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

[nadya w. <na...@sd...>]

Hi Conrad,
On Jan 17, 2012, at 2:04 PM, Conrad Huang 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:
what database are you using with opal: hibernate, mysql, or postgres?

>
> When the output file names contain a '|' character, the retrieval  
> of the
illegal character. The files may be generated but the databases do  
not except this character as a legal
in files names.
> 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
it is not opal error. We are using postgres or mysql DB with our opal  
installs on linux OS
the "|" is not a legal character in a file name under UNIX, so the  
best way is to avoid it.

> 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 are using mysql or postgres I would advise to create a DB for  
opal that has UTF8 encoding.
By default opal generated LATIN9 which will fail sometimes when users  
form other countries use some
characters for which there is no  encoding translation between LATIN9  
and UTF8.

If you are running on any unix flavor OS, then any charaacters that  
are allowed under unixwill be ok
for the db.


Nadya
>
> Thanks.  (And thanks for the great software.)
>
> Conrad
>
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Nadya Williams                 University of California, San Diego
na...@sd...             9500 Gilman Dr. MC 0446
+1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
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