From e96aa19ea301f3386b47043a435b3e0091eadbec Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 21 Mar 2006 17:18:41 +0000
Subject: [PATCH] intermediate cjeckin - nfs woes!

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@196 be28352e-c001-0410-b1a7-c7978e42abec
---
 src/org/vamsas/client/IClient.java                 |    2 +
 .../vamsas/client/simpleclient/ClientDocument.java |  226 ++++++++++++++------
 .../vamsas/client/simpleclient/SimpleClient.java   |   48 ++++-
 .../client/simpleclient/SimpleClientAppdata.java   |   56 ++++-
 .../client/simpleclient/SimpleDocBinding.java      |    2 +
 .../vamsas/client/simpleclient/SimpleDocument.java |    5 +-
 src/org/vamsas/objects/utils/AppDataReference.java |   19 ++
 7 files changed, 268 insertions(+), 90 deletions(-)

diff --git a/src/org/vamsas/client/IClient.java b/src/org/vamsas/client/IClient.java
index 51367c9..c73aaa4 100644
--- a/src/org/vamsas/client/IClient.java
+++ b/src/org/vamsas/client/IClient.java
@@ -83,6 +83,8 @@ public interface IClient {
      * New objects without provenance information will be 
      * given a default entry using the IClient's application, 
      * user (and session) handles
+     * Validity of IClientDocument object instances after this call is implementation dependent
+     * TODO: consider refactoring to remove the redundant IClientDocument parameter for this method
      */
     public void updateDocument(IClientDocument newdoc);
     /**
diff --git a/src/org/vamsas/client/simpleclient/ClientDocument.java b/src/org/vamsas/client/simpleclient/ClientDocument.java
index 71365ee..6b1d7fc 100644
--- a/src/org/vamsas/client/simpleclient/ClientDocument.java
+++ b/src/org/vamsas/client/simpleclient/ClientDocument.java
@@ -3,22 +3,20 @@
  */
 package org.vamsas.client.simpleclient;
 
-import java.util.Hashtable;
 import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.IClient;
+import org.vamsas.client.ClientHandle;
 import org.vamsas.client.IClientAppdata;
 import org.vamsas.client.IClientDocument;
-import org.vamsas.client.VorbaId;
 import org.vamsas.client.Vobject;
-import org.vamsas.objects.core.AppData;
+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.
@@ -40,6 +38,7 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
   public boolean isModified() {
     return isModified;
   }
+  private java.util.Hashtable objrefs=null;
   /**
    *
    *  prepare Application-side dataset from the vamsas Document archive
@@ -57,6 +56,7 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
     this.sclient = sclient;
     archive = docHandler;
     this.doc = doc;
+    objrefs = Factory.getVorbaIdHash();
   }
   
   /*
@@ -65,8 +65,9 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId)
    */
   public Vobject getObject(VorbaId id) {
-    // TODO: look up id in document Vobject
-    // retrieve Vobject and return
+    if (objrefs.containsKey(id))
+      return (Vobject) objrefs.get(id);
+    log.debug("Returning null Vobject reference for id "+id.getId());
     return null;
   }
   
