Hi Peter, On Feb 3, 2014, at 7:01 PM, Peter Cock <p.j.a.c...@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' 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_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' 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 > > 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/
___________________________________________________________ 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/
