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[17.09] Toolshed install stability improvements #5099



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mvdbeek commented Nov 30, 2017

This should go a long way to fixing #5031

I pulled these changes out of #5076 because the remaining errors are probably specific to setups that don't use the default tool-data location and occur only rarely when installing new data tables. To fix it the right way would probably require some larger changes that should go into 18.01 or later.

mvdbeek added some commits Nov 27, 2017

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/", line 217, in parse_xml
    root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))
  File "/usr/lib/python2.7/xml/etree/", line 657, in parse
    self._root = parser.close()
  File "/usr/lib/python2.7/xml/etree/", line 1654, in close
  File "/usr/lib/python2.7/xml/etree/", line 1506, in _raiseerror
    raise err
ParseError: no element found: line 1, column 0
reported in #5031.
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/", line 40, in __call__
    iterable = self.application(environ, start_response)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/", line 85, in __call__
    return self.application(environ, start_response)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/", line 136, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/", line 215, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/web/framework/", line 98, in decorator
    return func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/controllers/", line 1849, in update_to_changeset_revision
  File "tool_shed/galaxy_install/metadata/", line 30, in __init__
    metadata_dict=metadata_dict, user=None)
  File "tool_shed/metadata/", line 63, in __init__
    self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)}

@mvdbeek mvdbeek added this to the 18.01 milestone Nov 30, 2017

@dannon dannon merged commit e9f05cb into galaxyproject:release_17.09 Dec 7, 2017

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api test Build finished. 293 tests run, 4 skipped, 0 failed.
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framework test Build finished. 162 tests run, 0 skipped, 0 failed.
integration test Build finished. 46 tests run, 0 skipped, 0 failed.
lgtm analysis: JavaScript No alert changes
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toolshed test Build finished. 579 tests run, 0 skipped, 0 failed.

@mvdbeek mvdbeek deleted the mvdbeek:toolshed_install_stability branch Jun 12, 2018

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