@@ -76,8 +77,13 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#getObjects(org.vamsas.client.VorbaId[])
    */
   public Vobject[] getObjects(VorbaId[] ids) {
-    // TODO: getObject in bulk
-    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;
   }
   /**
    * internal reference to single copy of Document Roots array
@@ -121,7 +127,6 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
  * @return true if newVersion is a valid root that preserves original references
  */
   private boolean isValidUpdate(VAMSAS newVersion, final VAMSAS oldVersion) {
-    // LATER: IMPLEMENT
     // ideal - this cascades down the two structures, ensuring that all ID'd objects in one are present in the other.
     if (oldVersion==newVersion) {
       // may be a virgin root element.
@@ -140,6 +145,53 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
         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
@@ -186,60 +238,31 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
   /**
    * 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) {
-    
+    VAMSAS[] newr;
+    if (newroots==null) {
+      log.debug("setVamsasRoots(null) - do nothing.");
+      return;
+    }
     // are we dealing with same array ?
     if (_VamsasRoots!=newroots) {
-      // merge roots into 
-    }
-    // extract root objects
-    if (newroots != null) {
-      // check newroots for objects that were present in the old document
-      // 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 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)
@@ -264,6 +287,7 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
         } else {
           ids[i]=registerObject(unregistered[i]);
         }
+      log.debug("Registered "+unregistered.length+" objects - total of "+objrefs.size()+" ids.");
       return ids;
     }
     return null;
@@ -272,8 +296,11 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.Vobject)
    */
   public VorbaId registerObject(Vobject unregistered) {
-    if (unregistered!=null)
-      return _registerObject(unregistered);
+    if (unregistered!=null) {
+      VorbaId id = _registerObject(unregistered);
+      log.debug("Registered object - total of "+objrefs.size()+" ids.");
+      return id;
+    }
     log.warn("Null Vobject passed to registerObject.");
     return null;
   }
@@ -299,18 +326,6 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
     }
     return scappd;
   }
-  /* (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;
-    }
-    
-    super.finalize();
-  }
   /**
    * access the vamsas document
    * @return the session's vamsas document
@@ -330,4 +345,73 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
     }
     return null;
   }
+  protected boolean updateSessionDocument() throws java.io.IOException {
+    if (!isModified() && !scappd.isModified())
+      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;
+      scappd.closeForWriting();      
+      long newAppd = scappd.newAppData.sessionFile.length();
+      
+      if (scappd.appsGlobal==null) {
+        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()));
+      }
+      if (scappd.newAppData!=null && scappd.newAppData.sessionFile.exists()) {
+        if (scappd.appsGlobal.getData()!=null) {
+          scappd.appsGlobal.setData(null);
+          scappd.appsGlobal.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()));
+        }
+        
+          
+          
+      }
+      if (scappd.usersData==null) {
+        
+      }
+      
+    }
+    cdocument.archive.putVamsasDocument(vdoc);
+    // write the appHandle to the lastupdate file.
+  }
+  if (scappd!=null) {
+      if (scappd.accessedDocument)
+    }
+    va = new org.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();
+
+    return true; // successfully updated.
+  }
+  /* (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;
+    }
+    // TODO local garbage collection
+    super.finalize();
+  }
+
 }
diff --git a/src/org/vamsas/client/simpleclient/SimpleClient.java b/src/org/vamsas/client/simpleclient/SimpleClient.java
index efaf2ea..084c7f5 100644
--- a/src/org/vamsas/client/simpleclient/SimpleClient.java
+++ b/src/org/vamsas/client/simpleclient/SimpleClient.java
@@ -26,8 +26,11 @@ import org.vamsas.client.IClientDocument;
 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;
 
@@ -144,7 +147,23 @@ public class SimpleClient implements IClient {
   public UserHandle getUserHandle() {
     return user;
   }
-  
+  /**
+   * 
+   * @return user field for a provenance entry
+   */
+  protected String getProvenanceUser() {
+    return new String(user.getFullName()+" ["+client.getClientUrn()+"]");
+  }
+  /**
+   * construct a provenance entry for this client with the specified action string.
+   * @param action
+   * @return properly completed provenance entry
+   */
+  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(getProvenanceUser(), action);
+    return prov;
+  }
   private Hashtable handlers = initHandlers();
   
   private Vector listeners = new Vector();
@@ -220,7 +239,7 @@ public class SimpleClient implements IClient {
       // if session currently holds data - read it in - or get a dummy
       _session.slog.debug("Accessing document");
       doc = 
-        va.getVamsasDocument(user.getFullName()+" using "+client.getClientName(),
+        va.getVamsasDocument(getProvenanceUser(),
             "created new session document.", null);
       if (doc!=null)
         _session.slog.debug("Successfully retrieved document.");
@@ -239,18 +258,31 @@ public class SimpleClient implements IClient {
   
   /*
    * (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.");
     }
-    
-    // try to update the sessionFile
-    
-    // write the appHandle to the lastupdate file.
-    
+    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 {
+      if (cdocument.updateSessionDocument())
+        log.warn("Session document did not update properly for session directory "+_session.sessionDir);
+    }
+    // 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;
   }
   
