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fix duplicated attributes #403

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merged 1 commit into from Jan 16, 2016

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bgruening commented Jan 14, 2016

Remove one of the two prefix="" attributes from the resolvers_conf.xml which results in this error:

  File "/home/bag/projects/code/galaxy-test/lib/galaxy/tools/deps/__init__.py", line 44, in build_dependency_manager
    dependency_manager = DependencyManager( **dependency_manager_kwds )
  File "/home/bag/projects/code/galaxy-test/lib/galaxy/tools/deps/__init__.py", line 87, in __init__
    self.dependency_resolvers = self.__build_dependency_resolvers( conf_file )
  File "/home/bag/projects/code/galaxy-test/lib/galaxy/tools/deps/__init__.py", line 132, in __build_dependency_resolvers
    plugin_source = plugin_config.plugin_source_from_path( conf_file )
  File "/home/bag/projects/code/galaxy-test/lib/galaxy/util/plugin_config.py", line 74, in plugin_source_from_path
    return ('xml', ElementTree.parse( path ).getroot())
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1182, in parse
    tree.parse(source, parser)
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 656, in parse
    parser.feed(data)
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1642, in feed
    self._raiseerror(v)
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
    raise err
xml.etree.ElementTree.ParseError: duplicate attribute: line 2, column 66
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jmchilton commented Jan 15, 2016

I just added this though because I don't want to use Galaxy's default. Is there another way to fix this?

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jmchilton commented Jan 15, 2016

I reviewed 5e0b6d1 - I think we want this default but the "prefix" in attributes check is wrong. It should be something like if [a in attributes if "prefix" in a]: probably.

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bgruening commented Jan 15, 2016

I guess we could remove this line: https://github.com/galaxyproject/planemo/blob/fix_resolvers_conf/planemo/galaxy_config.py#L675

Not tested, but then the conda_prefix is also not added.

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bgruening commented Jan 15, 2016

Ok, will try this.

fix duplicated attributes
Remove one of the two prefix="" attributes from the `resolvers_conf.xml` which results in this error:

```
  File "/home/bag/projects/code/galaxy-test/lib/galaxy/tools/deps/__init__.py", line 44, in build_dependency_manager
    dependency_manager = DependencyManager( **dependency_manager_kwds )
  File "/home/bag/projects/code/galaxy-test/lib/galaxy/tools/deps/__init__.py", line 87, in __init__
    self.dependency_resolvers = self.__build_dependency_resolvers( conf_file )
  File "/home/bag/projects/code/galaxy-test/lib/galaxy/tools/deps/__init__.py", line 132, in __build_dependency_resolvers
    plugin_source = plugin_config.plugin_source_from_path( conf_file )
  File "/home/bag/projects/code/galaxy-test/lib/galaxy/util/plugin_config.py", line 74, in plugin_source_from_path
    return ('xml', ElementTree.parse( path ).getroot())
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1182, in parse
    tree.parse(source, parser)
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 656, in parse
    parser.feed(data)
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1642, in feed
    self._raiseerror(v)
  File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
    raise err
xml.etree.ElementTree.ParseError: duplicate attribute: line 2, column 66
```

@bgruening bgruening force-pushed the fix_resolvers_conf branch from 8612a58 to f7ed0d5 Jan 15, 2016

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bgruening commented Jan 15, 2016

@jmchilton like this?

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jmchilton commented Jan 15, 2016

Yeah - does that work?

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bgruening commented Jan 15, 2016

Seems so!

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bgruening commented Jan 15, 2016

@jmchilton ok it works here: https://travis-ci.org/galaxyproject/tools-iuc/builds/102700945

The planemo error looks strange but this is an other problem.

jmchilton added a commit that referenced this pull request Jan 16, 2016

@jmchilton jmchilton merged commit 86328a6 into master Jan 16, 2016

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@jmchilton jmchilton deleted the fix_resolvers_conf branch Jan 16, 2016

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