SessionHandle session = null;
ClientHandle client = null;
+
/*
* (non-Javadoc)
*
}
private Hashtable handlers = initHandlers();
+
private Vector listeners = new Vector();
+
/**
* make all the PropertyChangeSupport objects for the
* events described in org.vamsas.client.Event
}
return events;
}
+
/*
* (non-Javadoc)
*
public void addDocumentUpdateHandler(PropertyChangeListener evt) {
if (handlers.containsKey(Events.DOCUMENT_UPDATE)) {
Object handler;
- ((PropertyChangeSupport) (handler
- = handlers.get(Events.DOCUMENT_UPDATE))).addPropertyChangeListener(evt);
+ ((PropertyChangeSupport) (handler = handlers.get(Events.DOCUMENT_UPDATE)))
+ .addPropertyChangeListener(evt);
listeners.add(handler);
- listeners.add((Object) evt);
+ listeners.add((Object) evt);
}
}
// deregister listeners.
// mark this instance as finalized
}
-
+
/**
* writes the VamsasDocument to the given stream.
+ * TODO: ensure that (at least) default provenance entries are written for objects.
* @param outstream
* @param doc
* @throws IOException
* @throws MarshalException
* @throws ValidationException
*/
- private static void setVamsasDocument(Writer outstream, VamsasDocument doc) throws IOException, MarshalException, ValidationException {
- Marshaller marshaller = new Marshaller(outstream);
+ private static void setVamsasDocument(Writer outstream, VamsasDocument doc)
+ throws IOException, MarshalException, ValidationException {
+ Marshaller marshaller = new Marshaller(outstream);
marshaller.marshal(doc);
}
-
+
/**
* Unmarshals a vamsasDocument object from a stream, registers
- * any VorbaIds, and completes the org.vamsas.client.object housekeeping fields.
- *
+ * unregistered objects, records existing VorbaIds, and completes
+ * the org.vamsas.client.object housekeeping fields.
+ * For a valid unmarshalling, the array of returned objects also includes
+ * a <return>sync</return> parameter which is true if new VorbaIds
+ * were created. If sync is false, then the caller should ensure that the
+ * vamsasDocument is written back to disk to propagate the new VorbaIds.
+ * TODO: ensure that provenance is correct for newly registered objects
* @param instream - the XML input stream
* @param factory - the SimpleClient's properly configured VorbaId factory to make new references.
- * @return null or {(Object) VamsasDocument object, (Object) Hashtable of object references)
+ * @return null or {(Object) VamsasDocument object, (Object) Hashtable of object references, (Object) Boolean(sync) }
*/
- private static Object[] getVamsasDocument(Reader instream,
+private static Object[] getVamsasDocument(Reader instream,
IVorbaIdFactory factory) {
Unmarshaller unmarshaller = new Unmarshaller(instream);
unmarshaller.setIDResolver(new IDResolver() {
}
});
Hashtable refbase = new Hashtable();
+ Vector unrefed = new Vector();
final Hashtable objrefs = refbase;
final IVorbaIdFactory vorbafactory = factory;
+ final Vector unrefedObj = unrefed;
unmarshaller.setUnmarshalListener(new UnmarshalListener() {
/*
nobj.set__stored_in_document(true);
Field fd = null;
try {
- // look for the id field (should be an NCName string)
- fd = nobj.getClass().getField("id");
- String idstring;
- if (fd.getType().getClass().equals("astring".getClass())) {
+ if (nobj.isRegisterable()) {
+ // look for the id field (should be an NCName string)
+ nobj.__vorba = vorbafactory;
+ fd = nobj.getClass().getField("id");
+ String idstring;
if (fd.get(nobj) != null) {
idstring = (String) fd.get(nobj);
- if (idstring.length() > 0)
+ if (idstring.length() > 0) {
if (!objrefs.containsKey(idstring)) {
objrefs.put(idstring, nobj);
nobj.setVorbaId(VorbaId.newId(idstring));
- nobj.__vorba = vorbafactory;
+ } else {
+ System.err.println("Serious problem : duplicate id '"+idstring+"' found! expect badness.");
+ // TODO: HANDLE duplicate XML ids correctly
}
+ } else {
+ // add to list of objects without a valid vorbaId
+ unrefedObj.add(nobj);
+ }
+ } else {
+ // add to list of objects without a valid vorbaId
+ unrefedObj.add(nobj);
}
- }
+
nobj.doHash();
+ }
} catch (Exception e) {
return;
- }
- ;
+ };
+
}
}
try {
while (instream.ready()) {
Object obj = unmarshaller.unmarshal(instream);
+ boolean sync=true;
if (obj instanceof VamsasDocument) {
- return new Object[] { obj, objrefs};
+ if (unrefed.size()>0) {
+ sync=false; // document is out of sync - ids have been created.
