Taverna Workbench 1.3.1

[AljoshaNL]

Hello,

Me and my mother are trying to install Taverna Workbench on a Fedora Core 4 machine. When we run runme.sh we get a splash screen, but it crashes with the folowing output:

[jdmitrie@thestral taverna-workbench-1.3.1]$ ./runme.sh
java.util.ConcurrentModificationException
   at java.util.HashMap$HashIterator.hasNext() (/usr/lib/libgcj.so.6.0.0)
   at java.awt.image.BufferedImage$1.startProduction(java.awt.image.ImageConsumer) (/usr/lib/libgcj.so.6.0.0)
   at gnu.java.awt.peer.gtk.GtkToolkit.createImage(java.awt.image.ImageProducer) (/usr/lib/lib-gnu-java-awt-peer-gtk.so.6.0.0)
   at javax.swing.ImageIcon.ImageIcon(java.awt.Image, java.lang.String) (/usr/lib/libgcj.so.6.0.0)
   at javax.swing.ImageIcon.ImageIcon(java.awt.Image) (/usr/lib/libgcj.so.6.0.0)
   at org.embl.ebi.escience.scuflui.ScuflIcons.<clinit>() (Unknown Source)
   at java.lang.Class.initializeClass() (/usr/lib/libgcj.so.6.0.0)
   at org.embl.ebi.escience.scuflui.AdvancedModelExplorer.getIcon() (Unknown Source)
   at org.embl.ebi.escience.scuflui.UIComponentRegistry.loadInstances(java.lang.ClassLoader) (Unknown Source)
   at org.embl.ebi.escience.scuflui.UIComponentRegistry.instance() (Unknown Source)
   at org.embl.ebi.escience.scuflui.workbench.Workbench.main(java.lang.String[]) (Unknown Source)
   at java.lang.reflect.Method.invoke(java.lang.Object, java.lang.Object[]) (/usr/lib/libgcj.so.6.0.0)
   at org.embl.ebi.escience.scuflui.workbench.WorkbenchLauncher.main(java.lang.String[]) (Unknown Source)
   at gnu.java.lang.MainThread.call_main() (/usr/lib/libgcj.so.6.0.0)
   at gnu.java.lang.MainThread.run() (/usr/lib/libgcj.so.6.0.0)
java.util.ConcurrentModificationException
Found auth = www.mygrid.org.uk for ns = dataprovenance
Found auth = www.mygrid.org.uk for ns = person
Found auth = www.mygrid.org.uk for ns = formaloutputparameter
Found auth = www.mygrid.org.uk for ns = documentcollection
Found auth = www.mygrid.org.uk for ns = affiliationepisode
Found auth = www.mygrid.org.uk for ns = lsdocument
Found auth = www.mygrid.org.uk for ns = experimentinstance
Found auth = www.mygrid.org.uk for ns = creationtype
Found auth = www.mygrid.org.uk for ns = address
Found auth = www.mygrid.org.uk for ns = servicedescription
Found auth = www.mygrid.org.uk for ns = programme
Found auth = www.mygrid.org.uk for ns = experimentdesign
Found auth = www.mygrid.org.uk for ns = study
Found auth = www.mygrid.org.uk for ns = operationtype
Found auth = www.mygrid.org.uk for ns = operation
Found auth = www.mygrid.org.uk for ns = labbookview
Found auth = www.mygrid.org.uk for ns = datatype
Found auth = www.mygrid.org.uk for ns = actualoutputparameter
Found auth = www.mygrid.org.uk for ns = formalinputparameter
Found auth = www.mygrid.org.uk for ns = operationtrace
Found auth = www.mygrid.org.uk for ns = format
Found auth = www.mygrid.org.uk for ns = operationcontent
Found auth = www.mygrid.org.uk for ns = scuflworkflowtrace
Found auth = www.mygrid.org.uk for ns = actualinputparameter
Found auth = www.mygrid.org.uk for ns = studyparticipationepisode
Found auth = www.mygrid.org.uk for ns = organization
Exception in thread "main" java.lang.reflect.InvocationTargetException
   at java.lang.reflect.Method.invoke(java.lang.Object, java.lang.Object[]) (/usr/lib/libgcj.so.6.0.0)
   at org.embl.ebi.escience.scuflui.workbench.WorkbenchLauncher.main(java.lang.String[]) (Unknown Source)
   at gnu.java.lang.MainThread.call_main() (/usr/lib/libgcj.so.6.0.0)
   at gnu.java.lang.MainThread.run() (/usr/lib/libgcj.so.6.0.0)
Caused by: java.util.regex.PatternSyntaxException: At position 4 in regular expression pattern:
attempted to repeat a token that is already repeated
        \w++
            ^
   at java.util.regex.Pattern.Pattern(java.lang.String, int) (/usr/lib/libgcj.so.6.0.0)
   at java.util.regex.Pattern.compile(java.lang.String, int) (/usr/lib/libgcj.so.6.0.0)
   at java.util.regex.Pattern.compile(java.lang.String) (/usr/lib/libgcj.so.6.0.0)
   at java.util.regex.Pattern.matches(java.lang.String, java.lang.CharSequence) (/usr/lib/libgcj.so.6.0.0)
   at org.embl.ebi.escience.scufl.Processor.Processor(org.embl.ebi.escience.scufl.ScuflModel, java.lang.String) (Unknown Source)
   at org.embl.ebi.escience.scufl.InternalSinkPortHolder.InternalSinkPortHolder(org.embl.ebi.escience.scufl.ScuflModel) (Unknown Source)
   at org.embl.ebi.escience.scufl.ScuflModel.ScuflModel() (Unknown Source)
   at org.embl.ebi.escience.scuflui.workbench.Workbench.Workbench() (Unknown Source)
   at org.embl.ebi.escience.scuflui.workbench.Workbench.main(java.lang.String[]) (Unknown Source)
   at java.lang.reflect.Method.invoke(java.lang.Object, java.lang.Object[]) (/usr/lib/libgcj.so.6.0.0)

