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