started on ClientDocument implementation and Locked IO tests for VamsasArchive

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@149 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/client/simpleclient/ClientDocument.java b/src/org/vamsas/client/simpleclient/ClientDocument.java
index 05fe494..3e5fcfa 100644 (file)
--- a/src/org/vamsas/client/simpleclient/ClientDocument.java
+++ b/src/org/vamsas/client/simpleclient/ClientDocument.java
@@ -16,16 +16,11 @@ import org.vamsas.objects.core.VamsasDocument;
  * @author jimp Contains a collection of vamsas objects and reference to a
  *         specified ClientHandle's information.
  */
-public class ClientDocument implements IClientDocument {
+public class ClientDocument extends org.vamsas.client.ClientDocument implements IClientDocument {
   protected IClient vorba;
   protected org.vamsas.objects.core.VAMSAS[] roots;
   protected byte[] appData;
-
-  /**
-   * collection of org.vamsas.client.object references
-   */
-  protected Hashtable vamsasObjects;
-  
+  protected VamsasArchive archive = null;
   /*
    * (non-Javadoc)
    * 
@@ -33,18 +28,12 @@ public class ClientDocument implements IClientDocument {
    */
 
   /**
-   * 
-   * @param data
-   * @param doc
-   * @param objects
-   * @param vorba
    */
-  protected ClientDocument(byte[] data, VAMSAS[] roots, Hashtable objects, IClient vorba) {
-    // TODO Auto-generated constructor stub
-    appData = data;
-    this.roots =roots;
-    vamsasObjects = objects;
+  protected ClientDocument(VamsasArchive document, IdFactory Factory, IClient vorba) {
+    super(Factory.getVorbaIdHash(), Factory);
     this.vorba = vorba;
+    archive = document;
+    roots = null;
   }
 
   public byte[] getApplicationData() {
@@ -148,12 +137,10 @@ public class ClientDocument implements IClientDocument {
 /*
    * (non-Javadoc)
    * 
-   * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.object)
+   * @see org.vamsas.client.IClientDocument#setApplicationData(byte[])
    */
-public VorbaId registerObject(object unregistered) {
-    if (!unregistered.isRegistered())
-      unregistered.setVorbaId(unregistered.__vorba.makeVorbaId());
-    return unregistered.getVorbaId();
+  public void setApplicationData(byte[] newData) {
+    appData = newData;
   }
   /*
    * (non-Javadoc)
@@ -170,12 +157,11 @@ public VorbaId registerObject(object unregistered) {
     return null;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see org.vamsas.client.IClientDocument#setApplicationData(byte[])
+  /* (non-Javadoc)
+   * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.object)
    */
-  public void setApplicationData(byte[] newData) {
-    appData = newData;
+  public VorbaId registerObject(object unregistered) {
+    // TODO: add provenance stuff to newly registered object
+    return _registerObject(unregistered);
   }
 }

diff --git a/src/org/vamsas/client/simpleclient/IdFactory.java b/src/org/vamsas/client/simpleclient/IdFactory.java
index 36fd3bc..543730e 100644 (file)
--- a/src/org/vamsas/client/simpleclient/IdFactory.java
+++ b/src/org/vamsas/client/simpleclient/IdFactory.java
@@ -51,7 +51,14 @@ public class IdFactory extends VorbaIdFactory {
     idstring = client.getClientUrn()+":"+unique.getValue()+"/";
     extantids=new Hashtable();
   }
-
+  /**
+   * values for keys in this hash can be used to reference the org.vamsas.client.object instance for the VorbaId string.
+   * @return the hash of all VorbaIds
+   */
+  protected Hashtable getVorbaIdHash() {
+    return extantids;
+  }
+  
   /* (non-Javadoc)
    * @see org.vamsas.client.VorbaIdFactory#makeVorbaId()
    */

