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Improve tool validation and metadata generation #5119

merged 23 commits into from Dec 7, 2017


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3 participants

mvdbeek commented Dec 2, 2017

(Builds on #5099)
This introduces a ValidationConext object, that should contain just enough information to load tools and data tables and can be used in place of app. This avoids manipulation of app-wide settings during tool installations, metadata setting and browsing of toolshed repos.

mvdbeek added some commits Nov 26, 2017

Fix copying of loc.sample files
`filename` should be joined with the tool_path, as evidenced by other uses of
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)}
Use a temporary ToolDataTableManager when generating metadata
Otherwise loaded data tables bleed into the app-wide data tables. This can be
seen with lots of data tables pointing to (non-existing, at that point)
temporary files after a metadata reset in the galaxy admin panel,
but it can also cause failure to install tools with entirely new data tables.
from .bunch import Bunch
class MiniApp(object):

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jmchilton Dec 2, 2017


Entirely personal preference - but what about the path and name instead of galaxy.util.miniapp.MiniApp?

Edit: For more justification - it seems very tool specific - so I don't think it belongs in galaxy.util. I imagine there are other places we will want to decompose app - indeed there are other places we have already decomposed trans so we should make it clear what the purpose of a particular decomposition is I guess -for instance with the WorkContext alternative to trans.

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mvdbeek Dec 2, 2017


Sure, I can do that!

@mvdbeek mvdbeek changed the title from WIP: Improve tool validation and metadata generation to Improve tool validation and metadata generation Dec 3, 2017

@mvdbeek mvdbeek added status/review and removed status/WIP labels Dec 3, 2017

@galaxybot galaxybot added this to the 18.01 milestone Dec 3, 2017


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jmchilton commented Dec 7, 2017

Amazing, amazing, amazing... amazing! Keep up the amazing work!

@jmchilton jmchilton merged commit 30e2736 into galaxyproject:dev Dec 7, 2017

7 checks passed

api test Build finished. 332 tests run, 4 skipped, 0 failed.
continuous-integration/travis-ci/pr The Travis CI build passed
framework test Build finished. 165 tests run, 0 skipped, 0 failed.
integration test Build finished. 59 tests run, 0 skipped, 0 failed.
lgtm analysis: JavaScript No alert changes
selenium test Build finished. 117 tests run, 2 skipped, 0 failed.
toolshed test Build finished. 577 tests run, 0 skipped, 0 failed.

@mvdbeek mvdbeek deleted the mvdbeek:dev_toolshed_install_improvements_2 branch Jun 12, 2018

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