Ugh... sorry I missed this e-mail. I don't have any answers yet but I
have created a Trello card to track the issue.

https://trello.com/c/3yVLp8RA

Thanks for the detailed error report.

-John

On Fri, Oct 31, 2014 at 12:16 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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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