Hi all,

Occasionally I've seen TravisCI tool tests fail with an exeception
ValueError: No JSON object could be decoded, e.g.

https://travis-ci.org/peterjc/galaxy_blast/jobs/107255016

...
galaxy.jobs INFO 2016-02-16 14:17:41,118 Collecting metrics for Job 139
galaxy.jobs DEBUG 2016-02-16 14:17:41,143 job 139 ended (finish()
executed in (1049.363 ms))
galaxy.model.metadata DEBUG 2016-02-16 14:17:41,154 Cleaning up
external metadata files
...
======================================================================
ERROR: NCBI BLAST+ blastn ( ncbi_blastn_wrapper ) > Test-2
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/functional/test_toolbox.py",
line 291, in test_tool
    self.do_it( td )
  File 
"/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/functional/test_toolbox.py",
line 40, in do_it
    stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
  File 
"/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py",
line 41, in stage_data_in_history
    upload_wait()
  File 
"/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py",
line 278, in wait
    while not self.__history_ready( history_id ):
  File 
"/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py",
line 297, in __history_ready
    history_json = self._get( "histories/%s" % history_id ).json()
  File 
"/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/requests/models.py",
line 805, in json
    return complexjson.loads(self.text, **kwargs)
  File "/opt/python/2.6.9/lib/python2.6/json/__init__.py", line 307, in loads
    return _default_decoder.decode(s)
  File "/opt/python/2.6.9/lib/python2.6/json/decoder.py", line 319, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/opt/python/2.6.9/lib/python2.6/json/decoder.py", line 338, in
raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
-------------------- >> begin captured stdout << ---------------------
...


On this run there was no sign of an SQLite locking issue. This JSON problem
went away on a re-run, sadly instead the test-set failed further on with an
SQLite locking problem, see:

https://github.com/galaxyproject/galaxy/issues/1158#issuecomment-168714547

Does this "No JSON object could be decoded" point at a file system issue
(perhaps a race condition)? From searching the email archive this exception
(although not necessarily from the same area of the code) seems to occur
most often where Galaxy is being used with a cluster. But here this is all
running on a single TravisCI VM with the local job runner.

I appreciate there probably isn't enough information here to solve this,
but perhaps we need better logging here - are the JSON files simply
empty for example?

Regards,

Peter
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