Hi,

Thanks for the tips, Peter.  Hmm.  No amount of playing with my 
galaxy-dist/tool_conf.xml.sample file is enabling the tool to be found by 
run_tests.sh . In the run_functional_tests.html I see:

  File "/usr/lib64/python2.6/unittest.py", line 278, in run
    testMethod()

  File 
"/usr/local/galaxy/production1/galaxy-dist/eggs/nose-0.11.1-py2.6.egg/nose/failure.py",
 line 39, in runTest
    raise self.exc_class(self.exc_val)

   ValueError: No such test TestForTool_ffp_phylogeny

In the run_tests.sh stdout I see

  galaxy.jobs WARNING 2015-02-12 15:26:56,326 Job configuration 
"./job_conf.xml" does not exist, using legacy job configuration from Galaxy 
config file "/tmp/tmp8_2Kiq/functional_tests_wsgi.ini" instead
  ...
  galaxy.tools INFO 2015-02-12 15:26:59,958 Parsing the tool configuration 
./config/migrated_tools_conf.xml
  galaxy.tools DEBUG 2015-02-12 15:26:59,959 Loading section: BCCDC Tools 
  galaxy.tools DEBUG 2015-02-12 15:26:59,989 Loaded tool id: 
salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00,
 version: 0.1.00 into tool panel....
  galaxy.tools DEBUG 2015-02-12 15:27:00,018 Loaded tool id: 
salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00,
 version: 0.1.00 into tool panel....
  galaxy.tools DEBUG 2015-02-12 15:27:00,108 Loaded tool id: 
salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/select_subsets/bccdcSelectSubsets/1.0.0,
 version: 1.0.0 into tool panel....
   ...

   ======================================================================
   ERROR: Failure: ValueError (No such test TestForTool_ffp_phylogeny)
   ----------------------------------------------------------------------
   Traceback (most recent call last):
     File 
"/usr/local/galaxy/production1/galaxy-dist/eggs/nose-0.11.1-py2.6.egg/nose/failure.py",
 line 39, in runTest
       raise self.exc_class(self.exc_val)
   ValueError: No such test TestForTool_ffp_phylogeny

   ----------------------------------------------------------------------
   Ran 1 test in 0.002s


Now investigating that "/tmp/tmp8_2Kiq/functional_tests_wsgi.ini" file I SEE A 
STRANGE THING - the prefix shows "/galaxy" whereas I'm testing on a /galaxylab 
prefix install.  There is a /galaxy prefix ALREADY as another galaxy install on 
our server.  Is this relevant/irrelevant?

[galaxy_amqp]

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

[server:main]
use_threadpool = True
use = egg:Paste#http
threadpool_kill_thread_limit = 10800

[app:main]
use_nglims = False
database_connection = 
sqlite:////tmp/tmp1OhjFo/tmpQTWBB8/database/universe.sqlite
new_file_path = /tmp/tmp1OhjFo/tmpQTWBB8/new_files_path_XuJDZT
job_queue_workers = 5
...
tool_config_file = None
job_working_directory = /tmp/tmp1OhjFo/tmpQTWBB8/job_working_directory_bsFveu
tool_path = tools
tool_data_table_config_path = None
user_library_import_dir = 
/usr/local/galaxy/production1/galaxy-dist/test-data/users
galaxy_data_manager_data_path = 
/tmp/tmp1OhjFo/data_manager_test_tmpHUW6pF/data_manager_tool-datafebj6D
file_path = /tmp/tmp1OhjFo/tmpQTWBB8/database/files
datatype_converters_config_file = datatype_converters_conf.xml.sample
database_auto_migrate = True
...
allow_user_creation = True
use_heartbeat = False
allow_library_path_paste = True
api_allow_run_as = t...@bx.psu.edu
test_conf = test.conf
...
debug = True
library_import_dir = /usr/local/galaxy/production1/galaxy-dist/test-data
running_functional_tests = True

So the last thing I'd say is does anyone have comments about whether or not to 
use this "/job_conf.xml" file for a test setup?  I haven't the slightest about 
how it should be configured.  I see John Chilton's example files in the 
/config/ subfolder.

Regards,

Damion

Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
________________________________________
From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Thursday, February 12, 2015 3:39 AM
To: Dooley, Damion
Cc: galaxy-...@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Tool test failure - I could use some help...

On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion <damion.doo...@bccdc.ca> wrote:
> I was trying to track down why an attempt to test my tool is eventually 
> failing with:
>
> "ValueError: No such test TestForTool_ffp_phylogeny"
>

There are at least two reasons that can happen.

(a) The tool wasn't loaded by the test framework.

(b) Your tool was loaded, but no <test> and <tests> tags
were recognised.

My first set would be to check the test log output to see which
tools were loaded, and if your tool was mentioned.

Peter
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