I'm actually working on rolling out much better error capturing for the toolshed via sentry (getsentry.org) and expect to update the test toolshed again with it shortly. I'd guess the main toolshed won't be too far behind. On Fri Jan 30 2015 at 12:24:47 PM Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dannon, Nicola,
This sounds very promising - I'll rerun the TravisCI job and we can expect it to work this time :)
https://bitbucket.org/galaxy/galaxy-central/commits/ 3618b7a91e23096ecf7ce5842c1e16c749251a4d (half an hour ago!)
When will this reach the Tool Shed and Test Tool Shed? The upload job failure seems to be the root cause of many of the unexpected test failures.
Thanks,
Peter
Yep, the FutureWarning that that commit resolves would have caused the upload job to end up as an error; I'm betting this is what was causing Peter's issues too.
On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo <nsoranzo@tiscali.it> wrote:
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 <p.j.a.cock@googlemail.com> 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 The bad news is
On Fri, Jan 30, 2015 at 5:19 PM, Dannon Baker <dannon.baker@gmail.com> wrote: 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 tested 2015-01-25 11:21:12
https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss 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
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", line 356, in _state_ready 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 framework?
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