I have some Java code that determines the namespace of the root-level element of an xml document using SAX. If the namespace is "http://sbgn.org/libsbgn/pd/0.1", it should return version 1. If the namespace is "http://sbgn.org/libsbgn/0.2", the version should be 2. So all the code does is read the first element, and set a variable based on the namespace. Here is the code:
private static class VersionHandler extends DefaultHandler
{
private int version = -1;
#Override
public void startElement (String uri, String localName, String qName, Attributes attributes) throws SAXException
{
if ("sbgn".equals (qName))
{
System.out.println (uri);
if ("http://sbgn.org/libsbgn/0.2".equals(uri))
{
version = 2;
}
else if ("http://sbgn.org/libsbgn/pd/0.1".equals(uri))
{
version = 1;
}
else
{
version = -1;
}
}
}
public int getVersion() { return version; }
};
public static int getVersion(File file) throws SAXException, FileNotFoundException, IOException
{
XMLReader xr;
xr = XMLReaderFactory.createXMLReader();
VersionHandler versionHandler = new VersionHandler();
xr.setContentHandler(versionHandler);
xr.setErrorHandler(versionHandler);
xr.parse(new InputSource(
InputStreamToReader.inputStreamToReader(
new FileInputStream (file))));
return versionHandler.getVersion();
}
This works, but has two problems:
It is inefficient, because the whole document will be parsed even though only the first element is needed.
More importantly, this code sometimes (apparently depending on firewall configuration) triggers a UnknownHostException like so:
java.net.UnknownHostException: www.w3.org
at java.net.PlainSocketImpl.connect(Unknown Source)
at java.net.SocksSocketImpl.connect(Unknown Source)
at java.net.Socket.connect(Unknown Source)
at java.net.Socket.connect(Unknown Source)
at sun.net.NetworkClient.doConnect(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.http.HttpClient.(Unknown Source)
at sun.net.www.http.HttpClient.New(Unknown Source)
at sun.net.www.http.HttpClient.New(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown
Source)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown
Source)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown
Source)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown
Source)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown
Source)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown
Source)
at org.sbgn.SbgnVersionFinder.getVersion(SbgnVersionFinder.java:57)
So my questions are:
Apparently this bit of code is connecting to the internet. How can I avoid that? Besides leading to problems with firewalls, it is also needlessly slow.
Why is it connecting to the internet? Please help me understand the logic here, there should be absolutely no need for it.
Is there a more efficient way to determine the namespace of the root element of an xml document?
Edit: here is a link to a sample document that I'm trying to parse this way: https://libsbgn.svn.sourceforge.net/svnroot/libsbgn/trunk/test-files/PD/adh.sbgn
Edit2: A note regarding to the solution of this bug: In fact the problem was triggered because the wrong document was being parsed, instead of the intended document, I was parsing an XHMTML document that does in fact refer to www.w3.org. Of course the solution is to use the correct document. Nevertheless, I found it useful to add this line:
xr.setEntityResolver(null);
To prevent xerces from going over the internet when it's really completely unnecessary.
I believe you need to set the entity resolver. See the javadoc. Also, this article seems relevant.
It's probably connecting to the internet because your document is referring to a DTD or other external entity on the W3C web site. Earlier this year, W3C stopped serving these documents because they couldn't handle the traffic.
You can solve the problem of reading the whole document by throwing a SAXException from one of your callbacks once you've seen as much of the document as you need to see. Be sure in the code that calls the XMLReader.parse() method to distinguish this exception from exceptions thrown by the parser itself (for example, you could subclass SAXException: though not all parsers throw your original exception unchanged and you may need to experiment.)
