Re: [Opaltoolkit-users] Special characters in file names causing problem

[Luca C. <luc...@gm...>]

Dear Conrad,
see below...

On Tue, Jan 17, 2012 at 2:04 PM, Conrad Huang <co...@cg...> wrote:
> Hi,
>
> We are using Opal 2.2 on our RedHat Linux 6.2 cluster as a service
> provider for UCSF Chimera, our molecular modeling application written in
> Python.  Things are working quite well with one exception.
>
> Background:
>
> We provide an interface to Modeller, a structure prediction program from
> the Sali group.  Chimera sends a few input files and expects to retrieve
> some output files after the computation is complete.  The names of the
> output file are derived from names of protein or nucleic acid sequences.
>
> The problem:
>
> When the output file names contain a '|' character, the retrieval of the
> output file fails.  The files are generated properly (I can see them in
> the tomcat directory) but I see these errors in catalina.out:
>
> 2012-01-17 10:18:13,440 INFO
> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java:419) -
> called
> 2012-01-17 10:18:13,442 ERROR
> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java:435) -
> Can't get job outputs for job: app1326824032862
> 2012-01-17 10:18:13,442 ERROR
> edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java:421) -
> Can't get job outputs for job: app1326824032862
>
> The error does not occur if the file names are "normal", i.e., without
> odd characters.
>
> My question:
>
> Is this an error in Opal, or should Chimera avoid these characters?  If
> the former, is it fixed in 2.4?  If the latter, is there a guideline as
> to which characters are allowed or disallowed?

If you look at the URL rfc:
http://www.ietf.org/rfc/rfc1738.txt

Find the "Unsafe:" section for a list of character that "should" be avoided.


Luca

>
> Thanks.  (And thanks for the great software.)
>
> Conrad
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users