internal flags for added and updated since last read for Vobjects tested with Archive...

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@315 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/uk/ac/vamsas/client/Vobject.java b/src/uk/ac/vamsas/client/Vobject.java
index c5f2697..5029a31 100644 (file)
--- a/src/uk/ac/vamsas/client/Vobject.java
+++ b/src/uk/ac/vamsas/client/Vobject.java
@@ -35,6 +35,10 @@ public abstract class Vobject {
    */
   protected boolean __updated_since_last_read = false;
   /**
+   * true if Vobject appeared in the document after the last access by this vamsas library instance
+   */
+  protected boolean __added_since_last_read = false;
+  /**
    * memory of the last doHash() value computed for the Vobject 
    * @see doHash()
    */
@@ -275,10 +279,16 @@ public abstract class Vobject {
   /**
    * @return true if this object has been updated in the currently stored document since the last time a Vobject with the same ID was read from a Vamsas Document
    */
-  public boolean is__updated_since_last_read() {
+  public boolean isUpdated() {
     return __updated_since_last_read;
   }
-
+  /**
+   * 
+   * @return true if this object was added to the document after the last time the vamsas library acessed the session document
+   */
+  public boolean isNewInDocument() {
+    return __added_since_last_read;
+  }
   /**
    * Set internal flag to indicate this object was updated since the last document read
    * @param __updated_since_last_read the __updated_since_last_read to set
@@ -300,6 +310,13 @@ public abstract class Vobject {
   }
 
   /**
+   * @param __added_since_last_read the __added_since_last_read to set
+   */
+  protected void set__added_since_last_read(boolean __added_since_last_read) {
+    this.__added_since_last_read = __added_since_last_read;
+  }
+
+  /**
    * __last_hash is the hash value computed when the Vobject was last checked
    * against a IClientDocument generated by the Vobject's parent IClient
    * instance.

diff --git a/src/uk/ac/vamsas/client/VorbaId.java b/src/uk/ac/vamsas/client/VorbaId.java
index 8ffee9e..4ba6c0b 100644 (file)
--- a/src/uk/ac/vamsas/client/VorbaId.java
+++ b/src/uk/ac/vamsas/client/VorbaId.java
@@ -38,8 +38,13 @@ public class VorbaId {
       return vobject.vorbaId;
     }
   }
+  /**
+   * protected VorbaId constructor used when turning XML ID strings into vorba IDs
+   * @param id
+   * @return VorbaId object or null if string was null.
+   */
   protected static VorbaId newId(String id) {
-    return new VorbaId(id);
+    return (id==null) ? null : new VorbaId(id);
   }
   /**
    * @return Returns the id.

diff --git a/src/uk/ac/vamsas/client/VorbaXmlBinder.java b/src/uk/ac/vamsas/client/VorbaXmlBinder.java
index 1834e95..9a94047 100644 (file)
--- a/src/uk/ac/vamsas/client/VorbaXmlBinder.java
+++ b/src/uk/ac/vamsas/client/VorbaXmlBinder.java
@@ -42,7 +42,7 @@ public class VorbaXmlBinder implements UnmarshalListener {
   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;
@@ -81,7 +81,7 @@ public class VorbaXmlBinder implements UnmarshalListener {
    */
   public void initialized(Object 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.
@@ -102,7 +102,8 @@ 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
               }
@@ -115,23 +116,35 @@ 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();
+          // 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);
+                oldobjhashes.put(nobj_id, new Vobjhash(nobj));
+                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;
       };
-      
+
     }
   }
 
@@ -146,7 +159,7 @@ 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");
@@ -154,7 +167,7 @@ public class VorbaXmlBinder implements UnmarshalListener {
       doc.__vorba = vorba;
     doc.__ensure_instance_ids(); // this may take a while. Do we allow for cyclic references ? 
     doc.marshal(outstream);
-    
+
   }
   /**
    * creates new VorbaId references where necessary for newly unmarshalled objects
@@ -182,61 +195,61 @@ 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 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 }
-     */
+   * @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) {
+        VorbaXmlBinder.log.warn("Warning - id " + id
+            + " is not found in the Vamsas XML!");
+        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;
+  }
 }
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