From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 14 Dec 2006 18:42:43 +0000 (+0000)
Subject: refactoring org to uk
X-Git-Tag: Release_0.2~233
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=156b868f868ba0d3cbf61da2f327047508b3ea4d;p=vamsas.git

refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@287 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/org/vamsas/test/simpleclient/ArchiveClient.java b/src/org/vamsas/test/simpleclient/ArchiveClient.java
deleted file mode 100644
index dec872a..0000000
--- a/src/org/vamsas/test/simpleclient/ArchiveClient.java
+++ /dev/null
@@ -1,293 +0,0 @@
-/**
- * 
- */
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Date;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.ValidationException;
-import org.vamsas.test.objects.Core;
-
-import uk.ac.vamsas.client.ClientHandle;
-import uk.ac.vamsas.client.IVorbaIdFactory;
-import uk.ac.vamsas.client.SessionHandle;
-import uk.ac.vamsas.client.UserHandle;
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.client.VorbaId;
-import uk.ac.vamsas.client.simpleclient.AppDataOutputStream;
-import uk.ac.vamsas.client.simpleclient.FileWatcher;
-import uk.ac.vamsas.client.simpleclient.IdFactory;
-import uk.ac.vamsas.client.simpleclient.SessionFile;
-import uk.ac.vamsas.client.simpleclient.SimpleDocBinding;
-import uk.ac.vamsas.client.simpleclient.SimpleDocument;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.AppData;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.User;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-import uk.ac.vamsas.objects.utils.AppDataReference;
-import uk.ac.vamsas.objects.utils.DocumentStuff;
-import uk.ac.vamsas.objects.utils.ProvenanceStuff;
-import uk.ac.vamsas.objects.utils.SeqSet;
-import uk.ac.vamsas.objects.utils.document.VersionEntries;
-
-/**
- * @author jimp
- *  test the VamsasFile routines for watching, reading and updating a vamsas document jar file.
- *  simple document access base class.
- */
-public class ArchiveClient extends IdFactory {
-  
-  private Log log = LogFactory.getLog(ArchiveClient.class);
-  // protected UserHandle user=null;
-  // protected ClientHandle me = new ClientHandle("ArchiveClient","0.01");
-  VamsasFile vsess;
-  
-  /**
-   * @param user
-   * @param vsess
-   */
-  public ArchiveClient(UserHandle user, VamsasFile vsess) {
-    super(new SessionHandle("vamsasfile://"+vsess.getVamsasFile()), new ClientHandle("ArchiveClient","0.01"), user);
-    this.vsess = vsess;
-    valid();
-  }
-  private void _openVsess(File vsess) {
-    try {
-      this.vsess = new VamsasFile(vsess);
-    }
-    catch (Exception e) {
-      log.error("Couldn't open session for file "+vsess,e);
-      this.vsess = null;
-    }
-  }
-  public ArchiveClient(String username, String organization, File vsess) {
-    super(new SessionHandle("vamsasfile://"+vsess), new ClientHandle("ArchiveClient","0.01"), new UserHandle(username, organization));
-    _openVsess(vsess);
-    valid();
-  }
-  public ArchiveClient(String username, String organization, String clientName, String clientVersion, File vsess) {
-    super(new SessionHandle("vamsasfile://"+vsess), new ClientHandle(clientName, clientVersion), new UserHandle(username, organization));
-    _openVsess(vsess);
-    valid();
-  }
-  public void valid() {
-    if (vsess==null)
-      throw new Error("ArchiveClient instance is invalid!.");
-  }
-  /**
-   * set this to false if watch loop should end immediately
-   */
-  protected boolean watchForChange=true;
-  public static int WATCH_SLEEP=300;
-  /**
-   * watch the document file for updates.
-   * @param time - length of time to watch for.
-   * @return read only IO interface for session document.
-   */
-  public ClientDoc watch(long time) {
-    valid();
-    vsess.unLock(); // doh.
-    FileWatcher watcher = new FileWatcher(vsess.getVamsasFile());
-    // watcher.setState();
-    watchForChange=true;
-    long endtime=System.currentTimeMillis()+time;
-    try {
-      uk.ac.vamsas.client.simpleclient.Lock doclock;
-      do {
-        doclock=watcher.getChangedState();
-        if (doclock==null)
-          Thread.sleep(WATCH_SLEEP);
-      } while (watchForChange && doclock==null && (time==0 || endtime>System.currentTimeMillis())); // tuning.
-      if (doclock==null)
-        return null;
-      else {
-        return getUpdateable(vsess.getLock(doclock));
-        /*VamsasArchiveReader varc = new VamsasArchiveReader(vsess.getVamsasFile());
-        return _getReadonly(varc);*/
-      }
-    } catch (Exception e) {
-      log.error("Whilst watching file "+vsess.getVamsasFile(), e);
-    }
-    return null;
-  }
-
-  // from ClientDocument.getClientAppdata
-  private AppData[] getAppData(VamsasDocument doc) {
-    if (doc==null) {
-      log.debug("extractAppData called for null document object");
-      return null;
-    }
-    AppData appsGlobal=null, usersData=null;
-    Vector apldataset = AppDataReference.getUserandApplicationsData(
-        doc, this.getUserHandle(), this.getClientHandle());
-    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.
-      }
-    }
-    return new AppData[] { appsGlobal, usersData};
-  }
-  
-  protected ClientDoc _getReadonly(VamsasArchiveReader vreader) throws IOException, ValidationException, MarshalException {
-    valid();
-    if (vreader!=null) {
-      SimpleDocBinding docb = new SimpleDocBinding();
-      docb.setVorba(this);
-      VamsasDocument d;
-      d = docb.getVamsasDocument(vreader);
-      
-      if (d!=null) {
-        ClientDoc creader = new ClientDoc(d, null, vreader, getClientHandle().getClientUrn(), getProvenanceUser(), getVorbaIdHash());
-        return creader;
-      }
-    }
-    return null;
-  }  
-  /**
-   * from SimpleClient
-   * @return user field for a provenance entry
-   */
-  protected String getProvenanceUser() {
-    return new String(getUserHandle().getFullName()+" ["+getClientHandle().getClientUrn()+"]");
-  }
-  
-  public ClientDoc getUpdateable() {
-    return getUpdateable(null);
-  }
-  public ClientDoc getUpdateable(uk.ac.vamsas.client.simpleclient.Lock lock) {
-    getVorbaIdHash().clear();
-    valid();
-    try {
-      // patiently wait for a lock on the document.
-      long tries=5000;
-      while (lock==null && ((lock=vsess.getLock())==null || !lock.isLocked()) && --tries>0) {
-//        Thread.sleep(1);
-        log.debug("Trying to get a document lock for the "+tries+"'th time.");
-      }
-      VamsasArchive varc = new VamsasArchive(vsess, true, false); // read archive, write as vamsasDocument, don't erase original contents.
-      varc.setVorba(this);
-      VamsasDocument d = varc.getVamsasDocument(getProvenanceUser(), "Created new document.", VersionEntries.latestVersion()); // VAMSAS: provenance user and client combined
-      
-      if (d==null) {
-        log.warn("Backing out from opening a VamsasArchive writable IO session");
-        varc.cancelArchive();
-        return null;
-      }      
-      ClientDoc cdoc = new ClientDoc(d, varc, varc.getOriginalArchiveReader(), getClientHandle().getClientUrn(), getProvenanceUser(), getVorbaIdHash());
-      return cdoc;
-      // do appHandle?
-    } catch (Exception e) {
-      log.error("Failed to get Updateable version of "+vsess.getVamsasFile(), e);
-    }
-    return null;
-  }
-  /**
-   * trust client to not do anything stupid to the document roots which will now be written to the archive.