Related
I'm simply trying to run this sample code below:
import com.memetix.mst.language.Language;
import com.memetix.mst.translate.Translate;
public class Translator {
public static void main(String[] args) throws Exception {
Translate.setClientId("ID GOES HERE");
Translate.setClientSecret("SECRET GOES HERE");
String translatedText = Translate.execute("Bonjour le monde",
Language.FRENCH, Language.ENGLISH);
System.out.println(translatedText);
}
}
and I'm getting the following Exception:
Exception in thread "main" java.lang.Exception: [microsoft-translator-api] Error retrieving translation : datamarket.accesscontrol.windows.net
at com.memetix.mst.MicrosoftTranslatorAPI.retrieveString(MicrosoftTranslatorAPI.java:202)
at com.memetix.mst.translate.Translate.execute(Translate.java:61)
at Translator.main(Translator.java:10)
Caused by: java.net.UnknownHostException: datamarket.accesscontrol.windows.net
at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
at java.net.PlainSocketImpl.connect(Unknown Source)
at java.net.SocksSocketImpl.connect(Unknown Source)
at java.net.Socket.connect(Unknown Source)
at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
at sun.net.NetworkClient.doConnect(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source)
at com.memetix.mst.MicrosoftTranslatorAPI.getToken(MicrosoftTranslatorAPI.java:133)
at com.memetix.mst.MicrosoftTranslatorAPI.retrieveResponse(MicrosoftTranslatorAPI.java:160)
at com.memetix.mst.MicrosoftTranslatorAPI.retrieveString(MicrosoftTranslatorAPI.java:199)
... 2 more
I know it seems like I'm not even trying to figure this out on my own but I'm a complete beginner and can't really understand the Exception trace at all by myself. I'm pretty sure I got the right client Secret. In my azure account I only see an application ID and an Object ID. I'm using the application ID as the client ID.
Does anyone have any ideas on what might be causing this? Any help is greatly appreciated.
Thank you!
The third party Java wrapper boatmeme/microsoft-translator-java-api for MS Azure Translator API is too old & unavailable, because it wrappered the old Microsoft Translator - Text Translation which is old & unavailable now.
There is a notice at the page top of the site Azure datamarket.
DataMarket and Data Services are being retired and will stop accepting new orders after 12/31/2016. Existing subscriptions will be retired and cancelled starting 3/31/2017. Please reach out to your service provider for options if you want to continue service.
For using the new Azure Translator API on Azure portal, you need to refer to the document Announcements: Microsoft Translator Moves to the Azure portal to know how to create the new one on Azure portal and use it via the new REST APIs. Meanwhile, just as reference, you can see my answer in Java for the other SO thread Microsoft Translator API Java, How to get client new ID with Azure.
Hope it helps.
I am trying to create a SOAP based web service, which will call stateless EJB in other project. My configuration is Server: WAS 8.5,IDE: RAD 8.5,Java 1.6, EJB 3.1, and SOAP 1.1. When I write a simple addition method it properly create Web Service, WSDL and i can access the Web Service. But When i add another method which calls EJB it wont allows me to create service and WSDL, it throws below error popup :
Errors occurred during wsgen.
error: compilation failed, errors should have been reported
warning: The apt tool and its associated API are planned to be
removed in the next major JDK release. These features have been
superseded by javac and the standardized annotation processing API,
javax.annotation.processing and javax.lang.model. Users are
recommended to migrate to the annotation processing features of
javac; see the javac man page for more information.
Note: ap round: 1
Problem encountered during annotation processing;
see stacktrace below for more information.
java.lang.NullPointerException
at com.ibm.jtc.jax.tools.ws.processor.modeler.annotation.WebServiceVisitor.isLegalType(Unknown Source)
at com.ibm.jtc.jax.tools.ws.processor.modeler.annotation.WebServiceVisitor.isLegalMethod(Unknown Source)
at com.ibm.jtc.jax.tools.ws.processor.modeler.annotation.WebServiceVisitor.methodsAreLegal(Unknown Source)
at com.ibm.jtc.jax.tools.ws.processor.modeler.annotation.WebServiceVisitor.isLegalImplementation(Unknown Source)
at com.ibm.jtc.jax.tools.ws.processor.modeler.annotation.WebServiceVisitor.shouldProcessWebService(Unknown Source)
at com.ibm.jtc.jax.tools.ws.processor.modeler.annotation.WebServiceVisitor.visitClassDeclaration(Unknown Source)
at com.sun.tools.apt.mirror.declaration.ClassDeclarationImpl.accept(Unknown Source)
at com.ibm.jtc.jax.tools.ws.processor.modeler.annotation.WebServiceAP.buildModel(Unknown Source)
at com.ibm.jtc.jax.tools.ws.processor.modeler.annotation.WebServiceAP.process(Unknown Source)
at com.sun.mirror.apt.AnnotationProcessors$CompositeAnnotationProcessor.process(Unknown Source)
at com.sun.tools.apt.comp.Apt.main(Unknown Source)
at com.sun.tools.apt.main.AptJavaCompiler.compile(Unknown Source)
at com.sun.tools.apt.main.Main.compile(Unknown Source)
at com.sun.tools.apt.main.Main.compile(Unknown Source)
at com.sun.tools.apt.Main.processing(Unknown Source)
at com.sun.tools.apt.Main.process(Unknown Source)
at com.sun.tools.apt.Main.process(Unknown Source)
at com.ibm.jtc.jax.tools.ws.wscompile.WsgenTool.buildModel(Unknown Source)
at com.ibm.jtc.jax.tools.ws.wscompile.WsgenTool.run(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.ibm.ast.ws.jaxws.emitter.jws22.v85.command.AbstractWsGenCommand.execute(Unknown Source)
at com.ibm.ast.ws.jaxws.emitter.command.WsGenCommand.execute(Unknown Source)
....
