From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 14 Dec 2006 17:52:40 +0000 (+0000)
Subject: refactored org to uk
X-Git-Tag: Release_0.2~250
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fb053ddd3462c204422eac279f20eceae62e1d01;p=vamsas.git

refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@270 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/org/vamsas/client/simpleclient/AppDataInputStream.java b/src/org/vamsas/client/simpleclient/AppDataInputStream.java
deleted file mode 100644
index 0785ed6..0000000
--- a/src/org/vamsas/client/simpleclient/AppDataInputStream.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/**
- * 
- */
-package org.vamsas.client.simpleclient;
-
-import java.io.DataInput;
-import java.io.DataInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.jar.JarInputStream;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * @author jimp
- * LATER: this may not be a necessary or useful class to return from IClientAppdata get*InputStream() methods
- */
-public class AppDataInputStream extends DataInputStream implements DataInput {
-  private Log log = LogFactory.getLog(AppDataInputStream.class);
-  private boolean isOpen = false;
-  /**
-   * Wrapper for writing to/from AppData Entries in a Vamsas Document.
-   */
-  public AppDataInputStream(InputStream inputstream) {
-    super(inputstream);
-    isOpen=true;
-  }
-
-  /* (non-Javadoc)
-   * @see java.io.FilterInputStream#close()
-   */
-  public void close() throws IOException {
-    if (!isOpen) {
-      log.debug("close() called on closed AppDataInputStream.");
-      // throw new IOException("Attempt to close an already closed AppDataInputStream");
-    } else {
-      isOpen=false;
-    }
-  }
-
-  /**
-   * Will return zero if stream has been closed.
-   * @see java.io.FilterInputStream#available()
-   */
-  public int available() throws IOException {
-    if (isOpen)
-      return super.available();
-    else
-      return 0;
-  }
-  
-}
diff --git a/src/org/vamsas/client/simpleclient/AppDataOutputStream.java b/src/org/vamsas/client/simpleclient/AppDataOutputStream.java
deleted file mode 100644
index db13652..0000000
--- a/src/org/vamsas/client/simpleclient/AppDataOutputStream.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/**
- * 
- */
-package org.vamsas.client.simpleclient;
-
-import java.io.DataOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * @author jimp
- *
- */
-public class AppDataOutputStream extends DataOutputStream {
-  private Log log = LogFactory.getLog(AppDataOutputStream.class);
-  private boolean isOpen=true;
-  /**
-   * @param out
-   */
-  public AppDataOutputStream(OutputStream out) {
-    super(out);
-    isOpen=true;
-  }
-  /* (non-Javadoc)
-   * @see java.io.DataOutputStream#flush()
-   */
-  public void flush() throws IOException {
-    if (isOpen)
-      super.flush();
-    else
-      log.warn("flush() called on closed AppDataOutputStream");
-  }
-  /* (non-Javadoc)
-   * @see java.io.DataOutputStream#write(byte[], int, int)
-   */
-  public synchronized void write(byte[] b, int off, int len) throws IOException {
-    if (isOpen) {
-      super.write(b, off, len);
-    } else {
-      log.debug("write(b,off,len) called on closed AppDataOutputStream");
-      throw new IOException("Attempt to write to closed AppDataOutputStream");
-    }
-  }
-  /* (non-Javadoc)
-   * @see java.io.DataOutputStream#write(int)
-   */
-  public synchronized void write(int b) throws IOException {
-    if (isOpen) {
-      super.write(b);
-    } else {
-      log.debug("write(b) called on closed AppDataOutputStream");
-      throw new IOException("Attempt to write to closed AppDataOutputStream");
-    }
-  }
-  /**
-   * Sets an internal flag preventing further write operations 
-   * to the AppData output stream and flushes any pending writes.
-   * @see java.io.FilterOutputStream#close()
-   */
-  public void close() throws IOException {
-    isOpen=false;
-    super.flush();
-    log.debug("AppDataOutputStream was closed.");
-  }
-  /* (non-Javadoc)
-   * @see java.io.FilterOutputStream#write(byte[])
-   */
-  public void write(byte[] b) throws IOException {
-    if (isOpen) {
-      super.write(b);
-    } else {
-      log.debug("write(b[]) called on closed AppDataOutputStream");
-      throw new IOException("Attempt to write to closed AppDataOutputStream");
-    }
-  }
-  /**
-   * @return true if stream is still Open.
-   */
-  public boolean isOpen() {
-    return isOpen;
-  }
-  
-}
diff --git a/src/org/vamsas/client/simpleclient/ArchiveUrn.java b/src/org/vamsas/client/simpleclient/ArchiveUrn.java
deleted file mode 100644
index 304e1f2..0000000
--- a/src/org/vamsas/client/simpleclient/ArchiveUrn.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-import java.net.MalformedURLException;
-
-/**
- * Vamsas Document URN for files understood by ArchiveReader and 
- * written by VamsasArchive.
- * vdoc://{Absolute path to file}
- * @author jimp
- *
- */
-public class ArchiveUrn extends org.vamsas.client.SessionUrn {
-  /**
-   * a simple vamsas document urn prefix
-   */
-  public static String VAMSASDOCUMENT="vdoc";
-  static {
-    TYPES.put(ArchiveUrn.VAMSASDOCUMENT, ArchiveUrn.class);
-  }
-
-  public ArchiveUrn(File docLocation) throws MalformedURLException {
-    super(VAMSASDOCUMENT, docLocation.getAbsoluteFile().toURL());
-  }
-
-  /**
-   * TODO: LATER: think about this again.
-   * @return File(urn.getPath())
-   */
-  public File asFile() {
-    return new File(urn.getPath());
-  }
-  // TODO: add abstract 'handler' methods for resolving the URN to a particular class
-}
diff --git a/src/org/vamsas/client/simpleclient/ClientDocument.java b/src/org/vamsas/client/simpleclient/ClientDocument.java
deleted file mode 100644
index 3b654f8..0000000
--- a/src/org/vamsas/client/simpleclient/ClientDocument.java
+++ /dev/null
@@ -1,510 +0,0 @@
-/*
- *
- */
-package org.vamsas.client.simpleclient;
-
-import java.io.IOException;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.IClientAppdata;
-import org.vamsas.client.IClientDocument;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.VorbaId;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.User;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
-import org.vamsas.objects.utils.AppDataReference;
-import org.vamsas.test.objects.Core;
-
-/**
- * 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);
-  private VamsasDocument doc;
-  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;
-  }
-  private Vector updatedObjects=null;
-  /**
-   *
-   *  prepare Application-side dataset from the vamsas Document archive
-   * @param doc - the dataset
-   * @param docHandler - the sessionFile IO handler
-   * @param Factory - the source of current and new vorbaIds
-   * @param sclient - the simpleclient instance
-   */
-  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 = sclient;
-    archive = docHandler;
-    this.doc = doc;
-    updatedObjects=null;  /// TODO: correct this line
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId)
-   */
-  public Vobject getObject(VorbaId id) {
-    if (vamsasObjects==null) {
-      log.debug("getObject called on null objrefs list.");
-      return null;
-    }
-    if (vamsasObjects.containsKey(id))
-      return (Vobject) vamsasObjects.get(id);
-    log.debug("Returning null Vobject reference for id "+id.getId());
-    return null;
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClientDocument#getObjects(org.vamsas.client.VorbaId[])
-   */
-  public Vobject[] getObjects(VorbaId[] ids) {
-    if (vamsasObjects==null) {
-      log.debug("getObject[]  called on null vamsasObjects list.");
-      return null;
-    }
-    Vobject[] vo = new Vobject[ids.length];
-    for (int i=0,j=ids.length; i<j;i++) 
-      if (vamsasObjects.containsKey(ids[i]))
-        vo[i] = (Vobject) vamsasObjects.get(ids[i]);
-      else
-        log.debug("Returning null Vobject reference for id "+ids[i].getId());
-    return vo;
-  }
-  /**
-   * 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==null) {
-      log.debug("Null document for getVamsasRoots(), returning null");
-      return null;
-    }
-    if (archive==null) {
-      // LATER: decide on read-only status of ClientDocument object
-      log.warn("getVamsasRoots() called on possibly read-only document.");
-    }
-    if (_VamsasRoots!=null)
-      return _VamsasRoots;
-    VAMSAS[] roots = doc.getVAMSAS();
-    if (roots == null) {
-      // Make a new one to return to client to get filled. 
-      _VamsasRoots = new VAMSAS[] { new VAMSAS() };
-      // Do provenance now. just in case.
-      doc.getProvenance().addEntry(sclient.getProvenanceEntry("Created new document root [id="+_VamsasRoots[0].getId()+"]"));
-      doc.addVAMSAS(_VamsasRoots[0]);
-    } 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) {
-    // 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;
-    /**
-     * LATER isValidUpdate : Ideally. we efficiently walk down, comparing hashes, to deal with merging and verifying provenance for objects
-    
-    // extract root objects
-    if (newroots != null) {
-      // check newroots for objects that were present in the old document
-      // check to see if the 'old' objects have been modified
-      // if they have ? we overwrite them with their new version, ensuring that
-      // provenance is updated.
-      // if they haven't ? do nothing ?
-      
-      for (int i = 0, k = newroots.length; i < k; i++) {
-        if (newroots[i].isRegistered()) {
-          // 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 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()) {
-                // Vobject has been modified by another client since this
-                // client's
-                // last access to document.
-              }
-            }
-          } else {
-            throw new Error(
-                "SimpleClient error when using setVamsasRoots : The vorbaId for Vobject "
-                + i
-                + " does not refer to an Vobject of type VAMSAS in the current document!");
-          }
-        } else {
-          if (!newroots[i].is__stored_in_document()) {
-            // check if Vobject is modified
-            if (newroots[i].get__last_hash() != newroots[i].hashCode()) {
-              // it is - so we add newroots[i] as a new Vobject, with updated
-              // provenance.
-            } else {
-              // do nothing
-              newroots[i] = null;
-            }
-          } else {
-            // just add newroots[i] as a new Vobject in the document
-            // - with appropriate provenance.
-          }
-        }
-      }*/
-  }
-  /**
-   * 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()
-   * @see org.vamsas.IClientDocument.setVamsasRoots
-   */
-  public void setVamsasRoots(VAMSAS[] newroots) {
-    if (doc==null) {
-      log.debug("setVamsasRoots called on null document.");
-      return;
-    }
-    VAMSAS[] newr;
-    if (newroots==null) {
-      log.debug("setVamsasRoots(null) - do nothing.");
-      return;
-    }
-    // are we dealing with same array ?
-    if (_VamsasRoots!=newroots) {
-      // merge roots into local version.
-      newr = new VAMSAS[newroots.length];
-      for (int i=0;i<newr.length;i++)
-        newr[i] = newroots[i];
-      newr=_combineRoots(newr,_VamsasRoots,this);
-    } else {
-      newr = new VAMSAS[_VamsasRoots.length];
-      for (int i=0;i<newr.length;i++)
-        newr[i]=_VamsasRoots[i];
-    }
-    //  actually compare with document root set for final combination (to ensure nothing is lost)
-    _VamsasRoots = _combineRoots(newr, doc.getVAMSAS(), this); 
-  }
-  
-  
-  /* (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) {
-    if (doc==null) {
-      log.debug("addVamsasRoots called on null document.");
-      return;
-    }
-    VAMSAS[] newroots = _combineRoots(new VAMSAS[] {newroot}, _VamsasRoots, this);
-    _VamsasRoots = newroots;  
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClientDocument#registerObjects(org.vamsas.client.Vobject[])
-   */
-  public VorbaId[] registerObjects(Vobject[] unregistered) {
-    if (doc==null) {
-      log.warn("registerObjects[] called on null document.");
-      return null;
-    }
-    if (vamsasObjects==null) {
-      log.warn("registerObjects[] called for null vamsasObjects hasharray.");
-      return null;
-    }
-    if (unregistered!=null) {
-      VorbaId ids[] = new VorbaId[unregistered.length];
-      for (int i=0,k=unregistered.length; i<k; i++)
-        if (unregistered[i]!=null) {
-          log.warn("Null Vobject passed to registerObject[] at position "+i);
-          return null;
-        } else {
-          ids[i]=registerObject(unregistered[i]);
-        }
-      log.debug("Registered "+unregistered.length+" objects - total of "+vamsasObjects.size()+" ids.");
-      return ids;
-    }
-    return null;
-  }
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.Vobject)
-   */
-  public VorbaId registerObject(Vobject unregistered) {
-    if (doc==null) {
-      log.warn("registerObjects called on null document.");
-      return null;
-    }
-    if (vamsasObjects==null) {
-      log.warn("registerObjects called for null vamsasObjects hasharray.");
-      return null;
-    }
-    if (unregistered!=null) {
-      VorbaId id = _registerObject(unregistered);
-      log.debug("Registered object - total of "+vamsasObjects.size()+" ids.");
-      return id;
-    }
-    log.warn("Null Vobject passed to registerObject.");
-    return null;
-  }
-  /**
-   * IClientAppdata instance - if it exists.
-   */
-  SimpleClientAppdata scappd = null;
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientDocument#getClientAppdata()
-   */
-  public IClientAppdata getClientAppdata() {
-    if (doc==null) {
-      log.warn("getClientAppdata called on null document.");
-      return null;
-    }
-    if (scappd==null) {
-      log.debug("Creating new SimpleClientAppdata instance for "+sclient.getSessionHandle());
-      scappd = new SimpleClientAppdata(this);
-      if (scappd==null) {
-        // LATER: may not need this as a warning message.
-        log.warn("Null appdata object for "+sclient.getSessionHandle());
-      } else {
-        log.debug("Created SimpleClientAppdata successfully.");
-      }
-    } else {
-      log.debug("Returning existing SimpleClientAppdata reference.");
-    }
-    return scappd;
-  }
-  /**
-   * access the vamsas document
-   * @return the session's vamsas document
-   */
-  protected VamsasDocument getVamsasDocument() {
-    return doc;
-  }
-  /**
-   * returns the read-only IO interface for the vamsas document Jar file
-   * @return
-   */
-  protected VamsasArchiveReader getVamsasArchiveReader() {
-    try {
-      return archive.getOriginalArchiveReader();
-    } catch (Exception e) {
-      log.warn("Unable to create OriginalArchiveReader!", e);
-    }
-    return null;
-  }
-  protected boolean updateSessionDocument() throws java.io.IOException {
-    boolean docupdate = true; // 'non-serious' problems below set this false
-    if (doc==null) {
-      log.warn("updateSessionDocument called on null document.");
-      throw new java.io.IOException("Document is closed.");
-    }
-    if (archive==null) {
-      log.warn("updateSessionDocument called document archive handler.");
-      throw new java.io.IOException("Document is closed.");
-    }
-    
-    if (!isModified() && !scappd.isModified()) {
-      log.debug("Document update not necessary. returning false.");
-      return false;
-    }
-    VamsasSession session = sclient._session;
-    log.debug("updating Session Document in "+session.sessionDir);
-    // update the VamsasDocument structure with any new appData's.
-    // try to update the sessionFile
-    log.debug("Attempting to update session "+sclient.session.getSessionUrn());
-    if (scappd.isModified()) {
-      ClientHandle client = sclient.client;
-      UserHandle user = sclient.user;
-      scappd.closeForWriting();      
-      if (scappd.appsGlobal==null) {
-        log.debug("Creating new appData entry for this application...");
-        // first write for this application - add a new section in document
-        ApplicationData appd = scappd.appsGlobal = new ApplicationData();
-        appd.setName(client.getClientName());
-        // appd.setUrn(client.getClientUrn());
-        appd.setVersion(client.getVersion());
-        doc.addApplicationData(appd);
-        // embed or jarEntry ?  - for now only jarEntry's are dealt with.
-        appd.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()));
-        log.debug("... created.");
-      }
-      if (scappd.newAppData!=null && scappd.newAppData.sessionFile.exists()) {
-        log.debug("Beginning update for new Global Appdata...");
-        // new global appdata to write.
-        if (scappd.appsGlobal.getData()!=null) {
-          scappd.appsGlobal.setData(null);
-          scappd.appsGlobal.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()));
-        }
-        // LATER: use a switch to decide if the data should be written as a reference or as an embedded data chunk
-        scappd.updateAnAppdataEntry(archive, scappd.appsGlobal, scappd.newAppData);
-        log.debug("...Successfully updated Global Appdata Entry.");
-      }
-      if (scappd.newUserData!=null && scappd.newUserData.sessionFile.exists()) {
-        log.debug("Beginning to update Users Appdata entry....");
-        if (scappd.usersData==null) {
-          // create new user appdata
-          scappd.usersData = new User();
-          scappd.usersData.setFullname(user.getFullName());
-          scappd.usersData.setOrganization(user.getOrganization());
-          scappd.appsGlobal.addUser(scappd.usersData);
-        }
-        User appd = scappd.usersData;
-        if (appd.getData()!=null || appd.getDataReference()==null) {
-          // LATER make standard appDataReference constructor for client+user 
-          appd.setData(null);          
-          String safe_username = user.getFullName();
-          int t = safe_username.indexOf(" ");
-          if (t!=-1) {
-            safe_username = safe_username.substring(t);
-          }
-          appd.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()+safe_username));
-        }
-        scappd.updateAnAppdataEntry(archive, scappd.usersData, scappd.newUserData);
-        log.debug("...Successfully updated user AppData entry.");
-      }
-    }
-    log.debug("Updating Document...");
-    // now update the document.
-    try {
-      archive.putVamsasDocument(doc);
-      log.debug("Successfully written document entry.");
-    }
-    catch (Exception e) {
-      log.error("Marshalling error for vamsas document.",e);
-      docupdate = false; // pass on the (probable) object validation error 
-    }
-    if (archive.transferRemainingAppDatas())
-      log.debug("Remaining appdatas were transferred.");
-    else
-      log.debug("No remaining appdatas were transferred. (Correct?)");
-    archive.closeArchive();
-    log.debug("...successully finished and closed.");
-    return docupdate; // no errors ?
-  }
-  /* (non-Javadoc)
-   * @see java.lang.Object#finalize()
-   */
-  protected void finalize() throws Throwable {
-    log.debug("Garbage collecting on ClientDocument instance.");
-    if (scappd!=null) {
-      scappd.finalize();
-      scappd = null;
-    }
-    if (doc!=null) {
-      doc = null;
-    }
-    // disengage from client
-    if (sclient!=null)
-      sclient.cdocument = null;
-    sclient=null;
-    
-    super.finalize();
-  }
-  public Vector getUpdatedObjects() {
-    return updatedObjects;
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/ClientsFile.java b/src/org/vamsas/client/simpleclient/ClientsFile.java
deleted file mode 100644
index 96fa871..0000000
--- a/src/org/vamsas/client/simpleclient/ClientsFile.java
+++ /dev/null
@@ -1,295 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import org.vamsas.client.*;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutput;
-import java.io.ObjectOutputStream;
-import java.io.OutputStream;
-import java.util.Vector;
-
-/**
- * Handler for the clientsFile within a vamsas session thread.
- * @author jim 
- */
-public class ClientsFile extends ListFile {
-  private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog(ClientsFile.class);
-  /**
-   * number of my client in list - passed back when a client 
-   * is added to list, and used (if valid) for quickly 
-   * looking up presence of client handle in the list.
-   */
-  private int syncnum = 1;
-
-  public ClientsFile(File filelist) throws IOException {
-    super(filelist);
-  }
-
-  /**
-   * internal method for getting clientList - ensures a lock has been made but
-   * does not release it.
-   * 
-   * @return list of clients
-   */
-  private ClientHandle[] retrieveClientHandles() {
-    if (lockFile()) {
-      try {
-        ClientHandle[] clients=null;
-        if (fileLock.length()>0) {
-          
-          ObjectInputStream is = new ObjectInputStream(fileLock.getBufferedInputStream(true));
-          Object o;
-          o=is.readObject();
-          if (o!=null) {
-            try {
-              clients = (ClientHandle[]) o;
-            }
-            catch (Exception e) {
-              System.err.println("Garbage in the clientHandle list "+this.sessionFile);
-            }
-          }
-        }
-        return clients;
-      } catch (FileNotFoundException e) {
-        // TODO Auto-generated catch block
-        e.printStackTrace(System.err);
-      } catch (Exception e) {
-        e.printStackTrace(System.err);
-      }
-    }
-    return null;
-  }
-  /**
-   * get the clientList from the file. May return null if lock failed!
-   * @return clientList
-   */
-  public ClientHandle[] retrieveClientList() {
-    if (lockFile()) {
-      ClientHandle[] clients = retrieveClientHandles();
-      unlockFile();
-      return clients;
-    }
-    return null;
-  }
-  /**
-   * get list from the locked ClientList.
-   * @param extantlock
-   * @return clientList or null if lock failed (or file was empty)
-   */
-  public ClientHandle[] retrieveClientList(Lock extantlock) {
-    if (lockFile(extantlock)) {
-      ClientHandle[] clients = retrieveClientHandles();
-      unlockFile();
-      return clients;
-    }
-    return null;
-  }
-  /**
-   * adds clientHandle me to the clientList under an existing lock extantLock.
-   * @param me
-   * @param extantLock
-   * @return client index in list or 0 if lock was invalid or addClient operation failed.
-   */
-  public int addClient(ClientHandle me, Lock extantLock) {
-    return addClient(me, true, extantLock);
-  }
-  
-  /**
-   * adds clientHandle me to the clientList under an existing lock.
-   * @param me - clientHandle
-   * @param disambig - if true then add will fail if an identical clientHandle already exists
-   * @param extantLock - existing lock
-   * @return client index in list or 0 if addClient (or the lock) failed.
-   */
-  
-  public int addClient(ClientHandle me, boolean disambig, Lock extantLock) {
-    if (lockFile(extantLock)) {
-      syncnum = addClient(me, disambig);
-      unlockFile();
-      return syncnum;
-    }
-    return 0;
-  }
-  
-  /**
-   * adds the ClientHandle to the list - if it is not unique, then the
-   * ClientHandle object is modified to make it unique in the list. returns the
-   * clientNumber for the client in the session.
-   * 
-   * @param me
-   * @return
-   */
-
-  public int addClient(ClientHandle me) {
-    syncnum = addClient(me, true);
-    unlockFile();
-    return syncnum;
-  }
-
-  /**
-   * removes 'me' from the session ClientList without complaint if 'me' isn't in the clientList already.
-   * @param me client handle to be removed
-   * @param clientlock existing lock passed from watcher.
-   */
-  public void removeClient(ClientHandle me, Lock clientlock) {
-    int mynum=-1;
-    if (lockFile(clientlock)) {
-      ClientHandle[] clients = retrieveClientHandles();
-      if (clients != null) {
-        if ((syncnum<=0 || syncnum>clients.length) || clients[syncnum-1]!=me) {
-          for (int i = 0, j = clients.length; i < j; i++) 
-            if (clients[i].equals(me)) {
-              mynum=i;
-              break;
-            }
-        } else {
-          mynum=syncnum-1;
-        }
-        if (mynum>-1) {
-          ClientHandle[] newlist = new ClientHandle[clients.length - 1];
-          for (int k=0,i = 0, j = clients.length; i < j; i++)
-            if (i!=mynum)
-              newlist[k++] = clients[i];
-          if (!putClientList(newlist))
-            throw new Error("Failed to write new clientList!"); // failed to put the clientList to disk.