-   * @param cdoc
-   * @return true if write was a success.
-   */
-  public boolean doUpdate(ClientDoc cdoc) {
-    valid();
-    if (cdoc==null) {
-      log.warn("Invalid ClientDoc passed to org.vamsas.test.simpleclient.doUpdate()");
-      return false;
-    }
-    if (cdoc.iohandler==null) {
-      log.warn("Read only ClientDoc object passed to org.vamsas.test.simpleclient.doUpdate()");
-      return false;
-    }
-    if (cdoc.iohandler.getVorba()!=this) {
-      log.error("Mismatch between ClientDoc instances and ArchiveClient instances!");
-      return false;
-    }
-    try {
-      // do any appDatas first.
-      if (cdoc.iohandler.transferRemainingAppDatas())
-        log.debug("Remaining appdatas were transfered.");
-      cdoc.updateDocumentRoots();
-      cdoc.iohandler.putVamsasDocument(cdoc.doc);
-      cdoc.iohandler.closeArchive();
-      this.extantids.clear();// we forget our ids after we close the document.
-      cdoc.iohandler=null;
-      cdoc = null;
-      vsess.unLock();
-    } catch (Exception e) {
-      log.warn("While updating archive in "+vsess.getVamsasFile(),e);
-      return false;
-    }
-    return true;
-  }
-  /**
-   * @param args
-   */
-  public static void usage() {
-    throw new Error("Usage: Username Organization VamsasFile [command,args]*");
-  }
-  public static void main(String[] args) {
-    // really simple.
-    if (args.length<3)
-      usage();
-    
-    ArchiveClient client = new ArchiveClient(args[0],args[1], new File(args[2]));
-    ClientDoc cdoc=null;
-    // sanity test.
-    try {
-      cdoc = client.getUpdateable();
-      // ArchiveReports.reportDocument(cdoc.doc, cdoc.getReader(), true, System.out);
-      System.out.println("Report Roots :");
-      ArchiveReports.rootReport(cdoc.getVamsasRoots(), true, System.out);
-      cdoc.addVamsasRoot(Core.getDemoVamsas());
-      System.out.println("Doing update.");
-      client.doUpdate(cdoc);
-      cdoc.closeDoc();
-      cdoc = null;
-      int u=5;
-      while (--u>0) {
-        System.out.println("Watch for more... ("+u+" left)");
-        ClientDoc ucdoc = client.watch(0000);
-        if (ucdoc!=null) {
-          System.out.println("****\nUpdate detected at "+new Date());
-          ArchiveReports.reportDocument(ucdoc.doc, ucdoc.getReader(), true, System.out);
-          ucdoc.closeDoc();
-          ucdoc=null;
-        } else {
-          System.out.println("!!!! Null document update detected at "+new Date());
-        }
-      }
-    }
-    catch (Exception e) {
-      client.log.error("Broken!", e);
-    }
-    System.out.println("Finished at "+new Date());
-  }
-  public uk.ac.vamsas.client.Vobject getObject(VorbaId id) {
-    Hashtable idhash = this.getVorbaIdHash();
-    if (idhash!=null && idhash.containsKey(id))
-      return (Vobject) idhash.get(id);
-    return null;
-    }
-}
diff --git a/src/org/vamsas/test/simpleclient/ArchiveReader.java b/src/org/vamsas/test/simpleclient/ArchiveReader.java
deleted file mode 100644
index 971bfa0..0000000
--- a/src/org/vamsas/test/simpleclient/ArchiveReader.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-
-
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-public class ArchiveReader {
-  /**
-   * tests VamsasArchiveReader archive reader on a vamsas jar file
-   * @param args
-   */
-  public static void main(String args[]) {
-    
-    try {
-      File av = new File(args[0]);
-      VamsasArchiveReader var = new VamsasArchiveReader(av);
-      VAMSAS roots[]=null;
-      if (var.isValid()) {
-        InputStreamReader vdoc = new InputStreamReader(var.getVamsasDocumentStream());
-        VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
-        if (ArchiveReports.reportDocument(doc, var, true, System.out)) {
-          roots = doc.getVAMSAS();
-        }
-      } else {
-        InputStream vxmlis = var.getVamsasXmlStream();
-        
-        if (vxmlis!=null) { // Might be an old vamsas file.
-          BufferedInputStream ixml = new BufferedInputStream(var.getVamsasXmlStream());
-          InputStreamReader vxml = new InputStreamReader(ixml);
-          VAMSAS root;
-          // unmarshal seems to always close the stream (should check this)
-          if ((root = VAMSAS.unmarshal(vxml))!=null) {
-            System.out.println("Read a root.");
-            roots = new VAMSAS[1];
-            roots[0] = root;
-          }
-        }
-      }
-      if (!ArchiveReports.rootReport(roots, true, System.out))
-        System.err.print(args[0]+" is not a valid vamsas archive.");
-    } catch (Exception e) {
-      e.printStackTrace(System.err);
-    }
-  }
-}
diff --git a/src/org/vamsas/test/simpleclient/ArchiveReports.java b/src/org/vamsas/test/simpleclient/ArchiveReports.java
deleted file mode 100644
index a2a2dfe..0000000
--- a/src/org/vamsas/test/simpleclient/ArchiveReports.java
+++ /dev/null
@@ -1,187 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.io.InputStream;
-import java.io.PrintStream;
-import java.io.PrintWriter;
-
-
-import uk.ac.vamsas.client.ClientDocument;
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.Alignment;
-import uk.ac.vamsas.objects.core.AppData;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.DataSet;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.Instance;
-import uk.ac.vamsas.objects.core.Provenance;
-import uk.ac.vamsas.objects.core.Tree;
-import uk.ac.vamsas.objects.core.User;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-/**
- * this class contains static methods for writing info to stdout about a vamsas document
- * Methods have a 'cascade' switch to indicate if sub-objects should have info printed on them.
- * Methods return true or false - indicating if the Vobject was valid or not
- * TODO: LATER: propagate true/false return so that an invalid vamsas Vobject invalidates the whole document
- * @author jimp
- *
- */
-public class ArchiveReports {
-    /**
-     * print an informative summary on a VamsasDocument
-     * @param outstr TODO
-     * @param document - the document itself
-     * @param archive - document source archive for resolving any appData refs
-     * @return
-     */
-  public static boolean reportProvenance(Provenance p, PrintStream outstr) {
-    if (p==null) {
-      outstr.println("No Provenance");
-      return false;
-    }
-    Entry[] pe = p.getEntry();
-    for (int i=0; i<pe.length; i++)
-      outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getApp()+"\t'"+pe[i].getAction()+"'");
-    return true;
-  }
-  public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
-    if (appD!=null) {
-      boolean nulldata=false;
-      if (appD.getDataReference()!=null) {
-        String appData=appD.getDataReference();
-        if (appData==null) { outstr.println("Empty DataReference - not valid ?"); } 
-        else 
-          if (appData.length()>1) {
-          outstr.print("a reference ("+appData+")");
-          InputStream jstrm;
-          if ((jstrm=archive.getAppdataStream(appData))!=null)
-            outstr.println(" which resolves to a JarEntry.");
-          else {
-            outstr.println(" which does not resolve to a JarEntry.");
-            outstr.println("Unresolved appdata reference '"+appData+"'");
-          }
-        } else {
-          nulldata=true;
-        }
-      } else {
-        if (appD.getData()==null)
-          nulldata &= true;
-          else
-          outstr.println("an embedded chunk of "+appD.getData().length+" bytes.");
-      }
-      if (nulldata)
-        outstr.println("Null AppData reference/data chunk.");
-    }
-    return true;
-  }
-  
-  public static boolean appDataReport(ApplicationData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
-    if (appD!=null) {
-      // Report on root appData
-      appDataEntryReport(appD, archive, cascade, outstr);
-      if (appD.getInstanceCount()>0) {
-        Instance inst[] = appD.getInstance();
-        for (int i=0,j=inst.hashCode(); i<j; i++) {
-          outstr.println("Data for App Instance URN: '"+inst[i].getUrn());
-          appDataEntryReport(inst[i],archive,cascade,outstr);
-        }
-      }
-      if (appD.getUserCount()>0) {
-        User users[] = appD.getUser();
-        for (int i=0,j=users.length; i<j; i++) {
-          outstr.println("Data for User '"+users[i].getFullname()+"' of '"+users[i].getOrganization()+"'");
-          appDataEntryReport(users[i], archive, cascade, outstr);
-        }
-      }
-    }
-
-    return true;
-  }
-  public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
-    if (document!=null) {
-      outstr.println("Vamsas Document version '"+document.getVersion()+"'");
-      reportProvenance(document.getProvenance(), outstr);
-      outstr.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" Application data elements.\n");
-      if (document.getVAMSASCount()>0 && cascade)
-        rootReport(document.getVAMSAS(), true, outstr);
-      if (document.getApplicationDataCount()>0) {
-        outstr.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
-        ApplicationData appd[] = document.getApplicationData();
-        for (int i=0,j=appd.length; i<j; i++) {
-          outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\n");
-          outstr.print("AppData is :");
-          appDataReport(appd[i], archive, cascade, outstr);
-        }
-          
-      }
-      return true;
-    } else {
-      outstr.println("Document Object is null");
-    }
-    return false;
-  }
-
-  /**
-   * summarises all the datasets in a vamsas document.