This is my code which works fine
public class Operations {
public int addition(int x, int y){
return x+y;
}
public String Greetings(String name){
return "happy birthday"+name;
}
}
when i add
#EJB
private transient StatusEJBBeanLocal statusEJBBeanLocal;
public Product StatusFromProductId(int ProdutoID) {
Product produto = null;
produto = this.statusEJBBeanLocal.StatusFromProductId(ProdutoID);
return produto;
}
It shows error. Please help me out here with some tutorial link or tell me whats wrong with my code, how to call EJB from Web services. Thanks in advance.
I've got a little problem developing an Android app. I've got a client (running Android), using android-xmlrpc, that calls some methods on the server (standard Java app), using Apache XML-RPC. Everything runs fine and smoothly, with one exception. When I try to call a method that has a Long type parameter, the server throws out this exception :
21.12.2010 18:54:35 org.apache.xmlrpc.server.XmlRpcErrorLogger log
SEVERE: Failed to parse XML-RPC request: Unknown type: i8
org.apache.xmlrpc.XmlRpcException: Failed to parse XML-RPC request: Unknown type: i8
at org.apache.xmlrpc.server.XmlRpcStreamServer.getRequest(XmlRpcStreamServer.java:71)
at org.apache.xmlrpc.server.XmlRpcStreamServer.execute(XmlRpcStreamServer.java:199)
at org.apache.xmlrpc.webserver.Connection.run(Connection.java:208)
at org.apache.xmlrpc.util.ThreadPool$Poolable$1.run(ThreadPool.java:68)
Caused by: org.xml.sax.SAXParseException: Unknown type: i8
at org.apache.xmlrpc.parser.RecursiveTypeParserImpl.startElement(RecursiveTypeParserImpl.java:122)
at org.apache.xmlrpc.parser.XmlRpcRequestParser.startElement(XmlRpcRequestParser.java:122)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xmlrpc.server.XmlRpcStreamServer.getRequest(XmlRpcStreamServer.java:65)
... 3 more
Everything should be in order, the EnabledForExtensions flag on the Apache side, as mentioned here , is set like this :
serverConfig.setEnabledForExtensions(true);
What am I doing wrong?
It seems there are two dialects for Long parameters, and the client and server have to agree which to use. Eg on a c++ server you need to call:
myRegistry.setDialect(xmlrpc_dialect_apache)
Or
myRegistry.setDialect(xmlrpc_dialect_i8)
Or a corresonding method on your client/server.
I believe the default is i8.
