On Thu, May 9, 2013 at 10:59 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
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:
...
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.htm
Correction, I'm trying to update to the latest galaxy-central (I was using f8d07c98812903dc98de2665874a2c31b65b84da from 2013-04-29 where these tests pass). Peter