-        }
-      }
-      unlockFile();
-    } else {
-      throw new Error("Couldn't get lock for "+((sessionFile==null) ? "Unitialised sessionFile in ClientsFile" : sessionFile.getAbsolutePath()));
-    }
-  }
-  /**
-   * Adds a ClientHandle to the ClientList file - optionally disambiguating 
-   * the ClientHandle (modifes the URN). 
-   * Note: Caller is left to release the lock on the ClientList.
-   * @param me
-   * @param disambiguate -
-   *          flag indicating if the URN for me should be disambiguated to
-   *          differentiate between sessions.
-   * @return index of clientHandle in new list, or -1-position of existing
-   *         clientHandle (if disambiguate is true)
-   */
-  protected int addClient(ClientHandle me, boolean disambiguate) {
-    int newclient = 0;
-    int tries=5;
-    while (tries-->0 && !lockFile())
-      try { Thread.sleep(1); } catch (Exception e){};
-    if (lockFile()) {
-      ClientHandle[] clients = retrieveClientHandles();
-      if (me.getClientUrn()==null) {
-        // TODO: move this into ClientUrn as a standard form method.
-        me.setClientUrn("vamsas://"+me.getClientName()+":"+me.getVersion()+"/");
-      }
-      if (clients == null) {
-        clients = new ClientHandle[1];
-        clients[0] = me;
-        newclient = 1;
-      } else {
-        int k = 0;
-        for (int i = 0, j = clients.length; i < j; i++) {
-          if (clients[i].equals(me)) {
-            if (disambiguate) {
-              while (clients[i].equals(me)) {
-                me.setClientUrn(me.getClientUrn() + k++); // TODO: make a better
-                                                          // disambiguation of
-                                                          // urn.
-              }
-            } else {
-              // will not write the ambiguous clientHandle to disk, just return
-              // its index.
-              return -1 - i;
-            }
-          }
-        }
-        int i, j;
-        ClientHandle[] newlist = new ClientHandle[clients.length + 1];
-        for (i = 0, j = clients.length; i < j; i++)
-          newlist[i] = clients[i];
-        newlist[j] = me;
-        clients = newlist;
-        newclient = j+1;
-      }
-      if (!putClientList(clients))
-        return 0; // failed to put the clientList to disk.
-    }
-    return newclient;
-  }
-  /**
-   * when set true - get FileNotFoundExceptions on WinXP when writing to locked stream after the backup has been made (via the backupFile method)
-   */
-  boolean backup=false;
-  /**
-   * safely writes clients array to the file referred to by sessionFile.
-   * 
-   * @param clients
-   * @return true if successful write. Throws Errors otherwise.
-   */
-  protected boolean putClientList(ClientHandle[] clients) {
-    if (lockFile()) {
-      File templist=null;
-      if (!backup || (templist = backupSessionFile()) != null) {
-        int retries=3;
-        while (retries-->0) {
-          try {
-            ObjectOutputStream os = 
-              new ObjectOutputStream(fileLock.getBufferedOutputStream(true));
-            log.debug("About to write "+clients.length+" clientHandles to output stream.");
-            os.writeObject(clients);
-            os.close();
-          // All done - remove the backup.
-          if (backup)
-            templist.delete();
-          templist = null;
-          retries=-1;
-          } catch (Exception e) {
-            System.err
-            .println("Serious - problems writing to sessionFile.");
-            if (retries>0 && templist != null) {
-              System.err.println("Recovering from Backup in "
-                      + templist.getAbsolutePath());
-              templist.renameTo(fileLock.target);
-            }
-            e.printStackTrace(System.err);
-          }
-        }
-        if (retries>-2) {
-          System.err
-          .println("Serious - problems writing to sessionFile. Giving Up.");
-          return false;
-        }
-      } else {
-        throw new Error(
-            "Couldn't create backup of the clientList before writing to it!");
-      }
-    } else {
-      throw new Error("Could not lock the clientList: "
-          + ((sessionFile == null) ? "Unitialized ClientsFile"
-              : " failed to get lock on " + sessionFile.getAbsolutePath()));
-    }
-    // successful!
-    return true;
-  }
-
-  public void clearList() {
-    if (lockFile()) {
-      try {
-        FileOutputStream fout = fileLock.getFileOutputStream(true);
-        fout.flush();
-        fout.close();
-      } catch (Exception e) {
-        throw new Error("Problems trying to clear clientlist!",e);
-        
-      }
-    }
-    
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/EventGeneratorThread.java b/src/org/vamsas/client/simpleclient/EventGeneratorThread.java
deleted file mode 100644
index d9aa1db..0000000
--- a/src/org/vamsas/client/simpleclient/EventGeneratorThread.java
+++ /dev/null
@@ -1,277 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-import java.util.Hashtable;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.Events;
-
-/**
- * monitors watcher objects and generates events.
- */
-public class EventGeneratorThread extends Thread implements Runnable {
-  private static Log log = LogFactory.getLog(EventGeneratorThread.class);
-  private SimpleClient client;
-  private Hashtable handlers; // manager object
-  private VamsasSession session;
-
-  /** 
-   * list with all the clientHandles for the session
-   */
-  protected FileWatcher clientfile=null;
-  /**
-   * the session's vamsasDocument
-   */
-  protected FileWatcher vamsasfile=null;
-  /**
-   * written to by client when its app calls storeDocument.
-   */
-  protected FileWatcher storeFile=null;
-  
-  private boolean watch=false;
-  
-  
-  EventGeneratorThread(VamsasSession s, SimpleClient _client, Hashtable eventhandlers) {
-    if (eventhandlers==null || s==null || _client==null)
-      throw new Error("Null arguments to EventGeneratorThread constructor.");
-    handlers = eventhandlers;
-    session = s;
-    client = _client;
-    setName(s.sessionDir.getName());
-    initWatchers();
-  }
-  
-  private void initWatchers() {
-    if (clientfile==null)
-      clientfile = session.getClientWatcher();
-    if (vamsasfile ==null)
-      vamsasfile = session.getDocWatcher();
-    if (storeFile == null)
-      storeFile = session.getStoreWatcher();
-    clientfile.setState();
-    vamsasfile.setState();
-    storeFile.setState();
-  }
-  boolean ownsf = false;
-  /**
-   * scans all watchers and fires changeEvents if necessary
-   * @return number of events generated.
-   */
-  private int checkforEvents() {
-    Lock watchlock;
-    //TODO : leave slog.info messages for the events that occur.
-    int raised=0;
-    // could make this general - but for now keep simple
-    if ((watchlock=storeFile.getChangedState())!=null) {
-      // TODO: define the storeFile semaphore mechanism : file exists - all clients inform their apps, and then the client that wrote the file should delete the file (it should hold the lock to it).
-      if (storeFile.exists) { 
-        PropertyChangeSupport h = (PropertyChangeSupport) handlers.get(Events.DOCUMENT_FINALIZEAPPDATA);
-        if (h!=null) {
-          log.debug("Triggering DOCUMENT_FINALIZEAPPDATA");
-          raised++;
-          h.firePropertyChange(client.getSessionUrn(), null, client);
-          // expect client to 
-          vamsasfile.setState();
-        }
-      }
-    }
-    if ((watchlock=clientfile.getChangedState())!=null) {
-      // see what happened to the clientfile - compare our internal version with the one in the file, or just send the updated list out...?
-      //
-      /**
-       * Generated when a new vamsas client is attached to a session (Handle is
-       * passed) Note: the newly created client does not receive the event.
-       *
-      public static final String CLIENT_CREATION = "org.vamsas.client.events.clientCreateEvent";
-  */ // as the test
-      /**
-       * Generated when a vamsas client leaves a session (Handle is passed to all
-       * others).
-      public static final String CLIENT_FINALIZATION = "org.vamsas.client.events.clientFinalizationEvent";
-       */ // again - as the test.
-          raised++;
-    }
-    if ((watchlock=vamsasfile.getChangedState())!=null) {
-      
-      /**
-       * Generated when a client has finished updating the document. Passes
-       * applicationHandle of client so the updating client can recognise its own
-       * updates.
-      public static final String DOCUMENT_UPDATE = "org.vamsas.client.events.documentUpdateEvent";
-       */
-      // read apphandle from 'lastUpdate' session file.
-      // pass apphandle name to appHandler ?
-      
-    }
-    /**
-     * Generated when a new vamsas document is created (perhaps from some existing
-     * Vamsas data) so an application may do its own data space initialization.
-     * TODO: decide if this is called when an app is connected to a stored
-     * session...
-     public static final String DOCUMENT_CREATE = "org.vamsas.client.events.documentCreateEvent";
-    */
-    // check if this session's appInit flag is set - if not - generate event for this app.
-    // prolly don't need this at the moment - when an app does getDocument it can to the initing then.
-    
-
-    /**
-     * Generated prior to session Shutdown, after the last participating vamsas
-     * client has finalized.
-     *  TODO: decide on purpose of this ?  is this for benefit of multi-session Apps only ?
-    public static final String SESSION_SHUTDOWN = "org.vamsas.client.events.SessionShutdownEvent";
-     */
-
-    /**
-     * Generated for all clients when any client calls IClient.storeDocument() to
-     * allow them to store any updates before an offline copy of the session is
-     * created. Any client that handles this should call the
-     * IClient.getDocument(), update and then IClient.updateDocument in the same
-     * handler thread.
-     * EventName: <Vamsas-session URN>
-     * NewValue: org.vamsas.client.IClient for session.
-     *
-    public static final String DOCUMENT_FINALIZEAPPDATA = "org.vamsas.client.events.DocumentFinalizeAppData";
-*/
-    // watch for finalization semaphore (last finalised sessionFile).
-    
-    /**
-     * Generated by Vorba stub after the penultimate client makes a call to
-     * closeDocument(). Sequence is as follows : 1. All other vamsas clients have
-     * called closeDocument() 2. Final living client monitors closures, and
-     * realises that it is last. 3. Final client generates event to prompt
-     * associated application to inquire if the user wishes to save the document
-     * for future reference.
-     *  * Any call to closeDocument in a thread other than the registered
-     * EventListener will block until the RequestToClose handler has exited.
-     * 
-     */
-    //    public static final String DOCUMENT_REQUESTTOCLOSE = "org.vamas.client.DocumentRequestToCloseEvent";
-
-    return raised;
-  }
-  
-  private void initEvents() {
-    
-  }
-  /**
-   * Events raised by IClient and propagated to others in session
-   */
-  
-  /**
-   * number of milliseconds between any file state check.
-   */
-  long POLL_UNIT = 20;
-  protected void wait(int u) {
-    if (u<=0)
-      u=1;
-    long l = System.currentTimeMillis()+POLL_UNIT*u;
-      while (System.currentTimeMillis()<l)
-        ;
-  }
-    
-  
-  private boolean block_document_updates=false;
-  int STORE_WAIT=5; // how many units before we decide all clients have finalized their appdatas
-  
-  /**
-   * client App requests offline storage of vamsas data. 
-   * Call blocks whilst other apps do any appData finalizing
-   * and then returns (after locking the vamsasDocument in the session)
-   * Note - the calling app may also receive events through the EventGeneratorThread for document updates.
-   * 
-   * @return Lock for session.vamArchive 
-   * @param STORE_WAIT indicates how lock the call will block for when nothing appears to be happening to the session.
-   */
-  protected Lock want_to_store() {
-    log.debug("Setting flag for document_update requests to be ignored");
-    block_document_updates=true;
-    log.debug("Waiting for other apps to do FinalizeApp handling.");
-    try {
-      session.addStoreDocumentRequest(client.getClientHandle(), client.getUserHandle());
-    } catch (Exception e) {
-      log.warn("Whilst writing StoreDocumentRequest for "+client.getClientHandle().getClientUrn()+" "+client.getUserHandle(),
-          e);
-      log.info("trying to continue.");
-    }
-    // LATER: refine this semaphore process 
-    // to make a robust signalling mechanism:
-    // app1 requests, app1..n do something (or don't - they may be dead), 
-    // app1 realises all apps have done their thing, it then continues with synchronized data.
-    // this probably needs two files - a request file, 
-    //  and a response file which is acknowledged by the app1 requestor for each app.
-    //  eventually, no more responses are received for the request, and the app can then only continue with its store.
-    int units = 0;
-    while (units<STORE_WAIT) {
-      wait(1);
-      if (storeFile.hasChanged() || vamsasfile.hasChanged())
-        units=0;
-      else
-        units++;
-    }
-    
-    block_document_updates=false;
-    log.debug("Cleared flag for ignoring document_update requests");
-    // wait around again (until our own watcher has woken up and synchronized).
-    while (units<STORE_WAIT) {
-      wait(1);
-      if (storeFile.hasChanged() || vamsasfile.hasChanged())
-        units=0;
-      else
-        units++;
-    }
-    
-    
-    log.debug("finished waiting.");
-    return session.vamArchive.getLock();
-  }
-  /**
-   * count handlers for a particular vamsas event 
-   * @param event string enumeration from org.vamsas.client.Events
-   * @return -1 for an invalid event, otherwise the number of handlers
-   */
-  protected int countHandlersFor(String event) {
-    if (handlers.containsKey(event)) {
-      PropertyChangeSupport handler = (PropertyChangeSupport) handlers.get(event);
-      PropertyChangeListener[] listeners;
-      if (handler!=null)
-        return ((listeners=handler.getPropertyChangeListeners())==null) 
-        ? -1 : listeners.length;
-    }
-    return -1;
-  }
-  /**
-   * probably don't need any of these below.
-   */
-  /* (non-Javadoc)
-   * @see java.lang.Thread#destroy()
-   */
-  public void destroy() {
-    super.destroy();
-  }
-  /* (non-Javadoc)
-   * @see java.lang.Thread#interrupt()
-   */
-  public void interrupt() {
-    // TODO Auto-generated method stub
-    super.interrupt();
-  }
-  /* (non-Javadoc)
-   * @see java.lang.Thread#isInterrupted()
-   */
-  public boolean isInterrupted() {
-    // TODO Auto-generated method stub
-    return super.isInterrupted();
-  }
-  /* (non-Javadoc)
-   * @see java.lang.Thread#run()
-   */
-  public void run() {
-    // TODO Auto-generated method stub
-    super.run();
-  }
-  
-
-}
diff --git a/src/org/vamsas/client/simpleclient/FileLock.java b/src/org/vamsas/client/simpleclient/FileLock.java
deleted file mode 100644
index a1c0406..0000000
--- a/src/org/vamsas/client/simpleclient/FileLock.java
+++ /dev/null
@@ -1,205 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.nio.channels.FileChannel;
-import java.nio.channels.ReadableByteChannel;
-/**
- * File based Locking mechanism to get around some bizarre limitations of JarEntry seeking.
- * Abstract locks have a target file, to which access is controlled when a lock is held. Native locks on WindowsXP seem to conflict with Jar seek operations, so a file lock creates an advisory lock.
- * Method:
- * A lock file is created, if it doesn't already exist - the naming convention is TargetFile+suffixSeparator+_LockSuffix.
- * A lock is obtained by locking the lock file with a native lock. The NativeLock is used for this.
- * @author JimP
- *
- */
-public class FileLock extends Lock {
-  private File _lock = null;
-  protected static String _LockSuffix="lck";
-  private NativeLock advisory=null;
-  /**
-   * ensure that the _lock file exists
-   * and create a lock
-   */
-  private boolean ensureLockFile(boolean block) {
-    if (_lock==null)
-      return false;
-    if (advisory!=null && advisory.isLocked())
-      return true;
-    try { 
-      advisory=new NativeLock(_lock, block);
-    } catch (Exception e) {
-      log.fatal("Failed to create advisory lock file "+_lock,e);
-      throw new Error("Failed to create advisory lock file "+_lock);          
-    }
-    return advisory.isLocked();
-  }
-  /**
-   * call to clear up a filelock file after its been made
-   *
-   */
-  private void tidy() {
-    if (_lock!=null) { 
-      if ( advisory!=null) 
-        advisory.release(true);
-      advisory.target.deleteOnExit();
-      advisory=null;
-      _lock=null;
-    }
-  }
-  /**
-   * @param lockfile
-   * @param block true means thread blocks until FileLock is obtained.
-   */
-  public FileLock(File lockfile, boolean block) {
-    super(lockfile);
-    // try and get a lock.
-    try {
-      _lock = new File(lockfile.getParentFile(), lockfile.getName()+"."+_LockSuffix);
-      if (!ensureLockFile(block)) {
-        log.debug("Couldn't get lock on "+_lock);
-        tidy();
-        return;
-      }
-      // create target file ready to be written to if necessary.
-      if (!lockfile.exists())
-        if (!lockfile.createNewFile()) {
-          log.warn("Failed to create locked file "+lockfile);
-          return;
-        }
-      //openRaFile();
-    } catch (FileNotFoundException e) {
-      //
-      log.debug("FileLock failed with target="+lockfile+" and lockfile suffix of "+_LockSuffix);
-      //log.error("Error! Couldn't create a lockfile at "
-      //  + lockfile.getAbsolutePath(), e);
-    } catch (IOException e) {
-      log.error("Error! Problems with IO when creating a lock on "
-          + lockfile.getAbsolutePath(),e);
-    }
-  }
-  
-  private boolean openRaFile() throws IOException {
-    if (target==null)
-      return false;
-    if (advisory==null || !advisory.isLocked())
-      return false;
-    if (rafile==null || rafile.getFD()==null || !rafile.getFD().valid()) {
-      rafile=new RandomAccessFile(target,"rw");
-    } else {
-      if (log.isDebugEnabled())
-        log.debug("Reusing existing RandomAccessFile on "+target);
-    }
-    return (rafile.getChannel()!=null) && rafile.getChannel().isOpen();
-  }
-  
-  public boolean isLocked() {
-    if (advisory != null) {
-      if (advisory.isLocked())
-        return true;
-      advisory=null;
-      if (log.isDebugEnabled())
-        log.debug("Lockfile "+_lock+" unexpectedly deleted ?");
-    }
-    return false;
-  }
-  
-  public void release() {
-    release(true);
-  }
-  
-  public void release(boolean closeChannel) {
-    if (!isLocked())
-      return;
-    if (log.isDebugEnabled())
-      log.debug("Releasing advisory lock on "+target);
-    if (closeChannel) {
-      if (rafile!=null) 
-        try {
-          rafile.close();
-        } catch (Exception e) {
-          log.debug("Unexpected exception whilst closing RandomAccessFile on "+target, e);
-        }
-        rafile=null; 
-    }
-    tidy();
-  }
-  
-  public FileInputStream getFileInputStream(boolean atStart) throws IOException {
-    if (!isLocked()) {
-      log.debug("Don't hold lock on "+target+" to get locked FileInputStream.");
-      return null;
-    }
-    openRaFile();
-    if (atStart)
-      rafile.seek(0);
-    return new FileInputStream(rafile.getFD());
-  }
-  
-  
-  public FileOutputStream getFileOutputStream(boolean clear) throws IOException {
-    if (!isLocked()) {
-      log.debug("Don't hold lock on "+target+" to get locked FileOutputStream.");
-      return null;
-    }
-    openRaFile();
-    if (clear) {
-      rafile.seek(0);
-      rafile.setLength(0);
-    } else
-      rafile.seek(rafile.length());
-    return new LockedFileOutputStream(rafile.getFD());
-  }
-  
-  
-  public BufferedOutputStream getBufferedOutputStream(boolean clear) throws IOException {
-    log.debug("Getting BufferedOutputStream (clear="+clear+")");
-    FileOutputStream fos = getFileOutputStream(clear);
-    if (fos!=null)
-      return new BufferedOutputStream(fos);
-    return null;
-  }
-  
-  /* (non-Javadoc)
-   * @see org.vamsas.client.simpleclient.Lock#getLength()
-   */
-  public long length() {
-    if (isLocked()) {
-      if (!target.exists()) {
-        try {
-          target.createNewFile();
-        } catch (Exception e) {
-          log.error("Invalid lock:Failed to create target file "+target);
-          tidy();
-          return -1;
-        }
-        return 0;
-      }
-      return target.length();
-    }
-    return -1;
-  }
-  protected void finalize() throws Throwable {
-    release(true); // we explicitly lose the lock here.
-    super.finalize();
-  }
-  public RandomAccessFile getRaFile() throws IOException {
-    if (isLocked() && openRaFile()) {
-      return rafile;
-    }
-    log.debug("Failed to getRaFile on target "+target);
-    return null;
-  }
-  public FileChannel getRaChannel() throws IOException {
-    if (isLocked() && openRaFile()) {
-      return rafile.getChannel();
-    }
-    log.debug("Failed to getRaChannel on target "+target);
-    return null;
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/FileWatcher.java b/src/org/vamsas/client/simpleclient/FileWatcher.java
deleted file mode 100644
index fe72381..0000000
--- a/src/org/vamsas/client/simpleclient/FileWatcher.java
+++ /dev/null
@@ -1,168 +0,0 @@
-/**
- * 
- */
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-
-
-/**
- * Watches a particular file for its creation, deletion, or
- * modification. The watcher is thread safe and different 
- * instances watching the state of a particular file carry
- * their own state record for the file.
- */
-public class FileWatcher {
-
-  private File subject = null;
-
-  private long lastStat[];
-  boolean waslocked=false;
-  boolean exists = false;
-  /**
-   * transient lock on subject - can be passed back to calling class
-   * to preserve new state of file for immediate reading.
-   */
-  private Lock subjectLock = null;
-  /**
-   * clear local locks on subject.
-   *
-   */
-  private void clearLock() {
-    if (subjectLock!=null)
-      subjectLock.release();
-    subjectLock=null;
-  }
-  /**
-   *  
-   * @return true if subject exists and is locked by another process.
-   */
-  private boolean checkLock() {
-    if (subject!=null && subject.exists()) {
-      if (subjectLock!=null) {
-        subjectLock.release();
-      }
-      subjectLock = LockFactory.tryLock(subject);
-      if (subjectLock.isLocked()) {
-        return false;
-      }
-      clearLock();
-      return true;
-    }
-    return false;
-  }
-  
-  private long[] getStat(File subject) {
-    return new long[] { subject.lastModified(), subject.length() };
-  }
-  private boolean compStat(long[] stat, long[] newstat) {
-    if (stat[0]!=newstat[0] || stat[1]!=newstat[1])
-      return false;
-    return true;
-  }
-  /**
-   * Detect changes in file state and release of any
-   * lock in place during change.
-   * @return true if file state has changed. Leaves lock in subjectLock (ready to be passed to caller)
-   */
-  private boolean check() {
-    if (subject != null) {
-      if (!subject.exists()) {
-        if (exists) {
-          if (!waslocked) {
-            // !checkLock()) {
-          
-            exists = false;
-            // waslocked=false;
-            return true;
-          }
-        }
-        // locked - state change registered after lock is released
-        return false;
-      } else {
-        long[] newStat = getStat(subject); // subject.lastModified();
-        if (!checkLock()) {
-          // file is free to access, return state change
-          if (!exists || !compStat(lastStat, newStat)) {
-            waslocked=false;
-            exists=true;
-            lastStat=newStat;
-            return true;
-          }
-          // no change
-          return false;
-        } else {
-          waslocked=true;
-          return false;
-        }
-      }
-    }
-    return false;
-  }
-  /**
-   * updates internal record of file state when caller has intentionally
-   * modified subject. (ignores locked-state of subject)
-   */
-  public void setState() {
-    if (subject!=null) {
-      if (exists = subject.exists()) {
-        lastStat = getStat(subject);
-        waslocked = false;
-      }
-    }
-  }
-  
-  /**
-   * Make a watcher for a particular file. If the file doesn't exist, the
-   * watcher will watch for its creation (and indicate a change of state) 
-   * For locked files, the removal of a lock constitutes a change of 
-   * state if the file was modified.
