On Fri, Apr 11, 2014 at 6:06 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Apr 11, 2014 at 5:29 PM, Daniel Blankenberg <dan@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.sqli... $ 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