Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca954541... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b842117... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.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 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f88... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Commit: ef13e28578513f94014a705127585a42aba1c470 https://github.com/galaxyproject/galaxy/commit/ef13e28578513f94014a705127585... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/228623a133fd...ef13e2857851