On Feb 3, 2014, at 7:01 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

Moreover there is a similar problem with the matching repository
on the Test Tool Shed,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-04 showing failed tests for proteomics_search_tandem_1
2013-12-20 showing failed tests for proteomics_search_tandem_1
2013-12-18 tests for blastxml_to_top_descr passed
2013-12-17 tests for blastxml_to_top_descr passed

Like the same repository on the main tool shed, the above issue were fixed for the blastxml_to_top_descr on the test tool shed in https://bitbucket.org/galaxy/galaxy-central/commits/e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211

--

Returning to the MIRA4 problem, I got a meaningful test
failure which I fixed (I hadn't set an environment variable
in the install script), but I now get only partial test output:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Not datestamped (a glitch if there is only one test entry?):

Automated tool test results
Automated test environment
Time tested: 2014-02-03 16:25:08
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12332:d9f6f3f24671
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tools missing tests or test data
Tool id: mira_4_0_mapping
Tool version: 0.0.2
Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2
Missing components:
Functional test definitions missing for mira_4_0_mapping.
Tool id: mira_4_0_de_novo
Tool version: 0.0.2
Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2
Missing components:
Functional test definitions missing for mira_4_0_de_novo.

That's all fine, but where are the test results for mira_bait which
I would expect to pass?

It looks lie the mira_bait tests results are being populated, bu the tests are failing, not passing. This doesn't look like an issue with the Tool Shed's install and test framework.

Tests that failed

Tool id: mira_4_0_bait

Tool version: mira_4_0_bait

Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)

Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/a6a56440567c/mirabait'

Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 312, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error

Tool id: mira_4_0_bait

Tool version: mira_4_0_bait

Test: test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)

Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/a6a56440567c/mirabait'

Tool id: mira_4_0_bait

Tool version: mira_4_0_bait

Test: test_tool_000002 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)

Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/a6a56440567c/mirabait'

Thanks,

Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/