X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2FVorbaXmlBinder.java;h=94624943cf42597a0d8d697bc1d84e5507d3d08d;hb=0a868a9601b051aeaf439a8d73f6fc070044a02c;hp=330372a4c9621fbc4cb8382cd36aa72f6b3b2a1a;hpb=ea8b10ee787a2b1e2b35f2acb4dccaf12fd2a6fd;p=vamsas.git

diff --git a/src/uk/ac/vamsas/client/VorbaXmlBinder.java b/src/uk/ac/vamsas/client/VorbaXmlBinder.java
index 330372a..9462494 100644
--- a/src/uk/ac/vamsas/client/VorbaXmlBinder.java
+++ b/src/uk/ac/vamsas/client/VorbaXmlBinder.java
@@ -24,7 +24,8 @@ import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.UnmarshalListener;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
-import org.vamsas.objects.core.VamsasDocument;
+
+import uk.ac.vamsas.objects.core.VamsasDocument;
 /**
  * Implements the Vamsas Vobject ID machinery for translating 
  * between non-volatile XML IDs and Vobject references. Use the
@@ -40,14 +41,13 @@ public class VorbaXmlBinder implements UnmarshalListener {
   private final Vector obj;
   private final Hashtable oldobjhashes;
   private final Hashtable objrefs;
-  private final Vector updatedobjs;
-  
-  public VorbaXmlBinder(IVorbaIdFactory vorbafactory, Vector obj, Hashtable objrefs, Hashtable oldobjhashes, Vector updatedobjs) {
-    this.vorbafactory = vorbafactory;
-    this.obj = obj;
-    this.objrefs = objrefs;
+  private final Vector updatedobjs; // not yet used elswhere ?
+  public VorbaXmlBinder(IVorbaIdFactory vorbafactory2, Vector unrefedObj, Hashtable objrefs2, Hashtable oldobjhashes, Vector updatedObj) {
+    this.vorbafactory = vorbafactory2;
+    this.obj = unrefedObj;
+    this.objrefs = objrefs2;
     this.oldobjhashes = oldobjhashes;
-    this.updatedobjs = updatedobjs;
+    this.updatedobjs = updatedObj;
   }
 
   /*
@@ -56,6 +56,7 @@ public class VorbaXmlBinder implements UnmarshalListener {
    * @see org.exolab.castor.xml.UnmarshalListener#attributesProcessed(java.lang.Object)
    */
   public void attributesProcessed(Object object) {
+
   }
 
   /*
@@ -79,8 +80,11 @@ public class VorbaXmlBinder implements UnmarshalListener {
    * @see org.exolab.castor.xml.UnmarshalListener#initialized(java.lang.Object)
    */
   public void initialized(Object object) {
+    if (object instanceof Vobject) {
+      Vobject nobj = (Vobject) object;
+    }
   }
-  
+
   /*
    * Check if the object has an 'id' field - if it does, copy the value into
    * the VorbaId field of Vobject, and add the Vobject to the VorbaId hash.
@@ -101,7 +105,8 @@ public class VorbaXmlBinder implements UnmarshalListener {
           if (idstring!=null) { 
             if (idstring.length() > 0) {
               nobj.setVorbaId(VorbaId.newId(idstring));
-              if (objrefs.containsKey(nobj_id=nobj.getVorbaId()) && !objrefs.get(nobj.getVorbaId()).equals(nobj)) {
+              nobj_id=nobj.getVorbaId();
+              if (objrefs.containsKey(nobj_id) && !objrefs.get(nobj_id).equals(nobj)) {
                 System.err.println("Serious problem : duplicate id '"+idstring+"' found! expect badness.");
                 // TODO: HANDLE duplicate XML ids correctly
               }
@@ -114,23 +119,33 @@ public class VorbaXmlBinder implements UnmarshalListener {
             // TODO: add to list of objects without a valid vorbaId
             obj.add(nobj);
           }
-          
-        nobj.doHash();
-        // check to see if new object was present in old object hash
-        if (oldobjhashes.containsKey(nobj.getVorbaId())) {
-          Vobjhash oldhash = (Vobjhash) oldobjhashes.get(nobj.getVorbaId());
-          if (oldhash.isUpdated(nobj)) {
-            // mark the object as updated in this document read.
-            nobj.set__updated_since_last_read(true);
+          nobj.doHash(); // updates detected by comparing with last hash when marshalling
+          // check to see if new object was present in old object hash
+          if (nobj_id!=null) {
+            if (oldobjhashes.containsKey(nobj_id)) {
+              Vobjhash oldhash = (Vobjhash) oldobjhashes.get(nobj_id);
+              if (oldhash.isUpdated(nobj)) {
+                // mark the object as updated in this document read.
+                nobj.set__updated_since_last_read(true);
+                updatedobjs.addElement(nobj);
+              }
+            } else {
+              // object has no entry in the oldhashvalue list but
+              // there is a valid vorbaId so
+              nobj.set__added_since_last_read(true);
+            }
+            // and record the just-unmarshalled hash value
             oldobjhashes.put(nobj_id, new Vobjhash(nobj));
-            updatedobjs.addElement(nobj);
+          } else {
+            // for objects yet to get a valid vorba_id
+            nobj.set__added_since_last_read(true);
           }
         }
-      }
+
       } catch (Exception e) {
         return;
       };
-      
+
     }
   }
 
