Tool tests failing on Main Tool Shed with "Exception: Job in error state."

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Tool tests failing on Main Tool Shed with "Exception: Job in error state."

Peter Cock
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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Re: Tool tests failing on Main Tool Shed with "Exception: Job in error state."

Peter Cock
On Tue, Mar 3, 2015 at 9:51 AM, Peter Cock <[hidden email]> wrote:

> 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).

Sorry, my enthusiasm got away with me. There is actually more
bad news - I hadn't noticed the latest test was just over a month
old - were no tests run at all in February?

> 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
> ...

This was last tested on the Test Tool Shed back on 2015-01-25,
failing with my old enemy "Exception: History 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
> ...

Last tested on the Test Tool Shed on 2015-01-25, giving
a more complex "Exception: History in error state." plus
"IndexError: list index out of range" traceback.

> https://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
>
> 2015-01-29 05:11:05
> Automated test environment
> Tests that failed
> ...

Last tested on the Test Tool Shed on 2015-01-23, giving a
complex failure with "Exception: History in error state."
plus "IndexError: list index out of range" and finally:
"TypeError: error_unless_accessible() takes exactly 4 arguments (3 given)"

The last error was likely fixed later that day:
https://github.com/galaxyproject/galaxy/commit/cdabbe2af8e23cb7414b824b6d819e71f81dbdfc

> 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

Similarly, last tested on the Test Tool Shed on 2015-01-25 with
the same problem.

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:
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