-   * @param roots
-   * @param cascade TODO
-   * @param outstr TODO
-   * @return
-   */
-  public static boolean rootReport(VAMSAS[] roots, boolean cascade, PrintStream outstr) {
-    if (roots!=null) {
-      for (int i=0; i<roots.length; i++) {
-        VAMSAS r = roots[i];
-        int ds, tr;
-        outstr.print("Vamsas Root "+i+" (id="
-            +((r.getId()!=null) ? r.getId():"<none>")
-            +") contains "+(ds=r.getDataSetCount())+" DataSets, "
-            + (tr=r.getTreeCount())+" Global trees\n");
-        if (cascade) {
-          for (int j=0; j<ds; j++) {
-            outstr.println("Dataset "+j);
-            cascade = datasetReport(r.getDataSet(j), true, outstr) && cascade ;
-          }
-          for (int j=0; j<tr; j++) {
-            outstr.println("Global tree "+j);
-            cascade = treeReport(r.getTree(j), true, outstr) && cascade;
-          }
-        }
-      }
-      return true;
-    }
-    return false;
-  }
-  public static boolean datasetReport(DataSet ds, boolean cascade, PrintStream outstr) {
-    if (cascade)
-      reportProvenance(ds.getProvenance(), outstr);
-    outstr.println("Dataset contains : "+ds.getSequenceCount()
-        +" sequences, "+ds.getAlignmentCount()+" alignments and "+ds.getTreeCount()+" trees.");
-    if (cascade)
-      alignmentReport(ds.getAlignment(), true, outstr);
-    return true;
-  }
-  public static boolean alignmentReport(Alignment[] al, boolean cascade, PrintStream outstr) {
-    boolean val=true;
-    if (al!=null && al.length>0) {
-      for (int i=0; i<al.length; i++) {
-        outstr.println("Alignment "+i+(al[i].isRegistered() ? " ("+al[i].getVorbaId()+")" : " (unregistered)"));
-        if (cascade)
-          reportProvenance(al[i].getProvenance(), outstr);
-        outstr.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
-            +al[i].getAlignmentAnnotationCount()+" annotations and "+al[i].getTreeCount()+" trees.");
-        if (cascade) {
-          for (int t=0; t<al[i].getTreeCount(); t++)
-            treeReport(al[i].getTree(t), true, outstr);
-        }
-      }
-    }
-    return val;
-  }
-  public static boolean treeReport(Tree t, boolean cascade, PrintStream outstr) {
-    outstr.println("Tree: '"+t.getTitle()+"'");
-    return !cascade || reportProvenance(t.getProvenance(), outstr);
-  }
-
-}
diff --git a/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java b/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java
deleted file mode 100644
index c1f9b58..0000000
--- a/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java
+++ /dev/null
@@ -1,53 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-
-
-import uk.ac.vamsas.client.simpleclient.SessionFile;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-public class ArchiveStreamReader {
-  /**
-   * tests VamsasArchiveReader archive reader on a vamsas jar file opened as a stream
-   * @param args
-   */
-  public static void main(String args[]) {
-    
-    try {
-      VamsasFile av = new VamsasFile(new File(args[0]));
-      VamsasArchiveReader var = new VamsasArchiveReader(av.getLock());
-      VAMSAS roots[]=null;
-      if (var.isValid()) {
-        InputStreamReader vdoc = new InputStreamReader(var.getVamsasDocumentStream());
-        VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
-        if (ArchiveReports.reportDocument(doc, var, true, System.out)) {
-          roots = doc.getVAMSAS();
-        }
-      } else {
-        InputStream vxmlis = var.getVamsasXmlStream();
-        
-        if (vxmlis!=null) { // Might be an old vamsas file.
-          BufferedInputStream ixml = new BufferedInputStream(var.getVamsasXmlStream());
-          InputStreamReader vxml = new InputStreamReader(ixml);
-          VAMSAS root;
-          // unmarshal seems to always close the stream (should check this)
-          if ((root = VAMSAS.unmarshal(vxml))!=null) {
-            System.out.println("Read a root.");
-            roots = new VAMSAS[1];
-            roots[0] = root;
-          }
-        }
-      }
-      if (!ArchiveReports.rootReport(roots, true, System.out))
-        System.err.print(args[0]+" is not a valid vamsas archive.");
-    } catch (Exception e) {
-      e.printStackTrace(System.err);
-    }
-  }
-}
diff --git a/src/org/vamsas/test/simpleclient/ArchiveWatcher.java b/src/org/vamsas/test/simpleclient/ArchiveWatcher.java
deleted file mode 100644
index 08a6522..0000000
--- a/src/org/vamsas/test/simpleclient/ArchiveWatcher.java
+++ /dev/null
@@ -1,106 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.client.ClientHandle;
-import uk.ac.vamsas.client.simpleclient.FileWatcher;
-import uk.ac.vamsas.client.simpleclient.Lock;
-import uk.ac.vamsas.client.simpleclient.SimpleDocument;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-/**
- * demo of archive watching process - should mimic the clientsfileTest watcher/monitor process.
