Hi,
I have investigated the testing possibilities within a Galaxy local
instance and within a toolshed. I met some difficulties and I have 4
questions listed below.
1- Tests on tools installed in a local Galaxy instance (with
run_tests.sh) : It seems that it is only possible to test the tools that
have been manually installed (run_test.sh -id ...), not the tools that
have been installed through a toolshed. Is that true ? When I try to
launch the tests of a toolshed installed tool, I have the following
error message :
#########
Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR
======================================================================
ERROR: Failure: ValueError (No such test TestForTool_sartools_edger)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/projet/htdocs/galaxy-dev/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/failure.py",
line 39, in runTest
raise self.exc_class(self.exc_val)
ValueError: No such test TestForTool_sartools_edger
----------------------------------------------------------------------
Ran 1 test in 0.002s
FAILED (errors=1)
#########
2- Tests on tools installed in a local Galaxy instance (with
run_tests.sh) : Is it possible to test tools which have repository or
tool dependencies ? I have a tool (manually installed in
galaxy-dist/tools/) with a dependence to a datatype installed from a
toolshed. The datatype (no_unzip.zip) is defined in the <param> input
tag (in <test>) with attribute "ftype". When running run_tests.sh, it
seems that the dataype is not known :
#########
======================================================================
ERROR: test_tool_000001 (functional.test_toolbox.TestForTool_sartools_edger)
SARTools edgeR ( sartools_edger ) > Test-2
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py",
line 268, in test_tool
self.do_it( td )
File
"/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py",
line 37, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py",
line 36, in stage_data_in_history
upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py",
line 182, in stage_data_async
raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'file_type': u"An
invalid option was selected for file_type, u'no_unzip.zip', please
verify.", u'files_metadata': [u"An invalid option was selected for
file_type, u'no_unzip.zip', please verify."]}}}
#########
3- Toolshed Install and Test framework (
install_and_test_tool_shed_repositories.sh) : For my tool, the test
fails if I don't explicitely defined the dbkey attribute to "unknown"
(dbkey="?") in the <param> input tag (in <test>). The default dbkey
value seems to be "hg17" (whereas hg17 is not defined on the server
running my toolshed). So I have the following error message if I don't
add dbkey="?" in <test> :
#########
======================================================================
ERROR: test_tool_000001
(functional.test_toolbox.TestForTool_galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209)
SARTools edgeR (
galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209 )
> Test-2
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py",
line 268, in test_tool
self.do_it( td )
File
"/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py",
line 37, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py",
line 36, in stage_data_in_history
upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py",
line 182, in stage_data_async
raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'dbkey': u"An
invalid option was selected for dbkey, u'hg17', please verify."}}}
#########
4- Is it possible to launch the tests against an external server ? That
would be very useful to be able run the tests on a production Galaxy
instance in order to test the tools in real condition, within the whole
environment.
Thanks in advance for your answers.
Loraine
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/
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