I found the solution of this problem here: https://ws.apache.org/xmlrpc/advanced.html
I must create own implementation of the TypeFactory, something like this:
public class ExtendedTypeFactoryImpl extends TypeFactoryImpl {
private static final String LONG_XML_TAG_NAME = "i8";
public ExtendedTypeFactoryImpl(XmlRpcController pController) {
super(pController);
}
#Override
public TypeParser getParser(XmlRpcStreamConfig pConfig, NamespaceContextImpl pContext, String pURI, String pLocalName) {
if (LONG_XML_TAG_NAME.equals(pLocalName)) {
return new LongParser();
} else {
return super.getParser(pConfig, pContext, pURI, pLocalName);
}
}
}
Then I must set my type factory of my XMPRPC client:
XmlRpcClient client = new XmlRpcClient();
XmlRpcClientConfigImpl conf = new XmlRpcClientConfigImpl();
conf.setServerURL(url.toURL());
conf.setEncoding(Charsets.UTF_8.name());
conf.setEnabledForExtensions(true);
client.setTypeFactory(new ExtendedTypeFactoryImpl(client));
client.setConfig(conf);
I have the following XML:
<?xml version="1.0" encoding="UTF-8"?>
<details>
...
<address1>Test&Address</address1>
...
</details>
When I try to unmarshal it using JAXB, it throws the following exception:
Caused by: org.xml.sax.SAXParseException: The reference to entity "Address" must end with the ';' delimiter.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEntityReference(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at com.sun.xml.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:194)
But when I changed the & in the XML to ', it works. Looks like the problem is only with ampersand & and I cannot understand why.
The code to unmarshal is:
JAXBContext context = JAXBContext.newInstance("some.package.name", this.getClass().getClassLoader());
Unmarshaller unmarshaller = context.createUnmarshaller();
obj = unmarshaller.unmarshal(new StringReader(xml));
Anyone have some insight?
EDIT: I tried the solution suggested by #abhin4v below (ie, add a space after &), but it doesn't seem to work too. Here's the stacktrace:
Caused by: org.xml.sax.SAXParseException: The entity name must immediately follow the '&' in the entity reference.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEntityReference(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at com.sun.xml.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:194)
I've run into this too. First pass I simply replaced the & to a token string (AMPERSAND_TOKEN), sent it through JAXB, then re-replaced the ampersand. Not ideal, but it was a quick fix.
Second pass I made a lot of significant changes, so I'm not sure what exactly solved the problem. I suspect that providing JAXB access to the html dtds made it much happier, but that's only a guess and could be specific to my project.
HTH
Xerces converts & to & and then tries to resolve &Address which fails because it does not end with ;. Put a space between & and Address and it should work. Putting a space will not work as Xerces will now try to resolve & and throw the second error given in OP. You can wrap the test in a CDATA section and Xerces will not try to resolve the entities.
It turns out that the problem is because of the framework I'm using (Mentawai framework). The said XML comes from the POST body of an HTTP request.
Apparently, the framework converts the character entities in the XML body, therefore, & becomes & and the unmarshaller fails to unmarshal the XML.
I've tried using the standard serializing type things, stuff like:
FileOutputStream f_out;
try {
f_out = new FileOutputStream("MAOS.data");
ObjectOutputStream obj_out = new ObjectOutputStream (f_out);
obj_out.writeObject(s);
obj_out.flush();
obj_out.close();
} catch (FileNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} ;
But the problem seems to be that if my object s contains any recursion at ALL I get a stack overflow. If s is a graph that contains nodes and edges (with nodes knowing about edges for purposes of spreading activation, and edges knowing about nodes for the same reason) then it stack overflows. If I take edges out entirely, and just have nodes that know about which nodes they're supposed to spread activation too, the same thing happens! I can even just try to save the ArrayList of nodes that the graph knows about, and the stack overflows again!
I'm so frustrated!
Graphs aren't exactly strange and mysterious, surely SOMEONE has wanted to save one before me. I'm seeing something about saving them as XML files here...but if my problem is the recursiveness, wouldn't I still be having the same problems even if I saved it differently? I just can't think of how you could make a graph without there being connections!
Am I just doing things wrong, or is this object serialization less powerful than I thought? Or do I need to just abandon the idea of saving a graph?
