- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 30ac5d: Release scaffold tweaks.
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30ac5d90d937a28dc61aef5d4a6b6cb05c1a05bf https://github.com/galaxyproject/galaxy/commit/30ac5d90d937a28dc61aef5d4a6b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Release scaffold tweaks. Commit: 66b05cbfc591a5de2d5d248c1f060a67ff369c44 https://github.com/galaxyproject/galaxy/commit/66b05cbfc591a5de2d5d248c1f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Minor clarification Commit: 5d51492a538dddb5eb5c45dc117f090104f70652 https://github.com/galaxyproject/galaxy/commit/5d51492a538dddb5eb5c45dc117f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Getgalaxy links Commit: 2fb4ea1e689e03a44712fd18942d86717e773e36 https://github.com/galaxyproject/galaxy/commit/2fb4ea1e689e03a44712fd18942d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6935 from dannon/release-scaffold-tweaks Release issue scaffold tweaks. Compare: https://github.com/galaxyproject/galaxy/compare/6f6fffe9134e...2fb4ea1e689e **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 29 Oct '18

29 Oct '18

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.

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[galaxyproject/galaxy] cf2645: Fix toolshed error in display_tool if tool is inva...
by GitHub 29 Oct '18

29 Oct '18

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.

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[galaxyproject/galaxy]
by GitHub 29 Oct '18

29 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] 1fd184: Additional 18.09 bugfix
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy 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/e89f746a0713...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.

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[galaxyproject/galaxy] 9319dd: Rename "Test Dataset".
by GitHub 29 Oct '18

29 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 29 Oct '18

29 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 29 Oct '18

29 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 26 Oct '18

26 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 26 Oct '18

26 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.

1 0