - run conversion to YAML. Commit: 2b12d0b605732f918e075ae52ea3518e15e61598 https://github.com/galaxyproject/galaxy/commit/2b12d0b605732f918e075ae52ea3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: R config/galaxy.ini.sample A lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- convert_yaml - make sample a schema. Commit: 6901fa9371be28584957fe14a06c73c221ed223b https://github.com/galaxyproject/galaxy/commit/6901fa9371be28584957fe14a06c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: R tmp_config_convert/convert.py R tmp_config_convert/galaxy.ini.sample Log Message: ----------- convert_yaml - remove tmp directory for converting yaml. Commit: 8a9dc5907d377819989d9c0165929c0f378d0559 https://github.com/galaxyproject/galaxy/commit/8a9dc5907d377819989d9c016592… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M Makefile A lib/galaxy/webapps/galaxy/uwsgi_schema.yml Log Message: ----------- yaml_config - Add entry points (e.g. Makefile) for dealing with Galaxy YAML configs. Commit: d08dc05d9588e24a31de3a4a1ba9a07b42ae2e2e https://github.com/galaxyproject/galaxy/commit/d08dc05d9588e24a31de3a4a1ba9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A config/galaxy.yml.sample Log Message: ----------- yaml_config - Generate Galaxy yaml sample. Commit: 4f4928b38677475fd3d70b0435bc9910154ccaba https://github.com/galaxyproject/galaxy/commit/4f4928b38677475fd3d70b0435bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst A doc/source/admin/options.rst M lib/galaxy/webapps/config_manage.py Log Message: ----------- yaml_config - Add RST docs for Galaxy options. Automatically generated from the new specification. Commit: 7bae23e105a46378b6042b6d00b1c61778349c0f https://github.com/galaxyproject/galaxy/commit/7bae23e105a46378b6042b6d00b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M .travis.yml M scripts/common_startup.sh M scripts/galaxy-main M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M test/base/driver_util.py M test/docker/base/run_test_wrapper.sh Log Message: ----------- yaml_config - update code base for converting galaxy.ini.sample to YAML. Commit: ba35d474a012d2ef60a6191fbfe3ee03ed04e09c https://github.com/galaxyproject/galaxy/commit/ba35d474a012d2ef60a6191fbfe3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/authentication.md M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/reports.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- yaml_config - update admin docs for switch to YAML config. Commit: 14f0185b217fad83009f2f8822a75774af42ae42 https://github.com/galaxyproject/galaxy/commit/14f0185b217fad83009f2f8822a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- yaml_config - change test wrapper to work with either ini or yml in container. Commit: f06860a8fb200f01154e4822b3931f32c882a706 https://github.com/galaxyproject/galaxy/commit/f06860a8fb200f01154e4822b393… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- yaml_config - Don't parse YAML configurations as ini files. Commit: 60cbcfd1eeb07a8b93e96ce148e911f1dfddb22b https://github.com/galaxyproject/galaxy/commit/60cbcfd1eeb07a8b93e96ce148e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M .ci/first_startup.sh Log Message: ----------- yaml_config - Try to fix first startup CI job for uWSGI default. Commit: bce21ab3f3ef7948a53c251c45f36b386928a29e https://github.com/galaxyproject/galaxy/commit/bce21ab3f3ef7948a53c251c45f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Axe special amqp config handling not used by modern messaging stuff. It wasn't compatible with YAML config and looks unused as far as I can tell. xref https://github.com/galaxyproject/galaxy/commit/6b92bf6eb8ca8a5114fc2ecf7fda… Commit: 8f69d17e8612dd8f33355a4bfd7a46ba635f1403 https://github.com/galaxyproject/galaxy/commit/8f69d17e8612dd8f33355a4bfd7a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Don't use uWSGI master mode by default. Fixes Ctrl+C on macOS and is really only important in production configs where you should be using a config file anyway. Commit: cec42d1656f9e6ea5f28b3fd02dbe3eb3f1bf078 https://github.com/galaxyproject/galaxy/commit/cec42d1656f9e6ea5f28b3fd02db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- yaml_config - Update Conda FAQ to link out to last .ini variant of docs for those who need them. Commit: 33abb94252544686b313e7c238e19882bdcbc2af https://github.com/galaxyproject/galaxy/commit/33abb94252544686b313e7c238e1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Drop missing --safe-pidfile uWSGI arg until it is released. Commit: f5aa17df1893ed9901de629e602fa052c169fa25 https://github.com/galaxyproject/galaxy/commit/f5aa17df1893ed9901de629e602f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix the use of --set galaxy_config_file with uWSGI where the app name is the PasteDeploy default `app:main`. Commit: 8cd23970fbb1f6250a65f570c288579777464cbf https://github.com/galaxyproject/galaxy/commit/8cd23970fbb1f6250a65f570c288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix for None