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

[galaxyproject/galaxy] 9319dd: Rename "Test Dataset".
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9319ddf989aa33158b5a02e7a80e879e9e1bc10d https://github.com/galaxyproject/galaxy/commit/9319ddf989aa33158b5a02e7a80e… Author: jra001k <jra001k(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Rename "Test Dataset". Rename test dataset from "Test Dataset" to "Test_Dataset" to prevent CWL error below: <-- if not ACCEPTLIST_RE.match(f["basename"]): raise WorkflowException("Invalid filename: '%s' contains illegal characters" % (f["basename"])) ---> This error occur when running the test below: test/api/test_workflows_cwl.py:CwlWorkflowsTestCase.test_simplest_wf Commit: f0bf1694c54b8cbb06d90e11737c3a7859ffc571 https://github.com/galaxyproject/galaxy/commit/f0bf1694c54b8cbb06d90e11737c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Tweak testing toward being a bit more robust. Commit: 2d7e54831944246b327f06f93cfc22343ae5f9c9 https://github.com/galaxyproject/galaxy/commit/2d7e54831944246b327f06f93cfc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Merge pull request #6929 from jmchilton/testing_tweaks Small testing tweaks from the CWL branch. Compare: https://github.com/galaxyproject/galaxy/compare/91e2e841f717...2d7e54831944 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy]
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/tags/v18.09 Home: https://github.com/galaxyproject/galaxy **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] cf2645: Fix toolshed error in display_tool if tool is inva...
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: cf2645f9a658c5e122fea0309bf73a1f64590c39 https://github.com/galaxyproject/galaxy/commit/cf2645f9a658c5e122fea0309bf7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix toolshed error in display_tool if tool is invalid Fixes the following exception: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/translogger.py", line 69, in __call__ return self.application(environ, replacement_start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "routes/middleware.py", line 141, in __call__ response = self.app(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 143, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 222, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/tool_shed/controllers/repository.py", line 888, in display_tool tool_state = tool_util.new_state(trans, tool, invalid=False) File "tool_shed/util/tool_util.py", line 211, in new_state log.debug('Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e) ``` (from https://sentry.galaxyproject.org/sentry/toolshed/issues/279820/) Might also fix some other issues when redering workflow svg for workflows with invalid tools. Commit: e89f746a0713df76e1e86eb9507d3336aade9419 https://github.com/galaxyproject/galaxy/commit/e89f746a0713df76e1e86eb9507d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge pull request #6932 from mvdbeek/fix_toolshed_bugs [18.09] Fix toolshed error in display_tool if tool is invalid Compare: https://github.com/galaxyproject/galaxy/compare/165123863904...e89f746a0713 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 79cff3: Add 18.09_announce to releases index.
by GitHub 27 Oct '18

27 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 79cff3ea6b34056a9a24a130dab6b25b98ae7ee4 https://github.com/galaxyproject/galaxy/commit/79cff3ea6b34056a9a24a130dab6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Add 18.09_announce to releases index. Commit: 165123863904daa1d7e96651b16f2c6dfa0629a2 https://github.com/galaxyproject/galaxy/commit/165123863904daa1d7e96651b16f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6930 from dannon/index-update [18.09] Add 18.09_announce to releases index. Compare: https://github.com/galaxyproject/galaxy/compare/9b24afc5922b...165123863904 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 79cff3: Add 18.09_announce to releases index.
by GitHub 27 Oct '18

27 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 79cff3ea6b34056a9a24a130dab6b25b98ae7ee4 https://github.com/galaxyproject/galaxy/commit/79cff3ea6b34056a9a24a130dab6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Add 18.09_announce to releases index. Commit: 165123863904daa1d7e96651b16f2c6dfa0629a2 https://github.com/galaxyproject/galaxy/commit/165123863904daa1d7e96651b16f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6930 from dannon/index-update [18.09] Add 18.09_announce to releases index. Compare: https://github.com/galaxyproject/galaxy/compare/9b24afc5922b...165123863904 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 17cc83: Update TTS
by GitHub 27 Oct '18

27 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 17cc8348980f61618236022a62581170db6c91cd https://github.com/galaxyproject/usegalaxy-playbook/commit/17cc8348980f6161… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7bbe0e: Allocate more memory for selenium Python 3 client.
by GitHub 27 Oct '18

