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

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

Thank you for the quick answer.  I will fix Chimera not to send unsafe 
characters.

Conrad

On 1/17/12 2:43 PM, Luca Clementi wrote:
> 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
>>
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>