Hi Dave,

Did a Trello card get filled for this problem of failing tests on the Tool Shed?

Thanks,

Peter

On Tue, Jun 11, 2013 at 9:04 AM, Björn Grüning <bjo...@gruenings.eu> wrote:
>
> Hi,
>
> I also have that error in the latest toolshed:
>
> AssertionError: Attempting to set field 'topology' to value '['-c']' in
> form 'tool_form' threw exception: multiple matches to value/label "c" in
> list control control: <SelectControl(topology=[-c, -l])> If the above
> control is a DataToolparameter whose data type class does not include a
> sniff() method, make sure to include a proper 'ftype' attribute to the
> tag for the control within the <test> tag set.
>
> http://testtoolshed.g2.bx.psu.edu/view/bgruening/trna_prediction
>
> Any hint on how to resolve that, or is it a recent regression?
>
> Cheers,
> Björn
>
>
> > On Thu, May 9, 2013 at 10:49 AM, Peter Cock
> > <p.j.a.c...@googlemail.com> wrote:
> > >
> > > This one is more interesting, and appears to be a problem with the
> > > test framework (both tests pass locally via
> > > run_functional_tests.sh):
> > >
> > >
> > > http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
> > > Functional test results for changeset revision 16a1a5ae98e9 of
> > > seq_rename 0 tests passed, 2 tests failed, 0 tests missing test 
> > > components.
> > >
> > > I'll raise that on a new thread,
> >
> > Here's the output from the (Test) Tool Shed where the tests fail:
> >
> > Tests that failed
> > Tool id: seq_rename
> > Tool version: seq_rename
> > Test: test_tool_000000
> >
> > (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3)
> > Stderr:
> >
> > Traceback:
> > Traceback (most recent call last): File
> >
> > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> > line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File
> > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> > line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name,
> > **page_inputs ) File
> > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> > line 1320, in run_tool self.submit_form( **kwd ) File
> > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> > line 1270, in submit_form raise AssertionError( errmsg ) AssertionError:
> > Attempting to set field 'new_column' to value '['2']' in form 'tool_form'
> > threw exception: cannot find value/label "2" in list control control:
> > <SelectControl(new_column=[1])> If the above control is a DataToolparameter
> > whose data type class does not include a sniff() method, make sure to
> > include a proper 'ftype' attribute to the tag for the control within the
> > <test> tag set.
> > Tool id: seq_rename
> > Tool version: seq_rename
> > Test: test_tool_000001
> >
> > (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3)
> > Stderr:
> >
> > Traceback:
> > Traceback (most recent call last): File
> >
> > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> > line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File
> > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> > line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name,
> > **page_inputs ) File
> > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> > line 1320, in run_tool self.submit_form( **kwd ) File
> > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> > line 1270, in submit_form raise AssertionError( errmsg ) AssertionError:
> > Attempting to set field 'new_column' to value '['c2']' in form 'tool_form'
> > threw exception: cannot find value/label "c2" in list control control:
> > <SelectControl(new_column=[1])> If the above control is a DataToolparameter
> > whose data type class does not include a sniff() method, make sure to
> > include a proper 'ftype' attribute to the tag for the control within the
> > <test> tag set.
> >
> > Both tests fail with the following assertion:
> >
> > AssertionError: Attempting to set field 'new_column' to value '['c2']'
> > in form 'tool_form' threw exception: cannot find value/label "c2" in
> > list control control: <SelectControl(new_column=[1])> If the above
> > control is a DataToolparameter whose data type class does not include
> > a sniff() method, make sure to include a proper 'ftype' attribute to
> > the tag for the control within the <test> tag set.
> >
> > Both tests pass on my development machine run via:
> >
> > $ ./run_functional_tests.sh -id seq_rename
> >
> > The two tests are defined as follows - identical bar the style used
> > for the column arguments - I was wondering if the Tool Shed testing
> > was stricter about numeric column names, but that does not seem to be
> > relevant:
> >
> >
> >     <tests>
> >         <test>
> >             <param name="input_file" value="four_human_proteins.fasta"
> > ftype="fasta" />
> >             <param name="input_tabular"
> > value="four_human_proteins.rename.tabular" ftype="tabular" />
> >             <param name="old_column" value="1" />
> >             <param name="new_column" value="2" />
> >             <output name="output_file"
> > file="four_human_proteins.rename.fasta" ftype="fasta" />
> >         </test>
> >         <test>
> >             <param name="input_file" value="four_human_proteins.fasta"
> > ftype="fasta" />
> >             <param name="input_tabular"
> > value="four_human_proteins.rename.tabular" ftype="tabular" />
> >             <param name="old_column" value="c1" />
> >             <param name="new_column" value="c2" />
> >             <output name="output_file"
> > file="four_human_proteins.rename.fasta" ftype="fasta" />
> >         </test>
> >     </tests>
> >
> > I can retest with the latest galaxy-dist once this issue is resolved:
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.html
> >
> > Peter
> >

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