Hi Peter, I was also getting "Exception: History in error state" errors with BioBlend continuous integration testing, but those seem to be fixed with latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d . Nicola Il 30.01.2015 17:36 Peter Cock ha scritto:
Retitling thread,
On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock wrote:
Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer [1] The bad news is there are many unexpected failures with: "Exception: History in error state." I'm sure you'll learn more once you look over the logs, Thank you, Peter
Right now the mummer example given above is passing,
but I am still getting this error on some of my tools, e.g.
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go [3]
tested 2015-01-25 11:21:12
https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss [4]
tested 2015-01-25 10:52:03
(Many of my other tools are also
currently listed with
different unexpected failures, some of which include the "Exception: History in error state." traceback.)
Interestingly, I've just got what appears to be the same
exception from a TravisCI test run (following a trivial change to README files):
https://travis-ci.org/peterjc/galaxy_blast/builds/48893916 [5]
e.g. (one of many similar failing tests in this log)
======================================================================
ERROR: test_tool_000000
(functional.test_toolbox.TestForTool_blastxml_to_top_descr)
BLAST top hit descriptions ( blastxml_to_top_descr ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
line 268, in test_tool
self.do_it( td ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/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 "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 42, in stage_data_in_history
upload_wait() File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 279, in wait
while not self.__history_ready( history_id ):
File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 297, in __history_ready
return self._state_ready( state, error_msg="History in error state." ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
raise Exception( error_msg ) Exception: History in error state.
I do not recall seeing this problem locally when using my development instllation of galaxy-central.
The TravisCI failure suggests this could be a stochastic resource contention (I can re-run the TravisCI build and see if this works second time round?), which is more prone to fail under the Tool Shed
line 356, in _state_ready framework?
Peter
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