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_00
(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
