From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 21 Mar 2006 11:59:49 +0000 (+0000)
Subject: rearranged some todos and preparing to implement SimpleClient and ClientDocument... 
X-Git-Tag: Release_0.2~325
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=50dbf081e4cdad62da0a65993793e2382f0a5f92;p=vamsas.git

rearranged some todos and preparing to implement SimpleClient and ClientDocument IO stuff.


git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@195 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/org/vamsas/client/ClientDocument.java b/src/org/vamsas/client/ClientDocument.java
index 005cb60..0bbdebc 100644
--- a/src/org/vamsas/client/ClientDocument.java
+++ b/src/org/vamsas/client/ClientDocument.java
@@ -37,7 +37,7 @@ public abstract class ClientDocument implements IClientDocument {
     else
       if (unregistered.__vorba!=vorbafactory) {
         // LATER: decide if this is allowed - it isn't for the moment.
-        log.error("Attempt to overwrite info in a registered vorba Vobject (under a different IVorgaIdFactory) ! - Implementation fix needed.");
+        log.error("Attempt to overwrite info in a registered vorba Vobject (under a different IVorbaIdFactory) ! - Implementation fix needed.");
         return null;
       } else {
         // probably didn't need to call registerObject.
diff --git a/src/org/vamsas/client/simpleclient/ClientDocument.java b/src/org/vamsas/client/simpleclient/ClientDocument.java
index dd1d695..71365ee 100644
--- a/src/org/vamsas/client/simpleclient/ClientDocument.java
+++ b/src/org/vamsas/client/simpleclient/ClientDocument.java
@@ -21,8 +21,8 @@ import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.objects.utils.AppDataReference;
 
 /**
- * @author jimp Contains a collection of vamsas objects and reference to a
- *         specified ClientHandle's information.
+ * Maintains a collection of vamsas objects, appdatas and states, and provides api for a SimpleClient's client.
+ * @author jimp 
  */
 public class ClientDocument extends org.vamsas.client.ClientDocument implements IClientDocument {
   private static Log log = LogFactory.getLog(ClientDocument.class);
@@ -30,6 +30,17 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
   protected SimpleClient sclient;
   protected VamsasArchive archive = null;
   /**
+   * indicate if new data has been incorporated
+   */
+  private boolean isModified = false;
+  /**
+   * Public method for internal use by SimpleClient.
+   * @return true if document has been modified.
+   */
+  public boolean isModified() {
+    return isModified;
+  }
+  /**
    *
    *  prepare Application-side dataset from the vamsas Document archive
    * @param doc - the dataset
@@ -37,13 +48,13 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @param Factory - the source of current and new vorbaIds
    * @param sclient - the simpleclient instance
    */
-  protected ClientDocument(VamsasDocument doc, VamsasArchive docHandler, IdFactory Factory, SimpleClient vorba) {
+  protected ClientDocument(VamsasDocument doc, VamsasArchive docHandler, IdFactory Factory, SimpleClient sclient) {
     super(Factory.getVorbaIdHash(), Factory);
     
