On Fri, Oct 11, 2013 at 10:01 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>> Peter,
>>
>> As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning
>> valid test results. As for seq_rename, ...
>>
>>    --Dave B.
>
> Hi Dave,
>
> That fix is on galaxy-central and the Test Tool Shed, and my tests
> have been passing there :)
>
> However, the tests are currently still failing on the main Tool Shed:
> http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
> http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
>
> The commit for your fix is on the galaxy-central default branch,
> https://bitbucket.org/galaxy/galaxy-dist/commits/d34d6d1da813
> https://bitbucket.org/galaxy/galaxy-dist/src/default/lib/galaxy/datatypes/binary.py
>
> The fix is not on the stable branch:
> https://bitbucket.org/galaxy/galaxy-dist/src/stable/lib/galaxy/datatypes/binary.py
>
> Nor is the fix on the next-stable branch,
> https://bitbucket.org/galaxy/galaxy-dist/src/next-stable/lib/galaxy/datatypes/binary.py
>
> I'm not quite sure how fixes like this are propagated from galaxy-central
> to the stable branches on galaxy-dist, but has this been forgotten about?
>
> Thanks,
>
> Peter

It does appear to have been forgotten about - now that the main
Tool Shed is running next-stable in preparation for tentative  4 Nov
release, I am seeing these sniffer related test failures once again :(

http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus

Tool test results
Automated test environment
Tests that passed successfully
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000000
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
Tests that failed
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000001
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
Stderr:
Traceback:
Traceback (most recent call last):
  File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-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-main-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-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 1327, in run_tool
    self.submit_form( **kwd )
  File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 1276, in submit_form
    raise AssertionError( errmsg )
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.


http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3

Tool test results
Automated test environment
Tests that passed successfully
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000000
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
Tests that failed
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000001
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
Stderr:
Traceback:
Traceback (most recent call last):
  File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-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-main-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-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 1327, in run_tool
    self.submit_form( **kwd )
  File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 1276, in submit_form
    raise AssertionError( errmsg )
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.
Traceback (most recent call last):
  File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 1193, in submit_form
    for value in kwd[ control.name ]:
KeyError: 'restrict|type'
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:
base.twilltestcase: DEBUG:

(That looks like an extra Twill debug logging line as well)

Regards,

Peter
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