[MOBY-l] Taverna Parser

[Ismael Navas]

Hello,

I've Developer a tool that makes use of the Taverna parser, in order to read
and use Taverna workflows, and this tool runs correctly in windows. However,
when I've tried to run it in Linux, it doesn't work. First I had problems
with the classpath, so I've changed ';' for ':' in classpath definition, but
now I obtain this error:

java -classpath
.:./lib/mysql-connector-java-3.0.10-stable-bin.jar:./lib/taverna-1.0.jar:./l
ib/dom4j-1.5.jar:./lib/log4j-1.2.8.jar:./lib/martj.jar:./lib/jmoby.jar:./lib
/axis-nightly-11.01.05.jar:./lib/jaxrpc-nightly-11.01.05.jar:./lib/commons-l
ogging-1.0.4.jar:./lib/commons-discovery-0.2.jar:./lib/saaj-nightly-11.01.05
.jar:./lib/jdom-1.0.jar TavernaINB.LoadWorkflow 91
HomologySearchAndPhylogeneticStudy.xml 
java.lang.NoClassDefFoundError
        at
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja
va:438)
java.lang.NoClassDefFoundError
        at
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja
va:438)
java.lang.NoClassDefFoundError
        at
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja
va:438)
java.lang.InternalError: Can't connect to X11 window server using ':0.0' as
the value of the DISPLAY variable.
        at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
        at
sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:134)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:141)
        at
java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment
.java:62)
        at sun.awt.motif.MToolkit.<clinit>(MToolkit.java:81)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:141)
        at java.awt.Toolkit$2.run(Toolkit.java:748)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739)
        at javax.swing.ImageIcon.<init>(ImageIcon.java:119)
        at javax.swing.ImageIcon.<init>(ImageIcon.java:138)
        at
org.embl.ebi.escience.scuflworkers.ProcessorHelper.<clinit>(ProcessorHelper.
java:85)
        at
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja
va:438)
java.lang.NoClassDefFoundError
        at
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja
va:438)
org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to locate
processor with name 'Create_moby_data'
        at
org.embl.ebi.escience.scufl.ScuflModel.locateProcessor(ScuflModel.java:528)
        at
org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate(ScuflModel.java:49
9)
        at
org.embl.ebi.escience.scufl.DataConstraint.<init>(DataConstraint.java:32)
        at
org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:3
61)
        at
org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:1
47)
        at TavernaINB.LoadWorkflow.loadWorkflow(LoadWorkflow.java:194)
        at TavernaINB.LoadWorkflow.load(LoadWorkflow.java:437)
        at TavernaINB.LoadWorkflow.main(LoadWorkflow.java:471)

Could somebody help me?

Thanks,
	Ismael Navas


-----Mensaje original-----
De: Martin Senger [mailto:senger at ebi.ac.uk] 
Enviado el: viernes, 11 de marzo de 2005 10:05
Para: Ismael Navas
CC: moby-l at biomoby.org
Asunto: Re: [MOBY-l] Taverna Parser

Hi,
> I'm working with the parser for Taverna from Java
>
   Could you clarify please what parser you are referring to? Do you mean
the part of Taverna (the BioMoby plug-in in Taverna code), or some
outside-Taverna parser?

   Thanks,
   Martin

-- 
Martin Senger

EMBL Outstation - Hinxton                Senger at EBI.ac.uk     
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