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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