<?xml version='1.0' encoding='ISO-8859-1'?>
<!DOCTYPE rdf:RDF [
         <!ENTITY rdf 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
         <!ENTITY a 'http://www.w3.org/2000/01/rdf-schema#'>
]>
<rdf:RDF xmlns:rdf="&rdf;"
         xmlns:a="&a;">
<a:Class rdf:about="http://www.mygrid.org.uk/ontology#2D_alignment_quality_graph_plot">
        <a:subClassOf rdf:resource="http://www.mygrid.org.uk/ontology#2D_graph_plot"/>
        <a:subClassOf rdf:resource="http://www.mygrid.org.uk/ontology#diagram"/>
</a:Class>
<a:Class rdf:about="http://www.mygrid.org.uk/ontology#2D_dot_plot">
        <a:subClassOf rdf:resource="http://www.mygrid.org.uk/ontology#diagram"/>
</a:Class>
<!-- any many more. See URL -->
</rdf:RDF>

When running openjump using jamvm and the CVS version of GNU classpath
with workbench-state.xml present in the current directory, I get the
same exception from the XML parser.  To reproduce it, run openjump
twice.  The first run will create the workbench-state.xml file, and
the second will output the exception.

org.jdom.input.JDOMParseException: Error on line 2: required string: "?>"
   at org.jdom.input.SAXBuilder.build(SAXBuilder.java:381)
   at org.jdom.input.SAXBuilder.build(SAXBuilder.java:764)
   at com.vividsolutions.jump.util.java2xml.XML2Java.read(XML2Java.java:61)
   at com.vividsolutions.jump.workbench.ui.plugin.PersistentBlackboardPlugIn.restoreState(PersistentBlackboardPlugIn.java:73)
   at com.vividsolutions.jump.workbench.ui.plugin.PersistentBlackboardPlugIn.initialize(PersistentBlackboardPlugIn.java:52)
   at com.vividsolutions.jump.workbench.JUMPConfiguration.initializeBuiltInPlugIns(JUMPConfiguration.java:988)
   at com.vividsolutions.jump.workbench.JUMPConfiguration.setup(JUMPConfiguration.java:269)
   at com.vividsolutions.jump.workbench.JUMPWorkbench.main(JUMPWorkbench.java:234)
   at com.vividsolutions.jump.workbench.JUMPWorkbench.main(JUMPWorkbench.java:200)
Caused by: org.xml.sax.SAXParseException: required string: "?>"
   at gnu.xml.stream.SAXParser.parse(SAXParser.java:660)
   at org.jdom.input.SAXBuilder.build(SAXBuilder.java:370)
   ...8 more
Caused by: javax.xml.stream.XMLStreamException: required string: "?>"
   at gnu.xml.stream.XMLParser.error(XMLParser.java:4053)
   at gnu.xml.stream.XMLParser.require(XMLParser.java:1291)
   at gnu.xml.stream.XMLParser.readXMLDecl(XMLParser.java:1716)
   at gnu.xml.stream.XMLParser.next(XMLParser.java:1121)
   at gnu.xml.stream.XMLParser.hasNext(XMLParser.java:984)
   at gnu.xml.stream.SAXParser.parse(SAXParser.java:377)
   ...9 more
Caused by: org.xml.sax.SAXParseException: required string: "?>"
   at gnu.xml.stream.SAXParser.parse(SAXParser.java:660)
   at org.jdom.input.SAXBuilder.build(SAXBuilder.java:370)
   at org.jdom.input.SAXBuilder.build(SAXBuilder.java:764)
   at com.vividsolutions.jump.util.java2xml.XML2Java.read(XML2Java.java:61)
   at com.vividsolutions.jump.workbench.ui.plugin.PersistentBlackboardPlugIn.restoreState(PersistentBlackboardPlugIn.java:73)
   at com.vividsolutions.jump.workbench.ui.plugin.PersistentBlackboardPlugIn.initialize(PersistentBlackboardPlugIn.java:52)
   at com.vividsolutions.jump.workbench.JUMPConfiguration.initializeBuiltInPlugIns(JUMPConfiguration.java:988)
   at com.vividsolutions.jump.workbench.JUMPConfiguration.setup(JUMPConfiguration.java:269)
   at com.vividsolutions.jump.workbench.JUMPWorkbench.main(JUMPWorkbench.java:234)
   at com.vividsolutions.jump.workbench.JUMPWorkbench.main(JUMPWorkbench.java:200)
Caused by: javax.xml.stream.XMLStreamException: required string: "?>"
   at gnu.xml.stream.XMLParser.error(XMLParser.java:4053)
   at gnu.xml.stream.XMLParser.require(XMLParser.java:1291)
   at gnu.xml.stream.XMLParser.readXMLDecl(XMLParser.java:1716)
   at gnu.xml.stream.XMLParser.next(XMLParser.java:1121)
   at gnu.xml.stream.XMLParser.hasNext(XMLParser.java:984)
   at gnu.xml.stream.SAXParser.parse(SAXParser.java:377)
   ...9 more

I have successfully parsed http://taverna.cvs.sourceforge.net/*checkout*/taverna/taverna1.0/src/org/embl/ebi/escience/scufl/semantics/mygrid-reasoned-small.rdfs using the SAX parser in Classpath 0.91 and HEAD.

Note that this XML is well-formed but not valid, so if you use the SAX parser in validating mode it will produce the error

org.xml.sax.SAXParseException: attribute must be declared: "xmlns:rdf"
   at gnu.xml.stream.SAXParser.parse(SAXParser.java:660)
   ...

However I cannot reproduce the "required string" exception below. Please confirm the input being used, i.e. that it is not being modified somehow by JDOM. You can test the function of SAXParser yourself with

  $JAVA gnu.xml.stream.SAXParser <file>

Created attachment 11622 [details]
XML file giving parse error with openjump

Attached is a copy of workbench-state.xml generated by openjump.  When it is
present in cwd, openjump throws the exception mentioned above.  When it is
removed, openjump do not throw the exception.  Because of this, I believe
this is the file openjump complain about.

The exception is no longer happening when I run openjump.  So from my point of
view, the CVS version of classpath has fixed this bug.

Great, so openjump works with the cvs version. Egon could could you test Taverna using a recent build? http://builder.classpath.org/dist/ 
Or leave instructions how to reproduce the bug in some easy steps?

?

Richard, why did you resolve this as invalid?

Based on the comments, changing to 'WORKSFORME'.