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[17.09] Toolshed install stability improvements #5099

Merged
merged 2 commits into from
Dec 7, 2017
Merged

[17.09] Toolshed install stability improvements #5099

merged 2 commits into from
Dec 7, 2017

Commits on Nov 30, 2017

  1. 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 galaxyproject#5031.
    @mvdbeek
    mvdbeek committed Nov 30, 2017
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  2. 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)}
```
    @mvdbeek
    mvdbeek committed Nov 30, 2017
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