- * @author jimp
- *
- */
-public class ArchiveWatcher {
-  private static Log log = LogFactory.getLog(ArchiveWatcher.class);
-  private static CommandProcessor cproc=new CommandProcessor();
-  static {
-    cproc.addCommand("new", 0, "no args");
-    cproc.addCommand("delete", 0, "no args");    
-    cproc.addCommand("watch", 0, "no args");
-    cproc.addCommand("file", 1, "Need vamsas archive as argument.");    
-  }
-  
-  public static void main(String[] args) {
-    try {
-      
-      if (args!=null && args.length>0) {
-        File archive = new File(args[0]);
-        log.info("Watching file "+args[0]);
-        int argc=1;
-        while (argc < args.length) {
-          // vars needed for operations
-          ClientHandle ch;
-          int com = cproc.getCommand(args, argc);
-          argc++;
-          switch (com) {
-          case 0:
-            // new
-            log.info("Doing locked deletion and new-file creation.");
-            {
-              if (!archive.exists())
-                archive.createNewFile();
-              VamsasFile sf = new VamsasFile(archive);
-              Lock l = sf.getLock();
-              archive.delete();
-              archive.createNewFile();
-              sf.unLock();
-            }
-            break;
-          case 1:
-            // delete
-            log.info("Deleting "+archive+" without locking it first.");
-            archive.delete();
-            break;
-          case 2:
-            // watch
-            log.info("Endlessly Watching file "+archive);
-            /*        if (!archive.exists())
-                      archive.createNewFile();
-             */       // watch the new file... - taken straight from ClientsFileTest
-            FileWatcher w = new FileWatcher(archive);
-            while (true) {              
-              // get watcher's lock to ensure state change is fixed for retrieval
-              Lock chlock = w.getChangedState();
-              if (chlock != null) {
-                log.info("Got lock on "+archive+(archive.exists() ? " exists l="+archive.length() : "(non existant)"));
-                if (archive.length()>0) {
-                  VamsasArchiveReader vreader = new VamsasArchiveReader(archive);
-                  SimpleDocument sdoc = new SimpleDocument("testing vamsas watcher");
-                  try {
-                    VamsasDocument d = sdoc.getVamsasDocument(vreader);
-                    if (d!=null) {
-                      ArchiveReports.reportDocument(d, vreader, false, System.out);
-                    }
-                    System.out.println("Update at "+System.currentTimeMillis()+"\n\n********************************************************\n");
-                  } catch (Exception e) {
-                    log.error("Unmarshalling failed.",e);
-                  }
-                  vreader.close();
-                  w.setState();
-                }
-              }
-            }
-            // break;
-          case 3: // set file
-            archive = new File(args[argc++]);
-            break;
-          case 4:
-            break;
-            default:
-              log.warn("Unknown command  + "+args[argc++]);
-          }
-        }
-      }
-    } catch (Exception e) {
-      log.error(e);
-    }
-    
-  }
-}
diff --git a/src/org/vamsas/test/simpleclient/ArchiveWriter.java b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
deleted file mode 100644
index f99f400..0000000
--- a/src/org/vamsas/test/simpleclient/ArchiveWriter.java
+++ /dev/null
@@ -1,182 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
-import java.text.DateFormat;
-import java.util.Date;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-der;
-import uk.ac.vamsas.objects.core.Alignment;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.Instance;
-import uk.ac.vamsas.objects.core.Provenance;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-import uk.ac.vamsas.objects.ut
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-ils.ProvenanceStuff;
-
-public class ArchiveWriter {
-  
-  /**
-   * Test program for writing archive files.
-   * form is ArchiveWriter new/modified argive command list
-   */
-  
-  static Log log = LogFactory.getLog(ArchiveWriter.class);
-    
-  private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) {
-    int i;
-    for (i=0; i<svec1.length; i++)
-      destvec[i] = svec1[i];
-    for (int j=0; j<svec2.length; i++, j++)
-      destvec[i] = svec2[j];
-  }
-  // Merge appDataReferences require transfer of jar entries, perhaps with a renaming of the entry.
-  // Merge appDatas require eventually unique URNS
-  // TODO: merging global appdata from different documents where same app has written them causes conflict
-  
-  public static Hashtable hashOfAppDatas(Hashtable ht, Instance[] appdatas) {
-    if (ht==null)
-      ht = new Hashtable();
-    for (int i=0, j=appdatas.length; i<j; i++) {
-      if (!ht.containsKey(appdatas[i].getUrn())) {
-        Hashtable aphash = new Hashtable();
-        ht.put(appdatas[i].getUrn(), aphash);
-        aphash.put(appdatas[i], appdatas[i].getDataReference());
-      } else {
-        // ensure urns and references are unique
-        
-        
-      }
-          
-    }
-    return ht;
-  }
-  /**
-   * safely copies an appData from one archive to another.
-   * @param darc destination archive
-   * @param dest destination document Vobject
-   * @param sarc source archive reader
-   * @param entry application data to be copied from source archive
-   */
-  public static void addAppDataEntry(VamsasArchive darc, VamsasDocument dest,  VamsasArchiveReader sarc, ApplicationData entry) {
-    // TODO: fix instances
-    // check uniqueness of instance's[] entry.urn amongst dest.ApplicationData[].getInstances[].urn 
-    //  check uniqueness of entry.user[].urn amongst dest.ApplicationData[].user[].urn
-    // check uniqueness of entry.user
-    // entry.getAppDataChoice().getData() or getDataReference is unique
-    ApplicationData newo = new ApplicationData();
-    for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
-      ApplicationData o = dest.getApplicationData()[i];
-      // ensure new urn is really unique
-      //String urn = entry.getUrn();
-      int v = 1;
-      //while (o.getUrn().equals(urn)) {
-      //  urn = entry.getUrn()+v++;      
-     // }
-      // uniqueness of urn
-      // check each user ApplicationData
-      // uniqueness (again)
-      // copy over valid objects
-      // 
-    }
-  }
-  /**
-   * Copy new datasets and appdatas from one vamsas document to another.
-   * @param darc
-   * @param dest
-   * @param sarc
-   * @param source
-   * @return true if merge was successful.
-   */
-  public static boolean mergeDocs(VamsasArchive darc, VamsasDocument dest,  VamsasArchiveReader sarc, VamsasDocument source) {
-    log.debug("mergeDocs entered.");
-    // search for appDatas in cdoc
-    VAMSAS[] newr = new VAMSAS[dest.getVAMSASCount()+source.getVAMSASCount()];
-    mergeVecs(newr, dest.getVAMSAS(), source.getVAMSAS());
-    dest.setVAMSAS(newr);
-    /** TODO: LATER: should verify that all ids really are unique in newly merged document. If not then what ?
-     *  investigate possibility of having an id translation between appDatas and the core document - 
-     *  the mapping is stored when an external application performs a merge, but when the owning 
-     *  Application accesses the Vobject, the vorba_id is updated to the new one when it writes its 
-     *  references in to its appdata again
-     */
-    if (source.getApplicationDataCount()>0) {
-      ApplicationData[] newdat = new ApplicationData[source.getApplicationDataCount()+dest.getApplicationDataCount()];
-      ApplicationData[] sappd = source.getApplicationData();
-      // check refs and update/modify if necessary
-      for (int i=0; i<sappd.length; i++) {
-        addAppDataEntry(darc, dest, sarc, sappd[i]);
-      }
-      
-    }
-    
-    return true; // success    
-  }
-  
-  private static CommandProcessor cproc;
-  static {
-    cproc.addCommand("new", 0, "no args");
-    cproc.addCommand("add", 1, "Need another vamsas document archive filename as argument.");    
-    cproc.addCommand("repair", 0, "no args");
-    cproc.addCommand("list", 0, "no args");    
-    cproc.addCommand("monitor", 0, "no args");    
-  }
-  
-  public static void main(String argv[]) {
-    /**
-     * TODO: switches for setting user identities for writing to vamsas document
-     */ 
-    if (argv.length<1) {
-      log.fatal("Usage : <archive to create> [(commands)]");
-      return;
-    }
-    File newarch = new File(argv[0]);
-    int argpos = 0;
-    try {
-      // test fully fledged doc construction
-      VamsasArchive varc = new VamsasArchive(newarch, true);
-      VamsasDocument docroot;
-      docroot = new VamsasDocument();
-      docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "user", "Created new Vamsas Document"));
-      while (++argpos<argv.length) {
-        File archive = new File(argv[argpos]);
-        InputStream istream;
-        if (archive.exists()) {
-          VamsasArchiveReader vdoc = new VamsasArchiveReader(archive);
-          if (vdoc.isValid()) {
-            istream = vdoc.getVamsasDocumentStream(); 
-            if (istream!=null) {
-              VamsasDocument cdocroot = VamsasDocument.unmarshal(new InputStreamReader(istream));
-              if (cdocroot!=null) 
-                mergeDocs(varc, docroot, vdoc, cdocroot);
-            } else 
-              log.warn("Unexpectedly null document stream from existing document "+archive);
-          } else {
-              // updating an oldformat stream ?
