From 6a22a06cc820ff240f5b37866b768fd7c0df16d7 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 13 Sep 2006 14:24:57 +0000
Subject: [PATCH] bug fix to ensure valid and vorbaIds are generated and
 stored in vamsas object model

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@242 be28352e-c001-0410-b1a7-c7978e42abec
---
 src/org/vamsas/client/Vobject.java                |   40 ++++++++++++++++++++-
 src/org/vamsas/client/VorbaXmlBinder.java         |   12 +++----
 src/org/vamsas/client/simpleclient/IdFactory.java |    2 +-
 3 files changed, 46 insertions(+), 8 deletions(-)

diff --git a/src/org/vamsas/client/Vobject.java b/src/org/vamsas/client/Vobject.java
index 1c7388f..d120e6c 100644
--- a/src/org/vamsas/client/Vobject.java
+++ b/src/org/vamsas/client/Vobject.java
@@ -71,7 +71,7 @@ public abstract class Vobject {
     super();
     testInstanceForIdField();
   }
-
+  java.lang.reflect.Field ___id_field=null; // set to ease pain of reflection
   /**
    * set the isRegisterable flag based on the presence of a 'private String _id' field in
    * the reflected class instance.
@@ -86,6 +86,7 @@ public abstract class Vobject {
       try {
         java.lang.reflect.Field fd = thisclass.getDeclaredField("_id");
         if (String.class.isAssignableFrom(fd.getType())) {
+          ___id_field=fd;
           this.setRegisterable(true);
           break;
         }
@@ -132,6 +133,43 @@ public abstract class Vobject {
           + this.getClass().toString() + " (which cannot be given a vorbaId)");
     }
   }
+  
+  protected String __getInstanceIdField() {
+    /*if (!registerable && !__testedInstance) {
+      testInstanceForIdField();
+      __testedInstance=true;
+    }*/
+    if (registerable) {
+      if (__vorba != null)
+        try {
+          Method fd = this.getClass().getMethod("getId", (Class[]) null);
+          Object idstring = fd.invoke((Object) this, (Object[]) null);
+          log.debug(this.getClass().getName()+" called setInstanceVorbaIdField!");
+          if (idstring!=null && idstring instanceof String) {
+            if (((String) idstring).length()>0)
+              return (String) idstring;
+          }
+        } catch (InvocationTargetException e) { 
+          log.error("SourceGeneration of "
+              + this.getClass().toString()
+              + "\n has resulted in an inaccessible 'getId' method!\nCannot set ID from the vorbaId Vobject.", e);
+        }
+        catch (IllegalAccessException e) {
+          log.error("SourceGeneration of "
+                  + this.getClass().toString()
+                  + "\n has resulted in an inaccessible 'getId' method!\nCannot set ID from the vorbaId Vobject.", 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 Vobject class (Implementation error?)");
+          this.setRegisterable(false);
+        }
+    } else {
+      System.err.println("Client error. Trying to getInstanceIdField on a "
+          + this.getClass().toString() + " (which cannot be given a vorbaId)");
+    }
+    return null;
+  }
 
   /**
    * calculate a hash for the Vobject with all housekeeping fields at standard
diff --git a/src/org/vamsas/client/VorbaXmlBinder.java b/src/org/vamsas/client/VorbaXmlBinder.java
index 0f4feb1..c73d158 100644
--- a/src/org/vamsas/client/VorbaXmlBinder.java
+++ b/src/org/vamsas/client/VorbaXmlBinder.java
@@ -86,13 +86,13 @@ public class VorbaXmlBinder implements UnmarshalListener {
       nobj.set__stored_in_document(true);
       Field fd = null;
       try {
-        if (nobj.isRegisterable()) {
+        if (nobj.isRegisterable() && nobj.___id_field!=null) {
           // look for the id field (should be an NCName string)
           nobj.__vorba = vorbafactory;
-          fd = nobj.getClass().getDeclaredField("_id");
-          String idstring;
-          if (fd.get(nobj) != null) {
-            idstring = (String) fd.get(nobj);
+          fd = nobj.___id_field;
+          // use the Vobject accessor method to avoid unpleasant security exceptions.
+          String idstring = nobj.__getInstanceIdField();
+          if (idstring!=null) { 
             if (idstring.length() > 0) {
               if (!objrefs.containsKey(idstring)) {
                 objrefs.put(idstring, nobj);
@@ -106,7 +106,7 @@ public class VorbaXmlBinder implements UnmarshalListener {
               obj.add(nobj);
             }
           } else {
-            // add to list of objects without a valid vorbaId
+            // TODO: add to list of objects without a valid vorbaId
             obj.add(nobj);
           }
           
diff --git a/src/org/vamsas/client/simpleclient/IdFactory.java b/src/org/vamsas/client/simpleclient/IdFactory.java
index 0f3cc36..80f8f28 100644
--- a/src/org/vamsas/client/simpleclient/IdFactory.java
+++ b/src/org/vamsas/client/simpleclient/IdFactory.java
@@ -49,7 +49,7 @@ public class IdFactory extends VorbaIdFactory {
     unique.reset();
     unique.update(new Object[] { session, client, user}.toString().getBytes());
     // TODO: Ensure format of URNs and use standard composition methods.
-    idstring = client.getClientUrn()+":"+unique.getValue()+"/";
+    idstring = client.getClientName()+":"+unique.getValue()+".";
     extantids=new Hashtable();
   }
   /**
-- 
1.7.10.2