Branch: refs/heads/dev
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.
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
Commit: 1fd1848a81532ecd0fb36800e7f1ae1609661141
https://github.com/galaxyproject/galaxy/commit/1fd1848a81532ecd0fb36800e7f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M doc/source/releases/18.09.rst
Log Message:
-----------
Additional 18.09 bugfix
Commit: d0a93ff62808e7e1727c7deb4a48853639bd7ece
https://github.com/galaxyproject/galaxy/commit/d0a93ff62808e7e1727c7deb4a48…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M doc/source/releases/18.09.rst
Log Message:
-----------
Merge pull request #6934 from dannon/doc_update
[18.09] Additional 18.09 doc update for toolshed bugfix.
Commit: 6f6fffe9134e7becfd698340899a96c1cbd8a4fe
https://github.com/galaxyproject/galaxy/commit/6f6fffe9134e7becfd698340899a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M doc/source/releases/18.09.rst
M doc/source/releases/index.rst
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 remote-tracking branch 'upstream/release_18.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/2d7e54831944...6f6fffe9134e
**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/master
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
Commit: 1fd1848a81532ecd0fb36800e7f1ae1609661141
https://github.com/galaxyproject/galaxy/commit/1fd1848a81532ecd0fb36800e7f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M doc/source/releases/18.09.rst
Log Message:
-----------
Additional 18.09 bugfix
Commit: d0a93ff62808e7e1727c7deb4a48853639bd7ece
https://github.com/galaxyproject/galaxy/commit/d0a93ff62808e7e1727c7deb4a48…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M doc/source/releases/18.09.rst
Log Message:
-----------
Merge pull request #6934 from dannon/doc_update
[18.09] Additional 18.09 doc update for toolshed bugfix.
Compare: https://github.com/galaxyproject/galaxy/compare/165123863904...d0a93ff62808
**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.