On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:
>
> Hi Dave,
>
> As you hoped, these test now shows up on the tool page (as expected
> they are test failures - apparently my install script isn't quite right
yet):
>
> ...
>
> 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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