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.
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.