+ java.util.Iterator newobj = unrefed.listIterator();
+ while (newobj.hasNext()) {
+ object o = (object) newobj.next();
+ // forces registration and id field update.
+ VorbaId id = o.getVorbaId();
+ if (!objrefs.containsKey(id)) {
+ objrefs.put(id.id, o);
+ } else {
+ throw new Error("Serious! Duplicate reference made by vorbaIdFactory!");
+ }
+ }
+ }
+ return new Object[] { obj, objrefs, new Boolean(sync)};
}
}
} catch (MarshalException e) {
}
return null;
}
-/**
- * extract data appropriate for client, session and user
- * from vamsas document.
- * @return application's byte array
- */
+ /**
+ * extract data appropriate for client, session and user
+ * from vamsas document.
+ * @return application's byte array
+ */
private byte[] getApplicationData() {
+ // TODO: extract correct byte object from Jar and return it to application.
return null;
}
*/
public IClientDocument getClientDocument() {
Object[] vdoc;// TODO: = getVamsasDocument(new Reader());
- ClientDocument cdoc = new ClientDocument(getApplicationData(),
- ((VamsasDocument) vdoc[0]).getVAMSAS(), (Hashtable) vdoc[1], this);
+ // ClientDocument cdoc = new ClientDocument(getApplicationData(),
+ // ((VamsasDocument) vdoc[0]).getVAMSAS(), (Hashtable) vdoc[1], this);
//
return null;
}
*/
public void updateDocument(IClientDocument newdoc) {
// TODO Auto-generated method stub
-
+ //
}
/*
public void addVorbaEventHandler(String EventChain, PropertyChangeListener evt) {
if (handlers.containsKey(EventChain)) {
Object handler;
- ((PropertyChangeSupport) (handler
- = handlers.get(EventChain))).addPropertyChangeListener(evt);
+ ((PropertyChangeSupport) (handler = handlers.get(EventChain)))
+ .addPropertyChangeListener(evt);
listeners.add(handler);
- listeners.add((Object) evt);
+ listeners.add((Object) evt);
}
}
*/
public void pollUpdate() {
// TODO wake up UpdateWatcher thread to check for updates.
-
+
}
public static void main(String[] args) {
+++ /dev/null
-/**
- *
- */
-package org.vamsas.client.castor;
-
-import org.exolab.castor.mapping.GeneralizedFieldHandler;
-
-/**
- * @author jim
- *
- */
-public class VorbaIdFieldHandler extends GeneralizedFieldHandler {
-
- public VorbaIdFieldHandler() {
- super();
- // TODO Auto-generated constructor stub
- }
-
- /* (non-Javadoc)
- * @see org.exolab.castor.mapping.GeneralizedFieldHandler#convertUponGet(java.lang.Object)
- */
- public Object convertUponGet(Object arg0) {
- // TODO Auto-generated method stub
- return null;
- }
-
- /* (non-Javadoc)
- * @see org.exolab.castor.mapping.GeneralizedFieldHandler#convertUponSet(java.lang.Object)
- */
- public Object convertUponSet(Object arg0) {
- // TODO Auto-generated method stub
- return null;
- }
-
- /* (non-Javadoc)
- * @see org.exolab.castor.mapping.GeneralizedFieldHandler#getFieldType()
- */
- public Class getFieldType() {
- // TODO Auto-generated method stub
- return null;
- }
-
-}
*
*/
package org.vamsas.client;
+
/**
- * Base class for all Vamsas objects extracted
- * from an IClientDocument.
