Thanks for the report Peter. That API error message is really very unclear - I think this https://bitbucket.org/galaxy/galaxy-central/commits/7c6fce1fd9e7f7adb4811cd9... should make it slightly less unclear what is going on and I have created a Trello card here https://trello.com/c/iCdW0pt9 laying out how to make the error message even less bad. -John On Tue, Apr 15, 2014 at 10:00 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I am using TravisCI for testing my Galaxy Tools developed on GitHub, see: http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
Currently this uses a hard coded datatypes_conf.xml file consisting of the local datatypes in use (e.g. BLAST databases) plus a cut down list those core dataypes also being used (e.g. FASTA).
The following test run failed because one of the newly added tests used "sam" format, which was not defined:
https://travis-ci.org/peterjc/pico_galaxy/builds/23041174
I've added the SAM definition now, the reason for this email is to suggest clearer error messages from the test framework for undefined dataypes.
Currently Twill (default) said:
====================================================================== ERROR: test_tool_000001 (functional.test_toolbox.TestForTool_samtools_depad) BAM mapping statistics ( samtools_depad ) > Test-2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py", line 106, in test_tool self.do_it( td ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py", line 29, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py", line 30, in stage_data_in_history upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py", line 336, in stage_data_async wait=(not async) ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py", line 209, in upload_file self.refresh_form( "file_type", ftype ) # Refresh, to support composite files File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py", line 1369, in refresh_form tc.fv( f.name, control.name, value ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/eggs/twill-0.9-py2.7.egg/twill/commands.py", line 450, in formvalue set_form_control_value(control, value) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/eggs/twill-0.9-py2.7.egg/twill/utils.py", line 190, in set_form_control_value raise ClientForm.ItemNotFoundError('cannot find value/label "%s" in list control' % (val,)) ItemNotFoundError: cannot find value/label "sam" in list control
Similarly unclear, the API test framework said:
galaxy.web.framework: ERROR: Uncaught exception in exposed API method: Traceback (most recent call last): File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py", line 199, in decorator rval = func( self, trans, *args, **kwargs) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/api/tools.py", line 130, in create template, vars = tool.handle_input( trans, incoming, history=target_history, process_state=process_state, source="json" ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/tools/__init__.py", line 1921, in handle_input errors, params = self.__check_param_values( trans, incoming, state, old_errors, process_state, history=history, source=source ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/tools/__init__.py", line 2029, in __check_param_values errors = self.populate_state( trans, inputs, state.inputs, incoming, history, source=source ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/tools/__init__.py", line 2136, in populate_state current_case = input.get_current_case( value, trans ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/tools/parameters/grouping.py", line 462, in get_current_case raise Exception( "No case matched value:", self.name, str_value ) Exception: ('No case matched value:', 'files_metadata', u'sam') requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 500 None
In both cases, I would prefer something like a ValueError explicitly saying the problem is an undefined dataype (in this case, "sam" was not defined).
This will be most useful when dealing with 3rd party tools using 3rd part datatype definitions.
Thanks,
Peter