@@ -145,15 +160,16 @@ public class VorbaXmlBinder implements UnmarshalListener {
    * @throws ValidationException
    */
   public static void putVamsasDocument(PrintWriter outstream, VorbaIdFactory vorba, VamsasDocument doc)
-      throws IOException, MarshalException, ValidationException {
+  throws IOException, MarshalException, ValidationException {
     // Ensure references
     if (vorba==null)
       throw new Error("Null VorbaIdFactory Parameter");
     if (doc.__vorba==null)
       doc.__vorba = vorba;
     doc.__ensure_instance_ids(); // this may take a while. Do we allow for cyclic references ? 
-    doc.marshal(outstream);
-    
+    Marshaller mshl = new Marshaller(outstream);
+    mshl.marshal(doc);
+
   }
   /**
    * creates new VorbaId references where necessary for newly unmarshalled objects
@@ -181,61 +197,62 @@ public class VorbaXmlBinder implements UnmarshalListener {
     return sync;
   }
   /**
-     * Unmarshals a vamsasDocument Vobject from a stream, registers
-     * unregistered objects, records existing VorbaIds, and completes 
-     * the uk.ac.vamsas.client.Vobject 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
-     * as getVamsasObjects but will detect updated objects based on differing hash values
-     * obtained from the VorbaIdFactory's VorbaId, Vobject.get__last_Hash() pairs (if any) 
-     * @param instream - the XML input stream 
+   * Unmarshals a vamsasDocument Vobject from a stream, registers
+   * unregistered objects, records existing VorbaIds, and completes 
+   * the uk.ac.vamsas.client.Vobject 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
+   * as getVamsasObjects but will detect updated objects based on differing hash values
+   * obtained from the VorbaIdFactory's VorbaId, Vobject.get__last_Hash() pairs (if any) 
+   * @param instream - the XML input stream 
    * @param factory - the SimpleClient's properly configured VorbaId factory to make new references.
-   * @param root the root element's org.vamsas.objects.core Vobject.
-     * @return null or {(Object) VamsasDocument Vobject, (Object) Hashtable of Vobject references, (Object) Boolean(sync), (Object) Vector of updated objects in document }
-     */
+   * @param root the root element's uk.ac.vamsas.objects.core Vobject.
+   * @return null or {(Object) VamsasDocument Vobject, (Object) Hashtable of Vobject references, (Object) Boolean(sync), (Object) Vector of updated objects in document }
+   */
   public static Object[] getVamsasObjects(Reader instream,
-        VorbaIdFactory factory, Vobject root) {  
+      VorbaIdFactory factory, Vobject root) {  
     Unmarshaller unmarshaller = new Unmarshaller(root);
-      unmarshaller.setIDResolver(new IDResolver() {
-        public Object resolve(String id) {
-          VorbaXmlBinder.log.warn("Warning - id " + id
-              + " is not found in the Vamsas XML!");
+    unmarshaller.setIDResolver(new IDResolver() {
+      public Object resolve(String id) {
+        // TODO: allow for external ID resolution
+        VorbaXmlBinder.log.warn("Warning - id " + id
+            + " is not found in the Vamsas XML! (TODO: Ignore if this is a forward reference!)");
+        return null;
+      }
+    });
+    final Hashtable objrefs = new Hashtable();
+    if (factory.extanthashv==null)
+      factory.extanthashv=new Hashtable();
+    final Hashtable oobjhashes=factory.extanthashv;
+    final VorbaIdFactory vorbafactory = factory;
+    final Vector unrefedObj =  new Vector();
+    final Vector updatedObj = new Vector();
+    unmarshaller.setUnmarshalListener(new VorbaXmlBinder(vorbafactory, unrefedObj, objrefs, oobjhashes,updatedObj));
+    // Call the unmarshaller.
+    try {
+      while (instream.ready()) {
+        // TODO: mark objects in oobjhash prior to unmarshalling, to detect when objects have been lost through an update.
+        //tohere
+        Object obj = unmarshaller.unmarshal(instream);
+        boolean sync=ensure_references(unrefedObj, objrefs);
+        if (!(obj instanceof Vobject))
           return null;
-        }
-      });
-      final Hashtable objrefs = new Hashtable();
-      if (factory.extanthashv==null)
-        factory.extanthashv=new Hashtable();
-      final Hashtable oobjhashes=factory.extanthashv;
-      final VorbaIdFactory vorbafactory = factory;
-      final Vector unrefedObj =  new Vector();
-      final Vector updatedObj = new Vector();
-      unmarshaller.setUnmarshalListener(new VorbaXmlBinder(vorbafactory, unrefedObj, objrefs, oobjhashes, updatedObj));
-      // Call the unmarshaller.
-      try {
-        while (instream.ready()) {
-          // TODO: mark objects in oobjhash prior to unmarshalling, to detect when objects have been lost through an update.
-          //tohere
-          Object obj = unmarshaller.unmarshal(instream);
-          boolean sync=ensure_references(unrefedObj, objrefs);
-          if (!(obj instanceof Vobject))
-            return null;
-          vorbafactory.setNewIdHash(objrefs); // update the Document IO Handler's set of vorbaId<>Object bindings.
-          return new Object[] { obj, objrefs, new Boolean(sync),updatedObj};
-          }
-      } catch (MarshalException e) {
-        // TODO Auto-generated catch block
-        e.printStackTrace();
-      } catch (ValidationException e) {
-        // TODO Auto-generated catch block
-        e.printStackTrace();
-      } catch (IOException e) {
-        // TODO Auto-generated catch block
-        e.printStackTrace();
+        vorbafactory.setNewIdHash(objrefs); // update the Document IO Handler's set of vorbaId<>Object bindings.
+        return new Object[] { obj, objrefs, new Boolean(sync),updatedObj};
       }
-      return null;
+    } catch (MarshalException e) {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+    } catch (ValidationException e) {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+    } catch (IOException e) {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
     }
+    return null;
+  }
 }
\ No newline at end of file