[MOBY-l] Taverna Parser

[José María Fernández González]

Hi everybody,
	the easiest way to run java 1.4.x in a headless environment is using 
the system property java.awt.headless:

java -Djava.awt.headless=true ...

	Best regards,
		José María

Tom Oinn wrote:
> 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
>>
> 
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-- 
José María Fernández González		e-mail: jmfernandez at cnb.uam.es
Tlfn:	(+34) 91 585 54 50		Fax:	(+34) 91 585 45 06
Grupo de Diseño de Proteinas		Protein Design Group
Centro Nacional de Biotecnología	National Center of Biotechnology
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C/. Darwin nº 3 (Campus Cantoblanco, U. Autónoma), Madrid (Spain)