It seems to be happening during upload - so it is not unsurprising
that this error would affect multiple tools. I have checked out the
exact revision registered in the tests and the uploads seem fine to
me.

I am having trouble imagining a deployment problem short of an invalid
upload tool that might result in this error. Dave B, is it possible
that a problematic datatype is being installed by some repository and
affecting unrelated tools?

-John


On Mon, Mar 23, 2015 at 8:27 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi Dave,
>
> Now that you've fixed some of the test back log, the bad
> news is this issue I reported last week appears to be a major
> regression affecting multiple tools on the Test Tool Shed:
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
> ...
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
> ...
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
> ...
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
>
> These are all recent test runs from 2015-03-18. Note that
> some tool tests from the same date are passing, e.g.
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer
>
> I have not yet spotted any pattern in this division.
>
> (However this is clearly not linked to the test expect_failure
> test I'd added to the sample_seqs tool, as I speculated last
> week.)
>
> Regards,
>
> Peter
>
> On Wed, Mar 18, 2015 at 2:14 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Hi Dave,
>>
>> The following looks like a regression on the Test Tool Shed, the tests
>> pass locally (using a recent revision), and on TravisCI using the current
>> galaxy dev branch on GitHub:
>> https://travis-ci.org/peterjc/pico_galaxy/builds/54870500
>>
>> Problem tool: https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
>>
>> This may be unrelated, but by chance this is the first time I have
>> uploaded a tool to the Tool Shed which uses the new functionality
>> to test the stdout/stderr strings, and more importantly it includes a
>> test expected to fail via <test expect_failure="true" expect_exit_code="1">
>>
>> Revision on my development repository:
>> https://github.com/peterjc/pico_galaxy/commit/55ebb308b911b4acef912cc3b03f4371f4c6dfe6
>>
>> Test Tool Shed output from last night:
>>
>> Automated test environment
>> Time tested: 2015-03-18 02:46:55
>> System: Linux 3.13.0-36-generic
>> Architecture: x86_64
>> Python version: 2.7.6
>> Galaxy revision: 17050:6395e7035143
>> Galaxy database version: 128
>> Tool shed revision: 16867:0468d285f89c
>> Tool shed database version: 25
>> Tool shed mercurial version: 3.2.4
>> Tests that failed
>> Tool id: sample_seqs
>> Tool version: sample_seqs
>> Test: test_tool_000000
>> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.1)
>> Stderr:
>> Traceback:
>> Traceback (most recent call last):
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
>> line 268, in test_tool
>>     self.do_it( td )
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
>> line 37, in do_it
>>     stage_data_in_history( galaxy_interactor, testdef.test_data(),
>> test_history, shed_tool_id )
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
>> line 38, in stage_data_in_history
>>     upload_wait()
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
>> line 279, in wait
>>     while not self.__history_ready( history_id ):
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
>> line 297, in __history_ready
>>     return self._state_ready( state, error_msg="History in error state." )
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
>> line 356, in _state_ready
>>     raise Exception( error_msg )
>> Exception: History in error state.
>> Traceback (most recent call last):
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/__init__.py",
>> line 158, in prepare_job
>>     job_wrapper.prepare()
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/__init__.py",
>> line 828, in prepare
>>     tool_evaluator.set_compute_environment( compute_environment,
>> get_special=get_special )
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/evaluation.py",
>> line 53, in set_compute_environment
>>     incoming = self.tool.params_from_strings( incoming, self.app )
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/__init__.py",
>> line 1873, in params_from_strings
>>     return params_from_strings( self.inputs, params, app, ignore_errors )
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/__init__.py",
>> line 103, in params_from_strings
>>     value = params[key].value_from_basic( value, app, ignore_errors )
>>   File 
>> "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/grouping.py",
>> line 512, in value_from_basic
>>     raise e
>> KeyError: 'base_name'
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
>> connection (1): 127.0.0.1
>> galaxy.datatypes.metadata: DEBUG: Cleaning up external metadata files
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
>> connection (1): 127.0.0.1
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c/contents?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
>> connection (1): 127.0.0.1
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
>> connection (1): 127.0.0.1
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9/provenance?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>>
>> (All the tests for this tool seem to have failed the same way)
>>
>> Regards,
>>
>> Peter
>>
>>
>>
>> On Wed, Mar 18, 2015 at 1:46 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>>> Gentlemen,
>>>
>>> The issue with the nightly testing was due to a stalled test run blocking
>>> subsequent tests. I've cleared out that blockage and a manual test run
>>> appears to have completed successfully, as should future automated test
>>> runs. As always, feel free to let us know if you encounter any additional
>>> inexplicable behavior.
>>>
>>>    --Dave B.
>>>
>>> On 03/18/2015 07:00 AM, Peter Cock wrote:
>>>>
>>>> ... I can also confirm that the Test Tool Shed example I
>>>> gave was tested overnight, although it looks like a novel failure:
>>>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
>>>>
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