X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fclient%2Fobject.java;h=18054b7dbc3ea85ddecbe7d914f18688508ad6ad;hb=65a8158d49f3c25e78deba6ddd2f4a83fc695821;hp=c1a13da8d7435a0867eec2af0105984050e9a9e4;hpb=c8fa5246fcdb1fb5544a8116a48eda973ed2f222;p=vamsas.git

diff --git a/src/org/vamsas/client/object.java b/src/org/vamsas/client/object.java
index c1a13da..18054b7 100644
--- a/src/org/vamsas/client/object.java
+++ b/src/org/vamsas/client/object.java
@@ -2,70 +2,336 @@
  * 
  */
 package org.vamsas.client;
+
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.Iterator;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.exolab.castor.mapping.FieldDescriptor;
+import org.exolab.castor.mapping.FieldHandler;
+import org.exolab.castor.xml.util.XMLClassDescriptorImpl;
+import org.vamsas.test.simpleclient.VamsasArchive;
+
 /**
- * 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 {
+  static Log log = LogFactory.getLog(object.class);
+  
+  /**
+   * true if object was stored in a vamsas Document or has been retrieved from it
+   */
+  protected boolean __stored_in_document = false;
+  /**
+   * memory of the last doHash() value computed for the object 
+   * @see doHash()
+   */
+  protected long __last_hash = 0; 
+  /**
+   * set by testInstanceForIdField() if object should have a VorbaId
+   */
+  protected boolean registerable = false; 
 
-    /**
-     * unique id for all vamsas objects
-     * allows unambiguous referencing
-     * to any object in the vamsas document
-     */
-  	protected boolean __stored_in_document=false;
-    protected VorbaId __vorba__id=null;
-    protected VorbaIdFactory __vorba=null;
-    /**
-     * 
-     * @return true if object is registered
-     */
-    public boolean isRegistered() {
-      return (__vorba__id!=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 String getId() {
-      if (__vorba__id==null) {
-        // Try to use the associated factory.
-        if (__vorba!=null) 
-          if ((__vorba__id = __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 VorbaId vorbaId = null;
+
+  /**
+   * the source of unique VorbaIds.
+   */
+  protected IVorbaIdFactory __vorba = null;
+
+  /**
+   * 
+   */
+  protected object() {
+    super();
+    testInstanceForIdField();
+  }
+
+  /**
+   * set the isRegisterable flag based on the presence of a 'private 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().getDeclaredField("_id");
+      if (String.class.isAssignableFrom(fd.getType())) {
+        this.setRegisterable(true);
       }
-      return __vorba__id.getId();
+    } catch (SecurityException e) {
+      e.printStackTrace();
+    } catch (NoSuchFieldException e) {
+      this.setRegisterable(false);
     }
-    /**
-     * used by the IClient implementation
-     * to generate unique Id based on
-     * client applications current namespace.
-     */
-    protected void setVorbaId(VorbaId newid) {
-      __vorba__id = newid;
+  }
+
+  /**
+   * update the object instance's _id field, based on the contents of the
+   * VorbaId. Only call this if you mean to do it!
+   */
+  protected void setInstanceIdField() {
+    if (registerable) {
+      if (__vorba != null)
+        try {
+          Method fd = this.getClass().getMethod("setId", new Class[] { String.class });
+          fd.invoke((Object) this, new Object[] {new String(this.getVorbaId().id)});
+          log.debug(this.getClass().getName()+" called setInstanceIdField!");
+        } catch (InvocationTargetException e) { 
+          log.error("SourceGeneration of "
+              + this.getClass().toString()
+              + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId object.", e);
+        }
+        catch (IllegalAccessException e) {
+          log.error("SourceGeneration of "
+                  + this.getClass().toString()
+                  + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId object.", e);
+        } catch (SecurityException e) {
+          log.error("Security access violation for "+this.getClass().toString(),e);
+        } catch (NoSuchMethodException e) {
+          log.warn(this.getClass().toString()+" was erroneously marked as a Vorba object class (Implementation error?)");
+          this.setRegisterable(false);
+        }
+    } else {
+      System.err.println("Client error. Trying to setInstanceIdField on a "
+          + this.getClass().toString() + " (which cannot be given a vorbaId)");
     }
-    
-    /**
-     * @return true if object is present in Vamsas Document.
-     */
-    public boolean is__stored_in_document() {
-      return __stored_in_document;
+  }
+
+  /**
+   * calculate a hash for the object with all housekeeping fields at standard
+   * values. (isRegisterable is an immutable attribute property)
+   * TODO: decide if __stored_in_document should be included in the hash or not.
+   * @return true if new hash different to last hash
+   */
+  synchronized protected boolean doHash() {
+    long __old_hash = __last_hash;
+    __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 (__old_hash==0) || (__old_hash == __last_hash);
+  }
+
+  /**
+   * TODO: combine two versions of the same collection object to resolve
+   * asynchronous updates to the same vamsas object Merges two vamsas objects,
+   * one of which is a later version of the earlier (ie they have the same
+   * vorbaId but one is a later version recently read from the vamsasDocument
+   * collection.
+   * 
+   * @return
+   */
+  protected boolean merge(object laterCopy) {
+    log.warn(this.getClass().getName()+".merge() not implemented.");
+    return true;
+  }
+
+  /**
+   * 
+   * @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(this)) == null)
+          return null; // Factory not valid.