     /**
      * prepare Application-side dataset from the vamsas Document archive
      */
-    this.sclient = vorba;
+    this.sclient = sclient;
     archive = docHandler;
     this.doc = doc;
   }
@@ -68,23 +79,120 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
     // TODO: getObject in bulk
     return null;
   }
-  
+  /**
+   * internal reference to single copy of Document Roots array
+   */
+  private VAMSAS[] _VamsasRoots=null;
   /*
    * (non-Javadoc)
-   * 
+   * LATER: currently there is only one Vector of roots ever passed to client - decide if this is correct (means this is not thread safe and may behave unexpectedly)
    * @see org.vamsas.client.IClientDocument#getVamsasRoots()
    */
   public VAMSAS[] getVamsasRoots() {
-    if (doc.getVAMSAS() == null)
+    if (_VamsasRoots!=null)
+      return _VamsasRoots;
+    VAMSAS[] roots = doc.getVAMSAS();
+    if (roots == null) {
       // Make a new one to return to client : TODO: Decide if this is correct
-      return new VAMSAS[] { new VAMSAS() };
-    return doc.getVAMSAS();
+      _VamsasRoots = new VAMSAS[] { new VAMSAS() };
+    } else {
+      _VamsasRoots = new VAMSAS[roots.length];
+      for (int r=0;r<roots.length; r++)
+        _VamsasRoots[r] = roots[r];
+    }
+    return _VamsasRoots;
+  }
+  
+  private int _contains(VAMSAS root, VAMSAS[] docRoots) {
+    if (root==null)
+      return -1;
+    if (docRoots==null || docRoots.length==0)
+      return -1;
+    String r_id = root.getId();
+    for (int i=0,j=docRoots.length; i<j; i++)
+      if (docRoots[i]==root || (docRoots[i]!=null && docRoots[i].getId().equals(r_id)))
+        return i;
+    return -1;
+  }
+/**
+ * verify that newr version is really an intact version of the 
+ * @param newVersion (may be modified)
+ * @param oldVersion 
+ * @return true if newVersion is a valid root that preserves original references
+ */
+  private boolean isValidUpdate(VAMSAS newVersion, final VAMSAS oldVersion) {
+    // LATER: IMPLEMENT
+    // ideal - this cascades down the two structures, ensuring that all ID'd objects in one are present in the other.
+    if (oldVersion==newVersion) {
+      // may be a virgin root element.
+      if (!newVersion.isRegistered())
+        _registerObject(newVersion);
+      // Should retrieve original version and compare - unless local hashes can be used to determine if resultSet has been truncated.
+      // just do internal validation for moment.
+      if (newVersion.isValid())
+        return true;
+      return false;
+    } else {
+      // redundant ? if (oldVersion.is__stored_in_document())
+      if (!newVersion.isRegistered())
+        _registerObject(newVersion);
+      if (newVersion.isValid())
+        return true;
+    }
+    return false;
+  }
+  /**
+   * merge old and new root vectors
+   * @param newr This array may be written to
+   * @param original
+   * @param the client document (usually this) which this root set belongs to.
+   * @return merged vector of vamsas roots
+   */
+  private VAMSAS[] _combineRoots(VAMSAS[] newr, final VAMSAS[] original, ClientDocument modflag) {
+    Vector rts = new Vector();
+    boolean modified=false;
+    for (int i=0,j=original.length; i<j; i++) {
+      int k = _contains(original[i], newr);
+      if (k>-1) {
+        if (isValidUpdate(newr[k], original[i])) {
+          modified=true;
+          rts.add(newr[k]);
+          newr[k]=null;
+        } else {
+          // LATER: try harder to merge ducument roots.
+          log.warn("Couldn't merge new VAMSAS root "+newr[k].getId());
+          newr[k] = null; // LATER: this means we ignore mangled roots. NOT GOOD
+        }
+      } else {
+        // add in order.
+        rts.add(original[i]);
+      }
+    }
+    // add remaining (new) roots
+    for (int i=0,j=newr.length; i<j; i++) {
+      if (newr[i]!=null) {
+        rts.add(newr[i]);
+        modified=true;
+      }
+    }
+    newr = new VAMSAS[rts.size()];
+    for (int i=0,j=rts.size(); i<j; i++)
+      newr[i] = (VAMSAS) rts.get(i);
+    if (modflag!=null)
+      modflag.isModified = modified;
+    return newr;
   }
   
   /**
    * update the document with new roots.
+   * LATER: decide: this affects the next call to getVamsasRoots()
    */
   public void setVamsasRoots(VAMSAS[] newroots) {
+    
+    // are we dealing with same array ?
+    if (_VamsasRoots!=newroots) {
+      // merge roots into 
+    }
     // extract root objects
     if (newroots != null) {
       // check newroots for objects that were present in the old document
@@ -98,8 +206,7 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
           // easy - just check if anything has changed and do provenance
           Vobject oldversion = getObject(newroots[i].getVorbaId());
           if (oldversion instanceof VAMSAS) {
-            // LATER: appropriate merging behaviour when two clients have
-            // modified the same registered Vobject independently
+            // LATER: appropriate merging behaviour when two clients have improperly modified the same Vobject independently.
             if (newroots[i].get__last_hash() != newroots[i].hashCode()) {
               // client has modified this Vobject since last retrieval.
               if (newroots[i].get__last_hash() != oldversion.get__last_hash()) {
@@ -134,11 +241,12 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
   }
   
