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

[Conrad H. <co...@cg...>]

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?

Thanks.  (And thanks for the great software.)

Conrad