-   * 
-   * @param subject
-   */
-  
-  public FileWatcher(File subject) {
-    this.subject = subject;
-    setState();
-  }
-  /**
-   * Test for change in file state. Only indicates a change 
-   * after any lock on a file has been released.
-   * @return true if file has been modified.
-   */
-  public boolean hasChanged() {
-    boolean res = check();
-    clearLock();
-    return res;
-  }
-  /**
-   * passes lock back to caller if hasChanged returned true.
-   * @return
-   */
-  public Lock getChangedState() {
-    boolean res = check();
-    if (res)
-      return subjectLock;
-    else {
-      clearLock();
-      return null;
-    }
-  }
-  /**
-   * safely? getting current state of the watched file
-   * @return
-   */
-  public long[] getCurrentState() {
-    return getStat(subject);
-  }
-  /**
-   * safely compare an externally recorded state with the current state
-   * for significant modifications.
-   * @param a
-   * @param b
-   * @return
-   */
-  public boolean diffState(long[] a, long[] b) {
-    return compStat(a,b);
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/IdFactory.java b/src/org/vamsas/client/simpleclient/IdFactory.java
deleted file mode 100644
index 81581be..0000000
--- a/src/org/vamsas/client/simpleclient/IdFactory.java
+++ /dev/null
@@ -1,159 +0,0 @@
-/**
- * 
- */
-package org.vamsas.client.simpleclient;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.SessionHandle;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.VorbaId;
-import org.vamsas.client.VorbaIdFactory;
-import org.vamsas.client.Vobject;
-import org.vamsas.objects.utils.document.VersionEntries;
-
-import java.util.Hashtable;
-import java.util.zip.CRC32;
-/**
- * Simplest VorbaId constructor
- * @author jimp
- *
- */
-public class IdFactory extends VorbaIdFactory {
-  static Log log = LogFactory.getLog(IdFactory.class);
-  private SessionHandle session=null;
-  private ClientHandle client;
-  private UserHandle user;
-  private CRC32 unique=new CRC32(); // used to attempt a unique but predictable stream for IDs
-  private String idstring;
-  int sequence=1; // incrementing value for next new ID
-  /**
-   * 
-   */
-  public IdFactory() {
-    super();
-    // TODO Auto-generated constructor stub
-  }
-  
-  /**
-   * @param session
-   * @param client
-   * @param user
-   */
-  protected IdFactory(SessionHandle session, ClientHandle client, UserHandle user) {
-    super();
-    this.session = session;
-    this.client = client;
-    this.user = user;
-    unique.reset();
-    unique.update(new Object[] { session, client, user}.toString().getBytes());
-    // TODO: Ensure format of URNs and use standard composition methods.
-    idstring = client.getClientName()+":"+unique.getValue()+".";
-    extantids=new Hashtable();
-    this.extanthashv=new Hashtable();
-  }
-  /**
-   * values for keys in this hash can be used to reference the org.vamsas.client.Vobject instance for the VorbaId string.
-   * @return the hash of all VorbaIds
-   */
-  protected Hashtable getVorbaIdHash() {
-    return extantids;
-  }
-  /**
-   * values for keys in this hash are Vobjhash objects created for each Vobj with a VorbaId
-   * after this factory has been used to write a vamsas archive.
-   * @return the hash of all VorbaIds and their hash values.
-   */
-  protected Hashtable getVobjhashVals() {
-    return extanthashv;
-  }
-  /* (non-Javadoc)
-   * @see org.vamsas.client.VorbaIdFactory#makeVorbaId()
-   */
-  public VorbaId makeVorbaId(Vobject vobject) {
-    if (session==null)
-      throw new Error("makeVorbaId called on improperly initialised IdFactory Vobject!");
-    if (!vobject.isRegisterable())
-      throw new Error("makeVorbaId called on unregisterable object.");
-    if (vobject.isRegistered())
-      throw new Error("makeVorbaId called on already registered object.");
-    String newidstring;
-    do {
-      if (sequence>0) {
-        sequence++;
-      } else {
-        idstring+="1/";
-        sequence=1;
-      }
-      newidstring=idstring+Integer.toString(sequence);
-    } while (extantids.containsKey(newidstring));
-    extantids.put(newidstring, vobject); // hash the Vobject by its new Id
-    VorbaId id = newId(newidstring); // VorbaId.hash()==newidstring.hash() so we can still recover vobject
-    return id;
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.VorbaIdFactory#setSession(org.vamsas.client.SessionHandle)
-   */
-  protected void setSession(SessionHandle sessionhandle) {
-    if (sessionhandle!=null)
-      session=sessionhandle;
-    else
-      log.warn("setSession(null) called.");
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.VorbaIdFactory#getSessionHandle()
-   */
-  public SessionHandle getSessionHandle() {
-    return session;
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.VorbaIdFactory#setClient(org.vamsas.client.ClientHandle)
-   */
-  protected void setClient(ClientHandle appHandle) {
-    if (appHandle!=null)
-      client = appHandle;
-    else
-      log.warn("setClient(null) called.");
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.VorbaIdFactory#getClientHandle()
-   */
-  public ClientHandle getClientHandle() {
-    return client;
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.VorbaIdFactory#setUser(org.vamsas.client.UserHandle)
-   */
-  protected void setUser(UserHandle userHandle) {
-  if (userHandle!=null)
-    user = userHandle;
-  else
-    log.warn("setUser(null) called.");
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.VorbaIdFactory#getUserHandle()
-   */
-  public UserHandle getUserHandle() {
-    return user;
-  }
-  /**
-   * Convenience method used for default behaviour in testing 
-   * and any anonymous internal vamsasDocument unmarshalling
-   * @param clientname
-   * @return
-   */
-  protected  static IdFactory getDummyFactory(String clientname) {
-    if (clientname==null)
-      clientname="org.vamsas.client.simpleclient.IdFactory";
-    return new IdFactory(new SessionHandle("dummy.session"), 
-        new ClientHandle(clientname,VersionEntries.latestVersion()), 
-        new UserHandle(clientname, "Arnold User's Inc."));
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/ListFile.java b/src/org/vamsas/client/simpleclient/ListFile.java
deleted file mode 100644
index 30956e9..0000000
--- a/src/org/vamsas/client/simpleclient/ListFile.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/**
- * 
- */
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-
-
-/**
- * base class for generic list storage and retrieval operations from a locked IO file
- *  TODO: LATER: generalize for all list storage and retrieval operations 
- *  (pull-up from ClientsFile object)
- */
-public class ListFile extends SessionFile {
-
-  /**
-   * @param file
-   */
-  public ListFile(File file) throws java.io.IOException {
-    super(file);
-    if (!this.sessionFile.exists())
-      this.sessionFile.createNewFile();
-  }
-
-}
diff --git a/src/org/vamsas/client/simpleclient/Lock.java b/src/org/vamsas/client/simpleclient/Lock.java
deleted file mode 100644
index d3a5889..0000000
--- a/src/org/vamsas/client/simpleclient/Lock.java
+++ /dev/null
@@ -1,96 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.RandomAccessFile;
-import java.nio.channels.ByteChannel;
-import java.nio.channels.FileChannel;
-import java.nio.channels.ReadableByteChannel;
-
-import org.apache.commons.logging.LogFactory;
-
-/**
- * transient object representing a file lock
- * This lock should hold for all processes interacting in a session.
- * @author jimp
- */
-
-public abstract class Lock {
-  protected org.apache.commons.logging.Log log = LogFactory.getLog(Lock.class);
-  File target = null; // The file that is being locked
-  protected RandomAccessFile rafile=null;
-  
-  /**
-   * creates a valid Lock (test with <method>isLocked</method>)
-   * if a lock could be obtained for <param>lockfile</param>
-   * @param lockfile
-   */
-  protected Lock(java.io.File lockfile) {
-    target = lockfile;
-  }
-  /**
-   * 
-   * @return true if lock is held on the target
-   */
-  public abstract boolean isLocked();
-  /**
-   * release lock and close all managed channels to file
-   *
-   */
-  public abstract void release();
-  /**
-   * optionally close the open random access channel on the file when releasing lock
-   * @param closeChannel
-   */
-  public abstract void release(boolean closeChannel);
-
-  /**
-   * gets Locked Stream for reading from
-   * @param atStart true to start reading at beginning of file.
-   * @return null if file not locked
-   * @throws IOException
-   */
-  public abstract FileInputStream getFileInputStream(boolean atStart) throws IOException;
-
-  /**
-   * gets Locked stream to write to
-   * FileInput always starts at the *end* of the file (after any truncation)
-   * @param clear true means file will be cleared to zero length
-   * @return null if file is not locked
-   * @throws IOException
-   */
-  public abstract FileOutputStream getFileOutputStream(boolean clear) throws IOException;
-  /**
-   * return buffered output stream to locked file.
-   * @param clear - true means file is truncated to 0 length before writing 
-   * @return
-   */
-  public abstract BufferedOutputStream getBufferedOutputStream(boolean clear) throws IOException;
-  
-  protected void finalize() throws Throwable {
-    target=null;
-  }
-  /**
-   * return buffered input stream for locked file.
-   * @param atStart - true means read from begining of file
-   * @return null if file is not locked.
-   */
-  public BufferedInputStream getBufferedInputStream(boolean atStart) throws IOException {
-    FileInputStream fis = getFileInputStream(atStart);
-    if (fis!=null)
-      return new BufferedInputStream(fis);
-    return null;
-  }
-  /**
-   * safe lock target length() function.
-   * @return -1 for non-lockable target, otherwise target's file length 
-   */
-  public abstract long length();
-  public abstract RandomAccessFile getRaFile() throws IOException;
-  public abstract FileChannel getRaChannel() throws IOException;
-}
diff --git a/src/org/vamsas/client/simpleclient/LockFactory.java b/src/org/vamsas/client/simpleclient/LockFactory.java
deleted file mode 100644
index 5fdde6c..0000000
--- a/src/org/vamsas/client/simpleclient/LockFactory.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-public class LockFactory {
-  protected static Log log = LogFactory.getLog(LockFactory.class);
-  public static int locktype=0; // use file lock by default
-  public static String[] locktypes = {"file","native"};
-  {
-    String lockt = System.getProperty("vamsas.locktype");
-    if (lockt!=null) {
-      int i,j;
-      for (i=0, j=locktypes.length; i<j && locktypes[i].equalsIgnoreCase(lockt); i++)
-        ;
-      if (i>=j) {
-        String lt = "'"+locktypes[0]+"'";
-        for (i=1; i<j; i++)
-          lt += ",'"+locktypes[i]+"'";
-        log.warn("System property vamsas.locktype takes one of "+lt);
-        log.warn("Defaulting to Locktype of "+locktypes[locktype]);
-      }
-    } else
-      log.debug("Defaulting to Locktype of "+locktypes[locktype]);
-  }
-  /**
-   * lock target (blocks until lock is obtained)
-   * @param target
-   * @return lock
-   */
-  public static Lock getLock(java.io.File target) {
-    return getLock(target, true);
-  }
-  public static Lock getLock(java.io.File target, boolean block) { 
-    if (locktype==0)
-      return new FileLock(target, block);
-    if (locktype==1)
-      return new NativeLock(target, block);
-    log.fatal("Implementation Error! No valid Locktype value");
-    return null;
-  }
-  /**
-   * try to lock target 
-   * @param target
-   * @return null if lock was not possible
-   */
-  public static Lock tryLock(File target) {
-    return getLock(target, false);
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/LockTimeoutException.java b/src/org/vamsas/client/simpleclient/LockTimeoutException.java
deleted file mode 100644
index 8dc1317..0000000
--- a/src/org/vamsas/client/simpleclient/LockTimeoutException.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/**
- * 
- */
-package org.vamsas.client.simpleclient;
-
-/**
- * @author jimp
- *
- */
-public class LockTimeoutException extends Exception {
-  static final long serialVersionUID=1;
-  static final String defaultMessage = "Timeout whilst waiting for lock on VamsasDocument";
-  public LockTimeoutException() {
-    super(defaultMessage);
-  }
-  public LockTimeoutException(String arg0, Throwable arg1) {
-    super(arg0+" (timeout whilst waiting for lock)", arg1);
-    // TODO Auto-generated constructor stub
-  }
-  public LockTimeoutException(String arg0) {
-    super(arg0+" (timeout whilst waiting for lock)");
-    // TODO Auto-generated constructor stub
-  }
-  public LockTimeoutException(Throwable arg0) {
-    super(defaultMessage, arg0);
-    // TODO Auto-generated constructor stub
-  }
-  
-}
diff --git a/src/org/vamsas/client/simpleclient/LockedFileOutputStream.java b/src/org/vamsas/client/simpleclient/LockedFileOutputStream.java
deleted file mode 100644
index 1d59c8a..0000000
--- a/src/org/vamsas/client/simpleclient/LockedFileOutputStream.java
+++ /dev/null
@@ -1,159 +0,0 @@
-/**
- * 
- */
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-import java.io.FileDescriptor;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.nio.channels.FileChannel;
-
-import org.apache.commons.logging.LogFactory;
-
-/**
- * @author Jim
- *
- */
-public class LockedFileOutputStream extends FileOutputStream {
-  private static org.apache.commons.logging.Log log = LogFactory.getLog(LockedFileOutputStream.class);
-  //FileOutputStream ostream=null;
-  boolean closed=true;
-  private void init() {
-    FileChannel ch = super.getChannel();
-    if (ch!=null) {
-      try { closed = !ch.isOpen();
-      } catch (Exception e) {
-        closed=true;
-        log.debug("Invalid LockedOutputStream marked closed.",e);
-      }
-    }
-  }
-  /**
-   * @param file
-   * @throws FileNotFoundException
-   */
-  public LockedFileOutputStream(File file) throws FileNotFoundException {
-    super(file); // super(file);
-    init();
-  }
-
-  /**
-   * @param file
-   * @param append
-   * @throws FileNotFoundException
-   */
-  public LockedFileOutputStream(File file, boolean append)
-      throws FileNotFoundException {
-    super(file, append);
-    init();
-  }
-
-  /**
-   * @param fdObj
-   */
-  public LockedFileOutputStream(FileDescriptor fdObj) {
-    super(fdObj);
-    init();
-    if (fdObj.valid())
-      closed=false;
-  }
-
-  /**
-   * @param name
-   * @throws FileNotFoundException
-   */
-  public LockedFileOutputStream(String name) throws FileNotFoundException {
-    super(name);
-    init();
-  }
-
-  /**
-   * @param name
-   * @param append
-   * @throws FileNotFoundException
-   */
-  public LockedFileOutputStream(String name, boolean append)
-      throws FileNotFoundException {
-    super(name, append);
-    init();
-  }
-  /**
-   * closes - actually just flushes the stream instead.
-   */
-  public void close() throws IOException {
-    if (!closed) {
-      super.flush();
-      super.getChannel().force(true);
-      log.debug("Marking Lockedoutputstream closed.");
-    } else
-      throw new IOException("Close on already closed FileOutputStream.");
-    closed=true;
-  }
-
-
-  /**
-   * @throws IOException
-   * @see java.io.OutputStream#flush()
-   */
-  public void flush() throws IOException {
-    if (!closed)
-      super.flush();
-    else
-      throw new IOException("flush on closed FileOutputStream");
-  }
-
-  /**
-   * @return
-   * @see java.io.FileOutputStream#getChannel()
-   */
-  public FileChannel getChannel() {
-    if (!closed)
-      return super.getChannel();
-    else
-      return null;
-  }
-
-
-
-  /**
-   * @param b
-   * @param off
-   * @param len
-   * @throws IOException
-   * @see java.io.FileOutputStream#write(byte[], int, int)
-   */
-  public void write(byte[] b, int off, int len) throws IOException {
-    if (!closed)
-      super.write(b, off, len);
-    else
-      throw new IOException("write on Closed FileOutputStream");
-  }
-
-  /**
-   * @param b
-   * @throws IOException
-   * @see java.io.FileOutputStream#write(byte[])
-   */
-  public void write(byte[] b) throws IOException {
-    if (!closed)
-      super.write(b);
-    else
-      throw new IOException("write on Closed FileOutputStream");
-  }
-
-  /**
-   * @param b
-   * @throws IOException
-   * @see java.io.FileOutputStream#write(int)
-   */
-  public void write(int b) throws IOException {
-    if (!closed)
-      super.write(b);
-    else
-      throw new IOException("write on Closed FileOutputStream");
-  }
-  
-}
diff --git a/src/org/vamsas/client/simpleclient/NativeLock.java b/src/org/vamsas/client/simpleclient/NativeLock.java
deleted file mode 100644
index 6a624f1..0000000
--- a/src/org/vamsas/client/simpleclient/NativeLock.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.RandomAccessFile;
-import java.nio.channels.FileChannel;
-import java.nio.channels.FileLock;
-import java.nio.channels.ReadableByteChannel;
-
-/**
- * @author JimP
- *
- */
-public class NativeLock extends Lock {
-
-  protected FileLock lock = null;
-
-  /**
-   * @param lockfile
-   * @param block true means thread will block until a lock is obtained.
-   */
-  public NativeLock(File lockfile, boolean block) {
-    super(lockfile);
-    // try and get a lock.
-    lock = null;
-    
-    try {
-      if (!lockfile.exists())
-        if (!lockfile.createNewFile()) {
-          log.warn("Failed to create locked file "+lockfile);
-          return;
-        }
-      
-      rafile=new RandomAccessFile(lockfile,"rw");
-      if (block)
-        lock = rafile.getChannel().lock();
-      else
-        lock = rafile.getChannel().tryLock();
-      if (lock==null || !lock.isValid()) {
-        // failed to get lock. Close the file channel
-        log.debug("failed to get lock for "+lockfile);
-        rafile.getChannel().close();
-        lock=null;
-      }
-    } catch (FileNotFoundException e) {
-      //
-      log.debug("Lock failed - normal behaviour for windows locking.");
-      //log.error("Error! Couldn't create a lockfile at "
-      //  + lockfile.getAbsolutePath(), e);
-    } catch (IOException e) {
-      log.error("Error! Problems with IO when creating a lock on "
-          + lockfile.getAbsolutePath(),e);
-    }
-  }
-
-  public boolean isLocked() {
-    if (lock != null && lock.isValid()) {
-      return true;
-    }
-    return false;
-  }
-
-  public void release() {
-    release(true);
-  }
-
-  public void release(boolean closeChannel) {
-    try {
-      // channel.close should be called before release() for rigourous locking.
-      if (rafile!=null && rafile.getFD().valid() && rafile.getChannel()!=null && lock.isValid()) {
-        if (closeChannel && rafile.getChannel().isOpen()) {
-            rafile.close();
-            rafile=null; 
-        }
-        if (lock!=null && lock.isValid())
-          lock.release();
-        
-      }
-    } catch (IOException e) {
-      log.warn("Whilst releasing lock",e);
-    }
-    lock=null;
-  }
-
-  /**
-   * gets Locked Stream for reading from
-   * @param atStart true to start reading at beginning of file.
-   * @return null if file not locked
-   * @throws IOException
-   */
-  public FileInputStream getFileInputStream(boolean atStart) throws IOException {
-    if (!isLocked())
-      return null;
-    if (atStart)
-      rafile.seek(0);
-    return new FileInputStream(rafile.getFD());
-  }
-
-  /**
-   * gets Locked stream to write to
-   * FileInput always starts at the *end* of the file (after any truncation)
-   * @param clear true means file will be cleared to zero length
-   * @return null if file is not locked
-   * @throws IOException
-   */
-  public FileOutputStream getFileOutputStream(boolean clear) throws IOException {
-    if (!isLocked())
-      return null;
-    if (clear) {
-      rafile.seek(0);
-      rafile.setLength(0);
-    } else
-      rafile.seek(rafile.length());
-    return new LockedFileOutputStream(rafile.getFD());
-  }
-
-  /**
-   * return buffered output stream to locked file.
-   * @param clear - true means file is truncated to 0 length before writing 
-   * @return
-   */
-  public BufferedOutputStream getBufferedOutputStream(boolean clear) throws IOException {
-    OutputStream fos = getFileOutputStream(clear);
-    if (fos!=null)
-      return new BufferedOutputStream(fos);
-    return null;
-  }
-  /**
-   * @see org.vamsas.client.simpleclient.Lock#finalize()
-   */
-  protected void finalize() throws Throwable {
-    release(true); // we explicitly lose the lock here.
-    // log.debug("lock closing through garbage collection ?");
-    super.finalize();
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.simpleclient.Lock#getLength()
-   */
-  public long length() {
-    if (isLocked()){
-      try {
-        return rafile.length();
-      } catch (Exception e) {
-        log.debug("getLength exception:",e);
-      }
-    }
-    return -1;
-  }
-
-  public RandomAccessFile getRaFile() throws IOException {
-    if (isLocked())
-      return rafile;
-    else
-      log.debug("Failed to getRaFile on "+target);
-    return null;
-  }  
-  
-  public FileChannel getRaChannel() throws IOException {
-    if (isLocked())
-      return rafile.getChannel();
-    else
-      log.debug("Failed to getRaChannel on "+target);
-    return null;
-  }
-
-}
diff --git a/src/org/vamsas/client/simpleclient/SessionFile.java b/src/org/vamsas/client/simpleclient/SessionFile.java
deleted file mode 100644
index c9f9e67..0000000
--- a/src/org/vamsas/client/simpleclient/SessionFile.java
+++ /dev/null
@@ -1,215 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.nio.channels.ReadableByteChannel;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * Basic methods for classes handling locked IO on files 
- * monitored by all (simpleclient) clients in a vamsas session.
- * @author jimp
- *TODO: support non nio file locking capable systems
- */
-public class SessionFile {
-  private static Log log = LogFactory.getLog(SessionFile.class);
-  protected File sessionFile;
-  protected Lock fileLock = null;
-
-  protected SessionFile(File file) {
-    super();
-    sessionFile = file;
-  }
-
-  protected boolean lockFile(Lock extantlock) {
-    if (fileLock!=null && !fileLock.isLocked()) {
-      fileLock.release();// tidy up invalid lock
-      fileLock=null;
-    }
-    if (extantlock!=null && extantlock.isLocked())
-      fileLock=extantlock; // THIS IS BROKEN - lockFile then nulls the lock.
-    return lockFile();
-  }
-  private boolean ensureSessionFile() {
-    if (sessionFile != null) {
-      if (!sessionFile.exists()) {
-        // create new file
-        try {
-          if (!sessionFile.createNewFile()) {
-            log.error("Failed to create file prior to locking: "+sessionFile);
-            return false;
-          }
-        } catch (IOException e) {
-          log.error("Exception when trying to create file "+sessionFile, e);
-          return false;
-        }
-      }
-      return true;
-    }
-    log.error("ensureSessionFile called for non-initialised SessionFile!");
-    return false;
-  }
-  /**
-   * Get a lock for the SessionFile
-   * 
-   * @return true if lock was made
-   */
-  protected boolean lockFile() {
-    if (fileLock != null) {
-      if (fileLock.isLocked()) {
-        if (!ensureSessionFile())
-          return false;
-        return true;
-      } else {
-        // lock failed for some reason.