   /*
diff --git a/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java b/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java
index 52d5890..5bda46e 100644
--- a/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java
+++ b/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java
@@ -10,6 +10,7 @@ import java.io.DataInput;
 import java.io.DataInputStream;
 import java.io.DataOutput;
 import java.io.DataOutputStream;
+import java.io.IOException;
 import java.io.InputStream;
 import java.util.Vector;
 import java.util.jar.JarEntry;
@@ -48,6 +49,15 @@ public class SimpleClientAppdata implements IClientAppdata {
    */
   SessionFile newAppData=null;
   JarOutputStream newAppDataStream=null;
+  /**
+   * set by extractAppData
+   */
+  protected ApplicationData appsGlobal = null;
+  /**
+   * set by extractAppData
+   */
+  protected User usersData = null;
+  
   ClientDocument clientdoc;
   /**
    * state flags
@@ -71,14 +81,6 @@ public class SimpleClientAppdata implements IClientAppdata {
     this.clientdoc = clientdoc;
   }
   /**
-   * set by extractAppData
-   */
-  protected ApplicationData appsGlobal = null;
-  /**
-   * set by extractAppData
-   */
-  protected User usersData = null;
-  /**
    * 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.
    */
@@ -447,6 +449,44 @@ public class SimpleClientAppdata implements IClientAppdata {
       // 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();
+    }
+  }
+  /**
+   * copy data from the appData jar file to an appropriately 
+   * referenced jar or Data entry for the given ApplicationData 
+   * @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) {
+    
+  }
+
+  /**
+   * 
+   * @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()
    */
diff --git a/src/org/vamsas/client/simpleclient/SimpleDocBinding.java b/src/org/vamsas/client/simpleclient/SimpleDocBinding.java
index da453c2..408e651 100644
--- a/src/org/vamsas/client/simpleclient/SimpleDocBinding.java
+++ b/src/org/vamsas/client/simpleclient/SimpleDocBinding.java
@@ -19,6 +19,8 @@ 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
  */
   
diff --git a/src/org/vamsas/client/simpleclient/SimpleDocument.java b/src/org/vamsas/client/simpleclient/SimpleDocument.java
index 4226458..df569e7 100644
--- a/src/org/vamsas/client/simpleclient/SimpleDocument.java
+++ b/src/org/vamsas/client/simpleclient/SimpleDocument.java
@@ -5,9 +5,8 @@ import org.apache.commons.logging.LogFactory;
 import org.vamsas.client.VorbaIdFactory;
 
 /**
- * holds static vamsasDocument from XML routines and
- * state objects for a particular unmarshalled Document instance.
- * TODO Could be refactored ? only dependence is the IdFactory.getDummyFactory(String) method.
+ * @see SimpleDocBinding
+ * Additional constructors for 'headless' Vamsas Document access
  * @author jimp
  */
 public class SimpleDocument extends SimpleDocBinding {
diff --git a/src/org/vamsas/objects/utils/AppDataReference.java b/src/org/vamsas/objects/utils/AppDataReference.java
index 29c044b..50dc96b 100644
--- a/src/org/vamsas/objects/utils/AppDataReference.java
+++ b/src/org/vamsas/objects/utils/AppDataReference.java
@@ -6,6 +6,8 @@ import java.util.Vector;
 
 import org.vamsas.client.ClientHandle;
 import org.vamsas.client.UserHandle;
+import org.vamsas.client.simpleclient.VamsasArchive;
+import org.vamsas.client.simpleclient.VamsasArchiveReader;
 import org.vamsas.objects.core.*;
 /**
  * Form, accessors and validation for ApplicationData references in
@@ -137,4 +139,21 @@ public class AppDataReference {
     
     return searchAppDatas(doc, match, true); // only return AppDatas belonging to appdata app.
   }
+  /**
+   * safely creates a new appData reference
+   * @param dest destination document Vobject
+   * @param entry base application reference to make unique 
+   */
+  public static String uniqueAppDataReference(VamsasDocument dest,String base) {
+    String urn = new String(base);    
+    for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
+      ApplicationData o = dest.getApplicationData()[i];
+      // ensure new urn is really unique
+      int v = 1;
+      while (o.getUrn().equals(urn)) {
+        urn = base+"/"+v++;      
+      } 
+    }
+    return urn;
+  }
 }
-- 
1.7.10.2