On Thu, May 9, 2013 at 10:49 AM, Peter Cock p.j.a.cock@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