-        fileLock.release();
-        log.info("Unexpected session file lock failure. Trying to get it again.");
-        fileLock=null;
-      }
-    }
-    if (!ensureSessionFile())
-      return false;
-    // TODO: see if we need to loop-wait for locks or they just block until
-    // lock is made...
-    long tries=5000;
-    do {
-      tries--;
-      if (fileLock==null || !fileLock.isLocked()) {
-        //try { Thread.sleep(1); } catch (Exception e) {};
-        fileLock = LockFactory.getLock(sessionFile,true); // TODO: wait around if we can't get the lock.
-          }
-      } while (tries>0 && !fileLock.isLocked());
-    if (!fileLock.isLocked())
-      log.error("Failed to get lock for "+sessionFile);
-    // fileLock = new Lock(sessionFile);
-    return fileLock.isLocked();    
-  }
-
-  /**
-   * Explicitly release the SessionFile's lock.
-   * 
-   * @return true if lock was released.
-   */
-  protected void unlockFile() {
-    if (fileLock != null) {
-      fileLock.release();    
-      fileLock = null;
-    }
-  }
-
-  /**
-   * Makes a backup of the sessionFile.
-   * @return Backed up SessionFile or null if failed to make backup.
-   */
-  protected File backupSessionFile() {
-    return backupSessionFile(null, sessionFile.getName(),".old", sessionFile.getParentFile());
-  }
-
-  protected File backupSessionFile(Lock extantLock, String backupPrefix, String backupSuffix, File backupDir) {
-    File tempfile=null;
-    if (lockFile(extantLock)) {
-      try {
-        tempfile = File.createTempFile(backupPrefix, backupSuffix, backupDir);
-        if (fileLock.length()>0) {
-          FileOutputStream tos = new FileOutputStream(tempfile);
-          ReadableByteChannel channel;
-          tos.getChannel().transferFrom(channel=fileLock.getRaChannel(), 0,
-              fileLock.length());
-          tos.close();
-          if (!channel.isOpen())
-            throw new Error(tos.getChannel().getClass()+".transferFrom closes source channel!");
-          if (!lockFile(extantLock))
-            throw new Error("Lost lock for "+sessionFile.getName()+" after backup.");
-          
-        }
-      } catch (FileNotFoundException e1) {
-        log.warn("Can't create temp file for "+sessionFile.getName(),e1);
-        tempfile=null;
-      } catch (IOException e1) {
-        log.warn("Error when copying content to temp file for "+sessionFile.getName(),e1);
-        tempfile=null;
-      }
-    }
-    return tempfile;
-  }
-  /**
-   * Replaces data in sessionFile with data from file handled by another sessionFile
-   * passes up any exceptions.
-   * @param newData source for new data
-   */
-  protected void updateFrom(Lock extantLock, SessionFile newData) throws IOException {
-    log.debug("Updating "+sessionFile.getAbsolutePath()+" from "+newData.sessionFile.getAbsolutePath());
-    if (newData==null)
-      throw new IOException("Null newData object.");
-    if (newData.sessionFile==null)
-      throw new IOException("Null SessionFile in newData.");
-      
-    if (!lockFile(extantLock))
-      throw new IOException("Failed to get write lock for "+sessionFile);
-    if (!newData.lockFile())
-      throw new IOException("Failed to get lock for updateFrom "+newData.sessionFile);
-    RandomAccessFile nrafile = newData.fileLock.getRaFile();
-    nrafile.seek(0);
-    RandomAccessFile trafile = fileLock.getRaFile();
-    /*long tries=5000;
-    while (trafile==null && --tries>0) {
-      log.debug("Lost lock on "+sessionFile+"! Re-trying for a transfer.");
-      lockFile();
-      trafile = fileLock.getRaFile();
-    }*/
-    trafile.seek(0);
-    trafile.getChannel().transferFrom(nrafile.getChannel(), 0, 
-        nrafile.length());
-  }
-  /**
-   * remove all trace of the sessionFile file
-   *
-   */
-  protected void eraseExistence() {
-    unlockFile();
-    if (sessionFile!=null) {
-      sessionFile.delete();
-      sessionFile = null;
-    }
-  }
-  /* (non-Javadoc)
-   * @see org.vamsas.client.simpleclient.Lock#getBufferedInputStream(boolean)
-   */
-  public BufferedInputStream getBufferedInputStream(boolean atStart) throws IOException {
-    lockFile();
-    return fileLock.getBufferedInputStream(atStart);
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.simpleclient.Lock#getBufferedOutputStream(boolean)
-   */
-  public BufferedOutputStream getBufferedOutputStream(boolean clear) throws IOException {
-    lockFile();
-    return fileLock.getBufferedOutputStream(clear);
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.simpleclient.Lock#getFileInputStream(boolean)
-   */
-  public FileInputStream getFileInputStream(boolean atStart) throws IOException {
-    lockFile();
-    return fileLock.getFileInputStream(atStart);
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.simpleclient.Lock#getFileOutputStream(boolean)
-   */
-  public FileOutputStream getFileOutputStream(boolean clear) throws IOException {
-    lockFile();
-    return fileLock.getFileOutputStream(clear);
-  }
-  
-}
diff --git a/src/org/vamsas/client/simpleclient/SessionFlagFile.java b/src/org/vamsas/client/simpleclient/SessionFlagFile.java
deleted file mode 100644
index 7826fbc..0000000
--- a/src/org/vamsas/client/simpleclient/SessionFlagFile.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * methods for setting and checking 
- * binary flags in a vamsas session directory.
- * all methods apart from the constructor will 
- * throw a fatal error if the flagFile is not
- * a valid java.io.File object.
- * LATER: extract SessionFlag interface for generalizing the vamsas session code 
- * @author jimp
- *
- */
-public class SessionFlagFile {
-  private static Log log = LogFactory.getLog(SessionFlagFile.class);
-  protected File flagFile=null;
-  private void checkFlagFile() {
-    if (flagFile==null) {
-      log.fatal("Implementation error - uninitialized SessionFlagFile", 
-          new Error("Implementation error - uninitialized SessionFlagFile"));
-    }
-  }
-  /**
-   * will log a warning if exceptions occur during flag creation.
-   * @return true if flag was set successfully
-   */
-  public boolean setFlag() {
-    checkFlagFile();
-    try {
-      if (flagFile.createNewFile()) {
-        log.debug("Set session flag "+flagFile);
-      } else {
-        log.debug("Session flag already set "+flagFile);
-      }
-      return true;
-    }
-    catch (Exception e) {
-      log.warn("Couldn't set session flag "+flagFile, e);
-    }
-    return false;
-  }
-  /**
-   * 
-   * @return true if flag was cleared successfully
-   */
-  public boolean clearFlag() {
-    checkFlagFile();
-    if (flagFile.exists()) {
-      log.debug("clearing session flag "+flagFile);
-      if (!flagFile.delete()) {
-        log.warn("failed to clear session flag "+flagFile);
-        return false;
-      }
-    } else {
-      log.debug("clearFlag called for already cleared flag "+flagFile);
-    }
-    return true;
-  }
-    /**
-     * 
-     * @return state of session flag
-     */
-  public boolean checkFlag() {
-    checkFlagFile();
-    if (flagFile.exists()) {
-      if (log.isDebugEnabled())
-        log.debug("Flag '"+flagFile+"' is set.");
-      return true;
-    }
-    if (log.isDebugEnabled())
-      log.debug("Flag '"+flagFile+"' is not set.");    
-    return false;
-  }
-    /**
-     * @param flagFile
-     */
-    public SessionFlagFile(File flagFile) {
-      super();
-      this.flagFile = flagFile;
-    };
-}
diff --git a/src/org/vamsas/client/simpleclient/SessionUrn.java b/src/org/vamsas/client/simpleclient/SessionUrn.java
deleted file mode 100644
index 13b6f23..0000000
--- a/src/org/vamsas/client/simpleclient/SessionUrn.java
+++ /dev/null
@@ -1,40 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-import java.net.MalformedURLException;
-
-/**
- * SessionUrn for simpleclient sessions:
- * simpleclient://{Absolute path to session directory}
- * @author jimp
- *
- */
-public class SessionUrn extends org.vamsas.client.SessionUrn {
-  /**
-   * a simple client session urn prefix
-   */
-  public static final String SIMPLECLIENT="simpleclient";
-  public static String VAMSASDOCUMENT="vdoc";
-  static {
-    TYPES.put(SIMPLECLIENT, SessionUrn.class);
-    TYPES.put(SessionUrn.VAMSASDOCUMENT, SessionUrn.class);
-  }
-  
-  public SessionUrn(File sessionLocation) throws MalformedURLException {
-  // TODO: LATER: implement switch to have vamsas document or simpleclient sessions for same constructor
-    super(SIMPLECLIENT, sessionLocation.getAbsoluteFile().toURL());
-    //else
-      // super(VAMSASDOCUMENT, sessionLocation);
-  }
-  public SessionUrn(VamsasSession session) throws MalformedURLException {
-    super(SIMPLECLIENT, session.sessionDir.getAbsoluteFile().toURL());
-  }
-  /**
-   * TODO: LATER: think about this again.
-   * @return File(urn.getPath())
-   */
-  public File asFile() {
-    return new File(urn.getPath());
-  }
-  // TODO: add abstract 'handler' methods for resolving the URN to a particular class
-}
diff --git a/src/org/vamsas/client/simpleclient/SessionsFile.java b/src/org/vamsas/client/simpleclient/SessionsFile.java
deleted file mode 100644
index eb80f45..0000000
--- a/src/org/vamsas/client/simpleclient/SessionsFile.java
+++ /dev/null
@@ -1,342 +0,0 @@
-/* EMBL - The European Bioinformatics institute
-* MSD Group
-* VAMSAS Project
-*
-*  Copyright (c) 2005-2006 Thr European Bioinformatics Institute. All rights reserved.
-*
-*   Redistribution and use in source and binary forms, with or without
-*   modification, are permitted provided that the following conditions
-*   are met:
-*  
-*   1. Redistributions of source code must retain the above copyright
-*      notice, this list of conditions and the following disclaimer. 
-*  
-*   2. Redistributions in binary form must reproduce the above copyright
-*      notice, this list of conditions and the following disclaimer in
-*      the documentation and/or other materials provided with the
-*      distribution.
-*  
-*   3. The name MSD must not be used to endorse or promote products 
-*      derived from this software without prior written permission. For 
-*      written permission, please contact msd-help@ebi.ac.uk
-*  
-*   4. Products derived from this software may not be called "MSD"
-*      nor may "MSD" appear in their names without prior written
-*      permission of the MSD developers.
-*  
-*   5. Redistributions of any form whatsoever must retain the following
-*      acknowledgment:
-*      "This product includes software developed by MSD 
-*       (http://www.ebi.ac.uk/)"
-*  
-*   THIS SOFTWARE IS PROVIDED BY THE MSD GROUP ``AS IS'' AND ANY
-*   EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-*   IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-*   PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE ENSEMBL GROUP OR
-*   ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-*   SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
-*   NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-*   LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
-*   HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
-*   STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-*   ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
-*   OF THE POSSIBILITY OF SUCH DAMAGE.
-*
-* The European Bioinformatics Institute may publish revised and/or new
-* versions of this license with new releases of VAMSAS software.
-*==============================================================================
-*
-*  @author <a href="mailto:pierre@ebi.ac.uk">Pierre MARGUERITE</a>
-* 
-* Dec 13, 2006  - VamsasClientV4
-*
-*/
- 
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.SessionHandle;
-
-/**
- * @author <a href="mailto:pierre@ebi.ac.uk">Pierre MARGUERITE</a>
- * 
- * 
- */
-public class SessionsFile extends ListFile {
-  
-  private static Log log = LogFactory.getLog(SessionsFile.class);
-  /**
-   * when set true - get FileNotFoundExceptions on WinXP when writing to locked stream after the backup has been made (via the backupFile method)
-   */
-  boolean backup=false;
-  /**
-   * number of my session in list - passed back when a session 
-   * is added to list, and used (if valid) for quickly 
-   * looking up presence of session handle in the list.
-   */
-  private int syncnum = 1;
-  /**
-   * @param file
-   */
-  public SessionsFile(File file) throws java.io.IOException {
-    super(file);
-  }
-  
-  
-  /**
-   * internal method for getting sessionsList - ensures a lock has been made but
-   * does not release it.
-   * 
-   * @return list of clients
-   */
-  private SessionHandle[] retrieveSessionHandles() {
-    if (lockFile()) {
-      try {
-        SessionHandle[] clients=null;
-        if (this.fileLock.length()>0) {
-          
-          ObjectInputStream is = new ObjectInputStream(this.fileLock.getBufferedInputStream(true));
-          Object o;
-          o=is.readObject();
-          if (o!=null) {
-            try {
-              clients = (SessionHandle[]) o;
-            }
-            catch (Exception e) {
-              log.error("Garbage in the clientHandle list "+this.sessionFile,e);
-            }
-          }
-        }
-        return clients;
-      } catch (FileNotFoundException e) {
-       // e.printStackTrace(System.err);
-        log.error(e);
-      } catch (Exception e) {
-        log.error(e);
-        //e.printStackTrace(System.err);
-      }
-    }
-    return null;
-  }
-
-  /**
-   * get the SessionsList from the file. May return null if lock failed!
-   * @return sessionsList
-   */
-  public SessionHandle[] retrieveSessionsList() {
-    if (lockFile()) {
-      SessionHandle[] clients = retrieveSessionHandles();
-      unlockFile();
-      return clients;
-    }
-    return null;
-  }
-
-  /**
-   * get list from the locked ClientList.
-   * @param extantlock
-   * @return clientList or null if lock failed (or file was empty)
-   */
-  public SessionHandle[] retrieveSessionsList(Lock extantlock) {
-    if (lockFile(extantlock)) {
-     SessionHandle[] clients = retrieveSessionHandles();
-      unlockFile();
-      return clients;
-    }
-    return null;
-  }
- 
-  
-  /**
-   * adds clientHandle me to the clientList under an existing lock extantLock.
-   * @param me
-   * @param extantLock
-   * @return client index in list or 0 if lock was invalid or addClient operation failed.
-   */
-  public int addSession(SessionHandle me, Lock extantLock) {
-    return addSession(me, true, extantLock);
-  }
-  
-  /**
-   * adds SessionsHandle me to the sessionsList under an existing lock.
-   * @param me - sessionsHandle
-   * @param disambig - if true then add will fail if an identical clientHandle already exists
-   * @param extantLock - existing lock
-   * @return client index in list or 0 if addClient (or the lock) failed.
-   */
-  
-  public int addSession(SessionHandle session, boolean disambig, Lock extantLock) {
-    if (lockFile(extantLock)) {
-      this.syncnum = addSession(session, disambig);
-      unlockFile();
-      return this.syncnum;
-    }
-    return 0;
-  }
-  
-  /**
-   * removes the current session from the  SessionsList without complaint if the session isn't in the sessionsList already.
-   * @param me client handle to be removed
-   * @param clientlock existing lock passed from watcher.
-   */
-  public void removeSession(SessionHandle session, Lock clientlock) {
-    int mynum =-1;
-    if (lockFile(clientlock)) {
-      SessionHandle[] sessions = retrieveSessionHandles();
-      if (sessions != null) {
-        if ((this.syncnum<=0 || this.syncnum>sessions.length) || sessions[this.syncnum-1]!=session) {
-          for (int i = 0, j = sessions.length; i < j; i++) 
-            if (sessions[i].equals(session)) {
-              mynum=i;
-              break;
-            }
-        } else {
-          mynum=this.syncnum-1;
-        }
-        if (mynum>-1) {
-          SessionHandle[] newlist = new SessionHandle[sessions.length - 1];
-          for (int k=0,i = 0, j = sessions.length; i < j; i++)
-            if (i!=mynum)
-              newlist[k++] = sessions[i];
-          if (!putSessionsList(newlist))
-            throw new Error("Failed to write new sessionsList!"); // failed to put the sessionList to disk.
-        }
-      }
-      unlockFile();
-    } else {
-      throw new Error("Couldn't get lock for "+((sessionFile==null) ? "Unitialised sessionFile in SessionsFile" : this.sessionFile.getAbsolutePath()));
-    }
-  }
-  /**
-   * Adds a SessionHandle to the SessionList file - optionally disambiguating 
-   * the SessionHandle (modifes the URN). 
-   * Note: Caller is left to release the lock on the SessionList.
-   * @param me
-   * @param disambiguate -
-   *          flag indicating if the URN for me should be disambiguated to
-   *          differentiate between sessions.
-   * @return index of sessionHandle in new list, or -1-position of existing
-   *         sessionHandle (if disambiguate is true)
-   */
-  protected int addSession(SessionHandle session, boolean disambiguate) {
-    int newsession = 0;
-    int tries=5;
-    while (tries-->0 && !lockFile())
-      try { Thread.sleep(1); } catch (Exception e){};
-    if (lockFile()) {
-      SessionHandle[] sessions = retrieveSessionHandles();
-
-      if (sessions == null) {
-        sessions = new SessionHandle[1];
-        sessions[0] = session;
-        newsession = 1;
-      } else {
-        int k = 0;
-        for (int i = 0, j = sessions.length; i < j; i++) {
-          if ( sessions[i].equals(session)) {
-            if (disambiguate) {
-              while (sessions[i].equals(session)) {
-               // me.setClientUrn(me.getClientUrn() + k++); // TODO: make a better
-                                                          // disambiguation of
-                                                          // urn.
-              }
-            } else {
-              // will not write the ambiguous clientHandle to disk, just return
-              // its index.
-              return -1 - i;
-            }
-          }
-        }
-        int i, j;
-        SessionHandle[] newlist = new SessionHandle[sessions.length + 1];
-        for (i = 0, j = sessions.length; i < j; i++)
-          newlist[i] = sessions[i];
-        newlist[j] = session;
-        sessions = newlist;
-        newsession = j+1;
-      }
-      if (!putSessionsList(sessions))
-        return 0; // failed to put the clientList to disk.
-    }
-    return newsession;
-  }
-  
-  
-  /**
-   * safely writes sessions array to the file referred to by sessionFile.
-   * 
-   * @param clients
-   * @return true if successful write. Throws Errors otherwise.
-   */
-  protected boolean putSessionsList(SessionHandle[] clients) {
-    if (lockFile()) {
-      File templist=null;
-      if (!this.backup || (templist = backupSessionFile()) != null) {
-        int retries=3;
-        while (retries-->0) {
-          try {
-            ObjectOutputStream os = 
-              new ObjectOutputStream(this.fileLock.getBufferedOutputStream(true));
-            log.debug("About to write "+clients.length+" sessionHandles to output stream.");
-            os.writeObject(clients);
-            os.close();
-          // All done - remove the backup.
-          if (this.backup)
-            templist.delete();
-          templist = null;
-          retries=-1;
-          } catch (Exception e) {
-           // System.err
-            //.println("Serious - problems writing to sessionFile.");
-            log.error("Serious - problems writing to sessionFile.",e);
-            if (retries>0 && templist != null) {
-            //  System.err.println("Recovering from Backup in "
-              //        + templist.getAbsolutePath());
-              log.error("Recovering from Backup in "+ templist.getAbsolutePath());
-              templist.renameTo(this.fileLock.target);
-            }
-            //e.printStackTrace(System.err);
-            log.error(e);
-          }
-        }
-        if (retries>-2) {
-         // System.err
-         // .println("Serious - problems writing to sessionFile. Giving Up.");
-          log.error("Serious - problems writing to sessionFile. Giving Up.");
-          return false;
-        }
-      } else {
-        throw new Error(
-            "Couldn't create backup of the clientList before writing to it!");
-      }
-    } else {
-      throw new Error("Could not lock the clientList: "
-          + ((this.sessionFile == null) ? "Unitialized ClientsFile"
-              : " failed to get lock on " + this.sessionFile.getAbsolutePath()));
-    }
-    // successful!
-    return true;
-  }
-
-  public void clearList() {
-    if (lockFile()) {
-      try {
-        FileOutputStream fout = this.fileLock.getFileOutputStream(true);
-        fout.flush();
-        fout.close();
-      } catch (Exception e) {
-        throw new Error("Problems trying to clear clientlist!",e);
-        
-      }
-    }
-    
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/SimpleClient.java b/src/org/vamsas/client/simpleclient/SimpleClient.java
deleted file mode 100644
index 2041c11..0000000
--- a/src/org/vamsas/client/simpleclient/SimpleClient.java
+++ /dev/null
@@ -1,416 +0,0 @@
-/*
- * Created on 15-Sep-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.client.simpleclient;
-
-import java.beans.EventHandler;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.Events;
-import org.vamsas.client.IClient;
-import org.vamsas.client.IClientDocument;
-import org.vamsas.client.IObjectUpdate;
-import org.vamsas.client.InvalidSessionUrnException;
-import org.vamsas.client.SessionHandle;
-import org.vamsas.client.UserHandle;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.LockFile;
-import org.vamsas.objects.core.VamsasDocument;
-import org.vamsas.objects.utils.AppDataReference;
-import org.vamsas.objects.utils.ProvenanceStuff;
-import org.vamsas.objects.utils.document.VersionEntries;
-
-/**
- * @author jimp
- */
-public class SimpleClient implements IClient {
-  
-  private static Log log = LogFactory.getLog(SimpleClient.class);
-  
-  protected UserHandle user = null;
-  
-  protected SessionUrn session = null;
-  protected VamsasSession _session;
-  protected ClientHandle client = null;
-  protected EventGeneratorThread evgen = null;
-  protected ClientDocument cdocument = null;
-  /**
-   * object hash table that persists in each client holding vorbaIds and hash values after a document write
-   */
-  protected Hashtable extantobjects=null;
-  /**
-   * construct a transient IdFactory instance - this should last only as long as the 
-   * SimpleClient object holds the lock on the vamsas document being created/manipulated.
-   * @return
-   */
-  private IdFactory makeVorbaIdFactory() {
-    return new IdFactory(getSessionHandle(), client, user);
-  }
-  
-  /**
-   * construct SimpleClient for user, client and VamsasSession directory
-   * use the SimpleClientFactory rather than this constructor directly. 
-   * @param user
-   * @param client
-   * @param sess
-   */
-  protected SimpleClient(UserHandle user, ClientHandle client, VamsasSession sess) throws InvalidSessionUrnException {
-    // TODO: validate user/client/session
-    _session = sess;
-    this.user = user;
-    this.client = client;
-    try {
-      session = new SessionUrn(_session);
-    } catch (MalformedURLException e) {
-      log.error("Couldn't form a valid SessionUrn object!",e);
-      throw new InvalidSessionUrnException(_session.toString());
-    }
-  }
-  /**
-   * construct new session by importing objects from an existing vamsas document
-   * @param user
-   * @param client
-   * @param sess
-   * @param importingArchive
-   * @throws Exception IOExceptions for Session IO problems, and general Exception if importing document is invalid.
