[MOBY-l] Taverna Parser

[Tom Oinn]

Ismael,

This is a standard problem with running Java on a machine with no 
display configured - when Java creates a Graphics context (such as when 
loading an icon image, which is where I think the problem is occuring) 
it attempts to connect to an X server on unix like platforms. There are 
several generic workarounds.

1) Use a more recent version of java - they fixed this a while back, you 
might be using quite an old version?

2) Use something like the XVFB device, produces a virtual frame buffer 
which Java can then connect to to get font metrics etc.

A search for 'headless java' will produce more information, I don't know 
any more detail than this though.

Cheers,

Tom

Ismael Navas wrote:
> 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
>