config_file in web stack stuff. Commit: c99b4ece5bfb0b2d30049796cc9e415e05ef2092 https://github.com/galaxyproject/galaxy/commit/c99b4ece5bfb0b2d30049796cc9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 0585efaaa7d7d63d54088e120e3d5a7cd7e6ef33 https://github.com/galaxyproject/galaxy/commit/0585efaaa7d7d63d54088e120e3d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/cluster.md M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst Log Message: ----------- Update newer deployer config docs for switch to YAML config. Commit: 70ee8d00cc3708b866723de9fe784c9c6a2cda3c https://github.com/galaxyproject/galaxy/commit/70ee8d00cc3708b866723de9fe78… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Begin config schema for Galaxy (just the new not-in-galaxy.ini logging option for now, the rest will be autogenerated from the sample) Commit: 0664921e00ba5dac623c19f1f5344a7f367aaa62 https://github.com/galaxyproject/galaxy/commit/0664921e00ba5dac623c19f1f534… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: A doc/source/admin/application_server.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst Log Message: ----------- WIP admin documentation updates Commit: 8cf649b33186838f1de2364b696d36f962bc99bf https://github.com/galaxyproject/galaxy/commit/8cf649b33186838f1de2364b696d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: R doc/source/admin/application_server.rst M doc/source/admin/config.rst M doc/source/admin/index.rst M doc/source/admin/reports.rst M doc/source/admin/scaling.md Log Message: ----------- WIP admin docs updates for 18.01 Commit: 5ae0c323ec1ef374a24e18efb59df423424aa80c https://github.com/galaxyproject/galaxy/commit/5ae0c323ec1ef374a24e18efb59d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py Log Message: ----------- Expand number of parameters with custom conversion/linting for Galaxy. Add functionality and test case for converting parameter names (e.g. from allow_library_path_paste to allow_path_pate) during conversion. Commit: e8a9cc27ff9e7de6aa70aedc7005773d34d3d59d https://github.com/galaxyproject/galaxy/commit/e8a9cc27ff9e7de6aa70aedc7005… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Locate the Galaxy config file when multiple uWSGI --yaml/--json arguments are used. Commit: 542aa95fa40288b7b754d3908d87967a7ce92e34 https://github.com/galaxyproject/galaxy/commit/542aa95fa40288b7b754d3908d87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-08 (Mon, 08 Jan 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- uWSGI: Use --master when daemonizing (required when using http server w/ daemonization) and fix `run.sh --stop-daemon` Commit: 36ecca47e7c859a980c4e775db0ebedbb1c02cef https://github.com/galaxyproject/galaxy/commit/36ecca47e7c859a980c4e775db0e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Major updates to the scaling doc for uWSGI Commit: 18b3599207b12ff3019d7d1032101b6bdb99eb75 https://github.com/galaxyproject/galaxy/commit/18b3599207b12ff3019d7d103210… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Remove emperor mode reference Commit: daa7845580c08f7ded43af2aa1ff183fc95c5a05 https://github.com/galaxyproject/galaxy/commit/daa7845580c08f7ded43af2aa1ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Add docstring to LOGGING_CONFIG_DEFAULT so that it is part of the autodoc generated docs, so that it can be linked from statically written docs. Commit: 9204916ac8ffbfb5dad3734275fa3d4843300d20 https://github.com/galaxyproject/galaxy/commit/9204916ac8ffbfb5dad3734275fa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/config.rst Log Message: ----------- Galaxy config doc corrections Commit: e0891cac355d062711b645e5e4859cddd6f14cdd https://github.com/galaxyproject/galaxy/commit/e0891cac355d062711b645e5e485… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/conf.py Log Message: ----------- Add intersphinx mapping to the Python 2.7 documentation Commit: db00f97175c2870300617a8de8a5adac16e7b0d5 https://github.com/galaxyproject/galaxy/commit/db00f97175c2870300617a8de8a5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M .gitignore M doc/Makefile M doc/source/admin/config_logging.rst Log Message: ----------- Finish Galaxy logging configuration documentation Commit: adcf2138ae2f2013bed9386356b2b7c5d2d53648 https://github.com/galaxyproject/galaxy/commit/adcf2138ae2f2013bed9386356b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M .gitignore Log Message: ----------- Add missing generated docs to .gitignore Commit: 1e275e84f8d1ce2d1afb5974d62d988ccc0e2bfe https://github.com/galaxyproject/galaxy/commit/1e275e84f8d1ce2d1afb5974d62d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/index.rst Log Message: ----------- Add loggging configuration to admin docs TOC and move the cluster docs after the scaling docs Commit: 35b1e2c9e7ce349f8cc37d363bb637b96a37266b https://github.com/galaxyproject/galaxy/commit/35b1e2c9e7ce349f8cc37d363bb6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/jobs.md M doc/source/admin/scaling.md Log Message: ----------- Correct the handlers section of the job conf documentation. Commit: 1daa2ae6e5b11843912e2c42af2a0040a32d6030 https://github.com/galaxyproject/galaxy/commit/1daa2ae6e5b11843912e2c42af2a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Fix support for proxy prefix under uWSGI. Commit: 1b583fb851ebfc476f53daff7447b37ee8477561 https://github.com/galaxyproject/galaxy/commit/1b583fb851ebfc476f53daff7447… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M doc/source/admin/index.rst A doc/source/admin/nginx.