Hi Peter, On Nov 28, 2013, at 12:30 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Nov 28, 2013 at 5:16 PM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Peter,
On Nov 28, 2013, at 4:56 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Greg,
Things look much better today on the Test Tool Shed, with most of my tools under "Latest revision: all tool tests pass" again - or as expected a few under "Latest revision: missing tool tests" due to not yet having full test coverage.
I've only spotted one glitch so far, missing test results for: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
The above repository was not displaying the missing test components due to a problem in the previous test runs which I fixed yesterday. The problem resulted in test result data that could not be displayed.
Perhaps a fall back error message would be useful here (e.g. "Test failed but unable to display data"), which would be better than the "missing" test results?
When I introduced the new feature for stroing and displaying multiple test runs, I decided to not eliminate the bad data, but just to let enough test runs proceed that the bad data would eventually be eliminated. I forced new test runs, and now things should be displaying as expected. Here is the display for the above repository for the latest run this morning:
Thank you - that alerted me to a missing set of out output files for a recently added test, hopefully addressed in this revision: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045
But its not all good news - another test is now listed as failing, but with missing test results: http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
The bad data shoud now be eliminated, and there are 3 test runs displaying for this one. Do these look crrect to you? The oldest test run has a data of 'unknown' because I had not implemented the date deature at that point. Automated tool test results Test runs 2013-11-28 14:50:44 Automated test environment Time tested: 2013-11-28 14:50:44 System: Linux 3.8.0-30-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 11549:5aede225ebef Galaxy database version: 117 Tool shed revision: 11549:5aede225ebef Tool shed database version: 21 Tool shed mercurial version: 2.2.3 Tests that passed successfully Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000002 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000003 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tests that failed Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Stderr: 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 101, 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 31, 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 64, 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 303, 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 814, in verify_dataset_correctness self.wait( maxseconds=maxseconds ) # wait for job to finish File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1425, in wait return self.wait_for(lambda: self.get_running_datasets(), **kwds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1440, in wait_for assert slept < maxseconds AssertionError: 2013-11-28 09:24:20 Automated test environment Time tested: 2013-11-28 09:24:20 System: Linux 3.8.0-30-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 11548:7756b29bea29 Galaxy database version: 117 Tool shed revision: 11544:8b613225f1de Tool shed database version: 21 Tool shed mercurial version: 2.2.3 Tests that passed successfully Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000002 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000003 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) unknown_2 Automated test environment Time tested: unknown_2 System: Linux 3.8.0-30-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 11526:c0384bad246d Galaxy database version: 117 Tool shed revision: Tool shed database version: Tool shed mercurial version: Tests that passed successfully Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000002 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Tests that failed Tool id: get_orfs_or_cdss Tool version: get_orfs_or_cdss Test: test_tool_000003 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5) Stderr: 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 101, 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 31, 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 64, 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 303, 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 814, in verify_dataset_correctness self.wait( maxseconds=maxseconds ) # wait for job to finish File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1425, in wait return self.wait_for(lambda: self.get_running_datasets(), **kwds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1440, in wait_for assert slept < maxseconds AssertionError
Thanks,
Peter
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