-              if ((istream = vdoc.getVamsasXmlStream())!=null) {
-                // make a new vamsas document from the vamsas.xml entry
-                VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream)); // TODO: verify only one VAMSAS element per vamsas.xml entry.
-                docroot.getProvenance().addEntry(ProvenanceStuff.newProvenanceEntry("ArchiveWriter", "user", "added vamsas.xml from "+argv[argpos-1]));
-                docroot.addVAMSAS(root);
-              }
-          }
-        } else {
-          // Begin a new vamsas document
-          PrintWriter docwriter = varc.getDocumentOutputStream();
-        }
-      }
-    } catch (Exception e) {
-      log.error("Whilst manipulating "+argv[0], e);
-    }
-  }
-}
diff --git a/src/org/vamsas/test/simpleclient/ClientDoc.java b/src/org/vamsas/test/simpleclient/ClientDoc.java
deleted file mode 100644
index 0e88c1d..0000000
--- a/src/org/vamsas/test/simpleclient/ClientDoc.java
+++ /dev/null
@@ -1,356 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.client.IClientAppdata;
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.client.VorbaId;
-import uk.ac.vamsas.client.simpleclient.ClientDocument;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-import uk.ac.vamsas.objects.utils.ProvenanceStuff;
-
-// simple holder to pass to client.
-public class ClientDoc extends uk.ac.vamsas.client.ClientDocument {
-  /* (non-Javadoc)
-   * @see uk.ac.vamsas.client.IClientDocument#getClientAppdata()
-   */
-  public IClientAppdata getClientAppdata() {
-    throw new Error("Appdata access is not implemented in the test.simpleclient.ClientDoc instance."); // TODO Auto-generated method stub
-  }
-  protected boolean isModified=false;
-  private Log log = LogFactory.getLog(ClientDoc.class);
-  protected VamsasDocument doc;
-  public uk.ac.vamsas.objects.core.VAMSAS[] _VamsasRoots;
-  protected VamsasArchive iohandler=null;
-  protected VamsasArchiveReader reader=null;
-  private String user=null;
-  private String app=null;
-  
-  /**
-   * @param doc
-   * @param iohandler
-   * @param reader
-   * @param app
-   * @param user
-   */
-  public ClientDoc(VamsasDocument doc, VamsasArchive iohandler, VamsasArchiveReader reader, String app, String user, Hashtable objrefs) {
-    super(objrefs, (iohandler!=null) ? iohandler.getVorba() : null);
-    this.doc = doc;
-    this.iohandler = iohandler;
-    this.reader = reader;
-    this.app = app;
-    this.user = user;
-    this.objrefs = objrefs;
-    _VamsasRoots = doc.getVAMSAS();
-  }
-  // AppDataOutputStream appd;
-  //AppDataOutputStream userd;
-  /* (non-Javadoc)
-   * @see java.lang.Object#finalize()
-   */
-  protected Entry getProvenanceEntry(String action) {
-    // VAMSAS: modify schema to allow referencing of user field (plus other issues, ClientUrn field, machine readable action, input parameters, additional data generated notes
-    Entry prov = ProvenanceStuff.newProvenanceEntry(app, user, action);
-    return prov;
-  }
-  public VAMSAS[] getVamsasRoots() {
-    if (doc==null) {
-      log.debug("Null document for getVamsasRoots(), returning null");
-      return null;
-    }
-    if (iohandler==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(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;
-    VorbaId r_id = root.getVorbaId();
-    for (int i=0,j=docRoots.length; i<j; i++) {
-      VorbaId n_id=null;
-      if (docRoots[i]==root || (docRoots[i]!=null && (n_id=docRoots[i].getVorbaId())!=null && n_id.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())
-        iohandler.getVorba().makeVorbaId(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())
-        iohandler.getVorba().makeVorbaId(newVersion);
-      if (newVersion.isValid())
-        return true;
-    }
-    return false;
-  }
-    /**
-  /**
-   * merge old and new root vectors
-   * @param newr This array may be written to
-   * @param original
-   * @param the client document (usually this) which this root set belongs to.
-   * @return merged vector of vamsas roots
-   */
-  private VAMSAS[] _combineRoots(VAMSAS[] newr, final VAMSAS[] original, ClientDoc 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 uk.ac.vamsas.client.IClientDocument#addVamsasRoot(uk.ac.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;  
-  }
-
-  public VamsasArchiveReader getReader() {
-    return reader;
-  }
-  private void _finalize() {
-    log.debug("finalizing clientDoc");
-    if (doc!=null) {
-      doc = null;
-    }
-    if (_VamsasRoots!=null) {
-      for (int i=0; i<_VamsasRoots.length; i++)
-        _VamsasRoots[i]=null;
-      _VamsasRoots=null;
-       
-    }
-      
-    if (reader!=null) {
-      log.debug("Closing and removing reader reference");
-      reader.close();
-      reader=null;
-    }
-    if (iohandler!=null) {
-      log.debug("Removing ioHandler reference.");
-      iohandler.cancelArchive();
-      iohandler=null;
-    }
-  }
-  protected void finalize() throws Throwable {
-    _finalize();
-    super.finalize();
-  }
-  private java.util.Hashtable objrefs=null;
-  
-  public VorbaId[] registerObjects(Vobject[] unregistered) {
-    if (doc==null) {
-      log.warn("registerObjects[] called on null document.");
-      return null;
-    }
-    if (objrefs==null) {
-      log.warn("registerObjects[] called for null objrefs 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 "+objrefs.size()+" ids.");
-      return ids;
-    }
-    return null;
-  }
-  /* (non-Javadoc)
-   * @see uk.ac.vamsas.client.IClientDocument#registerObject(uk.ac.vamsas.client.Vobject)
-   */
-  public VorbaId registerObject(Vobject unregistered) {
-    if (doc==null) {
-      log.warn("registerObjects called on null document.");
-      return null;
-    }
-    if (objrefs==null) {
-      log.warn("registerObjects called for null objrefs hasharray.");
-      return null;
-    }
-    if (iohandler==null) {
-      log.warn("registerObjects called for read only document.");
-      return null;
-    }
-    
-    if (unregistered!=null) {
-      VorbaId id = this._registerObject(unregistered);
-      log.debug("Registered object - total of "+objrefs.size()+" ids.");
-      return id;
-    }
-    log.warn("Null Vobject passed to registerObject.");
-    return null;
-  }
-  /*
-   * (non-Javadoc)
-   * 
-   * @see uk.ac.vamsas.client.IClientDocument#getObject(uk.ac.vamsas.client.VorbaId)
-   */
-  public Vobject getObject(VorbaId id) {
-    if (objrefs==null) {
-      log.debug("getObject called on null objrefs list.");
-      return null;
-    }
-    if (objrefs.containsKey(id.getId()))
-      return (Vobject) objrefs.get(id.getId());
-    log.debug("Returning null Vobject reference for id "+id.getId());
-    return null;
-  }
-  
-  /*
-   * (non-Javadoc)
-   * 
-   * @see uk.ac.vamsas.client.IClientDocument#getObjects(uk.ac.vamsas.client.VorbaId[])
-   */
-  public Vobject[] getObjects(VorbaId[] ids) {
-    if (objrefs==null) {
-      log.debug("getObject[]  called on null objrefs list.");
-      return null;
-    }
-    Vobject[] vo = new Vobject[ids.length];
-    for (int i=0,j=ids.length; i<j;i++) 
-      if (objrefs.containsKey(ids[i]))
-        vo[i] = (Vobject) objrefs.get(ids[i]);
-      else
-        log.debug("Returning null Vobject reference for id "+ids[i].getId());
-    return vo;
-  }
-  protected void updateDocumentRoots() {
-    if (doc==null) {
-      log.error("updateDocumentRoots called on null document. Probably an implementation error.");
-      return;
-    }
-    if (isModified) {
-      if (_VamsasRoots!=null) {
-        doc.setVAMSAS(_VamsasRoots);
-        _VamsasRoots=null;
-      }
-    }
-  }
-  /**
-   * tell vamsas client to close the document and reset the object. Once closed, nothing can be done with the object.
