Hi, I am relatively new to Galaxy so if you get a difference answer from a core developer consider that one.
Personally I never got the run_test.sh -id ...) to run but I did use planemo http://planemo.readthedocs.org/en/latest/readme.html With success. It is much easier, does not need the tool to be installed in a local galaxy to test. It does require the tool xml config file See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax And depends on their being a <tests> section. See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Christian University of Manchester PS. I am not a developer of Planemo just a user so please keep all question on this mailing list ________________________________ From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Loraine Guéguen [loraine.gueg...@sb-roscoff.fr] Sent: Tuesday, June 02, 2015 9:14 AM To: Galaxy Dev List Subject: [galaxy-dev] errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh 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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