27 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7bbe0e98cd0fdb1c0a952cdb0c6c99e121c1f1e2 https://github.com/galaxyproject/galaxy/commit/7bbe0e98cd0fdb1c0a952cdb0c6c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh Log Message: ----------- Allocate more memory for selenium Python 3 client. Matching Python 2 fix in 4054ffc31165b533cb292c58edafac49b59de9de. Commit: 91e2e841f71734f1ad90c1679f5427fb4826336c https://github.com/galaxyproject/galaxy/commit/91e2e841f71734f1ad90c1679f54… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh Log Message: ----------- Merge pull request #6927 from jmchilton/py3_sel_fix Allocate more memory for selenium Python 3 client. Compare: https://github.com/galaxyproject/galaxy/compare/395778390c69...91e2e841f717 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] ac411e: Update MTS
by GitHub 27 Oct '18

27 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ac411e61016550c758f208bd48f8fc724754ef1e https://github.com/galaxyproject/usegalaxy-playbook/commit/ac411e61016550c7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update MTS **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7bd7ab: Fix linting of dev.
by GitHub 27 Oct '18

27 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7bd7abb5eeb1e3e73effde03498aedc979744939 https://github.com/galaxyproject/galaxy/commit/7bd7abb5eeb1e3e73effde03498a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M test/api/test_workflows_from_yaml.py Log Message: ----------- Fix linting of dev. Commit: 395778390c692cab247853a82a8d3ebfd6d7edd0 https://github.com/galaxyproject/galaxy/commit/395778390c692cab247853a82a8d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M test/api/test_workflows_from_yaml.py Log Message: ----------- Merge pull request #6928 from jmchilton/fix_linting_dev Fix linting of dev. Compare: https://github.com/galaxyproject/galaxy/compare/4919805f815e...395778390c69 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f7fa5a: Don't mask exceptions during job runner work threa...
by GitHub 27 Oct '18

27 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7fa5a94ba945d56e916deba84353bcf5b44c746 https://github.com/galaxyproject/galaxy/commit/f7fa5a94ba945d56e916deba8435… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Don't mask exceptions during job runner work thread shutdown Commit: 93b93a789ae51a5478553f062a50d74050c49ef5 https://github.com/galaxyproject/galaxy/commit/93b93a789ae51a5478553f062a50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Modify job runner work thread shutdown behavior from "wait at least this long per thread" to "wait at least (but pretty close to) this long for all threads" Commit: 33c3b74bf56f9c197e4d15cc4cd6f94882fc1240 https://github.com/galaxyproject/galaxy/commit/33c3b74bf56f9c197e4d15cc4cd6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Increase the value of monitor_thread_join_timeout to 30 now that it is the total wait time. Add more documentation about it and the uWSGI and supervisord options that changing it will have an effect upon. Commit: e7156bdd23a0621b3a98d50687041af2403241f3 https://github.com/galaxyproject/galaxy/commit/e7156bdd23a0621b3a98d5068704… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Restore monitor_thread_join_timeout to 5 for tests Commit: 7c6b184557dcfd052abf1424fc024f77838c4a70 https://github.com/galaxyproject/galaxy/commit/7c6b184557dcfd052abf1424fc02… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Clarify that maximum job runner worker shutdown time is a multiple of `monitor_thread_join_timeout` based on the configured number of runner plugins. Commit: ae12cc92eb12cada527cb44dc5c66ae7b355545e https://github.com/galaxyproject/galaxy/commit/ae12cc92eb12cada527cb44dc5c6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Catch all exceptions around runner shutdown so it doesn't prevent other runners from attempting shutdown. Commit: a6215ea68e4b8accfef5a5cec2133f440fec9fe0 https://github.com/galaxyproject/galaxy/commit/a6215ea68e4b8accfef5a5cec213… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- In fixing the incorrect behavior of what was previously in the handler shutdown method, I made the same mistake in a slightly different way. Commit: 4919805f815ef0e7f780b094ffd6c91f6d54c4b4 https://github.com/galaxyproject/galaxy/commit/4919805f815ef0e7f780b094ffd6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M lib/galaxy/config.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/base/driver_util.py Log Message: ----------- Merge pull request #6924 from natefoo/quiesce-handler Be more precise with the job runner worker thread join timeout and improve documentation Compare: https://github.com/galaxyproject/galaxy/compare/dda297c4089f...4919805f815e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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