-   *
-   */
-  public void closeDoc() {
-    if (doc!=null) {
-      log.debug("Closing open document.");
-      _finalize();
-    } else {
-      log.warn("Ignoring closeDoc on invalid document.");
-    }
-  }
-  
-}
\ No newline at end of file
diff --git a/src/org/vamsas/test/simpleclient/ClientsFileTest.java b/src/org/vamsas/test/simpleclient/ClientsFileTest.java
deleted file mode 100644
index 1a2ab35..0000000
--- a/src/org/vamsas/test/simpleclient/ClientsFileTest.java
+++ /dev/null
@@ -1,311 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.util.Iterator;
-import java.util.Vector;
-
-
-import uk.ac.vamsas.client.ClientHandle;
-import uk.ac.vamsas.client.simpleclient.ClientsFile;
-import uk.ac.vamsas.client.simpleclient.FileWatcher;
-import uk.ac.vamsas.client.simpleclient.Lock;
-
-public class ClientsFileTest {
-  private static CommandProcessor cproc;
-
-  private static Vector commands;
-  static {
-    cproc = new CommandProcessor();
-    ClientsFileTest.commands = new Vector();
-    ClientsFileTest.commands.add(new String("add"));
-    cproc.addCommand("add", 2, "for the Client's 'Name' and 'Version'");
-    ClientsFileTest.commands.add(new String("remove"));
-    cproc.addCommand("remove", 3, "for the Client's 'Name', Version and URN");
-    ClientsFileTest.commands.add(new String("list"));
-    cproc.addCommand("list", 0, "no args needed");
-    ClientsFileTest.commands.add(new String("clear"));
-    cproc.addCommand("clear", 0, "no args needed");
-    ClientsFileTest.commands.add(new String("watch"));
-    cproc.addCommand("watch", 0, "no args needed");
-    ClientsFileTest.commands.add(new String("monitor"));
-    cproc.addCommand("monitor", 2, "for the Client's 'Name' and 'Version'");
-  }
-
-  private static void complainArgs(int argl, int argpos, String cmd,
-      int argneed, String msg) {
-    if (argl - argpos < argneed)
-      throw new Error(cmd + " needs " + argneed + " arguments : " + msg);
-  }
-
-  public static void main(String[] args) {
-    java.io.File cf = new java.io.File(args[0]);
-    System.out.println("Connecting to clientFile " + args[0]);
-    ClientsFile cfhand;
-    try {
-      cfhand = new ClientsFile(cf);
-    } catch (Exception e) {
-      e.printStackTrace(System.err);
-      return;
-    }
-    int argc = 1;
-    while (argc < args.length) {
-      // vars needed for operations
-      ClientHandle ch;
-      int com = cproc.getCommand(args, argc);
-      argc++;
-      switch (com) {
-      case 0:
-        // Add
-        int pos = cfhand.addClient(ch = new ClientHandle(args[argc],
-            args[argc + 1]));
-        argc += 2;
-        if (pos != 0)
-          System.out.println("Client added at " + pos + " as urn:"
-              + ch.getClientUrn());
-        else
-          System.out.println("Client was not added.");
-        break;
-      case 1:
-        // remove
-        ch = new ClientHandle(args[argc], args[argc + 1]);
-        ch.setClientUrn(args[argc + 2]);
-        argc += 3;
-        cfhand.removeClient(ch, null);
-        System.out.println("Client removed (apparently)");
-        break;
-      case 2:
-        // list
-        ClientHandle[] chlist = cfhand.retrieveClientList();
-        if (chlist != null) {
-          for (int chi = 0, che = chlist.length; chi < che; chi++) {
-            System.out.println("Client " + chi + " ("
-                + chlist[chi].getClientName() + " " + chlist[chi].getVersion()
-                + " " + chlist[chi].getClientUrn() + ")");
-          }
-        } else {
-          System.out.println("Client list is empty.");
-        }
-        break;
-      case 3:
-        // clear
-        //cfhand.get = null;
-        //cf.delete();
-        try {
-          
-          cfhand.clearList();
-          
-        } catch (Exception e) {
-          System.err.println("Failed on new empty clientfile creation!");
-          e.printStackTrace(System.err);
-        }
-        break;
-      case 4:
-        // watch
-        FileWatcher w = new FileWatcher(cf);
-        while (cf.exists()) {
-          // get watcher's lock to ensure state change is fixed for retrieval
-          Lock chlock = w.getChangedState();
-          if (chlock != null) {
-            ClientHandle[] cl = cfhand.retrieveClientList(chlock);
-            System.out.println("-- Watching " + cf.getName());
-            //while (w.hasChanged())
-            //  ;
-            if (cl != null) {
-              for (int chi = 0, che = cl.length; chi < che; chi++) {
-                System.out.println("Client " + chi + " ("
-                    + cl[chi].getClientName() + " " + cl[chi].getVersion()
-                    + " " + cl[chi].getClientUrn() + ")");
-              }
-            } else {
-              System.out.println("Client list is empty.");
-            }
-          }
-
-        }
-        break;
-      case 5:
-        // monitor
-        int clpos = cfhand.addClient(ch = new ClientHandle(args[argc],
-            args[argc + 1]));
-        argc += 2;
-        if (clpos != 0)
-          System.out.println("Monitor Client added at " + clpos + " as urn:"
-              + ch.getClientUrn());
-        else {
-          System.err.println("Monitor Client was not added.");
-          break;
-        }
-        FileWatcher mon = new FileWatcher(cf);
-        while (cf.exists()) {
-          // get watcher's lock to ensure state change is fixed for retrieval
-          Lock chlock = mon.getChangedState();
-          if (chlock != null) {
-            ClientHandle[] cl = cfhand.retrieveClientList(chlock);
-            System.out.println("-- Monitor " + cf.getName());
-            //while (w.hasChanged())
-            //  ;
-            int newpos = -1;
-            if (cl != null) {
-              for (int chi = 0, che = cl.length; chi < che; chi++) {
-                if (ch.equals(cl[chi]))
-                  newpos = chi + 1;
-              }
-            }
-            if (newpos == -1) {
-              // add self again to cleared list.