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/index.rst R doc/source/admin/special_topics/nginx.md Log Message: ----------- Update nginx documentation for uWSGI Commit: 5a0d60537cdf9417c347921f06ae9b22e577274c https://github.com/galaxyproject/galaxy/commit/5a0d60537cdf9417c347921f06ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: A doc/source/admin/apache.md M doc/source/admin/index.rst M doc/source/admin/nginx.md M doc/source/admin/production.md M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/index.rst M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Update Apache documentation for uWSGI Commit: 78992968ecd0de1f95b99352b53ea2ecd246f954 https://github.com/galaxyproject/galaxy/commit/78992968ecd0de1f95b99352b53e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Correct documentation line endings Commit: f4131b8d2bcf75c1724e19265cf4ca93dfaefa73 https://github.com/galaxyproject/galaxy/commit/f4131b8d2bcf75c1724e19265cf4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Correct doc typos caught by @nsoranzo Commit: 5fcefe404f7d5cd5d2dbbf0628b265e9d24138f5 https://github.com/galaxyproject/galaxy/commit/5fcefe404f7d5cd5d2dbbf0628b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst M doc/source/admin/apache.md M doc/source/admin/nginx.md A doc/source/admin/proxy_package_layout.rst Log Message: ----------- Attempt to reduce duplication in the proxy documentation through the use of includes, move the multi-config-file discussion to a common page. 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lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py R openid/yahoo.xml R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py M scripts/build_universe_config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M 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scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/vue.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test-data/neostore.zip A test-data/new_element_sort_order.txt M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_1.ga M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml A test/functional/tools/multi_output_recurse.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_parsing.py A test/unit/tools/test_tool_validation.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into ini_to_yaml_config Commit: 3fdbaa3dec07078388ce63bdb1a6f9251ffeb3f1 https://github.com/galaxyproject/galaxy/commit/3fdbaa3dec07078388ce63bdb1a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- Regenerate galaxy.yml.sample and documentation for newly added/documented config options. Commit: dd0aeec50013e172a0f49c1e5681cc73ed635213 https://github.com/galaxyproject/galaxy/commit/dd0aeec50013e172a0f49c1e5681… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Fix lint error Commit: 7659efc68c92948e5e8e00404e537752158061cb https://github.com/galaxyproject/galaxy/commit/7659efc68c92948e5e8e00404e53… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M .gitignore M .travis.yml M Makefile R config/galaxy.ini.sample A config/galaxy.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/config_schema.yml A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M test/base/driver_util.py M test/docker/base/run_test_wrapper.sh A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py Log Message: ----------- Merge pull request #5105 from jmchilton/ini_to_yaml_config Convert options file to YAML and use uWSGI by default Compare: https://github.com/galaxyproject/galaxy/compare/b174dafa36f0...7659efc68c92

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[galaxyproject/usegalaxy-playbook] 73e398: Use IU for swarm communication since all the nodes...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 73e398cfa4693852eccccfe8d864c894842d4c38 https://github.com/galaxyproject/usegalaxy-playbook/commit/73e398cfa4693852… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M env/main/group_vars/galaxywebservers.yml M env/test/group_vars/galaxyservers/vars.yml M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Use IU for swarm communication since all the nodes are there anyway