-   */
-  protected SimpleClient(UserHandle user, ClientHandle client, VamsasSession sess, File importingArchive) throws Exception {
-    this(user, client, sess);
-    VamsasArchive sessdoc = _session.getVamsasDocument();
-    try {
-      VamsasArchiveReader odoc = new VamsasArchiveReader(importingArchive);
-      SimpleDocument sdoc = new SimpleDocument(makeVorbaIdFactory());
-      VamsasDocument doc = sdoc.getVamsasDocument(odoc);
-      sessdoc.putVamsasDocument(doc, sdoc.vorba);
-      sessdoc.closeArchive();
-    } catch (Exception e) {
-      sessdoc.cancelArchive();
-      // write a dummy archive
-      _session.slog.info("Exception when importing document data from "+importingArchive);
-      throw new Exception("Failed to import data from "+importingArchive, e);
-    }
-  }
-  
-  /*
-   * (non-Javadoc)
-   * LATER: check that build substitution variables are correct
-   * @see org.vamsas.client.IClient#getAbout()
-   */
-  public String getAbout() {
-    return new String("VORBA SimpleClient version $version$ build $build$");
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#getSessionUrn()
-   */
-  public String getSessionUrn() {
-    return session.getSessionUrn();
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#getSessionHandle()
-   */
-  public SessionHandle getSessionHandle() {
-    // TODO: eliminate SessionHandle ? need to refactor interfaces.
-    SessionHandle sh = new SessionHandle(session.getSessionUrn());
-    return sh;
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#getClientHandle()
-   */
-  public ClientHandle getClientHandle() {
-    return client;
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#getUserHandle()
-   */
-  public UserHandle getUserHandle() {
-    return user;
-  }
-  /**
-   * 
-   * @return user field for a provenance entry
-   */
-  protected String getProvenanceUser() {
-    return new String(user.getFullName());
-  }
-  /**
-   * construct a provenance entry for this client with the specified action string.
-   * @param action
-   * @return properly completed provenance entry
-   */
-  protected Entry getProvenanceEntry(String action) {
-    Entry prov = ProvenanceStuff.newProvenanceEntry(client.getClientUrn(), getProvenanceUser(), action);
-    return prov;
-  }
-  private Hashtable handlers = initHandlers();
-  
-  private Vector listeners = new Vector();
-  
-  /**
-   * make all the PropertyChangeSupport objects for the
-   * events described in org.vamsas.client.Event
-   * @return
-   */
-  private static Hashtable initHandlers() {
-    Hashtable events = new Hashtable();
-    java.util.Iterator evt = Events.EventList.iterator();
-    while (evt.hasNext()) {
-      Object ths = evt.next();
-      events.put(ths, (Object) new PropertyChangeSupport(ths));
-    }
-    return events;
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#addDocumentUpdateHandler(java.util.EventListener)
-   */
-  public void addDocumentUpdateHandler(PropertyChangeListener evt) {
-    if (handlers.containsKey(Events.DOCUMENT_UPDATE)) {
-      Object handler;
-      ((PropertyChangeSupport) (handler = handlers.get(Events.DOCUMENT_UPDATE)))
-      .addPropertyChangeListener(evt);
-      listeners.add(handler);
-      listeners.add((Object) evt);
-    }
-  }
-  boolean finalized=false;
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#finalizeClient()
-   */
-  public void finalizeClient() {
-    // TODO: determine if this is last client in session
-    // TODO: raise events like : ((lst_client && document.request.to.close), (client_finalization), (
-    
-    // if (handlers.containsKey(Events.))
-    // if (handlers.containsKey(Events.CLIENT_FINALIZATION))
-    // deregister listeners.
-    // mark this instance as finalized
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#getClientDocument()
-   */
-  public IClientDocument getClientDocument() throws IOException {
-    if (cdocument!=null) {
-      // cdocument is non-nill if the ClientDocument.finalise() method hasn't been called.
-      return cdocument;
-    }
-    VamsasArchive va = null;
-    try {
-      // LATER: bail out if it takes too long to get the lock ?
-      va = _session.getVamsasDocument();
-    }
-    catch (IOException e) {
-      throw new IOException("Failed to get lock on session document");
-    }
-    VamsasDocument doc=null;
-    IdFactory vorba = null;
-    // TODO: reduce size of vorba ids generated from these parameters to IdFactory (mainly sessionHandle rationalization ?)
-    try {
-      va.setVorba(vorba=makeVorbaIdFactory());
-      // if session currently holds data - read it in - or get a dummy
-      _session.slog.debug("Accessing document");
-      doc = 
-        va.getVamsasDocument(getProvenanceUser(),
-            "created new session document.", null);
-      if (doc!=null)
-        _session.slog.debug("Successfully retrieved document.");
-      else
-        log.error("Unexpectedly retrieved null document!");
-    }
-    catch (Exception e) {
-      log.error("Failed to get session document for session directory '"+_session.sessionDir+"'", e);
-      throw new IOException("Failed to get session document for session directory '"+_session.sessionDir+"'");
-    }
-    // Construct the IClientDocument instance
-    
-    ClientDocument cdoc = new ClientDocument(doc, va, vorba, this);
-    return cdoc;
-  }
-  
-  /*
-   * (non-Javadoc)
-   * @throws Errors for invalid newdoc parameter
-   * @see org.vamsas.client.IClient#updateDocument(org.vamsas.client.IClientDocument)
-   */
-  public void updateDocument(IClientDocument newdoc) {
-    if (!(newdoc instanceof ClientDocument)) {
-      throw new Error("Invalid IClientDocument instance for SimpleClient.");
-    }
-    if (cdocument==null)
-      throw new Error("Client Error - updateDocument() called before getClientDocument().");
-    if (newdoc!=cdocument)
-      throw new Error("Client Error - SimpleClient.updateDocument() can only take the IClientDocument instance returned from SimpleClient.getClientDocument()");
-    if (!cdocument.isModified()) {
-      if (log.isDebugEnabled())
-        log.debug("updateDocument for "+session.getSessionUrn()+" with unmodified IClientDocument.");
-    } else {
-      try {
-        if (!cdocument.updateSessionDocument()) {
-          log.warn("Session document did not update properly for session directory "+_session.sessionDir);
-          // cdocument.archive.cancelArchive(); // LATER: could be done - would need to prevent updateSessionDocument closing the archive.
-          _session.slog.warn("Session Document updated but may not be valid (false return from org.vamsas.simpleclient.ClientDocument.updateSessionDocument()");
-        }
-      }
-      catch (IOException e) {
-        log.warn("IO Problems when updating document!",e);
-        _session.slog.error("IO problems when attempting to update document.");
-      }
-    }
-    // garbage collect the ClientDocument instance.
-    try {
-      cdocument.finalize();
-
-    } catch (Throwable e) {
-      log.error("Exception when trying to garbage collect ClientDocument for "+session.getSessionUrn(), e);
-    }
-    cdocument = null; // this is probably done by finalize
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#storeDocument(java.io.File)
-   */
-  public void storeDocument(File location) {
-    
-    // write storeDocument file to inform other clients that they should raise
-    Lock vamlock = evgen.want_to_store();
-    // Events.DOCUMENT_FINALIZEAPPDATA
-    try {
-      _session.writeVamsasDocument(location, vamlock);
-      _session.clearUnsavedFlag();
-    } catch (Exception e) {
-      log.warn("Exception whilst trying to store document in "+location,e);
-    }
-    
-    vamlock.release();
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClient#addVorbaEventHandler(java.lang.String,
-   *      java.beans.PropertyChangeListener)
-   */
-  public void addVorbaEventHandler(String EventChain, PropertyChangeListener evt) {
-    if (handlers.containsKey(EventChain)) {
-      Object handler;
-      ((PropertyChangeSupport) (handler = handlers.get(EventChain)))
-      .addPropertyChangeListener(evt);
-      listeners.add(handler);
-      listeners.add((Object) evt);
-    }
-  }
-  
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClient#pollUpdate()
-   */
-  public void pollUpdate() {
-    
-    if (evgen==null) {
-      log.warn("pollUpdate called on incomplete SimpleClient object.");
-      return;
-    }
-    
-    if (!evgen.isAlive()) {
-      log.warn("pollUpdate called before joinSession() - trying to do this.");
-      try {
-        joinSession();
-      } catch (Exception e) {
-        log.error("Unexpected exception on default call to joinSession",e);
-      }
-    }
-    
-    //TODO ensure event generator robustly handles these interrupts.
-    log.debug("interrrupting event generator.");
-    evgen.interrupt();
-    log.debug("interrrupted event generator.");
-  }
-  
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClient#joinSession()
-   */
-  public void joinSession() throws Exception {
-    // start the EventGenerator thread.
-    if (evgen==null) {
-      log.warn("joinSession called on incomplete SimpleClient object.");
-      return;
-    }
-    if (evgen.isAlive())
-      throw new Error("Join session called twice for the same SimpleClient (IClient instance).");
-    evgen.start();
-    if (evgen.isAlive())
-      log.debug("Started EventGenerator thread.");
-    else {
-      log.warn("Failed to start EventGenerator thread.");
-      throw new Exception("Failed to start event generator thread - client cannot be instantiated.");
-    }
-    if (evgen.countHandlersFor(Events.DOCUMENT_CREATE)>0) {
-      //TODO: is this application connecting to a newly created session document ?
-      //evgen.raise(Events.DOCUMENT_CREATE);
-    }
-  }
-  
-  
-  
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClient#importDocument(java.io.File)
-   */
-  public void importDocument(File location) {
-    // TODO LATER: implement SimpleClient.importDocument()
-    log.error("importDocument is not yet implemented for a SimpleClient Session.");
-  }
-
-  public IObjectUpdate getUpdateHandler(Class rootObject) {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  public IObjectUpdate[] getUpdateHandlers() {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  public void removeUpdateHandler(Class rootObject) {
-    // TODO Auto-generated method stub
-    
-  }
-
-  public void setUpdateHandler(IObjectUpdate handler) {
-    // TODO Auto-generated method stub
-    
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java b/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java
deleted file mode 100644
index 84bc48a..0000000
--- a/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java
+++ /dev/null
@@ -1,543 +0,0 @@
-/**
- * 
- */
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.DataInput;
-import java.io.DataInputStream;
-import java.io.DataOutput;
-import java.io.DataOutputStream;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.IClientAppdata;
-import org.vamsas.objects.core.AppData;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.User;
-import org.vamsas.objects.utils.AppDataReference;
-
-/**
- * @author jimp
- * Access interface to data chunks read from a VamsasArchiveReader stream 
- * (or byte buffer input stream) or written to a VamsasArchive stream.
- * // TODO: get VamsasArchiveReader from sclient
- */
-public class SimpleClientAppdata implements IClientAppdata {
-  private static Log log = LogFactory.getLog(SimpleClientAppdata.class);
-  /**
-   * has the session's document been accessed to get the AppData entrys?
-   */
-  protected boolean accessedDocument = false;
-  /**
-   * has the user datablock been modified ? 
-   * temporary file containing new user specific application data chunk
-   */
-  SessionFile newUserData=null;
-  JarOutputStream newUserDataStream = null;
-  /**
-   * has the apps global datablock been modified ?
-   * temporary file containing new global application data chunk
-   */
-  SessionFile newAppData=null;
-  JarOutputStream newAppDataStream=null;
-  /**
-   * set by extractAppData
-   */
-  protected ApplicationData appsGlobal = null;
-  /**
-   * set by extractAppData
-   */
-  protected User usersData = null;
-  
-  ClientDocument clientdoc;
-  /**
-   * state flags
-   * - accessed ClientAppdata
-   * - accessed UserAppdata
-   * => inputStream from embedded xml or jar entry of backup has been created
-   * - set ClientAppdata
-   * - set UserAppdata
-   * => an output stream has been created and written to - or a data chunk has been written.
-   *  - need flag for switching between embedded and jar entry mode ? - always write a jar entry for a stream.
-   *  - need code for rewind and overwriting if the set*Appdata methods are called more than once.
-   *  - need flags for streams to except a call to set*Appdata when an output stream exists and is open.
-   *  - need 
-   * @param clientdoc The ClientDocument instance that this IClientAppData is accessing
-   */
-  protected SimpleClientAppdata(ClientDocument clientdoc) {
-    if (clientdoc==null) {
-      log.fatal("Implementation error - Null ClientDocument for SimpleClientAppdata construction.");
-      throw new Error("Implementation error - Null ClientDocument for SimpleClientAppdata construction.");
-    }
-    this.clientdoc = clientdoc;
-  }
-  /**
-   * gets appropriate app data for the application, if it exists in this dataset
-   * Called by every accessor to ensure data has been retrieved from document.
-   */
-  private void extractAppData(org.vamsas.objects.core.VamsasDocument doc) {
-    if (doc==null) {
-      log.debug("extractAppData called for null document object");
-      return;
-    }
-    if (accessedDocument) {
-      return;
-    }
-    Vector apldataset = AppDataReference.getUserandApplicationsData(
-        doc, clientdoc.sclient.getUserHandle(), clientdoc.sclient.getClientHandle());
-    accessedDocument = true;
-    if (apldataset!=null) {
-      if (apldataset.size()>0) {
-        AppData clientdat = (AppData) apldataset.get(0);
-        if (clientdat instanceof ApplicationData) {
-          appsGlobal = (ApplicationData) clientdat;
-          if (apldataset.size()>1) {
-            clientdat = (AppData) apldataset.get(1);
-            if (clientdat instanceof User) {
-              usersData = (User) clientdat;
-            }
-            if (apldataset.size()>2)
-              log.info("Ignoring additional ("+(apldataset.size()-2)+") AppDatas returned by document appdata query.");
-          } 
-        } else {
-          log.warn("Unexpected entry in AppDataReference query: id="+clientdat.getVorbaId()+" type="+clientdat.getClass().getName());
-        }
-        apldataset.removeAllElements(); // destroy references.
-      }
-    }
-  }
-  /**
-   * LATER: generalize this for different low-level session implementations (it may not always be a Jar)
-   * @param appdata
-   * @param docreader
-   * @return
-   */
-  private JarInputStream getAppDataStream(AppData appdata, VamsasArchiveReader docreader) {
-    String entryRef = appdata.getDataReference();
-    if (entryRef!=null) {
-      log.debug("Resolving appData reference +"+entryRef);
-      InputStream entry = docreader.getAppdataStream(entryRef);
-      if (entry!=null) {
-        if (entry instanceof JarInputStream) {
-          return (JarInputStream) entry;
-        }
-        log.warn("Implementation problem - docreader didn't return a JarInputStream entry.");
-      }
-    } else {
-      log.debug("GetAppDataStream called for an AppData without a data reference.");
-    }
-    return null;
-  }
-  /**
-   * yuk - size of buffer used for slurping appData JarEntry into a byte array.
-   */
-  private final int _TRANSFER_BUFFER=4096*4;
-
-  /**
-   * Resolve AppData object to a byte array.
-   * @param appdata
-   * @param archiveReader
-   * @return null or the application data as a byte array
-   */
-  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();
-      try {
-        byte buff[] = new byte[_TRANSFER_BUFFER];
-        int olen=0;
-        while (entry.available()>0) {
-          int len = entry.read(buff, olen, _TRANSFER_BUFFER);
-          bytes.write(buff, 0, len);
-          olen+=len;
-        }
-        buff=null;
-      } catch (Exception e) {
-        log.warn("Unexpected exception - probable truncation when accessing VamsasDocument entry "+appdata.getDataReference(), e);
-      }
-      if (bytes.size()>0) {
-        // LATER: deal with probable OutOfMemoryErrors here
-        log.debug("Got "+bytes.size()+" bytes from AppDataReference "+appdata.getDataReference());
-        byte data[] = bytes.toByteArray();
-        bytes = null;
-        return data;
-      }
-      return null;
-    } else {
-      log.debug("Returning inline AppData block for "+appdata.getVorbaId());
-      return appdata.getData();
-    }
-  }
-  /**
-   * internal method for getting a DataInputStream from an AppData object.
-   * @param appdata
-   * @param docreader
-   * @return data in object or null if no data is accessible
-   */
-  private DataInput getAppDataAsDataInputStream(AppData appdata, VamsasArchiveReader docreader) {
-    if (appdata!=null && docreader!=null) {
-      String entryRef = appdata.getDataReference();
-      if (entryRef!=null) {
-        log.debug("Resolving AppData reference for "+entryRef);
-        InputStream jstrm = docreader.getAppdataStream(entryRef);
-        if (jstrm!=null)
-          return new AppDataInputStream(jstrm);
-        else {
-          log.debug("Returning null input stream for unresolved reference ("+entryRef+") id="+appdata.getVorbaId());
-          return null;
-        }
-      } else {
-        // return a byteArray input stream
-        byte[] data=appdata.getData();
-        if (data.length>0) {
-          ByteArrayInputStream stream = new ByteArrayInputStream(data);
-          return new DataInputStream(stream);
-        } else {
-          log.debug("Returning null input stream for empty Appdata data block in id="+appdata.getVorbaId());
-          return null;
-        }
-      }
-    } else {
-      log.debug("Returning null DataInputStream for appdata entry:"+appdata.getVorbaId());
-    }
-    return null;
-  }
-
-  /**
-   * internal method for getting ByteArray from AppData object
-   * @param clientOrUser - true for returning userData, otherwise return Client AppData.
-   * @return null or byte array
-   */
-  private byte[] _getappdataByteArray(boolean clientOrUser) {
-    if (clientdoc==null)
-      throw new Error("Implementation error, Improperly initialized SimpleClientAppdata.");
-    byte[] data=null;
-    String appdName;
-    if (!clientOrUser) {
-      appdName = "Client's Appdata";
-    } else {
-      appdName = "User's Appdata";
-    }    
-    log.debug("getting "+appdName+" as a byte array");
-    extractAppData(clientdoc.getVamsasDocument());
-    AppData object;
-    if (!clientOrUser) {
-      object = appsGlobal;
-    } else {
-      object = usersData;
-    }
-    if (object!=null) {
-      log.debug("Trying to resolve "+appdName+" object to byte array.");
-      data = getAppDataAsByteArray(object, clientdoc.getVamsasArchiveReader());
-    }
-    if (data == null)
-      log.debug("Returning null for "+appdName+"ClientAppdata byte[] array");
-    return data;
-    
-  }
-  
-  /**
-   * common method for Client and User AppData->InputStream accessor
-   * @param clientOrUser - the appData to resolve - false for client, true for user appdata.
-   * @return null or the DataInputStream desired.
-   */
-  private DataInput _getappdataInputStream(boolean clientOrUser) {
-    if (clientdoc==null)
-      throw new Error("Implementation error, Improperly initialized SimpleClientAppdata.");
-    String appdName;
-    if (!clientOrUser) {
-      appdName = "Client's Appdata";
-    } else {
-      appdName = "User's Appdata";
-    }
-    if (log.isDebugEnabled())
-      log.debug("getting "+appdName+" as an input stream.");
-    extractAppData(clientdoc.getVamsasDocument());
-    AppData object;
-    if (!clientOrUser) {
-      object = appsGlobal;
-    } else {
-      object = usersData;
-    }
-    if (object!=null) {
-      log.debug("Trying to resolve ClientAppdata object to an input stream.");
-      return getAppDataAsDataInputStream(object, clientdoc.getVamsasArchiveReader());
-    }
-    log.debug("getClientInputStream returning null.");
-    return null;
-  }
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#getClientAppdata()
-   */
-  public byte[] getClientAppdata() {
-    return _getappdataByteArray(false);
-  }
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#getClientInputStream()
-   */
-  public DataInput getClientInputStream() {
-    return _getappdataInputStream(false);
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#getUserAppdata()
-   */
-  public byte[] getUserAppdata() {
-    return _getappdataByteArray(true);
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#getUserInputStream()
-   */
-  public DataInput getUserInputStream() {
-    return _getappdataInputStream(true);
-  }
-  /**
-   * methods for writing new AppData entries.
-   */
-  private DataOutput _getAppdataOutputStream(boolean clientOrUser) {
-    String apdname;
-    SessionFile apdfile=null;
-    if (!clientOrUser) {
-      apdname = "clientAppData";
-      apdfile = newAppData;
-    } else {
-      apdname = "userAppData";
-      apdfile = newUserData;
-    }
-    try {
-      if (apdfile==null) {
-        apdfile=clientdoc.sclient._session.getTempSessionFile(apdname,".jar");
-        log.debug("Successfully made temp appData file for "+apdname);
-      } else {
-        // truncate to remove existing data.
-        apdfile.fileLock.getRaFile().setLength(0);
-        log.debug("Successfully truncated existing temp appData for "+apdname);
-      }
-      } catch (Exception e) {
-      log.error("Whilst opening temp file in directory "+clientdoc.sclient._session.sessionDir, e);
-    }
-    // we do not make another file for the new entry if one exists already
-    if (!clientOrUser) {
-      newAppData = apdfile;
-    } else {
-      newUserData = apdfile;
-    }
-    try {
-      apdfile.lockFile();
-      // LATER: Refactor these local AppDatastream IO stuff to their own class.
-      JarOutputStream dstrm = 
-        new JarOutputStream(apdfile.fileLock.getBufferedOutputStream(true));
-      if (!clientOrUser) {
-        newAppDataStream = dstrm;
-      } else {
-        newUserDataStream = dstrm;
-      }
-      dstrm.putNextEntry(new JarEntry("appData_entry.dat"));
-      // LATER: there may be trouble ahead if an AppDataOutputStream is written to by one thread when another truncates the file. This situation should be prevented if possible
-      return new AppDataOutputStream(dstrm);
-    }
-    catch (Exception e) {
-      log.error("Whilst opening jar output stream for file "+apdfile.sessionFile);
-    }
-    // tidy up and return null
-    apdfile.unlockFile();
-    return null;
-   }
-  /**
-   * copy data from the appData jar file to an appropriately 
-   * referenced jar or Data entry for the given ApplicationData
-   * Assumes the JarFile is properly closed. 
-   * @param vdoc session Document handler
-   * @param appd the AppData whose block is being updated
-   * @param apdjar the new data in a Jar written by this class
-   */
-  protected void updateAnAppdataEntry(VamsasArchive vdoc, AppData appd, SessionFile apdjar) throws IOException {
-    if (apdjar==null || apdjar.sessionFile==null || !apdjar.sessionFile.exists()) {
-      throw new IOException("No temporary Appdata to recover and transfer.");
-    }
-    if (vdoc==null) {
-      log.fatal("FATAL! NO DOCUMENT TO WRITE TO!");
-      throw new IOException("FATAL! NO DOCUMENT TO WRITE TO!");
-    }
-    log.debug("Recovering AppData entry from "+apdjar.sessionFile);
-    JarInputStream istrm = new JarInputStream(apdjar.getBufferedInputStream(true));
-    JarEntry je=null;
-    while (istrm.available()>0 && (je=istrm.getNextJarEntry())!=null && !je.getName().equals("appData_entry.dat")) {
-      if (je!=null)
-        log.debug("Ignoring extraneous entry "+je.getName());
-    }
-    if (istrm.available()>0 && je!=null) {
-      log.debug("Found appData_entry.dat in Jar");
-      String ref = appd.getDataReference();
-      if (ref==null) {
-        throw new IOException("Null AppData.DataReference passed.");
-      }
-      if (vdoc.writeAppdataFromStream(ref, istrm)) {
-        log.debug("Entry updated successfully.");
-      } else {
-        throw new IOException("writeAppdataFromStream did not return true - expect future badness."); // LATER - verify why this might occur.
