[MOBY-dev] Skeleton and input for the service

[Martin Senger]

Hi,
   Thanks for the input file and the skeleton. (Wow, it seems unusual,
to say "thanks for the skeleton" :-)).
   I have tried to reproduce your error, but I failed.

   I found that your input data were interesing because they seem to be
non-valid XML - they contain '>' in the seguence name (FASTA format).
Interesting is that it does not invalidate XML (the rules about XML
validity allows the '>' to be present without being escaped). So this is
not the problem.

   Then I found that your input data were not strictly speaking compliant
with the Biomoby API because the Simple should have an article name. But
this also did not cause the problem because the jMoby classes are
relatively forgiving on this.

   Then, I have written my own trivial implementation of your skeleton,
and run it with your input data. Unforunately, the error that happened to
you has not occured to me. This is my implementatation:

--- begin ---
package org.jmoby.tutorial.service;

import PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel;

import org.biomoby.shared.MobyException;
import org.biomoby.shared.parser.MobyPackage;
import org.biomoby.shared.parser.MobyJob;
import org.biomoby.shared.datatypes.*;


public class RunHotSpotFromFASTAImpl
    extends RunHotSpotFromFASTASkel {

    public void processIt (MobyJob request,
			   MobyJob response,
			   MobyPackage outputContext)
	throws MobyException {
	System.out.println (get_FASTA_AA (request));
    }

}
--- end ---

And this is how I tested:

build/run/run-service -service RunHotSpotFromFASTA -xml FASTA.xml \
        -class org.jmoby.tutorial.service.RunHotSpotFromFASTAImpl

I have not got any errors.

So, the only thing I can think about is that perhaps you do not have the
latest version of jMoby (even though I have not found any concrete case
where this should matter). Please cvs update again, generate your skeleton
again, compile and run it. Try also my implementation class shown
above. If it still gives you an error, consider to show me your own
implementation class (you can remove there all sensistive pieces, of
course).

Sorry that I have not found yet a solution for you. But bear with me, we
will find it.

   Regards,
   Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)