- * An object maybe registered or unregistered.
+ * Base class for all Vamsas objects extracted from an IClientDocument. An
+ * object maybe registered or unregistered.
*
* @author jimp
- *
+ *
*/
public abstract class object {
- /**
- * unique id for all vamsas objects
- * allows unambiguous referencing
- * to any object in the vamsas document
- */
- protected boolean __stored_in_document=false;
- protected long __last_hash=0;
-
- protected VorbaId vorbaId=null;
- protected IVorbaIdFactory __vorba=null;
- /**
- * calculate a hash
- * for the object with all housekeeping
- * fields at standard values.
- */
- synchronized protected void doHash() {
- __last_hash = 0;
- VorbaId thisid = vorbaId;
- IVorbaIdFactory factory = __vorba;
- boolean stored = __stored_in_document;
- vorbaId = null;
- __vorba = null;
- __last_hash = this.hashCode();
- vorbaId = thisid;
- __vorba = factory;
- __stored_in_document = stored;
- }
-
- /**
- *
- * @return true if object is registered
- */
- public boolean isRegistered() {
- return (vorbaId!=null);
- }
- /**
- * Method to get fixed reference for
- * the object in the vamsas document.
- * @returns null if object is neither registered
- * or not associated with a properly instantiated
- * VorbaIdFactory.
- */
- public VorbaId getVorbaId() {
- if (vorbaId==null) {
- // Try to use the associated factory.
- if (__vorba!=null)
- if ((vorbaId = __vorba.makeVorbaId())==null)
- return null; // Factory not valid.
- else
- return null;
+ /**
+ * unique id for all vamsas objects allows unambiguous referencing to any
+ * object in the vamsas document
+ */
+ protected boolean __stored_in_document = false;
+
+ protected long __last_hash = 0;
+
+ protected boolean registerable = false;
+
+ protected VorbaId vorbaId = null;
+
+ protected IVorbaIdFactory __vorba = null;
+
+ /**
+ *
+ */
+ protected object() {
+ super();
+ testInstanceForIdField();
+ }
+
+ /**
+ * set the isRegisterable flag based on the presence of a 'String id' field in
+ * the reflected class instance.
+ */
+ private void testInstanceForIdField() {
+ // look for the id field (should be an NCName string)
+ // TODO: decide if 'id' is an appropriate reserved attribute name for the
+ // VorbaId
+ try {
+ java.lang.reflect.Field fd = this.getClass().getField("id");
+ if (fd.getType().getClass().equals("astring".getClass())) {
+ this.setRegisterable(true);
}
- return vorbaId;
- }
- /**
- * used by the IClient implementation
- * to generate unique Id based on
- * client applications current namespace.
- */
- protected void setVorbaId(VorbaId newid) {
- vorbaId = newid;
+ } catch (SecurityException e) {
+ e.printStackTrace();
+ } catch (NoSuchFieldException e) {
+ this.setRegisterable(false);
}
-
- /**
- * @return true if object is present in Vamsas Document.
- */
- public boolean is__stored_in_document() {
- return __stored_in_document;
- }
- /**
- * for use by Vorba agent to reflect state of
- * vamsas object to client application.
- * @param __stored_in_document The __stored_in_document to set.
- */
- protected void set__stored_in_document(boolean __stored_in_document) {
- this.__stored_in_document = __stored_in_document;
+ }
+
+ /**
+ * update the object instance's String id field, based on the contents of the
+ * VorbaId. Only call this if you mean to do it!
+ */
+ protected void setInstanceIdField() {
+ if (registerable) {
+ if (vorbaId!=null)
+ try {
+ java.lang.reflect.Field fd = this.getClass().getField("id");
+ fd.set((Object) this, (Object) new String(vorbaId.id));
+ } catch (IllegalAccessException e) {
+ System.err.println("SourceGeneration of "+this.getClass().toString()
+ +"\n has resulted in an inaccessible 'id' field!\nCannot set ID from the vorbaId object.")