-      }
-    } else {
-      throw new IOException("Couldn't find appData_entry.dat in temporary jar file "+apdjar.sessionFile.getAbsolutePath());
-    }
-    istrm.close();
-  }
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#getClientOutputStream()
-   */
-  public DataOutput getClientOutputStream() {
-    if (clientdoc==null)
-      throw new Error("Implementation error, Improperly initialized SimpleClientAppdata.");
-    if (log.isDebugEnabled())
-      log.debug("trying to getClientOutputStream for "+clientdoc.sclient.client.getClientUrn());   
-    return _getAppdataOutputStream(false);
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#getUserOutputStream()
-   */
-  public DataOutput getUserOutputStream() {
-    if (clientdoc==null)
-      throw new Error("Implementation error, Improperly initialized SimpleClientAppdata.");
-    if (log.isDebugEnabled())
-      log.debug("trying to getUserOutputStream for ("
-          +clientdoc.sclient.getUserHandle().getFullName()+")"+clientdoc.sclient.client.getClientUrn());   
-    return _getAppdataOutputStream(true);
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#hasClientAppdata()
-   */
-  public boolean hasClientAppdata() {
-    if (clientdoc==null)
-      throw new Error("Implementation error, Improperly initialized SimpleClientAppdata.");
-    extractAppData(clientdoc.getVamsasDocument());
-    // LATER - check validity of a DataReference before we return true
-    if ((appsGlobal!=null) && (appsGlobal.getDataReference()!=null || appsGlobal.getData()!=null))
-      return true;
-    return false;
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#hasUserAppdata()
-   */
-  public boolean hasUserAppdata() {
-    if (clientdoc==null)
-      throw new Error("Implementation error, Improperly initialized SimpleClientAppdata.");
-    extractAppData(clientdoc.getVamsasDocument());
-    // LATER - check validity of a DataReference before we return true
-    if ((appsGlobal!=null) && (appsGlobal.getDataReference()!=null || appsGlobal.getData()!=null))
-      return true;
-    return false;
-  }
-  private boolean _writeAppDataStream(JarOutputStream ostrm, byte[] data) {
-    try {
-      if (data!=null && data.length>0) 
-        ostrm.write(data);
-      ostrm.closeEntry();
-      return true;
-    }
-    catch (Exception e) {
-      log.error("Serious! - IO error when writing AppDataStream to file "+newAppData.sessionFile, e);
-    }
-    return false;
-  }
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#setClientAppdata(byte[])
-   */
-  public void setClientAppdata(byte[] data) {
-    if (clientdoc==null)
-      throw new Error("Implementation error, Improperly initialized SimpleClientAppdata.");
-    _getAppdataOutputStream(false);
-    if (newAppDataStream==null) {
-      // LATER: define an exception for this ? - operation may fail even if file i/o not involved
-      log.error("Serious! - couldn't open new AppDataStream in session directory "+clientdoc.sclient._session.sessionDir);
-    } else {
-      _writeAppDataStream(newAppDataStream, data);
-      // LATER: deal with error case - do we make session read only, or what ?
-    }
-  }
-
-  /* (non-Javadoc)
-   * @see org.vamsas.client.IClientAppdata#setUserAppdata(byte[])
-   */
-  public void setUserAppdata(byte[] data) {
-    if (clientdoc==null)
-      throw new Error("Implementation error, Improperly initialized SimpleClientAppdata.");
-    _getAppdataOutputStream(true);
-    if (newUserDataStream==null) {
-      // LATER: define an exception for this ? - operation may fail even if file i/o not involved
-      log.error("Serious! - couldn't open new UserDataStream in session directory "+clientdoc.sclient._session.sessionDir);
-    } else {
-      _writeAppDataStream(newUserDataStream, data);
-      // LATER: deal with error case - do we make session read only, or what ?
-    }
-  }
-  /**
-   * flush and close outstanding output streams. 
-   *  - do this before checking data length.
-   * @throws IOException
-   */
-  protected void closeForWriting() throws IOException {
-    if (newAppDataStream!=null) {
-      newAppDataStream.flush();
-      newAppDataStream.closeEntry();
-      newAppDataStream.close();
-    }
-    if (newUserDataStream!=null) {
-      newUserDataStream.flush();
-      newUserDataStream.closeEntry();
-      newUserDataStream.close();
-    }
-  }
-
-
-  /**
-   * 
-   * @return true if any AppData blocks have to be updated in session Jar
-   */
-  protected boolean isModified() {
-    // LATER differentiate between core xml modification and Jar Entry modification.
-    if (newAppData.sessionFile.exists() || newUserData.sessionFile.exists())
-      return true;
-    return false;
-  }
-  /* (non-Javadoc)
-   * @see java.lang.Object#finalize()
-   */
-  protected void finalize() throws Throwable {
-    if (newAppDataStream!=null) {
-      newAppDataStream = null;
-    }
-    if (newAppDataStream!=null) {
-      newUserDataStream = null;
-    }
-    if (newAppData!=null) {
-      newAppData.eraseExistence();
-      newAppData = null;
-    }
-    if (newUserData!=null) {
-      newUserData.eraseExistence();
-      newUserData = null;
-    }
-    super.finalize();
-  }
-
-}
diff --git a/src/org/vamsas/client/simpleclient/SimpleClientFactory.java b/src/org/vamsas/client/simpleclient/SimpleClientFactory.java
deleted file mode 100644
index 6f5509a..0000000
--- a/src/org/vamsas/client/simpleclient/SimpleClientFactory.java
+++ /dev/null
@@ -1,262 +0,0 @@
-/*
-* VAMSAS Project
-*
-
-* 
-* Dec 13, 2006 
-*
-*/
- 
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-
-import java.io.IOException;
-
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.IClient;
-import org.vamsas.client.IClientFactory;
-import org.vamsas.client.InvalidSessionUrnException;
-import org.vamsas.client.NoDefaultSessionException;
-import org.vamsas.client.SessionHandle;
-import org.vamsas.client.UserHandle;
-
-/**
- * 
- * 
- */
-public class SimpleClientFactory implements IClientFactory {
-
-  private static Log log = LogFactory.getLog(SimpleClientFactory.class);
-
-  private File sessionArena = null;
-  
-  private String vamsasSubdirectoryName = ".vamsas";
-  
-  private SessionsFile sessionFile = null;
-  private static final String SESSION_LIST="sessions.obj";
-  
-  //private   String[] currentlyAvailableDessions = null; 
-  
-  /**
-   * default constructor - called by CreateClientFactory only.
-   *
-   *Inits the sessionarena to the directory .vamsas of the user home directory. 
-   *
-   */
-  public SimpleClientFactory() throws IOException
-  {
-   // sessionArena
-    
-    //retrieves user home directory
-    String userHomeDirectory = System.getProperty("user.home");
-    if (userHomeDirectory == null || userHomeDirectory.length()<1)
-      {
-        new IOException("Unable to detect user home directory");
-      }
-    String sessionArenaPath =  userHomeDirectory.concat(File.separator.concat(this.vamsasSubdirectoryName));
-    
-    this.initSessionArena(sessionArenaPath);
-    this.initFactoryObjects();
-  }
-  
-  
-  /**
-   * Create a client factory that works with sessions at the given
-   * path.
-   * @param path path to directory called  session arena, where will be created session directories and session files.
-   */
-  public SimpleClientFactory(String path) throws IOException
-  {
-    this.initSessionArena(path);
-  }
-  /**
-   * Inits sessionArena to a given path.
-   * checks if path is valid.
-   * 
-   * @param path path to a directory to use 
-   * @throws IOException if the path is incorrect
-   */
-  private void  initSessionArena (String path) throws IOException
-  {
-    // Check path is valid and read/writeable.
-    File arenaFile = new File (path);
-    if (!arenaFile.exists())
-    {
-      if (! arenaFile.mkdirs())
-      {
-        this.sessionArena = null;
-        throw(new IOException("Unable to create a directory called "+path));
-      }
-    }
-    if (arenaFile.exists() && arenaFile.isDirectory() && arenaFile.canRead() && arenaFile.canWrite()) 
-      {
-        this.sessionArena = arenaFile;
-      } 
-    else
-      {
-      this.sessionArena = null;
-        throw(new IOException("Cannot read and write to a directory called "+path));
-      }
-  }
-  
-  /**
-   * construct SessionFile objects and watchers for each
-   */
-  private void initFactoryObjects() throws IOException {
-    if (this.sessionFile!=null )
-      throw new IOException("initFactoryObjects called for initialised ClientFactory object.");
-    this.sessionFile = new SessionsFile(new File(this.sessionArena,SESSION_LIST));
-
-  }
-  /**
-   * @see org.vamsas.client.IClientFactory#getCurrentSessions()
-   */
-  public String[] getCurrentSessions() 
-  { 
-    String[] sessions = null;
-    if (this.sessionFile!=null )
-      {
-        SessionHandle[] sessionHandles =  this.sessionFile.retrieveSessionsList();
-        if (sessionHandles != null)
-          {
-            sessions = new String[sessionHandles.length];
-            for (int i = sessionHandles.length -1; i > 0; i--)
-              {
-                SessionHandle sessionHandle = sessionHandles[i];
-                sessions [i] = sessionHandle.getSessionUrn();
-              }
-          }
-      }
-    return sessions;
-  }
-  
-  
-  private void discoverSession()
-  {
-   
-  }
-
-  /**
-   * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle)
-   * 
-   * Creates a IClient object, using default UserHandle with system variables:"user.name" or "USERNAME")),
-            "host.name" or "HOSTNAME" 
-   */
-  public IClient getIClient(ClientHandle applicationHandle)
-      throws NoDefaultSessionException {
-    
-    return this.getIClient(applicationHandle, (UserHandle) null);
-  }
-
-  /**
-   * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, java.lang.String)
-   */
-  public IClient getIClient(ClientHandle applicationHandle, String sessionUrn) {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /**
-   * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, org.vamsas.client.UserHandle, java.lang.String)
-   */
-  public IClient getIClient(ClientHandle applicationHandle, UserHandle userId,
-      String sessionUrn) {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /**
-   * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, org.vamsas.client.UserHandle)
-   */
-  public IClient getIClient(ClientHandle applicationHandle, UserHandle userId)
-      throws NoDefaultSessionException {
-    SimpleClient client = null;
-    if (this.sessionArena==null)
-      throw new Error("Improperly initialised SimpleClientFactory object - null sessionArena.");
-    
-    ClientHandle clientHandle =applicationHandle;
-    //create default clientHandle with "SimpleVamsasClientApp","0.1",
-    if (clientHandle == null)
-     clientHandle = new ClientHandle("SimpleVamsasClientApp","0.1");
-    
-    //check if any available session(s)
-    String[] availableSessions = this.getCurrentSessions();
-    if (availableSessions != null) 
-      {//there are available sessions
-        if (availableSessions.length>1)
-          {//more than one session if available... can not choose
-          
-          //represents list of session as String
-            StringBuffer sessionURNs = new StringBuffer("");
-            for (int i = 0; i< availableSessions.length ; i++)
-              {
-                sessionURNs.append(availableSessions[i]+" ");
-              }
-            throw new  NoDefaultSessionException("Several sessions available, please pick one: "+sessionURNs);
-          }
-      
-        //check if only one session available. if yes, open it
-        if (availableSessions.length == 1)
-          {
-          //only one session available, open it.
-            return this.getIClient(clientHandle,  availableSessions[0]);
-          }
-      }
-    //no session available  - create a new one
-    
-    
-    try 
-      {
-        //create sessionDirectory
-        File sessdir = File.createTempFile("sess", ".simpleclient", this.sessionArena);
-        log.debug("Creating new session  directory");
-       if (!(sessdir.delete() && sessdir.mkdir()))
-          throw new IOException("Could not make session directory "+sessdir);
-      //create session
-        VamsasSession vamsasSession = new VamsasSession(sessdir);
-      
-        this.getSessionFile().addSession(new SessionHandle(new SessionUrn(vamsasSession).getSessionUrn()), false);
-        if (userId == null)
-          {
-      //create a default userHandle
-      //with current OS user and hostname
-            userId = new UserHandle(System.getProperty("user.name", System.getProperty("USERNAME","Joe Doe")),
-              System.getProperty("host.name",System.getProperty("HOSTNAME", "Unknown") ));// clientName, clientVersion,  sessionPath);
-          }
-     
-      
-      //create simple client
-         client = new SimpleClient(userId,  clientHandle,  vamsasSession);
-      } 
-    catch (IOException e) 
-      {
-        log.error("error while creating new IClient",e);
-      }
-    catch (InvalidSessionUrnException e) 
-      {
-        log.error("Unable to create new IClient. The session urn is incorrect ",e);
-      }
-   
-      return client;
-  }
-
-
-  /**
-   * @return the sessionFile
-   */
-  private SessionsFile getSessionFile()  throws IOException
-    {
-      if (this.sessionFile == null)
-        {
-          this.sessionFile = new SessionsFile( new File (this.sessionArena, SESSION_LIST));
-        }
-      return this.sessionFile;
-    }
-
-  
-
-}
diff --git a/src/org/vamsas/client/simpleclient/SimpleDocBinding.java b/src/org/vamsas/client/simpleclient/SimpleDocBinding.java
deleted file mode 100644
index c0c8084..0000000
--- a/src/org/vamsas/client/simpleclient/SimpleDocBinding.java
+++ /dev/null
@@ -1,138 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.Vector;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.VorbaIdFactory;
-import org.vamsas.client.VorbaXmlBinder;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
-import org.vamsas.objects.utils.AppDataReference;
-import org.vamsas.objects.utils.DocumentStuff;
-import org.vamsas.objects.utils.ProvenanceStuff;
-import org.vamsas.objects.utils.document.VersionEntries;
-
-/**
- * Base class for SimpleClient Vamsas Document Object Manipulation
- * holds static vamsasDocument from XML routines and
- * state objects for a particular unmarshalled Document instance.
- * @author jimp
- */
-  
-
-public class SimpleDocBinding {
-
-  protected VorbaIdFactory vorba;
-  protected static Log log = LogFactory.getLog(SimpleDocBinding.class);
-
-  /**
-   * @return Returns the vorba.
-   */
-  public VorbaIdFactory getVorba() {
-    return vorba;
-  }
-
-  /**
-   * @param vorba The vorba to set.
-   */
-  public void setVorba(VorbaIdFactory vorba) {
-    this.vorba = vorba;
-  }
-
-  /**
-   * Uses VorbaXmlBinder to retrieve the VamsasDocument from the given stream
-   */
-  public VamsasDocument getVamsasDocument(VamsasArchiveReader oReader) throws IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-    if (oReader!=null) {
-      // check the factory
-      if (vorba==null) {
-        log.error("Invalid SimpleDocument construction - no VorbaIdFactory defined!");
-        return null;
-      }
-  
-      if (oReader.isValid()) {
-        // Read vamsasDocument.xsd instance
-        InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
-        Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vdoc, vorba, new VamsasDocument());
-        if (unmarsh==null)
-          log.fatal("Couldn't unmarshall document!");
-        
-        Vobject vobjs = (Vobject) unmarsh[0];
-        if (vobjs!=null) { 
-          VamsasDocument doc=(VamsasDocument) vobjs;
-          if (doc!=null)
-            return doc;
-        }
-        log.debug("Found no VamsasDocument object in properly formatted Vamsas Archive.");
-      } else {        
-        // deprecated data handler (vamsas.xsd instance)
-        InputStream vxmlis = oReader.getVamsasXmlStream();
-        if (vxmlis!=null) { // Might be an old vamsas file.
-          BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
-          InputStreamReader vxml = new InputStreamReader(ixml);
-          Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vxml, vorba, new VAMSAS());
-          
-          if (unmarsh==null)
-            log.fatal("Couldn't unmarshall document!");
-          
-          VAMSAS root[]= new VAMSAS[] { null};
-          root[0] = (VAMSAS) unmarsh[0]; 
-          
-          if (root[0]==null) {
-            log.debug("Found no VAMSAS object in VamsasXML stream.");
-          } else {
-            log.debug("Making new VamsasDocument from VamsasXML stream.");
-            VamsasDocument doc = DocumentStuff.newVamsasDocument(root, 
-                ProvenanceStuff.newProvenance(
-                    vorba.getUserHandle().getFullName(), 
-                    "Vamsas Document constructed from vamsas.xml"), VersionEntries.ALPHA_VERSION);
-            // VAMSAS: decide on 'system' operations provenance form
-            // LATER: implement classes for translating Vorba properties into provenance user fields.
-            // VAMSAS: decide on machine readable info embedding in provenance should be done
-            root[0]=null;
-            root=null;
-            return doc;
-          }
-        }
-      }
-    }
-    // otherwise - there was no valid original document to read.
-    return null;    
-  }
-
-  /**
-   * Extract all jarEntries in an archive referenced by the vamsas document
-   * LATER: a family of methods for finding extraneous jarEntries , and invalid appDataReferences
-   * @param doc
-   * @param oReader
-   * @return array of the subset of JarEntry names that are referenced in doc 
-   */
-  public Vector getReferencedEntries(VamsasDocument doc, VamsasArchiveReader oReader) {
-    if (oReader==null)
-     return null;
-    if (doc==null) {
-     try { doc = getVamsasDocument(oReader); } 
-     catch (Exception e) { log.warn("Failed to get document from "+oReader.jfile.getName()); };
-    }
-    Vector docrefs = AppDataReference.getAppDataReferences(doc);
-    if (docrefs==null)
-      return null;
-    Vector entries = oReader.getExtraEntries();
-    if (entries!=null && docrefs.size()>0) {
-      int i=0, j=entries.size();
-      do {
-        if (!docrefs.contains(entries.get(i))) {
-            entries.remove(i);
-            j--;
-        } else
-          i++;
-      } while (i<j);
-    }
-    return entries;
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/SimpleDocument.java b/src/org/vamsas/client/simpleclient/SimpleDocument.java
deleted file mode 100644
index df569e7..0000000
--- a/src/org/vamsas/client/simpleclient/SimpleDocument.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.VorbaIdFactory;
-
-/**
- * @see SimpleDocBinding
- * Additional constructors for 'headless' Vamsas Document access
- * @author jimp
- */
-public class SimpleDocument extends SimpleDocBinding {
-  private static Log log = LogFactory.getLog(SimpleDocument.class);
-  
-  private VorbaIdFactory makeDefaultFactory(String name) {
-    return IdFactory.getDummyFactory(name);
-  }
-
-  public SimpleDocument(String name) {
-    vorba = makeDefaultFactory(name);
-  }
-  public SimpleDocument(VorbaIdFactory Vorba) {
-    if (Vorba!=null)
-      vorba = Vorba;
-    else
-      log.error("Invalid SimpleDocument construction - no VorbaIdFactory defined!");
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
deleted file mode 100644
index 68c366f..0000000
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ /dev/null
@@ -1,809 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarOutputStream;
-import java.util.jar.Manifest;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.IVorbaIdFactory;
-import org.vamsas.client.SessionHandle;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.VorbaIdFactory;
-import org.vamsas.client.VorbaXmlBinder;
-import org.vamsas.client.Vobject;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
-import org.vamsas.objects.utils.AppDataReference;
-import org.vamsas.objects.utils.DocumentStuff;
-import org.vamsas.objects.utils.ProvenanceStuff;
-import org.vamsas.objects.utils.document.VersionEntries;
-
-/**
- * Class for high-level io and Jar manipulation involved in creating 
- * or updating a vamsas archive (with backups).
- * Writes to a temporary file and then swaps new file for backup.
- * uses the sessionFile locking mechanism for safe I/O
- * @author jimp
- *
- */
-public class VamsasArchive {
-  private static Log log = LogFactory.getLog(VamsasArchive.class);
-  /**
-   * Access original document if it exists, and get VAMSAS root objects.
-   * @return vector of vamsas roots from original document
-   * @throws IOException
-   */
-  public static Vobject[] getOriginalRoots(VamsasArchive ths) throws IOException, 
-  org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-    VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
-    if (oReader!=null) {
-      
-      if (oReader.isValid()) {
-        InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
-        VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
-        if (doc!=null) 
-          return doc.getVAMSAS();
-        // TODO ensure embedded appDatas are garbage collected to save memory
-      } else {
-        InputStream vxmlis = oReader.getVamsasXmlStream();
-        if (vxmlis!=null) { // Might be an old vamsas file.
-          BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
-          InputStreamReader vxml = new InputStreamReader(ixml);
-          VAMSAS root[] = new VAMSAS[1];
-          root[0] = VAMSAS.unmarshal(vxml);
-          if (root[0]!=null)
-            return root;
-        }
-      }
-    }
-    return null;
-  }
-  /**
-   * Access the original vamsas document for a VamsasArchive class, and return it.
-   * Users of the VamsasArchive class should use the getVamsasDocument method to retrieve
-   * the current document - only use this one if you want the 'backup' version.
-   * TODO: catch OutOfMemoryError - they are likely to occur here.
-   * NOTE: vamsas.xml datastreams are constructed as 'ALPHA_VERSION' vamsas documents.
-   * @param ths
-   * @return null if no document exists.
-   * @throws IOException
-   * @throws org.exolab.castor.xml.MarshalException
-   * @throws org.exolab.castor.xml.ValidationException
-   */
-  public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths) throws IOException, 
-  org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-    return VamsasArchive.getOriginalVamsasDocument(ths, null);
-  } 
-  /**
-   * Uses VorbaXmlBinder to retrieve the VamsasDocument from the original archive referred to by ths
-   * @param ths
-   * @param vorba
-   * @return
-   * @throws IOException
-   * @throws org.exolab.castor.xml.MarshalException
-   * @throws org.exolab.castor.xml.ValidationException
-   */
-  public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths, VorbaIdFactory vorba) throws IOException, 
-  org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-    VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
-    if (oReader!=null) {
-      ths.setVorba(vorba);
-      return ths.vorba.getVamsasDocument(oReader);
-    }
-    // otherwise - there was no valid original document to read.
-    return null;    
-  }
-  /**
-   * destination of new archive data (tempfile if virginarchive=true, original archive location otherwise)
-   */
-  java.io.File archive=null;
-  /**
-   * locked IO handler for new archive file
-   */
-  SessionFile rchive=null;
-  /**
-   * original archive file to be updated (or null if virgin) where new data will finally reside
-   */
-  java.io.File original=null;
-  /**
-   * original archive IO handler
-   */
-  SessionFile odoclock = null;
-  Lock destinationLock = null;
-  /**
-   * Original archive reader class
-   */
-  VamsasArchiveReader odoc = null;
-  /**
-   * true if a real vamsas document is being written.
-   */
-  boolean vamsasdocument=true;
-  /**
-   * Output stream for archived data
-   */
-  JarOutputStream newarchive=null;
-  /**
-   * JarEntries written to archive
-   */
-  Hashtable entries = null;
-  
-  /**
-   * true if we aren't just updating an archive
-   */
-  private boolean virginArchive=false;
-  
-  /**
-   * name of backup of existing archive that has been updated/overwritten.
-   * only one backup will be made - and this is it.
-   */
-  File originalBackup = null;
-  
-  boolean donotdeletebackup=false;
-  private final int _TRANSFER_BUFFER=4096*4;
-  protected SimpleDocument vorba = null;
-  /**
-   * LATER: ? CUT'n'Paste error ?
-   * Access and return current vamsas Document, if it exists, or create a new one 
-   * (without affecting VamsasArchive object state - so is NOT THREAD SAFE)
-   * _TODO: possibly modify internal state to lock low-level files 
-   * (like the IClientDocument interface instance constructer would do) 
-   * @see org.vamsas.simpleclient.VamsasArchive.getOriginalVamsasDocument for additional caveats
-   * 
-   * @return
-   * @throws IOException
-   * @throws org.exolab.castor.xml.MarshalException
-   * @throws org.exolab.castor.xml.ValidationException
-   * ????? where does this live JBPNote ?
