hg summary:

parent: 9320:47ddf167c9f1 tip
Use Galaxy's ErrorMiddleware since Paste's doesn't return start_response. Fixes downloading tarballs from the Tool Shed when use_debug = false.
branch: stable
commit: 18 modified, 178 unknown
update: (current)


Geert

On 05/21/2013 04:59 PM, Dannon Baker wrote:
Geert,

This should be fixed in the up-to-date stable branch as far as I know. Can you tell me what 'hg summary' states?

-Dannon


On Mon, May 20, 2013 at 4:43 PM, Geert Vandeweyer <geert.vandewey...@ua.ac.be <mailto:geert.vandewey...@ua.ac.be>> wrote:

    Hi,

    After the latest upgrade (april), I'm having issues when starting
    (batch) workfows. Sometimes, it seems that step dependencies are
    not stored correctly, leading to some steps being started too
    soon, without prior datasets being completed. Specifically, for
    some workflows, some of the later steps start immediately. The
    issue seems to be random: in batch workflow submission, some run
    flawlessly, others show the issue, at different steps. I use one
    handler in the job_conf to exclude race conditions and shared
    variable clashes.

    I suspect there is an issue with fetching or storing the steps
    to/from the database (a remote mysql database in my case). On the
    mysql-side there are no errors in the log files, and the
    galaxy-logs don't show clear issues either.

    Does the job new job handler check for failed database
    connections? If not, could somebody point me to the code that
    performs these steps, I'd like to add a check & retry routine to
    see if this improves the situation.

    best,

    Geert

--
    Geert Vandeweyer, Ph.D.
    Department of Medical Genetics
    University of Antwerp
    Prins Boudewijnlaan 43
    2650 Edegem
    Belgium
    Tel: +32 (0)3 275 97 56
    E-mail: geert.vandewe...@ua.ac.be <mailto:geert.vandewe...@ua.ac.be>
    http://ua.ac.be/cognitivegenetics
    http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

___________________________________________________________
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