-Jenny
Edit, part of the HUGE stack trace:
Exception in thread "main" java.lang.StackOverflowError
at java.io.ObjectStreamClass.getPrimFieldValues(Unknown Source)
at java.io.ObjectOutputStream.defaultWriteFields(Unknown Source)
at java.io.ObjectOutputStream.writeSerialData(Unknown Source)
at java.io.ObjectOutputStream.writeOrdinaryObject(Unknown Source)
at java.io.ObjectOutputStream.writeObject0(Unknown Source)
at java.io.ObjectOutputStream.writeObject(Unknown Source)
at java.util.ArrayList.writeObject(Unknown Source)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at java.io.ObjectStreamClass.invokeWriteObject(Unknown Source)
at java.io.ObjectOutputStream.writeSerialData(Unknown Source)
at java.io.ObjectOutputStream.writeOrdinaryObject(Unknown Source)
at java.io.ObjectOutputStream.writeObject0(Unknown Source)
at java.io.ObjectOutputStream.defaultWriteFields(Unknown Source)
at java.io.ObjectOutputStream.writeSerialData(Unknown Source)
at java.io.ObjectOutputStream.writeOrdinaryObject(Unknown Source)
at java.io.ObjectOutputStream.writeObject0(Unknown Source)
at java.io.ObjectOutputStream.writeObject(Unknown Source)
at java.util.ArrayList.writeObject(Unknown Source)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at java.io.ObjectStreamClass.invokeWriteObject(Unknown Source)
at java.io.ObjectOutputStream.writeSerialData(Unknown Source)
at java.io.ObjectOutputStream.writeOrdinaryObject(Unknown Source)
at java.io.ObjectOutputStream.writeObject0(Unknown Source)
at java.io.ObjectOutputStream.defaultWriteFields(Unknown Source)
at java.io.ObjectOutputStream.writeSerialData(Unknown Source)
at java.io.ObjectOutputStream.writeOrdinaryObject(Unknown Source)
at java.io.ObjectOutputStream.writeObject0(Unknown Source)
at java.io.ObjectOutputStream.writeObject(Unknown Source)
at java.util.ArrayList.writeObject(Unknown Source)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at java.io.ObjectStreamClass.invokeWriteObject(Unknown Source)
at java.io.ObjectOutputStream.writeSerialData(Unknown Source)
at java.io.ObjectOutputStream.writeOrdinaryObject(Unknown Source)
at java.io.ObjectOutputStream.writeObject0(Unknown Source)
at java.io.ObjectOutputStream.defaultWriteFields(Unknown Source)
at java.io.ObjectOutputStream.writeSerialData(Unknown Source)
at java.io.ObjectOutputStream.writeOrdinaryObject(Unknown Source)
at java.io.ObjectOutputStream.writeObject0(Unknown Source)
at java.io.ObjectOutputStream.writeObject(Unknown Source)
at java.util.ArrayList.writeObject(Unknown Source)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at java.io.ObjectStreamClass.invokeWriteObject(Unknown Source)
at java.io.ObjectOutputStream.writeSerialData(Unknown Source)
These sort of structures are best saved like this:
collection of nodes, each node has a unique ID
collection of edges, each edge has two node IDs (or however many nodes an edge connects to)
without using any recursion. On reading the nodes, create a dictionary of nodes indexed by their ID. Then use the dictionary to fix up the edges when they're read. The IDs do not need to be part of the objects' run time structure, they only need to be unique within the data stream when the stream is written/read.
You could use the JGraphT library which supports serializing graphs into a text file with the ML format. GraphMLExporter Javadoc.
Java serialisation can cope with arbitrary graphs (although not necessarily very efficiently). Probably the problem lies with a custom implementation of writeObject. Perhaps a section of stack trace might help.
A useful serialization format you should consider is JSON, where dictionaries (as suggested by #Skizz) are easily represented:
A JSONObject is an unordered collection of name/value pairs. Its external form is a string wrapped in curly braces with colons between the names and values, and commas between the values and names. The internal form is an object having get() and opt() methods for accessing the values by name, and put() methods for adding or replacing values by name. The values can be any of these types: Boolean, JSONArray, JSONObject, Number, and String, or the JSONObject.NULL object.
Java serialization is capable of handling cyclic references (I assume this is what you mean by recursion), but there is a known problem with large graphs that is described here.
Don't let the date of the article throw you off, just follow chain of comments after it.
It seems you will have to use another serialization technique to accomplish this. Several have been mentioned, and some performance metrics give JSON high marks.
Hmmm. One solution would be to make it into a java bean and use XMLEncoder/XMLDecoder. This is a solution I've used in the past to save and load classes.