On Mon, Jun 8, 2015 at 6:30 AM, Loraine Guéguen <loraine.gueg...@sb-roscoff.fr> wrote: > Thanks for your answers ! > > I will try "./run_tests.sh -installed" and see if it can solve the 2 first > points. By the way, I didn't know this option (not displayed with > run_tests.sh --help) or documented on the wiki if I'm not mistaken.
I have opened a PR correcting this oversight - https://github.com/galaxyproject/galaxy/pull/323 - thanks for the catch. > > For point 3, I'll try the new "planemo shed_test" subcommand. The subcommand > "planemo test" uses the run_tests.sh script, isn't it ? Does the "planemo > shed_test" subcommand use all or any part of the Tool Shed Install and Test > Framework (https://wiki.galaxyproject.org/AutomatedToolTests) or is it > completely different ? It doesn't leverage the install and test framework - it uses run_tests.sh (with the -installed option) but it sets many extra things up. It may well not work with installed datatypes for the same reason - I am not sure. I've created an issue and will try to look into this (https://github.com/galaxyproject/planemo/issues/226). > > Is there any way to launch the tool tests against an external server (point > 4) with Planemo ? Nope - not at this time. Thanks for the detailed e-mail and follow up. I hope this helps. There are a lot of discussions ongoing about datatypes and whether they belong in the tool shed. I generally discourage putting them there - I think the framework is sort of broken by design for datatypes. Certain team and community members disagree - hopefully they will help and put some effort into making datatypes in the Tool Shed more usable :). -John > > Loraine > > > > Le 02/06/2015 15:16, John Chilton a écrit : >> >> 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/ >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ > > > -- > 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 > 29680 Roscoff > tel: ++33 (0)2 98 29 25 50 > http://abims.sb-roscoff.fr/ > http://www.sb-roscoff.fr/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