+        else {
+          this.setInstanceIdField();
+          return vorbaId;
+        }
     }
-    /**
-     * 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;
+    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.
+   * Setting stored_in_document on a registerable object without a 
+   * vorbaId will mean is will *never* get a vorbaId and 
+   * horrible things will happen.
+   * @param __stored_in_document true if object has been marshalled into current document.
+   */
+  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 true if object can have a vorbaId
+   */
+  public boolean isRegisterable() {
+    return registerable;
+  }
+
+  /**
+   * Called by __testInstanceForidField and the post-unmarshalling handler
+   * to indicate if object will have a vorbaId.
+   * @param registerable 
+   */
+  protected void setRegisterable(boolean registerable) {
+    this.registerable = registerable;
+  }
+  /**
+   * ensure's internal id field corresponds to vorbaId and
+   * cascade through all fields referring to an instance of object
+   * calling the same method on them.
+   * TODO: LATER: properly apply castors own field mechanisms to get at accessors
+   * TODO: FIX CYCLIC __ensure+instance_ids
+   * Implementation note for the todo:
+   * this works like a depth-first search over all vamsas objects in an vamsasDocument. 
+   * The doHash() function is used as the 'visited' flag - 
+   * this *is not* a valid heuristic, although it will work "most of the time".
+   * TODO: LATER? Add another method for setDefaultProvenanceField (in the spirit of setInstanceIdField) using the info from the __vorba.getClient/User/Session methods 
+   */
+  protected void __ensure_instance_ids() {
+    if (__vorba==null)
+      throw new Error("Improperly intialised org.vamsas.client.object - no VorbaFactory given.");
+    log.debug("doing "+this.getClass()+".__ensure_instance_ids()");
+    if (!__stored_in_document && registerable)
+      setInstanceIdField();
+    if (!doHash())
+      return; // nothing has changed in this object - probably visited it before.
+    Class descriptor = null;
+    XMLClassDescriptorImpl descimpl = null;
+    try {
+      // castor descriptor resolver magic
+      descriptor = this.getClass().getClassLoader().loadClass(this.getClass().getName()+"Descriptor");
+      descimpl = (XMLClassDescriptorImpl) descriptor.getConstructor(null).newInstance(null);
+    } catch (Exception e) {
+      log.fatal("Source Generation Error!: Couldn't resolve descriptor for "
+          +this.getClass().getName()
+          +" was 'generate descriptors' set for castorbuilder.properties?");
+      return;
     }
+    FieldDescriptor fields[] = descimpl.getFields();
+    for (int i=0,j=fields.length; i<j; i++) {
+      Class type= fields[i].getFieldType();
+      if (type.isArray()) {
+        if (object[].class.isAssignableFrom(type)) {
+          try {
+            Object val = fields[i].getHandler().getValue(this);
+            if (val!=null) {
+              object vals[] = (object[]) val; 
+              for (int k=0, l=vals.length; k<l; k++) {
+                if (vals[k].__vorba==null)
+                  vals[k].__vorba = __vorba; // propagate IVorbaIdFactory
+                vals[k].__ensure_instance_ids();
+              }
+            }
+          }
+          catch (Exception e) {
+            log.error("Client error - could not access array "+type.getName()+" in "+this.getClass().getName(), e);
+          }
+        }
+      } else
+        if (object.class.isAssignableFrom(type)) {
+          try {
+            FieldHandler fh = fields[i].getHandler();
+            object rf = null;
+            if (fh != null) {
+              Object fval = fh.getValue(this);
+              if (fval!=null) {
+                if (fval.getClass().isArray()) {
+                  //if (object[].class.isAssignableFrom(type)) {
+                    try {
+                      object vals[] = (object[]) fval; 
+                      for (int k=0, l=vals.length; k<l; k++) {
+                        if (vals[k].__vorba==null)
+                          vals[k].__vorba = __vorba; // propagate IVorbaIdFactory
+                        vals[k].__ensure_instance_ids();
+                      }
+                    }
+                    catch (Exception e) {
+                      log.error("Client error - could not access (fhval)array "+type.getName()+" in "+this.getClass().getName(), e);
+                    }
+                  //}
+                } else {
+                  rf = (object) fval;
+                  log.debug("Got value for "+fields[i].getFieldName());
+                }
+              }
+            } else {
+              // fuck around, fuck around, jump up jump up and get down! */
+              Object o = fields[i].getClassDescriptor();
+              if (o!=null) {
+                // XMLClassDescriptorImpl fclasdes = (XMLClassDescriptorImpl) o;
+                String methname = "get"+fields[i].getFieldName();
+                Method fgetmeth = this.getClass().getMethod(methname,null);
+                if (fgetmeth!=null) {
+                  Object fval = fgetmeth.invoke(this,null);
+                  if (fval!=null)
+                    rf = (object) fval;
+                } else {
+                  log.warn("Couldn't find "+this.getClass().getName()+"."+methname);
+                }
+              }
+            }
+            if (rf!=null) {
+              if (rf.__vorba==null)
+                rf.__vorba = __vorba; // propagate IVorbaIdFactory
+              rf.__ensure_instance_ids();
+            }
+          }
+          catch (Exception e) {
+            log.error("Client error - could not access "+type.getName()+" in "+this.getClass().getName(), e);
+          }
+        }
+    }
+    
+  }
 }