soaplab-users

[Soaplab-users] Classloaders in Soaplab

[<and...@bc...>]

Hi,

I have written a shell script for a custom soaplab ws that calls a 
number of command line tools in sequence, creating and reading temporary 
files as it goes. Some of the calls are to java classes available in my 
classpath. However, these do not seem to work (NoClassDefFoundError). It 
does work when I call it directly rather than as a WS.

Is this because the system classpath is not used even from the shell?  
How can I fix it?

Cheers,
Anders

-- 
Anders Lanzén, MSc
Programmer
Computational Biology Unit
Bergen Center for Computational Science
http://www.bccs.uib.no
phone: +47 5558 4045 
email: and...@bc...

Re: [Soaplab-users] Classloaders in Soaplab

[Martin S. <se...@eb...>]

Hi,
   I am sorry to be late with an answer to your problem (I was off my
office). It seems that you have already solved your problem (my thanks
also to Marc for his comments). Neverthelsss, I will try to summarize how 
CLASSPATH variable is treated in Soaplab.
   As you noticed, the run-AppLab-server script sets its CLASSPATH from
the scratch - so if you have anything in your CLASSPATH (e.g. from your
user profile, from .bashrc) it is gone. And it is intentional because
otherwise there may be hard-to-find bugs when Soaplab (respectively
AppLab) gets mixed versions of various Java packages.
   And this practice - to clean the CLASSPATH first and then to fill it
only with classes needed for a particular java program - is considered a
"best practices". That means that - in your case - your script that
invokes Java program should first set the full CLASSPATH without expecting
anything there. And that's exactly what you did by using option
'-classpath' (the same could be reached also by setting and exporting
CLASSPATH in your script before calling java).

   Please let me know if there are still unsolved and new questions.
   With regards,
   Martin

-- 
Martin Senger

EMBL Outstation - Hinxton                Se...@EB...     
European Bioinformatics Institute        Phone: (+44) 1223 494636      
Wellcome Trust Genome Campus             (Switchboard:     494444)
Hinxton                                  Fax  : (+44) 1223 494468
Cambridge CB10 1SD
United Kingdom                           http://industry.ebi.ac.uk/~senger