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.html
http://dev.list.galaxyproject.org/test-base-twilltestcase-py-Converting-local-test-data-bam-to-sam-failed-tc4666509.html

Regards,

Peter
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