   /* (non-Javadoc)
+   * LATER: decide: this affects the next call to getVamsasRoots()
    * @see org.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
    */
   public void addVamsasRoot(VAMSAS newroot) {
-    // TODO Auto-generated method stub
-    
+    VAMSAS[] newroots = _combineRoots(new VAMSAS[] {newroot}, _VamsasRoots, this);
+    _VamsasRoots = newroots;  
   }
   
   /*
@@ -150,18 +258,24 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
     if (unregistered!=null) {
       VorbaId ids[] = new VorbaId[unregistered.length];
       for (int i=0,k=unregistered.length; i<k; i++)
-        ids[i]=registerObject(unregistered[i]);
+        if (unregistered[i]!=null) {
+          log.warn("Null Vobject passed to registerObject[] at position "+i);
+          return null;
+        } else {
+          ids[i]=registerObject(unregistered[i]);
+        }
       return ids;
     }
     return null;
   }
-  
   /* (non-Javadoc)
    * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.Vobject)
    */
   public VorbaId registerObject(Vobject unregistered) {
-    // TODO: add provenance stuff to newly registered Vobject
-    return _registerObject(unregistered);
+    if (unregistered!=null)
+      return _registerObject(unregistered);
+    log.warn("Null Vobject passed to registerObject.");
+    return null;
   }
   /**
    * IClientAppdata instance - if it exists.
@@ -202,15 +316,18 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @return the session's vamsas document
    */
   protected VamsasDocument getVamsasDocument() {
-    // TODO: IMPLEMENT
-    return null;
+    return doc;
   }
   /**
    * returns the read-only IO interface for the vamsas document Jar file
    * @return
    */
   protected VamsasArchiveReader getVamsasArchiveReader() {
-    // TODO: IMPLEMENT getVamsasArchiveReader
+    try {
+      return archive.getOriginalArchiveReader();
+    } catch (Exception e) {
+      log.warn("Unable to create OriginalArchiveReader!", e);
+    }
     return null;
   }
 }
diff --git a/src/org/vamsas/client/simpleclient/SimpleClient.java b/src/org/vamsas/client/simpleclient/SimpleClient.java
index b15a3f5..efaf2ea 100644
--- a/src/org/vamsas/client/simpleclient/SimpleClient.java
+++ b/src/org/vamsas/client/simpleclient/SimpleClient.java
@@ -206,7 +206,7 @@ public class SimpleClient implements IClient {
     }
     VamsasArchive va = null;
     try {
-      // TODO: bail out if it takes too long to get the lock ?
+      // LATER: bail out if it takes too long to get the lock ?
       va = _session.getVamsasDocument();
     }
     catch (IOException e) {
diff --git a/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java b/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java
index 99dc336..52d5890 100644
--- a/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java
+++ b/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java
@@ -148,6 +148,10 @@ public class SimpleClientAppdata implements IClientAppdata {
    */
   private byte[] getAppDataAsByteArray(AppData appdata, VamsasArchiveReader docreader) {
     if (appdata.getData()==null) {
+      if (docreader==null) {
+        log.warn("Silently failing getAppDataAsByteArray with null docreader.",new Exception());
+        return null;
+      }
       // resolve and load data
       JarInputStream entry = getAppDataStream(appdata, docreader); 
       ByteArrayOutputStream bytes = new ByteArrayOutputStream();
@@ -183,7 +187,7 @@ public class SimpleClientAppdata implements IClientAppdata {
    * @return data in object or null if no data is accessible
    */
   private DataInput getAppDataAsDataInputStream(AppData appdata, VamsasArchiveReader docreader) {
-    if (appdata!=null) {
+    if (appdata!=null && docreader!=null) {
       String entryRef = appdata.getDataReference();
       if (entryRef!=null) {
         log.debug("Resolving AppData reference for "+entryRef);