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[galaxyproject/galaxy] 3681a4: Move the client build for selenium to run_tests.sh...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3681a4b77f29a9bbb6cbbd6841fc0a9c8a41106e https://github.com/galaxyproject/galaxy/commit/3681a4b77f29a9bbb6cbbd6841fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Move the client build for selenium to run_tests.sh instead of in the external jenkins job configuration. Has the added benefit of skipping the client build when we don't want to run it. Commit: e61d5cdadfdd17b8879b6ec9a74937cb3eac3479 https://github.com/galaxyproject/galaxy/commit/e61d5cdadfdd17b8879b6ec9a749… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Build sourcemaps for the jenkins selenium tests -- I don't know that this actually gets resolved, but it doesn't have a huge impact on build time anyway Commit: b174dafa36f08b7903a3469856672f85cf88e2ec https://github.com/galaxyproject/galaxy/commit/b174dafa36f08b7903a346985667… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #5333 from dannon/jenkins_client_build_tweak Move the client build for selenium to in-repo script Compare: https://github.com/galaxyproject/galaxy/compare/a48d0e9a7faa...b174dafa36f0

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[galaxyproject/galaxy] a847db: Fix tool report submission
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a847dbd3d5e312b13cfe8a90844c8f88d3aedc78 https://github.com/galaxyproject/galaxy/commit/a847dbd3d5e312b13cfe8a90844c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Fix tool report submission Commit: a6e9504dde8b5c96f6f5fc183c56d9458b996588 https://github.com/galaxyproject/galaxy/commit/a6e9504dde8b5c96f6f5fc183c56… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5303 from mvdbeek/sentry_hotfix [17.09] Fix tool report submission with sentry Commit: 6bef1fcbaa1df5690658f7b14512d212c115a0e5 https://github.com/galaxyproject/galaxy/commit/6bef1fcbaa1df5690658f7b14512… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- remove an extra F from the folder ID Commit: c3d145ce995e9e5f8e54dd7e81333bcc712bf4ab https://github.com/galaxyproject/galaxy/commit/c3d145ce995e9e5f8e54dd7e8133… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Merge pull request #5327 from martenson/fix-structured-lib-link [17.09] fix link to library from history structure view Commit: d94148ff7999e0ecee9b617c4daec24da28ea1a5 https://github.com/galaxyproject/galaxy/commit/d94148ff7999e0ecee9b617c4dae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Prevent reloading when data table is being modified Fixes https://github.com/galaxyproject/galaxy/issues/4783. Commit: 8c1807c2879950ef47ccd162b6a7eebc83bc892b https://github.com/galaxyproject/galaxy/commit/8c1807c2879950ef47ccd162b6a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Trigger reload for each modified data table In unindeted one level too much in the previous commit, which would only reload the last table (thanks @dannon). The alternative would be to reload all tables, but I think this is more efficient. Commit: 8f91ae0db9f0ebdc06e6e284fb2fb254db553181 https://github.com/galaxyproject/galaxy/commit/8f91ae0db9f0ebdc06e6e284fb2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Reload tool data tables for 'undeclared_tables' Thanks @nsoranzo! Commit: 3c85407ec80186166a6cb58f35bcb6eda6cc739b https://github.com/galaxyproject/galaxy/commit/3c85407ec80186166a6cb58f35bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #5331 from mvdbeek/data_manager_reload_fix [17.09] Prevent reloading when data table is being modified Commit: a48d0e9a7faabe79045011117f060fd655adc510 https://github.com/galaxyproject/galaxy/commit/a48d0e9a7faabe79045011117f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/toolbox/watcher.py M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bf2c9bab344c...a48d0e9a7faa

1 0

[galaxyproject/galaxy] d94148: Prevent reloading when data table is being modifie...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: d94148ff7999e0ecee9b617c4daec24da28ea1a5 https://github.com/galaxyproject/galaxy/commit/d94148ff7999e0ecee9b617c4dae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Prevent reloading when data table is being modified Fixes https://github.com/galaxyproject/galaxy/issues/4783. Commit: 8c1807c2879950ef47ccd162b6a7eebc83bc892b https://github.com/galaxyproject/galaxy/commit/8c1807c2879950ef47ccd162b6a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Trigger reload for each modified data table In unindeted one level too much in the previous commit, which would only reload the last table (thanks @dannon). The alternative would be to reload all tables, but I think this is more efficient. Commit: 8f91ae0db9f0ebdc06e6e284fb2fb254db553181 https://github.com/galaxyproject/galaxy/commit/8f91ae0db9f0ebdc06e6e284fb2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Reload tool data tables for 'undeclared_tables' Thanks @nsoranzo! Commit: 3c85407ec80186166a6cb58f35bcb6eda6cc739b https://github.com/galaxyproject/galaxy/commit/3c85407ec80186166a6cb58f35bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #5331 from mvdbeek/data_manager_reload_fix [17.09] Prevent reloading when data table is being modified Compare: https://github.com/galaxyproject/galaxy/compare/c3d145ce995e...3c85407ec801

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