I have "solved" this by commenting out the apparently harmless test:

https://github.com/peterjc/pico_galaxy/commit/f3d4261846566a86f9c85a158fb95877ca8bc7c5

Peter

On Wed, Oct 29, 2014 at 5:39 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> I'm getting the following exception in a failing unit test:
> https://travis-ci.org/peterjc/pico_galaxy/builds/39398677
>
> Testing this tool (where two of the three near identical tests passed):
> https://github.com/peterjc/pico_galaxy/blob/dd03346710e6a46cb6ec9dda1eed23d5fd301d03/tools/mummer/mummer.xml
>
> ```
> Traceback (most recent call last):
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
> line 116, in test_tool
>     self.do_it( td )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
> line 35, in do_it
>     self._verify_outputs( testdef, test_history, jobs, shed_tool_id,
> data_list, galaxy_interactor )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
> line 75, in _verify_outputs
>     galaxy_interactor.verify_output( history, jobs, output_data,
> output_testdef=output_testdef, shed_tool_id=shed_tool_id,
> maxseconds=maxseconds )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py",
> line 89, in verify_output
>     self._verify_metadata( history_id, hid, attributes )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py",
> line 102, in _verify_metadata
>     dataset = self._get( "histories/%s/contents/%s" % ( history_id,
> hid ) ).json()
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/eggs/requests-2.2.1-py2.7.egg/requests/models.py",
> line 740, in json
>     return json.loads(self.content.decode(encoding), **kwargs)
>   File "/usr/lib/python2.7/dist-packages/simplejson/__init__.py", line
> 413, in loads
>     return _default_decoder.decode(s)
>   File "/usr/lib/python2.7/dist-packages/simplejson/decoder.py", line
> 402, in decode
>     obj, end = self.raw_decode(s, idx=_w(s, 0).end())
>   File "/usr/lib/python2.7/dist-packages/simplejson/decoder.py", line
> 418, in raw_decode
>     obj, end = self.scan_once(s, idx)
> JSONDecodeError: Unpaired high surrogate: line 1 column 785 (char 785)
> ```
>
> Probably relevant:
>  - https://github.com/simplejson/simplejson/issues/62
>  - http://bugs.python.org/issue11489
>
> Any thoughts? What does Galaxy write to these job-associated JSON
> metadata files?
>
> Thanks,
>
> Peter
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