Hello all,

Good news - automated testing on the Galaxy Tool Shed seems to be mostly working again (after a period of trouble in the New Year). Thanks Dave B. et al, I'm sure this has been a lot of effort behind the scenes. I'm looking forward to getting a clean sweep of passing tests again...

I currently have 18 repositories listed with no failing tests :)

The bad news is I currently have four Tool Shed repositories with unexpectedly failing tests (all of which I expected to pass based on past testing, including locally and on TravisCI).

I will need some assistance to debug the first three which all fail with the cryptic message "Exception: Job in error state."

(Where a tool has more than one test, I've only shown the first error)

https://toolshed.g2.bx.psu.edu/view/peterjc/blast2go

Test runs 2015-01-29 05:12:50 Automated test environment Tests that failed Tool id: blast2go Tool version: blast2go Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.8) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 40, in do_it self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, galaxy_interactor ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 80, in _verify_outputs galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 62, in verify_output self.wait_for_job( job[ 'id' ], history_id, maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 119, in wait_for_job self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 2448, in wait_for result = func() File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 119, in <lambda> self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 277, in __job_ready return self._state_ready( state, error_msg="Job in error state." ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 346, in _state_ready raise Exception( error_msg ) Exception: Job in error state.

http://toolshed.g2.bx.psu.edu/view/peterjc/clinod

2015-01-29 05:07:17 Automated test environment Tests that failed Tool id: clinod Tool version: clinod Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/clinod/clinod/0.0.7) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 40, in do_it self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, galaxy_interactor ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 80, in _verify_outputs galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 62, in verify_output self.wait_for_job( job[ 'id' ], history_id, maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 119, in wait_for_job self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 2448, in wait_for result = func() File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 119, in <lambda> self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 277, in __job_ready return self._state_ready( state, error_msg="Job in error state." ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 346, in _state_ready raise Exception( error_msg ) Exception: Job in error state.

https://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3

2015-01-29 05:11:05 Automated test environment Tests that failed Tool id: effectiveT3 Tool version: effectiveT3 Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.13) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 40, in do_it self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, galaxy_interactor ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 80, in _verify_outputs galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 62, in verify_output self.wait_for_job( job[ 'id' ], history_id, maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 119, in wait_for_job self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 2448, in wait_for result = func() File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 119, in <lambda> self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 277, in __job_ready return self._state_ready( state, error_msg="Job in error state." ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 346, in _state_ready raise Exception( error_msg ) Exception: Job in error state.

The fourth and final failure on the main Tool Shed this morning is from: https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

This is different, "Converting local (test-data) bam to sam failed", already reported (27 Jan): https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-January/021383.htm... http://dev.list.galaxyproject.org/test-base-twilltestcase-py-Converting-loca...

Regards,

Peter