X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fclient%2Fobject.java;h=6498d7047a59945313fbff895c6c065a90cdc886;hb=8d474dd77c01354948a5db3ee135e04af8f97503;hp=fc13b4fedc618eee815a18f32d2936b33f93fd98;hpb=49874b2de657c9b2cfbb00d7600941f7cb7f2552;p=vamsas.git

diff --git a/src/org/vamsas/client/object.java b/src/org/vamsas/client/object.java
index fc13b4f..6498d70 100644
--- a/src/org/vamsas/client/object.java
+++ b/src/org/vamsas/client/object.java
@@ -3,6 +3,18 @@
  */
 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.
@@ -11,7 +23,8 @@ package org.vamsas.client;
  * 
  */
 public abstract class object {
-
+  static Log log = LogFactory.getLog(object.class);
+  
   /**
    * unique id for all vamsas objects allows unambiguous referencing to any
    * object in the vamsas document
@@ -40,11 +53,10 @@ public abstract class object {
    */
   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
+    // 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())) {
+      java.lang.reflect.Field fd = this.getClass().getDeclaredField("_id");
+      if (String.class.isAssignableFrom(fd.getType())) {
         this.setRegisterable(true);
       }
     } catch (SecurityException e) {
@@ -60,25 +72,35 @@ public abstract class object {
    */
   protected void setInstanceIdField() {
     if (registerable) {
-      if (vorbaId!=null) 
+      if (__vorba != 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);
+          Method fd = this.getClass().getMethod("setId", new Class[] { String.class });
+          fd.invoke((Object) this, new Object[] {new String(this.getVorbaId().id)});
+          log.info(this.getClass().getName()+" called setInstanceIdField!");
+        } catch (InvocationTargetException e) { 
+          System.err
+          .println("SourceGeneration of "
+              + this.getClass().toString()
+              + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId object.");
+          e.printStackTrace(System.err);
         }
-        catch (SecurityException e) {
+        catch (IllegalAccessException e) {
+          System.err
+              .println("SourceGeneration of "
+                  + this.getClass().toString()
+                  + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId object.");
           e.printStackTrace(System.err);
-        } catch (NoSuchFieldException e) {
+        } catch (SecurityException e) {
+          e.printStackTrace(System.err);
+        } catch (NoSuchMethodException e) {
           this.setRegisterable(false);
         }
     } else {
       System.err.println("Client error. Trying to setInstanceIdField on a "
-          +this.getClass().toString()+" (which cannot be given a vorbaId)");
+          + this.getClass().toString() + " (which cannot be given a vorbaId)");
     }
   }
+
   /**
    * calculate a hash for the object with all housekeeping fields at standard
    * values. (isRegisterable is an immutable attribute property)
@@ -97,6 +119,19 @@ public abstract class object {
   }
 
   /**
+   * 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) {
+    return true;
+  }
+
+  /**
    * 
    * @return true if object is registered
    */
@@ -178,4 +213,103 @@ public abstract class object {
   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
+   *
+   */
+  protected void __ensure_instance_ids() {
+    if (__vorba==null)
+      throw new Error("Improperly intialised org.vamsas.client.object - no VorbaFactory given.");
+    log.info(this.getClass()+".__ensure_instance_ids()");
+    if (!__stored_in_document && registerable)
+      setInstanceIdField();
+    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.error("Couldn't resolve descriptor for "+this.getClass().getName());
+      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.info("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);
+          }
+        }
+    }
+    
+  }
 }