Retitling thread to focus on a regression in the (Tool Shed) test framework
to do with input file types and sniffers.

On Thu, Aug 1, 2013 at 11:47 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>>> Peter,
>>>
>>> The issue with seq_rename incorrectly failing functional tests has been
>>> resolved in 10266:fe04978dadac, and the test results will be corrected the
>>> next time the automated testing framework runs. I'm still looking into the
>>> other issues you reported.
>>>
>>>    --Dave B.
>>
>> Hi Dave,
>>
>> The seq_rename test results (apparently) from last night are still failing,
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c
>>
>> 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.
>
> Same issue here?,
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
>
> AssertionError: Attempting to set field 'fasta_file' to value
> '['empty.fasta']' in form 'tool_form' threw exception: cannot find
> value/label "empty.fasta" in list control control:
> <SelectControl(fasta_file=[])> 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.

And another case which looks the same,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120

AssertionError: Attempting to set field 'fasta_file' to value
'['empty.fasta']' in form 'tool_form' threw exception: cannot find
value/label "empty.fasta" in list control control:
<SelectControl(fasta_file=[])> 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.

Note that for the nlstradamus and effectivet3 tests this is using
an empty FASTA file with no sequences in it, so the sniffer will
not be able guess this is a FASTA file - which is why the tool
text gives the ftype explicitly.

I originally used a literally empty fasta file (0 bytes) but as I recall
the (non-Tool Shed) framework at the time didn't like me doing
that in the test framework, so this empty.fasta file just has a
couple of blank lines in it.

I am testing with empty FASTA files deliberately - they can
often occur in gene/protein selection pipelines where an
early part of the pipeline is stringent enough to reject all
the sequences.

However, the seq_rename sniffer problem is not to do with
an 'empty' fasta file - it uses a non-empty tabular file.

My guess is somewhere in the test framework the ftype
attribute is being lost. This is still working locally,

$ ./run_functional_tests.sh -id seq_rename
$ ./run_functional_tests.sh -id nlstradamus
$ ./run_functional_tests.sh -id effectiveT3

Regards,

Peter
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