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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