At first, when we ran runme.sh it gave out the java help screen. We altered the command a bit, after that we got the output. We also installed some compatiblity gcj libraries, and after that we restored the command found in the runme.sh script to what is was. Here is the runme.sh script:

#!/bin/sh

## resolve links - $0 may be a symlink
PRG="$0"
progname=`basename "$0"`
saveddir=`pwd`

# need this for relative symlinks
cd `dirname "$PRG"`
  
while [ -h "$PRG" ] ; do
    ls=`ls -ld "$PRG"`
    link=`expr "$ls" : '.*-> \(.*\)$'`
    if expr "$link" : '.*/.*' > /dev/null; then
    PRG="$link"
    else
    PRG=`dirname "$PRG"`"/$link"
    fi
done

TAVERNA_HOME=`dirname "$PRG"`

cd "$saveddir"

# make it fully qualified
TAVERNA_HOME=`cd "$TAVERNA_HOME" && pwd`


CLASSP=$TAVERNA_HOME/resources:$TAVERNA_HOME/conf:$TAVERNA_HOME/taverna-1.3.1-launcher.jar

for i in $TAVERNA_HOME/libext/*.jar
do
  CLASSP=$CLASSP:$i
done

case "`uname`" in
  CYGWIN*) CLASSP=`cygpath --path --type windows $CLASSP`;;
esac

# echo "java -classpath" $CLASSP "-Djava.protocol.handler.pkgs=uk.ac.rdg.resc.jstyx.client -Dtaverna.home=$TAVERNA_HOME -ea" "org.embl.ebi.escience.scuflui.workbench.WorkbenchLauncher"

java -classpath $CLASSP -Djava.protocol.handler.pkgs=uk.ac.rdg.resc.jstyx.client -Dtaverna.home=$TAVERNA_HOME -ea org.embl.ebi.escience.scuflui.workbench.WorkbenchLauncher

Help is very much appreciated, were sitting here already for some hours, we really dont know what to try next.

Aljosha and Julia

[jro]

Without looking at the source directly it looks like a syntax error in one of the Regular Expressions in this file:
org.embl.ebi.escience.scufl.Processor.Processor

Did you try adding some stuff or are there optional modules that are included? If so try compiling without them.

[AljoshaNL]

I think I'm e-mailing the guys who made Taverna. It really ain't for humans. The only documentation I found didn't work, on 2 (totally) different distros.

[jro]

That would probably be my next course of action. Either that or post the error to the programs discussion board or mailing list. It didn't appear to be a problem on your end.

[AljoshaNL]

I needed to get sun's java. Now it works. They promised to make it clearer in the manual

[jro]

Ah ha, I looked right over the fact that you were compiling with gcj. Glad you got it working.

[AljoshaNL]

Here a short tutorial how to install J2RE on a debian (-based) system:

1) Go to http://java.sun.com and look for java J2RE
2) Meanwhile get these dependencies with apt-get : fakeroot java-package java-common
Important: NO! Do NOT (!) use sudo instead of fakeroot! It really ain't the same!
3) Make a .deb archive of the java package you downloaded: fakeroot make-jpkg jre-<thing you downloaded>
4) Install the package: sudo dpkg -i sun-j2re1.5_1.5.0+update05_i386.deb
5) Select Sun's java as the default java compiler and bytecode interpreter:
sudo update-alternatives --config java

Done this, you should be able to use Taverna Workbench