Re: [galaxy-dev] Test failure, JSONDecodeError: Unpaired high surrogate

2014-10-31 Thread Peter Cock 
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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Re: [galaxy-dev] Test failure, JSONDecodeError: Unpaired high surrogate

2014-10-31 Thread John Chilton 
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
 ___
 Please keep all replies on the list by using reply all
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

 To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/
___
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[galaxy-dev] Test failure, JSONDecodeError: Unpaired high surrogate

2014-10-29 Thread Peter Cock 
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
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/