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Tim, there's a Powerpoint from Jake Berberich on the EGL Cafe that 
discusses accessing an image file in the IFS, which would conceptually 
be similar to other IFS stream file accesses.
http://www-949.ibm.com/software/rational/cafe/thread/1815
If your users have a drive mapped to the IBM i NetServer, you should be 
able to use drive letter notation to specify the IFS file name (i.e. 
Z:\sharename\subpath\file.name)
If your users have the same userid/password on the PC as on IBM i, you 
could perhaps use UNC notation (i.e. \\IBMiName\sharename\subpath\file.name)
Probably the best thing (which is what the Powerpoint walks through) 
would be to identify your IFS directory to the HTTP server, and use URL 
notation (something like http:\\localhost:80\map\file.name   or 
file:\\localhost:80\map\file.name).  I'm not clear on this - I've never 
done this.
The tricky thing is that you said you are running Tomcat on a middle 
tier (or DMZ) with the IFS and DB2 stuff on a 3rd tier IBM i (i.e. not 
running application server on the same physical system as data).   
However, I guess if there is an HTTP Server running on IBM i, you could 
identify your IFS directory to that IBM i HTTP server, and you should be 
able to find the file since it's a URL lookup.  The gotcha would be 
you'd need the IBM i HTTP Server to be up & running all the time, as 
well as your Tomcat on Windows server.
There probably is a widget or JSP Control (for old EGL) for a local file 
selection browse button/window to help your user pick the local PC file 
they want to copy to the IFS.
I have called Java programs from EGL located in the IFS before using 
WebSphere's Shared Library support specified via the Administration 
Console.   That let me specify the location and name of the jar that I 
wanted to call classes from.  But I haven't dealt with copying IFS 
files.  Sorry I couldn't provide more specific help, but I think you 
probably would get an answer on the Cafe if posted or searched there 
some more.
By the way, PHP would have had the exact same issue here with the files 
being on a different physical system than the application server.  Still 
would need a way to handle the 3 tier architecture with some sort of 
file redirection/aliasing/mapping.
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