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index fb7ddd8..f55d3d8 100644 (file)
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchive.java
@@ -88,7 +88,11 @@ public class VamsasArchive {
    * @throws IOException if call to accessOriginal failed for updates, or openArchive failed.
    */
   public VamsasArchive(File archive, boolean vamsasdocument) throws IOException {
+    this(archive, vamsasdocument, null);
+  }
+  public VamsasArchive(File archive, boolean vamsasdocument, Lock extantLock) throws IOException {
     super();
+    
     if (archive==null || (archive!=null && !(archive.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"));
@@ -97,6 +101,8 @@ public class VamsasArchive {
     this.vamsasdocument = vamsasdocument;
     if (archive.exists()) {
       this.original = archive;
+      this.odoclock = new SessionFile(archive); // lock the file *immediatly*
+      odoclock.lockFile(extantLock);
       this.archive = null;       // archive will be a temp file when the open method is called
       virginArchive=false;
       try {
@@ -107,6 +113,11 @@ public class VamsasArchive {
     } else {
       this.original = null;
       this.archive = archive; // archive is written in place.
+      if (archive!=null) {
+        archive.createNewFile();
+        rchive=new SessionFile(archive); // lock the file *immediatly*
+        rchive.lockFile(extantLock);
+      }
       virginArchive = true;
     }
     this.openArchive(); // open archive
@@ -227,6 +238,7 @@ public class VamsasArchive {
    * 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 TODO
    * @throws IOException
    */
   private void openArchive() throws IOException {
@@ -249,8 +261,12 @@ public class VamsasArchive {
         log.warn("New archive file name already in use! Possible lock failure imminent?");
     }
     
-    rchive = new SessionFile(archive);
-    rchive.lockFile();
+    if (rchive==null)
+      rchive = new SessionFile(archive);
+    archive.createNewFile();
+    if (!rchive.lockFile()) 
+      throw new IOException("Failed to get lock on file "+archive);
+  
     newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));  
     entries = new Hashtable();
   }
@@ -282,7 +298,7 @@ public class VamsasArchive {
    */
   public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
     if (newarchive==null)
-      openArchive();
+      throw new IOException("Attempt to write to closed VamsasArchive object.");
     if (addValidEntry(appdataReference)) {
       return new AppDataOutputStream(newarchive);
     }
@@ -357,7 +373,7 @@ public class VamsasArchive {
   private void closeAndReset() {
     if (rchive!=null) {
       rchive.unlockFile();
-      rchive = null;
+      rchive=null;
     }
     if (original!=null) {
       if (odoc!=null) {

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java b/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
index b00ebce..3b03137 100644 (file)
--- a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
@@ -3,6 +3,7 @@ package org.vamsas.client.simpleclient;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.RandomAccessFile;
 import java.util.Enumeration;
 import java.util.Iterator;
 import java.util.Vector;
@@ -23,6 +24,9 @@ import org.apache.commons.logging.LogFactory;
 public class VamsasArchiveReader {
   private static Log log = LogFactory.getLog(VamsasArchiveReader.class);
   JarFile jfile;
+  boolean stream=false; // true if we are seeking on the stream.
+  RandomAccessFile rfile; 
+  JarInputStream jstream;
   public VamsasArchiveReader(File vamsasfile) {
     jfile=null;
     if (vamsasfile.exists()) {
@@ -36,6 +40,21 @@ public class VamsasArchiveReader {
     
   }
   /**
+   * 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) {
+    rfile = vamsaslock.rafile;
+    stream = true;
+    // TODO: Implement stream based JarFile access
+    log.error("NOT IMPLEMENTED STREAM-BASED JAR ACCESS");
+    throw new Error("Can't access a locked VamsasArchive file as a random access stream yet.");
+    // rfile.seek(0);
+    
+  }
+  /**
    * the vamsas document version(s) handled by this Reader
    */
   final public static String DOCUMENT_VERSION="0.1"; 

diff --git a/src/org/vamsas/client/simpleclient/VamsasFile.java b/src/org/vamsas/client/simpleclient/VamsasFile.java
index 6ad634b..4199dd2 100644 (file)
--- a/src/org/vamsas/client/simpleclient/VamsasFile.java
+++ b/src/org/vamsas/client/simpleclient/VamsasFile.java
@@ -63,6 +63,12 @@ public class VamsasFile extends SessionFile {
    * gets a locked Reader for the vamsas document.
    * @return reader for vamsasdocument.xml enrty
    */
+  public Lock getLock() {
+    while (!lockFile())
+      ;
+    return fileLock;
+  }
+  
   public java.io.Reader getDocumentReader() {
     
     try {