+ e.printStackTrace(System.err);
+ }
+ catch (SecurityException e) {
+ e.printStackTrace(System.err);
+ } catch (NoSuchFieldException e) {
+ this.setRegisterable(false);
+ }
+ } else {
+ System.err.println("Client error. Trying to setInstanceIdField on a "
+ +this.getClass().toString()+" (which cannot be given a vorbaId)");
}
- /**
- * __last_hash is the hash value computed
- * when the object was last checked against
- * a IClientDocument generated by the
- * object's parent IClient instance.
- * @return Returns the __last_hash.
- */
- public long get__last_hash() {
- return __last_hash;
+ }
+ /**
+ * calculate a hash for the object with all housekeeping fields at standard
+ * values. (isRegisterable is an immutable attribute property)
+ */
+ synchronized protected void doHash() {
+ __last_hash = 0;
+ VorbaId thisid = vorbaId;
+ IVorbaIdFactory factory = __vorba;
+ boolean stored = __stored_in_document;
+ vorbaId = null;
+ __vorba = null;
+ __last_hash = this.hashCode();
+ vorbaId = thisid;
+ __vorba = factory;
+ __stored_in_document = stored;
+ }
+
+ /**
+ *
+ * @return true if object is registered
+ */
+ public boolean isRegistered() {
+ return (registerable) ? (vorbaId != null) : false;
+ }
+
+ /**
+ * Method to get fixed reference for the object in the vamsas document.
+ *
+ * @returns null if object is neither registered or not associated with a
+ * properly instantiated VorbaIdFactory.
+ */
+ public VorbaId getVorbaId() {
+ if (registerable && vorbaId == null) {
+ // Try to use the associated factory.
+ if (__vorba != null)
+ if ((vorbaId = __vorba.makeVorbaId()) == null)
+ return null; // Factory not valid.
+ else {
+ this.setInstanceIdField();
+ return vorbaId;
+ }
}
+ return vorbaId;
+ }
+
+ /**
+ * used by the IClient implementation to generate unique Id based on client
+ * applications current namespace.
+ */
+ protected void setVorbaId(VorbaId newid) {
+ vorbaId = newid;
+ }
+
+ /**
+ * @return true if object is present in Vamsas Document.
+ */
+ public boolean is__stored_in_document() {
+ return __stored_in_document;
+ }
+
+ /**
+ * for use by Vorba agent to reflect state of vamsas object to client
+ * application.
+ *
+ * @param __stored_in_document
+ * The __stored_in_document to set.
+ */
+ protected void set__stored_in_document(boolean __stored_in_document) {
+ this.__stored_in_document = __stored_in_document;
+ }
+
+ /**
+ * __last_hash is the hash value computed when the object was last checked
+ * against a IClientDocument generated by the object's parent IClient
+ * instance.
+ *
+ * @return Returns the __last_hash.
+ */
+ public long get__last_hash() {
+ return __last_hash;
+ }
+
+ /**
+ * @return Returns the registerable.
+ */
+ public boolean isRegisterable() {
+ return registerable;
+ }
+
+ /**
+ * Called during unmarshalling - if object has an id string, it is
+ * registerable.
+ *
+ * @param registerable
+ * The registerable to set.
+ */
+ protected void setRegisterable(boolean registerable) {
+ this.registerable = registerable;
+ }
}
}
return null;
}
- /**
- * opens a locked UTF-8 stream to the vamsas document.
- * @return reader for vamsasdocument.xml enrty
- */
- public java.io.PrintWriter getDocumentWriter() {
- if (vamsasWriterStream!=null && vamsasWriterStream.checkError()) {
- return vamsasWriterStream;
- }
-
- try {
-
- newVamsasJarLock = new Lock(lockfile);
- if (newVamsasJarLock = !=null) {
- JarOutputStream session = new JarOutputStream(new FileOutputStream(vamsasJar));
- JarEntry vamsasDocument = session.getJarEntry("vamsasDocument.xml");
- if (vamsasDocument!=null)
- return new java.io.PrintWriter(OutputStreamWriter(session.Stream(vamsasDocument)), "UTF-8");
- }
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
+
}
git://source.jalview.org / vamsas.git / commitdiff