On Fri, Oct 11, 2013 at 10:01 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier dave@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/bi...
The fix is not on the stable branch: https://bitbucket.org/galaxy/galaxy-dist/src/stable/lib/galaxy/datatypes/bin...
Nor is the fix on the next-stable branch, https://bitbucket.org/galaxy/galaxy-dist/src/next-stable/lib/galaxy/datatype...
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