-              newpos = cfhand.addClient(ch);
-              mon.setState();
-              if (newpos == 0) {
-                System.err
-                    .println("Monitor client could not be re-added to list.");
-                break;
-              }
-            }
-            if (newpos != clpos) {
-              System.out.println("Monitor client moved from " + clpos + " to "
-                  + newpos);
-              clpos = newpos;
-            }
-          }
-        }
-        break;
-      default:
-        if (com == -1) {
-          System.err
-              .println("Unknown command : " + args[argc++] + "*Ignored!*");
-        } else
-          System.err.println("Command " + args[argc++]
-              + " *Ignored!* - its not implemented.");
-      }
-      
-      for (int j = 0; j < 900000; j++) {
-        Integer i = Integer.getInteger("1");
-        Integer q = i;
-      }
-    }
-
-  }
-
-  /*      Iterator coms = commands.iterator();
-   int com=-1;
-   while ((coms!=null) && coms.hasNext()) {
-   com++;
-   if (args[argc].toLowerCase().equals((String) coms.next())) {
-   System.out.println("Doing "+args[argc]);
-   ClientHandle ch;
-   argc++;
-   switch (com) {
-   case 0:
-   // Add
-   ClientsFileTest.complainArgs(args.length, argc, "add", 2, "for the Client's 'Name' and 'Version'");
-   int pos = cfhand.addClient(ch=new ClientHandle(args[argc],args[argc+1]));
-   argc+=2;
-   if (pos!=0)
-   System.out.println("Client added at "+pos+" as urn:"+ch.getClientUrn());
-   else
-   System.out.println("Client was not added.");
-   break;
-   case 1:
-   // remove
-   ClientsFileTest.complainArgs(args.length, argc, "remove", 3, "for the Client's 'Name', Version and URN");
-   ch=new ClientHandle(args[argc], args[argc+1]);
-   ch.setClientUrn(args[argc+2]);
-   argc+=3;
-   cfhand.removeClient(ch, null);
-   System.out.println("Client removed (apparently)");
-   break;
-   case 2:
-   // list
-   ClientHandle[] chlist = cfhand.retrieveClientList();
-   if (chlist!=null) {
-   for (int chi=0,che=chlist.length; chi<che; chi++) {
-   System.out.println("Client "+chi+" ("+chlist[chi].getClientName()+" "+chlist[chi].getVersion()+" "+chlist[chi].getClientUrn()+")");
-   }
-   } else {
-   System.out.println("Client list is empty.");
-   }
-   break;
-   case 3:
-   // clear
-   cfhand = null;
-   cf.delete();
-   try {
-   cf.createNewFile();
-   cfhand = new ClientsFile(cf);
-   }
-   catch (Exception e) {
-   System.err.println("Failed on new empty clientfile creation!");
-   e.printStackTrace(System.err);
-   }
-   break;
-   case 4:
-   // watch
-   FileWatcher w=new FileWatcher(cf);
-   while (cf.exists()) {
-   // get watcher's lock to ensure state change is fixed for retrieval
-   Lock chlock=w.getChangedState();
-   if (chlock!=null) {
-   ClientHandle[] cl = cfhand.retrieveClientList(chlock);
-   System.out.println("-- Watching "+cf.getName());
-   //while (w.hasChanged())
-   //  ;
-   if (cl!=null) {
-   for (int chi=0,che=cl.length; chi<che; chi++) {
-   System.out.println("Client "+chi+" ("+cl[chi].getClientName()+" "+cl[chi].getVersion()+" "+cl[chi].getClientUrn()+")");
-   }
-   } else {
-   System.out.println("Client list is empty.");
-   }
-   }
-   
-   }
-   break;
-   case 5:
-   // monitor
-   ClientsFileTest.complainArgs(args.length, argc, "monitor", 2, "for the Client's 'Name' and 'Version'");
-   int clpos = cfhand.addClient(ch=new ClientHandle(args[argc],args[argc+1]));
-   argc+=2;
-   if (clpos!=0)
-   System.out.println("Monitor Client added at "+clpos+" as urn:"+ch.getClientUrn());
-   else {
-   System.err.println("Monitor Client was not added.");
-   break;
-   }
-   FileWatcher mon=new FileWatcher(cf);
-   while (cf.exists()) {
-   // get watcher's lock to ensure state change is fixed for retrieval
-   Lock chlock=mon.getChangedState();
-   if (chlock!=null) {
-   ClientHandle[] cl = cfhand.retrieveClientList(chlock);
-   System.out.println("-- Monitor "+cf.getName());
-   //while (w.hasChanged())
-   //  ;
-   int newpos=-1;
-   if (cl!=null) {
-   for (int chi=0,che=cl.length; chi<che; chi++) {
-   if (ch.equals(cl[chi]))
-   newpos=chi+1;
-   }
-   }
-   if (newpos==-1) {
-   // add self again to cleared list.
-   newpos=cfhand.addClient(ch);
-   mon.setState();
-   if (newpos==0) {
-   System.err.println("Monitor client could not be re-added to list.");
-   break;
-   }
-   }
-   if (newpos!=clpos) {
-   System.out.println("Monitor client moved from "+clpos+" to "+newpos);
-   clpos=newpos;
-   }
-   }
-   }
-   
-   }
-   coms = null;
-   }
-   } */
-
-}
diff --git a/src/org/vamsas/test/simpleclient/CommandProcessor.java b/src/org/vamsas/test/simpleclient/CommandProcessor.java
deleted file mode 100644
index 0cf0701..0000000
--- a/src/org/vamsas/test/simpleclient/CommandProcessor.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.util.Iterator;
-import java.util.Vector;
-
-public class CommandProcessor {
-  /**
-   * this is not getOPT!!!! - processes a *series* of space separated commands - some of which take arguments.
-   */
-  private Vector commands;
-  /* static {
-    ClientsFileTest.commands=new Vector();
-    ClientsFileTest.commands.add(new String("add"));
-    ClientsFileTest.commands.add(new String("remove"));
-    ClientsFileTest.commands.add(new String("list"));    
-    ClientsFileTest.commands.add(new String("clear"));
-    ClientsFileTest.commands.add(new String("watch"));    
-    ClientsFileTest.commands.add(new String("monitor"));    
-  } */
-
-  public int addCommand(String cmd, int argneed, String complainString) {
-    int cnum=0;
-    if (commands==null)
-      commands = new Vector();
-    else 
-      cnum = commands.size();
-    Vector cv = new Vector();
-    cv.add(new String(cmd));
-    cv.add(new Integer(argneed));
-    cv.add(new String(complainString));
-    commands.add(cv);
-    return cnum;
-  }
- 
-  /**
-   * Integer argl, Integer argpos, String cmd, Integer argneed, String msg in vector
-   */
-  public void complainArgs(int argl, int argpos, Vector ca) {
-    int argneed = ((Integer) ca.get(1)).intValue();
-    if (argl-argpos<argneed)
-      throw new Error(((String) ca.get(0))+" at position "+argpos+" needs "+argneed+" arguments : "+(String) ca.get(2));
-  }
-  /**
-   * find and verify a command
-   * @param args argstring
-   * @param argpos position to check for command
-   * @return matching command or -1
-   */
-  public int getCommand(String[]args, int argpos) {
-    Iterator coms = commands.iterator();
-    int com=-1, argc;
-    argc=argpos;
-    while ((coms!=null) && coms.hasNext()) {
-      com++;
-      Vector comnext = (Vector) coms.next();
-      if (args[argc].toLowerCase().equals((String) comnext.get(0))) {
-        if (comnext.size()>2)
-          complainArgs(args.length, argc+1, comnext);
-        return com;
-      }
-    }
-    return -1;
-        
-  }
-}
diff --git a/src/org/vamsas/test/simpleclient/VamsasArchive.java b/src/org/vamsas/test/simpleclient/VamsasArchive.java
deleted file mode 100644
index c98b4b7..0000000
--- a/src/org/vamsas/test/simpleclient/VamsasArchive.java
+++ /dev/null
@@ -1,206 +0,0 @@
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.io.ObjectOutputStream;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.test.objects.Core;
-
-import uk.ac.vamsas.client.simpleclient.Lock;
-import uk.ac.vamsas.client.simpleclient.SessionFile;
-import uk.ac.vamsas.client.simpleclient.SimpleDocument;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.User;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-public class VamsasArchive {
-  /**
-   * test the org.vamsas.simpleclient.vamsasArchive class
-   */
-  static Log log = LogFactory.getLog(VamsasArchive.class);
-  public static ApplicationData makeDemoAppdata(uk.ac.vamsas.client.simpleclient.VamsasArchive va, String apname, String userName, String userOrg) {
-    if (va==null)
-      return null;
-    VamsasArchiveReader vread=null;
-    try {
-      vread = va.getOriginalArchiveReader();
-    }
-    catch (Exception e) {
-      log.error("Failed to get original archive reader!",e);
-      return null;
-    }
-    ApplicationData appdata = new ApplicationData();
-    appdata.setName("org.vamsas.test.simpleclient.VamsasArchive");
-    appdata.setData(new String("this is some test data.").getBytes());
-    User apuser = new User();
-    apuser.setFullname(userName);
-    apuser.setOrganization(userOrg);
-    String appdata_ref = "vamsas:"+apname+"/"+apuser.getOrganization()+"/"+apuser.getFullname();
-    SimpleDocument sdoc = new SimpleDocument("test.simpleclient.VamsasArchive");
-    if (vread!=null) {
-      VamsasDocument orignalnew;
-      try {
-        orignalnew = sdoc.getVamsasDocument(vread);
-        log.info("*** Dump follows ***");
-        
-        ArchiveReports.reportDocument(orignalnew, vread, false, System.out);
-        log.info("*** Dump precedes ***");
-      } catch (Exception e) {
-        log.info("makeDemoAppdata: Problems accessing original document");
-      }
-      
-      log.info("Reading (and avoiding references to) original data");
-      if (vread.getAppdataStream(appdata_ref)!=null) {
-        // transfer over
-        try {
-          va.transferAppDataEntry(appdata_ref);
-        } catch (Exception e) {
-          log.warn("Exception when transferring appdata reference : "+appdata_ref, e);
-        }
-        int i=0;
-        while (vread.getAppdataStream(appdata_ref+"/"+Integer.toString(++i))!=null) {
-          try {
-            // copy over another duplicate.