-   */
-  private VamsasDocument _doc=null;
-  
-  /**
-   * Create a new vamsas archive
-   * File locks are made immediately to avoid contention
-   *  
-   * @param archive - file spec for new vamsas archive
-   * @param vamsasdocument true if archive is to be a fully fledged vamsas document archive
-   * @throws IOException if call to accessOriginal failed for updates, or openArchive failed.
-   */
-  public VamsasArchive(File archive, boolean vamsasdocument) throws IOException {
-    this(archive, false, vamsasdocument, null);
-  }
-  public VamsasArchive(File archive, boolean vamsasdocument, boolean overwrite) throws IOException {
-    this(archive, overwrite, vamsasdocument, null);
-  }
-  /**
-   * Constructor for accessing Files under file-lock management (ie a session file)
-   * @param archive
-   * @param vamsasdocument
-   * @param overwrite
-   * @throws IOException
-   */
-  public VamsasArchive(VamsasFile archive, boolean vamsasdocument, boolean overwrite) throws IOException {
-    this(archive.sessionFile, overwrite, vamsasdocument, archive);
-    // log.debug("using non-functional lock-IO stream jar access constructor");
-  }
-  /**
-   * read and write to archive - will not overwrite original contents, and will always write an up to date vamsas document structure.
-   * @param archive
-   * @throws IOException
-   */
-  public VamsasArchive(VamsasFile archive) throws IOException {
-    this(archive, true, false); 
-  }
-  /**
-   * 
-   * @param archive file to write
-   * @param overwrite true if original contents should be deleted
-   * @param vamsasdocument true if a proper VamsasDocument archive is to be written.
-   * @param extantLock SessionFile object holding a lock for the <object>archive</object> 
-   * @throws IOException
-   */
-  public VamsasArchive(File archive, boolean overwrite, boolean vamsasdocument, SessionFile extantLock) throws IOException {
-    super();
-    if (archive==null || (archive!=null && !(archive.getAbsoluteFile().getParentFile().canWrite() && (!archive.exists() || archive.canWrite())))) {
-      log.fatal("Expect Badness! -- Invalid parameters for VamsasArchive constructor:"+((archive!=null) 
-          ? "File cannot be overwritten." : "Null Object not valid constructor parameter"));
-      return;
-    }
-    
-    this.vamsasdocument = vamsasdocument;
-    if (archive.exists() && !overwrite) {
-      this.original = archive;
-      if (extantLock!=null) {
-        this.odoclock = extantLock;
-        if (odoclock.fileLock==null || !odoclock.fileLock.isLocked())
-          odoclock.lockFile();
-      } else { 
-        this.odoclock = new SessionFile(archive);
-      }
-      odoclock.lockFile(); // lock the file *immediatly*
-      this.archive = null;       // archive will be a temp file when the open method is called
-      virginArchive=false;
-      try {
-        this.accessOriginal();
-      } catch (IOException e)  {
-        throw new IOException("Lock failed for existing archive"+archive);
-      }
-    } else {
-      this.original = null;
-      this.archive = archive; // archive is written in place.
-      if (extantLock!=null)
-        rchive=extantLock;
-      else
-        rchive = new SessionFile(archive);
-      rchive.lockFile();
-      if (rchive.fileLock==null || !rchive.fileLock.isLocked())
-        throw new IOException("Lock failed for new archive"+archive);
-      rchive.fileLock.getRaFile().setLength(0); // empty the archive.
-      virginArchive = true;
-    }
-    this.openArchive(); // open archive
-  }
-  /**
-   * open original archive file for exclusive (locked) reading.
-   * @throws IOException
-   */
-  private void accessOriginal() throws IOException {
-    if (original!=null && original.exists()) {
-      if (odoclock==null) 
-        odoclock = new SessionFile(original);
-      odoclock.lockFile();
-      if (odoc == null) 
-        odoc = new VamsasArchiveReader(original);
-        // this constructor is not implemented yet odoc = new VamsasArchiveReader(odoclock.fileLock);
-    }
-  }
-  
-  /**
-   * Add unique entry strings to internal JarEntries list.
-   * @param entry
-   * @return true if entry was unique and was added.
-   */
-  private boolean addEntry(String entry) {
-    if (entries!=null)
-      entries=new Hashtable();
-    if (entries.containsKey(entry))
-      return false;
-    entries.put(entry, new Integer(entries.size()));
-    return true;
-  }
-  /**
-   * adds named entry to newarchive or returns false.
-   * @param entry
-   * @return true if entry was unique and could be added
-   * @throws IOException if entry name was invalid or a new entry could not be made on newarchive
-   */
-  private boolean addValidEntry(String entry) throws IOException {
-    JarEntry je = new JarEntry(entry);
-    if (!addEntry(entry))
-      return false;
-    newarchive.flush();
-    newarchive.putNextEntry(je);
-    return true;
-  }
-  /**
-   * called by app to get name of backup if it was made.
-   * If this is called, the caller app *must* delete the backup themselves.
-   * @return null or a valid file object
-   */
-  public File backupFile() {
-    
-    if (!virginArchive) {
-      makeBackup();
-      donotdeletebackup=false; // external reference has been made.
-      return ((original!=null) ? originalBackup : null);
-    }
-    return null;
-  }
-  
-  /**
-   * Stops any current write to archive, and reverts to the backup if it exists.
-   * All existing locks on the original will be released. All backup files are removed.
-   */
-  public boolean cancelArchive() {
-    if (newarchive!=null) {
-      try { 
-        newarchive.closeEntry();
-        newarchive.putNextEntry(new JarEntry("deleted"));
-        newarchive.closeEntry();
-        newarchive.close();
-        
-      } catch (Exception e) {
-        log.debug("Whilst closing newarchive",e);
-      };
-      if (!virginArchive) {
-        // then there is something to recover.
-        try {
-          recoverBackup();
-        }
-        catch (Exception e) {
-          log.warn("Problems when trying to cancel Archive "+archive.getAbsolutePath(), e);
-          return false;
-        }
-      }
-      
-    } else {
-      log.warn("Client Error: cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
-    }
-    closeAndReset(); // tidy up and release locks.
-    return true;
-  }
-  
-  /**
-   * only do this if you want to destroy the current file output stream
-   *
-   */
-  private void closeAndReset() {
-    if (rchive!=null) {
-      rchive.unlockFile();
-      rchive=null;
-    }
-    if (original!=null) {
-      if (odoc!=null) {
-        odoc.close();
-        odoc=null;
-      }
-      if (archive!=null)
-        archive.delete();
-      if (odoclock!=null) {
-        odoclock.unlockFile();
-        odoclock = null;
-      }
-    }
-    removeBackup();
-    newarchive=null;
-    original=null;
-    entries=null;
-  }
-  /**
-   * Tidies up and closes archive, removing any backups that were created.
-   * NOTE: It is up to the caller to delete the original archive backup obtained from backupFile()
-   * TODO: ensure all extant AppDataReference jar entries are transferred to new Jar
-   * TODO: provide convenient mechanism for generating new unique AppDataReferences and adding them to the document
-   */
-  public void closeArchive() throws IOException {
-    if (newarchive!=null) {
-      newarchive.flush();
-      newarchive.closeEntry();
-      if (!isDocumentWritten())
-        log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
-      newarchive.finish();// close(); // use newarchive.finish(); for a stream IO
-      newarchive.flush();
-      //
-      updateOriginal();
-      closeAndReset();
-    } else {
-      log.warn("Attempt to close archive that has not been opened for writing.");
-    }
-  }
-  /**
-   * Opens and returns the applicationData output stream for the appdataReference string.
-   * @param appdataReference
-   * @return Output stream to write to
-   * @throws IOException
-   */
-  public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
-    if (newarchive==null)
-      throw new IOException("Attempt to write to closed VamsasArchive object.");
-    if (addValidEntry(appdataReference)) {
-      return new AppDataOutputStream(newarchive);
-    }
-    return null;
-  }
-  
-  /**
-   * 
-   * @return JarEntry name for the vamsas XML stream in this archive
-   */
-  protected String getDocumentJarEntry() {
-    if (vamsasdocument)
-      return VamsasArchiveReader.VAMSASDOC;
-    return VamsasArchiveReader.VAMSASXML;
-  }
-  /**
-   * Safely initializes the VAMSAS XML document Jar Entry. 
-   * @return Writer to pass to the marshalling function.
-   * @throws IOException if a document entry has already been written. 
-   */
-  public PrintWriter getDocumentOutputStream() throws IOException {
-    if (newarchive==null)
-      openArchive();
-    if (!isDocumentWritten()) {
-      try {
-        if (addValidEntry(getDocumentJarEntry())) 
-          return new PrintWriter(new java.io.OutputStreamWriter(newarchive, "UTF-8"));
-      } catch (Exception e) {
-        log.warn("Problems opening XML document JarEntry stream",e);
-      }
-    } else {
-      throw new IOException("Vamsas Document output stream is already written.");
-    }
-    return null;
-  }
-  
-  /**
-   * Access original archive if it exists, pass the reader to the client
-   * Note: this is NOT thread safe and a call to closeArchive() will by necessity 
-   * close and invalidate the VamsasArchiveReader object.
-   * @return null if no original archive exists.
-   */
-  public VamsasArchiveReader getOriginalArchiveReader() throws IOException {
-    if (!virginArchive) {
-      accessOriginal();
-      return odoc;
-    }
-    return null;
-  }
-  /**
-   * returns original document's root vamsas elements.
-   * @return
-   * @throws IOException
-   * @throws org.exolab.castor.xml.MarshalException
-   * @throws org.exolab.castor.xml.ValidationException
-   */
-  public Vobject[] getOriginalRoots() throws IOException, 
-  org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException  {
-    return VamsasArchive.getOriginalRoots(this);
-  }
-  /**
-   * @return original document or a new empty document (with default provenance)
-   * @throws IOException
-   * @throws org.exolab.castor.xml.MarshalException
-   * @throws org.exolab.castor.xml.ValidationException
-   */
-  public VamsasDocument getVamsasDocument() throws IOException, 
-  org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-    return getVamsasDocument("org.vamsas.simpleclient.VamsasArchive", "Created new empty document", null);
-  }
-  /**
-   * Return the original document or a new empty document with initial provenance entry.
-   * @param provenance_user (null sets user to be the class name)
-   * @param provenance_action (null sets action to be 'created new document')
-   * @param version (null means use latest version)
-   * @return (original document or a new vamsas document with supplied provenance and version info)
-   * @throws IOException
-   * @throws org.exolab.castor.xml.MarshalException
-   * @throws org.exolab.castor.xml.ValidationException
-   */
-  public VamsasDocument getVamsasDocument(String provenance_user, String provenance_action, String version) throws IOException, 
-  org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-    if (_doc!=null)
-      return _doc;
-    _doc = getOriginalVamsasDocument(this, getVorba());
-    if (_doc!=null)
-      return _doc;
-    // validate parameters
-    if (provenance_user==null)
-      provenance_user = "org.vamsas.simpleclient.VamsasArchive";
-    if (provenance_action == null)
-      provenance_action="Created new empty document";
-    if (version==null)
-      version = VersionEntries.latestVersion();
-    // Create a new document and return it
-    _doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { new VAMSAS()}, 
-        ProvenanceStuff.newProvenance(provenance_user, provenance_action), version);
-    return _doc;
-  }
-  /**
-   * @return Returns the current VorbaIdFactory for the archive.
-   */
-  public VorbaIdFactory getVorba() {
-    if (vorba==null)
-      vorba = new SimpleDocument("simpleclient.VamsasArchive");
-    return vorba.getVorba();
-  }
-  /**
-   * @return true if Vamsas Document has been written to archive
-   */
-  protected boolean isDocumentWritten() {
-    if (newarchive==null)
-      log.warn("isDocumentWritten() called for unopened archive.");
-    if (entries!=null) {
-      if (entries.containsKey(getDocumentJarEntry()))
-        return true;
-    }
-    return false;
-  }
-  private void makeBackup() {
-    if (!virginArchive) {
-      if (originalBackup==null && original!=null && original.exists()) {
-        try {
-          accessOriginal();
-          originalBackup = odoclock.backupSessionFile(null, original.getName(), ".bak", original.getParentFile());
-        }
-        catch (IOException e) {
-          log.warn("Problem whilst making a backup of original archive.",e);
-        }
-      }
-    }
-  }
-  /**
-   * opens the new archive ready for writing. If the new archive is replacing an existing one, 
-   * then the existing archive will be locked, and the new archive written to a temporary file. 
-   * The new archive will be put in place once close() is called.
-   * @param doclock LATER - pass existing lock on document, if it exists.... no need yet?
-   * @throws IOException
-   */
-  private void openArchive() throws IOException {
-    
-    if (newarchive!=null) {
-      log.warn("openArchive() called multiple times.");
-      throw new IOException("Vamsas Archive '"+archive.getAbsolutePath()+"' is already open.");
-    }
-    if (archive==null && (virginArchive || original==null)) {
-      log.warn("openArchive called on uninitialised VamsasArchive object.");
-      throw new IOException("Badly initialised VamsasArchive object - no archive file specified.");
-    }
-    if (!virginArchive) {
-      // lock the original
-      accessOriginal();
-      // make a temporary file to write to
-      archive = File.createTempFile(original.getName(), ".new",original.getParentFile());
-    } else {
-      if (archive.exists())
-        log.warn("New archive file name already in use! Possible lock failure imminent?");
-    }
-    
-    if (rchive==null)
-      rchive = new SessionFile(archive);
-    if (!rchive.lockFile()) 
-      throw new IOException("Failed to get lock on file "+archive);
-    // LATER: locked IO stream based access.
-    Manifest newmanifest = new Manifest();
-    newarchive = new JarOutputStream(rchive.fileLock.getBufferedOutputStream(true), newmanifest);  
-    //newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));  
-    entries = new Hashtable();
-  }
-  public void putVamsasDocument(VamsasDocument doc) throws IOException, 
-  org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-    putVamsasDocument(doc, getVorba());
-  }
-  /**
-   * 
-   * @param doc
-   * @param vorba
-   * @return (vorbaId string, Vobjhash) pairs for last hash of each object in document
-   * @throws IOException
-   * @throws org.exolab.castor.xml.MarshalException
-   * @throws org.exolab.castor.xml.ValidationException
-   */
-  public void putVamsasDocument(VamsasDocument doc, VorbaIdFactory vorba) throws IOException, 
-  org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-    if (vamsasdocument)
-      doc.setVersion(VersionEntries.latestVersion()); // LATER: ensure this does the correct thing.
-    VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);
-  }
-  
-  /**
-   * recovers the original file's contents from the (temporary) backup. 
-   * @throws Exception if any SessionFile or file removal operations fail.
-   */
-  private void recoverBackup() throws Exception {
-    if (originalBackup!=null) {
-      // backup has been made.
-      // revert from backup and delete it (changing backup filename)
-      if (rchive==null) {
-        rchive = new SessionFile(original);
-      }
-      SessionFile bckup = new SessionFile(originalBackup);
-      
-      rchive.updateFrom(null, bckup); // recover from backup file.
-      bckup.unlockFile();
-      bckup=null;
-      removeBackup();
-    }
-  }
-  
-  /**
-   * forget about any backup that was made - removing it first if it was only temporary.
-   */
-  private void removeBackup() {
-    if (originalBackup!=null) {
-      log.debug("Removing backup in "+originalBackup.getAbsolutePath());
-      if (!donotdeletebackup)
-        if (!originalBackup.delete())
-          log.info("VamsasArchive couldn't remove temporary backup "+originalBackup.getAbsolutePath());
-      originalBackup=null;
-    }
-  } 
-  /**
-   * @param vorba the VorbaIdFactory to use for accessing vamsas objects.
-   */
-  public void setVorba(VorbaIdFactory Vorba) {
-    if (Vorba!=null) {
-      if (vorba==null)
-        vorba = new SimpleDocument(Vorba);
-      else
-        vorba.setVorba(Vorba);
-    } else
-      getVorba();
-  }
-  /**
-   * Convenience method to copy over the referred entry from the backup to the new version.
-   * Warning messages are raised if no backup exists or the 
-   * entry doesn't exist in the backed-up original.
-   * Duplicate writes return true - but a warning message will also be raised.
-   * @param AppDataReference
-   * @return true if AppDataReference now exists in the new document
-   * @throws IOException
-   */
-  public boolean transferAppDataEntry(String AppDataReference) throws IOException {
-    return transferAppDataEntry(AppDataReference, AppDataReference);
-  }
-  /**
-   * Validates the AppDataReference: not null and not already written to archive.
-   * @param AppDataReference
-   * @return true if valid. false if not
-   * @throws IOException for really broken references!
-   */
-  protected boolean _validNewAppDataReference(String newAppDataReference) throws IOException {
-    // LATER: Specify valid AppDataReference form in all VamsasArchive handlers
-    if (newAppDataReference==null)
-      throw new IOException("null newAppDataReference!");
-    if (entries.containsKey(newAppDataReference)) {
-      log.warn("Attempt to write '"+newAppDataReference+"' twice! - IGNORED");
-      // LATER: fix me? warning message should raise an exception here.
-      return false;
-    }
-    return true;
-  }
-  /**
-   * Transfers an AppDataReference from old to new vamsas archive, with a name change.
-   * @see transferAppDataEntry(String AppDataReference)
-   * @param AppDataReference
-   * @param NewAppDataReference - AppDataReference in new Archive
-   * @return
-   * @throws IOException
-   */
-  public boolean transferAppDataEntry(String AppDataReference, String NewAppDataReference) throws IOException {
-    if (original==null || !original.exists()) {
-      log.warn("No backup archive exists.");
-      return false;
-    }
-    if (AppDataReference==null)
-      throw new IOException("null AppDataReference!");
-
-    if (!_validNewAppDataReference(NewAppDataReference))
-      return false;
-    
-    accessOriginal();
-    
-    java.io.InputStream adstream = odoc.getAppdataStream(AppDataReference);
-    
-    if (adstream==null) {
-      log.warn("AppDataReference '"+AppDataReference+"' doesn't exist in backup archive.");
-      return false;
-    }
-    
-    java.io.OutputStream adout = getAppDataStream(NewAppDataReference);
-    // copy over the bytes
-    int written=-1;
-    long count=0;
-    byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer
-    do {
-      if ((written = adstream.read(buffer))>-1) {
-        adout.write(buffer, 0, written);
-        log.debug("Transferring "+written+".");
-        count+=written;
-      }
-    } while (written>-1);
-    log.debug("Sucessfully transferred AppData for '"
-        +AppDataReference+"' as '"+NewAppDataReference+"' ("+count+" bytes)");
-    return true;
-  }
-  /**
-   * write data from a stream into an appData reference.
-   * @param AppDataReference - New AppDataReference not already written to archive
-   * @param adstream Source of data for appData reference - read until .read(buffer) returns -1
-   * @return true on success.
-   * @throws IOException for file IO or invalid AppDataReference string
-   */
-  public boolean writeAppdataFromStream(String AppDataReference, java.io.InputStream adstream) throws IOException {
-    if (!_validNewAppDataReference(AppDataReference)) {
-      log.warn("Invalid AppDataReference passed to writeAppdataFromStream");
-      throw new IOException("Invalid AppDataReference! (null, or maybe non-unique)!");
-    }
-      
-    if (AppDataReference==null) {
-      log.warn("null appdata passed.");
-      throw new IOException("Null AppDataReference");
-    }
-    
-    java.io.OutputStream adout = getAppDataStream(AppDataReference);
-    // copy over the bytes
-    int written=-1;
-    long count=0;
-    byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer
-    do {
-      if ((written = adstream.read(buffer))>-1) {
-        adout.write(buffer, 0, written);
-        log.debug("Transferring "+written+".");
-        count+=written;
-      }
-    } while (written>-1);
-    return true;
-  }
-  /**
-   * transfers any AppDataReferences existing in the old document 
-   * that haven't already been transferred to the new one
-   * LATER: do the same for transfers requiring a namechange - more document dependent.
-   *  @return true if data was transferred.
-   */
-  public boolean transferRemainingAppDatas() throws IOException {
-    boolean transfered=false;
-    if (original==null || !original.exists()) {
-      log.warn("No backup archive exists.");
-      return false;
-    }
-    accessOriginal();
-    
-    if (getVorba()!=null) {
-      Vector originalRefs=null;
-      try {
-        originalRefs = vorba.getReferencedEntries(getVamsasDocument(), getOriginalArchiveReader());
-      } catch (Exception e) {
-        log.warn("Problems accessing original document entries!",e);
-      }
-      if (originalRefs!=null) {
-        Iterator ref = originalRefs.iterator();
-        while (ref.hasNext()) {
-          String oldentry = (String) ref.next();
-          if (oldentry!=null && !entries.containsKey(oldentry)) {
-            log.debug("Transferring remaining entry '"+oldentry+"'");
-            transfered |= transferAppDataEntry(oldentry);
-          }
-        }
-      }
-    } 
-    return transfered;
-  }
-  /**
-   * called after archive is written to put file in its final place
-   */
-  private void updateOriginal() {
-    if (!virginArchive) {
-      // make sure original document really is backed up and then overwrite it.
-      if (odoc!=null) {
-        // try to shut the odoc reader.
-        odoc.close();
-        odoc = null;
-      }
-      // Make a backup if it isn't done already
-      makeBackup();
-      try {
-        // copy new Archive data that was writen to a temporary file
-        odoclock.updateFrom(null, rchive);
-      }
-      catch (IOException e) {
-        // LATER: decide if leaving nastily named backup files around is necessary.
-        File backupFile=backupFile();
-        if (backupFile!=null)
-          log.error("Problem updating archive from temporary file! - backup left in '"
-            +backupFile().getAbsolutePath()+"'",e);
-        else
-          log.error("Problems updating, and failed to even make a backup file. Ooops!", e);
-      }
-      // Tidy up if necessary.
-      removeBackup();
-    } else {
-      
-      
-    }
-  }
-}
diff --git a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java b/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
deleted file mode 100644
index 2df47f5..0000000
--- a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
+++ /dev/null
@@ -1,313 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.BufferedInputStream;
-import java.io.FileInputStream;
-import java.io.RandomAccessFile;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarFile;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.document.VersionEntries;
-/**
- * Basic methods for accessing an existing Vamsas Archive, 
- * and Jar entry names for creating new vamsas archives.
- * 
- * @author jimp
- *
- */
-public class VamsasArchiveReader {
-  private static Log log = LogFactory.getLog(VamsasArchiveReader.class);
-  JarFile jfile=null;
-  boolean stream=false; // true if we are seeking on the stream.
-  RandomAccessFile rfile;
-  ZipInputStream jstream=null;
-  Hashtable strmentries = null;
-  private void streamInit() {
-    //throw new Error("VamsasArchiveReader(Stream) Not implemented!");
-     if (!stream) {
-      log.debug("Skipping init for Jar Stream input.");
-      return;
-    }
-    strmentries = new Hashtable();
-    log.debug("Jar Stream input Initialisation");
-    try {
-      rfile.seek(0);
-      // no buffering - we need to be able to move around the random access stream.
