On Fri, Apr 11, 2014 at 6:06 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Fri, Apr 11, 2014 at 5:29 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
>> Hi Peter,
>>
>> Looks like you are missing the -data_managers flag, try this:
>>
>> run_functional_tests.sh -data_managers -id data_manager_blast_db
>>
>> Let us know if you encounter more issues.
>>
>> Thanks,
>>
>> Dan
>
> Thank you! That was my silly mistake, it was clearly stated here:
> https://wiki.galaxyproject.org/Admin/Tools/DataManagers/Testing
>
> However, adding the switch seems to prevent testing traditional
> tools at the same time - is that deliberate? e.g.
> https://travis-ci.org/peterjc/galaxy_blast/builds/22788397
>
> Also note the test fails which I suspect is due to the database
> changing slightly? Mike is proposing to switch to a regex based
> test out the output JSON files for this tool...
>
> $ ./run_functional_tests.sh -data_managers -id data_manager_blast_db
> ...
> base.twilltestcase: DEBUG: Files diff for
> '/mnt/galaxy/galaxy-central/test-data/est_out.json' vs
> '/tmp/tmpIk35vy/tmpTNneBG/new_files_path_Q3kSF9/tmpl9xH_Qest_out.json'
> base.twilltestcase: INFO: ## files diff on
> /mnt/galaxy/galaxy-central/test-data/est_out.json and
> /tmp/tmpIk35vy/tmpTNneBG/new_files_path_Q3kSF9/tmpl9xH_Qest_out.json
> lines_diff=0, found diff = 2
> --------------------- >> end captured logging << ---------------------
>
> ----------------------------------------------------------------------
> Ran 1 test in 24.030s
>
> FAILED (failures=1)
> ...

After a few missteps, I got this to run under TravisCI.

This time the twill based test failed to download the est database
(perhaps just a network glitch), but more interestingly this appears
to show a bug with the API based testing (Hi John!):

https://travis-ci.org/peterjc/galaxy_blast/builds/22938945

Running this locally,

$ export 
GALAXY_TEST_DB_TEMPLATE=https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0117.sqlite
$ export GALAXY_TEST_DEFAULT_INTERACTOR=api
$ ./run_functional_tests.sh -data_managers -id data_manager_blast_db
...
galaxy.jobs.handler DEBUG 2014-04-14 12:19:39,558 (1) Dispatching to
local runner
ERROR

======================================================================
ERROR: Blast DB ( data_manager_blast_db ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/galaxy/galaxy-central/test/functional/test_data_managers.py",
line 99, in test_tool
    self.do_it( td )
  File "/mnt/galaxy/galaxy-central/test/functional/test_data_managers.py",
line 34, in do_it
    for assoc in reversed( test_history.user.data_manager_histories ):
AttributeError: 'unicode' object has no attribute 'user'
-------------------- >> begin captured logging << --------------------
galaxy.web.framework: INFO: Session authenticated using Galaxy master api key
galaxy.web.framework: INFO: Session authenticated using Galaxy master api key
galaxy.web.framework: INFO: Session authenticated using Galaxy master api key
galaxy.jobs: DEBUG: (1) Working directory for job is:
/tmp/tmpE6lJPe/tmpNq68Jz/job_working_directory_5lfI0i/000/1
galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner
--------------------- >> end captured logging << ---------------------

----------------------------------------------------------------------
Ran 1 test in 3.060s

FAILED (errors=1)
...
galaxy.jobs.handler ERROR 2014-04-14 12:19:39,895 Exception in monitor_step
Traceback (most recent call last):
  File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line
154, in __monitor
    self.__monitor_step()
  File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line
264, in __monitor_step
    log.exception( "failure running job %d" % job.id )
...
  File 
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 281, in connect
    return self.dbapi.connect(*cargs, **cparams)
OperationalError: (OperationalError) unable to open database file None None
...


Regards,

Peter
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