-            va.transferAppDataEntry(appdata_ref+"/"+Integer.toString(i));
-          } catch (Exception e) {
-            log.warn("Exception when transferring appdata reference : "+appdata_ref, e);
-          }
-        }
-        // this one must be unique!
-        appdata_ref+="/"+Integer.toString(i);
-      }
-    }
-    
-    log.info("Adding new data stuff.");
-    log.info("Writing an apdata reference using AppDataStream interface.");
-    apuser.setDataReference(appdata_ref);
-    appdata.addUser(apuser);
-    appdata.setVersion("noggin");
-    //TODO: write instance appdata  appdata.setUrn("program:/the.nog/");
-    try {
-      ObjectOutputStream ost = new ObjectOutputStream(va.getAppDataStream(appdata_ref));
-      ost.writeObject(appdata);
-      ost.close();
-    } catch (Exception e) {
-      log.warn("Couldn't write appdata reference "+appdata_ref);
-    }
-    return appdata;
-  }
-  public static void main(String args[]) {
-    
-    try {
-      File av;
-      if (args.length>0)
-        av = new File(args[0]);
-      else
-        av = new File("test/vamsas.zip");
-      log.info("Opening archive "+av);
-      uk.ac.vamsas.client.simpleclient.VamsasArchive varchive = new uk.ac.vamsas.client.simpleclient.VamsasArchive(av, true);
-      
-      VAMSAS[] roots = (VAMSAS[]) varchive.getOriginalRoots();
-      
-      if (roots!=null) {
-        log.info("Report on Original roots in archive:");
-        ArchiveReports.rootReport(roots, true, System.out);
-      }
-      log.info("Getting current vamsas document.");
-      VamsasDocument doc = varchive.getVamsasDocument();
-      ArchiveReports.reportDocument(doc, varchive.getOriginalArchiveReader(), true, System.out); // not modified document so references will still be valid
-      // do some stuff
-      log.info("Retrieving backup");
-      File backup = varchive.backupFile();
-      if (backup==null)
-        log.info(av+" is a New Archive.");
-      else 
-        log.info(av+" has been backed up as "+backup);
-      File newf=new File(av.getAbsolutePath()+"_new.zip");
-      VamsasFile sfile = new VamsasFile(newf);
-      /* if (newf.exists()) {
-        int q=1;
-        do {
-          newf=new File(av.getAbsolutePath()+"_"+q+++"_new.zip");
-        }
-        while (newf.exists()); 
-      } */
-      if (newf.exists()) {
-        log.info("Removing existing "+newf);
-        newf.delete();
-      }
-        
-      log.info("Now writing new Archive into "+newf.getAbsolutePath());
-      uk.ac.vamsas.client.simpleclient.VamsasArchive va=null;
-      { // hold lock over deletion and write of new archive.
-        //Lock wlock = sfile.getLock();
-        //newf.delete(); // clear out old file.
-        sfile.getLock();
-        va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, true, true, sfile);
-        // open another and...
-        ApplicationData appdata = makeDemoAppdata(va, 
-            "org.vamsas.test.simpleclient.VamsasArchive", "arnold Bugger esq", "disOrganised");
-        log.info("Preparing to write new document.");
-        doc.addApplicationData(appdata);
-        doc.addVAMSAS(Core.getDemoVamsas());
-        va.putVamsasDocument(doc); // gets stream and puts it.
-        va.closeArchive();
-        sfile.unLock();
-      }
-      log.info("Dump of new vamsas document :");
-      log.info("Testing update: ");
-      {
-        Lock lock=sfile.getLock();
-        if (lock==null)
-          while ((lock=sfile.getLock())==null) {
-            log.info("Waiting for lock.");
-            Thread.sleep(100);
-          }
-        VamsasArchiveReader vreader = new VamsasArchiveReader(sfile.getVamsasFile());// lock); // cannot do new JarFile on a locked file. // newf);
-        SimpleDocument sdoc = new SimpleDocument("testing new vamsas write");
-        ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out);
-        sfile.unLock();
-      }
-      // backup.delete(); // tidy up
-      
-      log.info("Now Cancelling write to original archive "+av);
-      if (varchive.cancelArchive())
-        log.info("Successfully cancelled.");
-      else
-        log.info("Didn't cancel.");
-      long t=System.currentTimeMillis()+200; while (t>System.currentTimeMillis());
-      log.info("Now testing archive update.");
-      va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, false, true, sfile);
-      doc = va.getVamsasDocument();
-      doc.addVAMSAS(Core.getDemoVamsas());
-      doc.addApplicationData(makeDemoAppdata(va, 
-          "org.vamsas.test.simpleclient.VamsasArchive", "another old Bugger esq", "rescinded"));
-      if (va.transferRemainingAppDatas())
-        log.info("Remain appdatas were transferred.");
-      else
-        log.warn("No appdatas were transferred. This is wrong.");
-      va.putVamsasDocument(doc);
-      va.closeArchive();
-      sfile.unLock();
-      log.info("Testing update: ");
-      {
-        Lock lock=sfile.getLock();
-        if (lock==null)
-          while ((lock=sfile.getLock())==null)
-            log.info("Waiting for lock.");
-        // VamsasArchiveReader vreader = new VamsasArchiveReader(lock);
-        VamsasArchiveReader vreader = new VamsasArchiveReader(newf);
-        
-        SimpleDocument sdoc = new SimpleDocument("testing vamsas update");
-        VamsasDocument finaldoc = sdoc.getVamsasDocument(vreader);
-        if (finaldoc!=null)
-          ArchiveReports.reportDocument(finaldoc, vreader, true, System.out);
-        else 
-          log.error("Null Document Read from "+newf);
-      }
-    } catch (Exception e) {
-      e.printStackTrace(System.err);
-    }
-  }
-}