-      jstream = new ZipInputStream(new FileInputStream(rfile.getFD())); // no manifest (probably)
-      if (jstream.available()==0)
-        log.warn("Can't read from JarInputStream (Locked stream!)");
-      ZipEntry entry=null;
-      long pos=0;
-      do {
-        if ((entry=jstream.getNextEntry())!=null) {
-          if (strmentries.containsKey(entry.getName())) {
-            log.info("Only recording last of duplicate entries '"+entry.getName()+"'");
-          } 
-          strmentries.put(entry.getName(), new Long(pos++));
-          jstream.closeEntry();
-        }
-      } while (entry!=null);
-    }
-    catch (Exception e) {
-      log.warn("Exceptions during init!",e);
-      jstream=null;
-    }
-  }
-  
-  public VamsasArchiveReader(File vamsasfile) {
-    jfile=null;
-    if (vamsasfile.exists()) {
-      try {
-        jfile=new JarFile(vamsasfile);
-      }
-      catch (Exception e) {
-        log.debug("non-serious? couldn't open new JarFile on "+vamsasfile,e);
-        jfile=null;
-      }
-    }
-    
-  }
-  /**
-   * in an ideal world - this constructor will create a reader object
-   * for the locked file's random access stream.
-   * 
-   * @param vamsaslock
-   */
-  public VamsasArchiveReader(Lock vamsaslock) {
-    // LATER: implement or remove
-    if (vamsaslock==null || !vamsaslock.isLocked())
-      throw new Error("IMPLEMENTATION ERROR: Cannot create a VamsasArchiveReader without a valid lock.");
-    // throw new Error("VamsasArchiveReading from locked IO stream not yet implemented.");
-    try {
-      rfile = vamsaslock.getRaFile();
-    } catch (Exception e) {
-      log.warn("Unexpected IO Exception when accessing locked vamsas archive stream "+vamsaslock.target,e);
-    }
-    stream = true;
-    streamInit();
-    if (jstream==null)
-      throw new Error("Failed to open archive from Locked random access stream.");
-  }
-  
-  /**
-   * the vamsas document version(s) handled by this Reader
-   */
-  final public static String DOCUMENT_VERSION=VersionEntries.BETA_VERSION; 
-  /**
-   * name of the jarEntry containing a well formatted vamsas XML Document
-   */
-  
-  final public static String VAMSASDOC="vamsasDocument.xml";
-  
-  /**
-   * name of the jarEntry containing a root VAMSAS element, and containing a 
-   * random sequence of VAMSAS DataSet elements 
-   */
-  
-  final public static String VAMSASXML="vamsas.xml";
-  /**
-   * seeks jstream to the given entry name and reads it.
-   * @param entryname
-   * @return
-   */
-  private JarEntry seekEntry(String entryname) {
-    if (jstream==null)
-      return null;
-    if (!strmentries.containsKey(entryname)) 
-      return null;
-    Long entrypos = (Long) strmentries.get(entryname);
-    if (entrypos==null) {
-      log.error("Null entry position for "+entryname);
-      return null;
-    }
-    try {
-      jstream=null;
-      rfile.seek(0);
-      jstream = new ZipInputStream(new FileInputStream(rfile.getFD()));
-      ZipEntry entry = null;
-      long epos = entrypos.longValue();
-      do {
-        entry = jstream.getNextEntry();
-      } while (entry!=null && --epos>=0);  
-        // rfile.seek(entrypos.longValue());
-      // make a Jar entry from a zip entry.
-      return new JarEntry(entry);
-    }
-    catch (Exception e) {
-      log.warn("Whilst seeking for "+entryname, e);
-    }
-    return null;
-  }
-  /**
-   * 
-   * @return JarEntry for VamsasArchiveReader.VAMSASDOC
-   */
-  protected JarEntry getVamsasDocumentEntry() {
-    return getJarEntry(VAMSASDOC);
-  }
-  /**
-   * 
-   * @return JarEntry for VamsasArchiveReader.VAMSASXML
-   */
-  protected JarEntry getVamsasXmlEntry() {
-    return getJarEntry(VAMSASXML);
-  }
-  /**
-   * Test for valid vamsas document archive
-   * @return true if getVamsasDocumentStream will return a stream likely to contain valid XML
-   */
-  public boolean isValid() {
-    // TODO: check if VAMSASDOC is well formed (follows www.vamsas.ac.uk/schemas/vamsasDocument.xsd) and all appData references are resolvable - preferably as jar entries
-    if (jfile!=null || jstream!=null)
-      return (getVamsasDocumentEntry()!=null);
-    return false;   
-  }
-  
-  
-  protected JarEntry getAppdataEntry(String AppdataRef) {
-    JarEntry entry;
-    if ((jfile==null && jstream==null) || !isValid() || (entry=getJarEntry(AppdataRef))==null)
-      return null;
-    
-    return entry;
-  }
-  
-  public InputStream getAppdataStream(String AppdataRef) {
-    JarEntry entry=getAppdataEntry(AppdataRef);
-    try {
-      if (entry!=null)
-        return getInputStream(entry);
-    } catch (IOException e) {
-      log.error("Failed when opening AppdataStream for "+AppdataRef, e);
-    }
-    return null;
-  }
-  /**
-   * get the VamsasDocument input stream, if it exists.
-   * @return null or valid input stream
-   */
-  public InputStream getVamsasDocumentStream() {
-    InputStream vdoc;
-    if ((jfile==null && jstream==null) || !isValid())
-      return null;
-    try {
-      vdoc = getInputStream(getVamsasDocumentEntry());
-    } catch (IOException e) {
-      log.error("Whilst geting document stream",e);
-      vdoc=null;
-    }
-    return vdoc;
-  }
-  
-  /**
-   * get the VamsasXML input stream, if it exists.
-   * Note: Deprecated beyond our prealpha testing.
-   * @return null or valid input stream.
-   */
-  
-  public InputStream getVamsasXmlStream() {
-    // log.warn("Deprecated call");
-    JarEntry xmle=getVamsasXmlEntry();
-    InputStream vdoc;
-    if (xmle==null)
-      return null;
-    try {
-      vdoc = getInputStream(xmle);
-    } catch (IOException e) {
-      log.error("Whilst getting VamsasXmlStream",e);
-      vdoc=null;
-    }
-    return vdoc;
-  }
-  
-  /**
-   * silently close the jar file.
-   *
-   */
-  public void close() {
-    if (jfile!=null) {
-      try {
-        jfile.close();
-      } catch (IOException e) {
-        log.error("Whilst closing JarFile "+jfile.getName(), e);
-      }
-    }
-    if (jstream!=null) {
-      try {
-        jstream.closeEntry();
-        jstream=null;
-        // LATER: reference counting for random access file instances is necessary.
-      }
-      catch (Exception e) {
-        log.error("Whilst finishing reading from jar input stream",e);
-      }
-    }
-  }
-  
-  /**
-   * returns all entries not matching the filespec of a vamsas xml entry
-   * @return array of entries.
-   */
-  public Vector getExtraEntries() {
-    if ((jfile==null && jstream==null)|| !isValid())
-      return null;
-    Vector e = new Vector();
-    if (jstream!=null) {
-      Enumeration entries = strmentries.keys();
-      if (entries!=null && entries.hasMoreElements()) {
-        do {
-          JarEntry el = (JarEntry) entries.nextElement();
-          if (!el.getName().equals(VAMSASDOC) && !el.getName().equals(VAMSASXML))
-            e.add(new String(el.getName())); // avoid references
-        } while (entries.hasMoreElements());
-      }
-    } else {
-      Enumeration entries = jfile.entries();
-      if (entries!=null && entries.hasMoreElements()) {
-        do {
-          JarEntry el = (JarEntry) entries.nextElement();
-          if (!el.getName().equals(VAMSASDOC) && !el.getName().equals(VAMSASXML))
-            e.add(new String(el.getName())); // avoid references
-        } while (entries.hasMoreElements());
-      }
-      return e;
-    }
-    return null;
-  }
-  
-  /* (non-Javadoc)
-   * @see java.util.jar.JarFile#getInputStream(java.util.zip.ZipEntry)
-   */
-  private InputStream getInputStream(ZipEntry ze) throws IOException {
-    if (jfile!=null)
-      return jfile.getInputStream(ze);
-    if (jstream!=null) {
-      seekEntry(ze.getName());
-      return new AppDataInputStream(jstream);
-    }
-    return null;
-  }
-    
-    /* (non-Javadoc)
-     * @see java.util.jar.JarFile#getJarEntry(java.lang.String)
-     */
-    private JarEntry getJarEntry(String name) {
-      if (jfile!=null)
-        return jfile.getJarEntry(name);
-      if (jstream!=null)
-        return seekEntry(name);
-      return null;
-    }
-  }
diff --git a/src/org/vamsas/client/simpleclient/VamsasFile.java b/src/org/vamsas/client/simpleclient/VamsasFile.java
deleted file mode 100644
index 3dd2581..0000000
--- a/src/org/vamsas/client/simpleclient/VamsasFile.java
+++ /dev/null
@@ -1,100 +0,0 @@
-
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
-import java.util.Timer;
-import java.util.jar.JarEntry;
-import java.util.jar.JarFile;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import org.vamsas.objects.core.LockFileDescriptor;
-
-/**
- * low level vamsas document management routines
- * analogous to ClientsFile
- * Grew out of io tests on VamsasArchive class in org.vamsas.test.simpleclient.VamsasArchive
- * This class is not thread safe.
- * @author jimp
- *
- */
-public class VamsasFile extends SessionFile {
-  /**
-   * 
-   * Connect to an existing Vamsas document in a given sessionDir
-   * or create a new one.
-   * 
-   * @param sessionDir
-   * @throws java.io.IOException
-   */
-  public VamsasFile(File sessionFile) throws java.io.IOException {
-    super(sessionFile);
-  }
-  /**
-   * 
-   * @return the VamsasFile
-   */
-  public File getVamsasFile() {
-    return sessionFile;
-  }
-  /**
-   * Expand a previously stored session into the sessionDir
-   * @param sessionDir
-   * @param storedSession
-   
-   public VamsasFile(File sessionDir, JarFile storedSession) throws IOException {
-    // check if sessionDir is live or not
-    if (!sessionDir.exists()) {
-      sessionDir.mkdir();
-    }
-    
-    {
-      // check its actually a writable directory
-    }
-    
-    File sfile = new File(sessionDir, "vamsas.jar");
-    VamsasFile(sfile);
-    // if live - try to merge storedSession with sessionDir
-    //  - will probably fail through duplicate Vobject references needing to be dereferenced.
-    // TODO: think of a way of specifying vorba_id scope for an application's references to allow merging of one vamsasDocument with another.
-    
-  }
-  */
-  /**
-   * public interface for getting a lock.
-   * The lock object is internally referenced 
-   * so the lock will persist even after the
-   * return value of the method goes out of scope.
-   * @return null if lock couldn't be got or a valid Lock object.
-   */
-  public Lock getLock() {
-    if (lockFile())
-      return fileLock;
-    return null;
-  }
-  /**
-   * 
-   * @param extantLock
-   * @return null, extantLock or new Lock.
-   */
-  public Lock getLock(Lock extantLock) {
-    if (lockFile(extantLock))
-      return fileLock;
-    return null;
-  }
-  /**
-   * explicitly unlocks vamsas file.
-   * if you have called getLock() you *must* 
-   * call this to release the lock.
-   */
-  public void unLock() {
-    this.unlockFile();
-  }
-  
-}
diff --git a/src/org/vamsas/client/simpleclient/VamsasSession.java b/src/org/vamsas/client/simpleclient/VamsasSession.java
deleted file mode 100644
index a5359ad..0000000
--- a/src/org/vamsas/client/simpleclient/VamsasSession.java
+++ /dev/null
@@ -1,312 +0,0 @@
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.io.PrintWriter;
-import java.io.RandomAccessFile;
-import java.io.Writer;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.apache.log4j.Appender;
-import org.apache.log4j.Logger;
-import org.apache.log4j.FileAppender;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.UserHandle;
-/**
- * Does all the IO operations for a SimpleClient instance accessing 
- * a SimpleClient vamsas session.
- * 
- * Basically, it defines the various standard names for the files 
- * in the session directory (that maps to the sessionUrn), 
- * provides constructors for the file handlers and watchers of 
- * those file entities, and some higher level methods 
- * to check and change the state flags for the session.
- * 
- * TODO: move the stuff below to the SimpleClientFactory documentation.
- * much may not be valid now :
- * Vamsas client is intialised with a path to create live session directories. 
- * This path may contain a vamsas.properties file 
- * that sets additional parameters (otherwise client 
- * just uses the one on the classpath).
- * 
- * A vamsas session consists of :
- *  SessionDir - translates to urn of a live session.
- *  Contains: Vamsas Document (as a jar), Session client list file, 
- *  both of which may be locked, and additional 
- *  temporary versions of these files when write 
- *  operations are taking place.
- * 
- * Zip file entries
- *  - vamsasdocument.xml : core info
- *  one or more:
- *  - <applicationname>.version.sessionnumber.raw (string given in vamsasdocument.xml applicationData entry)
- *  
- * Lockfile
- *  - filename given in the vamsasdocument.xml. Should be checked for validity by any client and rewritten if necessary. 
- *    The lockfile can point to the jar itself.
- * Mode of operation.
- * Initially - documentHandler either:
- *  - creates a zip for a new session for the client
- *  - connect to an existing session zip 
- *   1. reads session urn file
- *   2. waits for lock
- *   3. examines session - decide whether to create new application data slice or connect to one stored in session.
- *   4. writes info into session file
- *   5. releases lock and generates local client events.
- *   6. Creates Watcher thread to generate events.
- * 
- * During the session
- *  - Update watcher checks for file change - 
- * 
- * Procedures for file based session message exchange
- *  - session document modification flag
- *    
- */
-
-public class VamsasSession {
-  /**
-   * indicator file for informing other processes that 
-   * they should finalise their vamsas datasets for 
-   * storing into a vamsas archive.
-   */
-  public static final String CLOSEANDSAVE_FILE="stored.log";
-  /**
-   * session file storing the last_stored_stat data 
-   */
-  public static final String MODIFIEDDOC_FILE="modified";
-
-  /**
-   * called to clear update flag after a successful offline storage event
-   */
-  protected void clearUnsavedFlag() {
-    SessionFlagFile laststored = new SessionFlagFile(new File(sessionDir, MODIFIEDDOC_FILE));
-    if (!laststored.clearFlag())
-      log.warn("Unsaved flag was not cleared for "+sessionDir);
-  }
-  /**
-   * called to indicate session document has been modified.
-   *
-   */
-  protected void setUnsavedFlag() {
-    SessionFlagFile laststored = new SessionFlagFile(new File(sessionDir, MODIFIEDDOC_FILE));
-    if (!laststored.setFlag())
-      log.warn("Couldn't set the Unsaved flag for "+sessionDir);
-  }
-  /**
-   * 
-   * @return true if session document has been modified since last offline storage event 
-   */
-  protected boolean getUnsavedFlag() {
-    SessionFlagFile laststored = new SessionFlagFile(new File(sessionDir, MODIFIEDDOC_FILE));
-    return laststored.checkFlag();
-  }
-  /**
-   * log file location
-   */
-  public static final String SESSION_LOG="Log.txt";
-  private static Log log = LogFactory.getLog(VamsasSession.class);
-  protected Logger slog = Logger.getLogger("org.vamsas.client.SessionLog");
-  /**
-   * setup the sessionLog using Log4j.
-   * @throws IOException
-   */
-  private void initLog() throws IOException {
-    // LATER: make dedicated appender format for session log.
-    Appender app = slog.getAppender("SESSION_LOG");
-    slog.addAppender(new FileAppender(app.getLayout(), new File(sessionDir, SESSION_LOG).getAbsolutePath()));
-  }
-  
-  /**
-   * the sessionDir is given as the session location for new clients.
-   */
-  protected File sessionDir;
-  /**
-   * holds the list of attached clients
-   */
-  ClientsFile clist;
-  public static final String CLIENT_LIST="Clients.obj";
-  /**
-   * holds the data
-   */
-  VamsasFile vamArchive; 
-  public static final String VAMSAS_OBJ="VamDoc.jar";
-  
-  /**
-   * sets up the vamsas session files and watchers in sessionDir
-   * @param sessionDir
-   */
-  protected VamsasSession(File sessionDir) throws IOException {
-    if (sessionDir==null)
-      throw new Error("Null directory for VamsasSession.");
-    if (sessionDir.exists()) {
-      if (!sessionDir.isDirectory() || !sessionDir.canWrite() || !sessionDir.canRead())
-        throw new IOException("Cannot access '"+sessionDir+"' as a read/writable Directory.");
-      if (checkSessionFiles(sessionDir)) {
-        // session files exist in the directory
-        this.sessionDir = sessionDir;
-        initSessionObjects();
-        slog.debug("Initialising additional VamsasSession instance");
-        log.debug("Attached to VamsasSession in "+sessionDir);
-      } 
-    } else {
-      // start from scratch
-      if (!sessionDir.mkdir())
-        throw new IOException("Failed to make VamsasSession directory in "+sessionDir);
-      this.sessionDir = sessionDir; 
-      createSessionFiles();
-      initSessionObjects();
-      slog.debug("Session directory created.");
-      log.debug("Initialised VamsasSession in "+sessionDir);
-    }
-  }
-  /**
-   * tests presence of existing sessionfiles files in dir
-   * @param dir
-   * @return
-   */
-  private boolean checkSessionFiles(File dir) throws IOException {
-    File c_file = new File(dir,CLIENT_LIST);
-    File v_doc = new File(dir,VAMSAS_OBJ);
-    if (c_file.exists() && v_doc.exists())
-      return true;
-    return false;
-  }
-  /**
-   * create new empty files in dir
-   *
-   */
-  private void createSessionFiles() throws IOException {
-    if (sessionDir==null)
-      throw new IOException("Invalid call to createSessionFiles() with null sessionDir");
-    File c_file = new File(sessionDir,CLIENT_LIST);
-    File v_doc = new File(sessionDir,VAMSAS_OBJ);
-    if (c_file.createNewFile())
-      log.debug("Created new ClientFile "+c_file); // don't care if this works or not
-    if (v_doc.createNewFile())
-      log.debug("Created new Vamsas Session Document File "+v_doc); 
-  }
-  /**
-   * construct SessionFile objects and watchers for each
-   */
-  private void initSessionObjects() throws IOException {
-    if (clist!=null || vamArchive!=null)
-      throw new IOException("initSessionObjects called for initialised VamsasSession object.");
-    clist = new ClientsFile(new File(sessionDir,CLIENT_LIST));
-    vamArchive = new VamsasFile(new File(sessionDir,VAMSAS_OBJ));
-    initLog();
-  }
-  /**
-   * make a new watcher object for the clientFile
-   * @return new ClientFile watcher instance
-   */
-  public FileWatcher getClientWatcher() {
-    return new FileWatcher(clist.sessionFile);
-  }
-  FileWatcher session_doc_watcher=null;
-  /**
-   * make a new watcher object for the vamsas Document
-   * @return new ClientFile watcher instance
-   */
-  public FileWatcher getDocWatcher() {
-    if (session_doc_watcher==null)
-      return session_doc_watcher = new FileWatcher(vamArchive.sessionFile);
-    return new FileWatcher(vamArchive.sessionFile);
-  }
-  FileWatcher store_doc_file=null;
-  /**
-   * make a new watcher object for the messages file
-   * (thread safe - keeps a reference to the first watcher)
-   * @return new watcher instance
-   */
-  public FileWatcher getStoreWatcher() {
-    if (store_doc_file==null)
-      return store_doc_file = new FileWatcher(new File(CLOSEANDSAVE_FILE));
-    return new FileWatcher(new File(CLOSEANDSAVE_FILE));
-
-  }
-  /**
-   * write to the StoreWatcher file to indicate that a storeDocumentRequest has been made.
-   * The local client's storeWatcher FileWatcher object is updated so the initial change is not registered.
-   * @param client
-   * @param user
-   * @return
-   */
-  public void addStoreDocumentRequest(ClientHandle client, UserHandle user) throws IOException {
-    SessionFile sfw = new SessionFile(new File(sessionDir, CLOSEANDSAVE_FILE));
-    while (!sfw.lockFile())
-      log.debug("Trying to get lock for "+CLOSEANDSAVE_FILE);
-    RandomAccessFile sfwfile=sfw.fileLock.getRaFile();
-    sfwfile.setLength(0); // wipe out any old info.
-    // TODO: rationalise what gets written to this file (ie do we want other clients to read the id of the requestor?)
-    sfwfile.writeUTF(client.getClientUrn()+":"+user.getFullName()+"@"+user.getOrganization());
-    sfw.unlockFile();
-    if (store_doc_file!=null)
-      store_doc_file.setState();
-    slog.info("FinalizeAppData request from "+user.getFullName()+" using "+client.getClientUrn()+"");
-  }
-  /**
-   * create a new session with an existing vamsas Document - by copying it into the session.
-   * @param archive
-   */
-  public void setVamsasDocument(File archive) throws IOException {
-    log.debug("Transferring vamsas data from "+archive+" to session:"+vamArchive.sessionFile);
-    SessionFile xtantdoc = new SessionFile(archive);
-    vamArchive.updateFrom(null, xtantdoc);
-    // LATER: decide if session archive provenance should be updated to reflect access.
-    // TODO: soon! do a proper import objects from external file 
-    log.debug("Transfer complete.");
-  }
-  /**
-   * write session as a new vamsas Document (this will overwrite any existing file without warning)
-   * TODO: test
-   * TODO: verify that lock should be released for vamsas document.
-   * @param destarchive
-   */
-  protected void writeVamsasDocument(File destarchive, Lock extlock) throws IOException {
-    log.debug("Transferring vamsas data from "+vamArchive.sessionFile+" to session:"+destarchive);
-    SessionFile newdoc = new SessionFile(destarchive);
-    if (extlock==null && !vamArchive.lockFile())
-      while (!vamArchive.lockFile())
-        log.info("Trying to get lock for "+vamArchive.sessionFile);
-    // TODO: LATER: decide if session archive provenance should be written in vamsasDocument file for this export.
-    newdoc.updateFrom(extlock, vamArchive);
-    // LATER: LATER: fix use of updateFrom for file systems where locks cannot be made (because they don't have a lockManager, ie NFS/Unix, etc).
-    vamArchive.unLock();
-    newdoc.unlockFile();
-    log.debug("Transfer complete.");
-  }
-  
-  /**
-   * Creates a VamsasArchive Vobject for accessing and updating document
-   * Note: this will lock the Vamsas Document for exclusive access to the client.
-   * @return session vamsas document
-   * @throws IOException if locks fail or vamsas document read fails.
-   */
-  protected VamsasArchive getVamsasDocument() throws IOException {
-    // TODO: check we haven't already done this once
-    if (!vamArchive.lockFile()) 
-      throw new IOException("Failed to get lock for vamsas archive.");
-    
-    VamsasArchive va = new VamsasArchive(vamArchive.sessionFile, false, true, vamArchive);
-    
-    return va;
-  }
-  /**
-   * create a uniquely named file in the session Directory
-   * @see java.io.File.createTempFile
-   * @param pref Prefix for name
-   * @param suff Suffix for name
-   * @return SessionFile object configured for the new file (of length zero)
-   * @throws IOException
-   */
-  protected SessionFile getTempSessionFile(String pref, String suff) throws IOException {
-    File tfile = File.createTempFile(pref,suff,sessionDir);
-    SessionFile tempFile = new SessionFile(tfile);
-    return tempFile;
-  }
-}
-
-