On Tue, Jun 2, 2015 at 4:14 AM, Loraine Guéguen
<loraine.gueg...@sb-roscoff.fr> wrote:
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)
./run_tests.sh -installed runs the tests of all installed tool shed
tools. It might be possible to combine that with -id - for a specific
tool but I am not sure. It may be possible to construct that test even
if -id doesn't work - but it is probably pretty hacky. Let me know if
-installed works for you but not when combined with -id and we can
work out the details.
#########
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."]}}}
#########
It is possible it is the case that tool shed datatypes are not loaded
unless running with the -installed flag. I would either setup the
tests to run locally (manually add datatypes and tools) or run
installed tools with -installed.
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."}}}
#########
Well that is frustrating. I am not aware of the internals of that
script or why that is happening - but my personal recommendation would
be not to use the install and test framework at this point - it seems
rather un-maintained. I recently added a subcommnd to planemo called
shed_test
(http://planemo.readthedocs.org/en/master/commands.html#shed-test-command)
- that will install and test a tool shed repository. It probably
requires modifying your tool shed development process to use planemo
(http://planemo.readthedocs.org/en/latest/publishing.html#shed).
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.
This would be great - but as I understand it - it is not possible at
this time. The test framework needs local access to some aspects of
the Galaxy app. Last year I outlined a Trello card to add this option
back to Galaxy (https://trello.com/c/8K86l4Qk) - it was available
years ago.
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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