From 25968adf9bc0c109749c5c59c4fdbd16e524f9d0 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 22 Mar 2006 17:04:50 +0000
Subject: [PATCH] more fixes for clientdocument/simpleclient. Testign the
 vamsasArchive reader and sessionfile mechanism (windows
 patches)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@199 be28352e-c001-0410-b1a7-c7978e42abec
---
 .../vamsas/client/simpleclient/ClientDocument.java |   67 +++++++++++++++++++-
 .../vamsas/client/simpleclient/SessionFile.java    |   30 ++++++---
 .../vamsas/client/simpleclient/SimpleClient.java   |    7 +-
 .../vamsas/client/simpleclient/VamsasArchive.java  |    2 +
 4 files changed, 90 insertions(+), 16 deletions(-)

diff --git a/src/org/vamsas/client/simpleclient/ClientDocument.java b/src/org/vamsas/client/simpleclient/ClientDocument.java
index f89f713..d360085 100644
--- a/src/org/vamsas/client/simpleclient/ClientDocument.java
+++ b/src/org/vamsas/client/simpleclient/ClientDocument.java
@@ -68,6 +68,10 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#getObject(org.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))
       return (Vobject) objrefs.get(id);
     log.debug("Returning null Vobject reference for id "+id.getId());
@@ -80,6 +84,10 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#getObjects(org.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]))
@@ -98,12 +106,23 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#getVamsasRoots()
    */
   public VAMSAS[] getVamsasRoots() {
+    if (doc==null) {
+      log.debug("Null document for getVamsasRoots(), returning null");
+      return null;
+    }
+    if (archive==null) {
+      // LATER: decide on read-only status of ClientDocument object
+      log.warn("getVamsasRoots() called on possibly read-only document.");
+    }
     if (_VamsasRoots!=null)
       return _VamsasRoots;
     VAMSAS[] roots = doc.getVAMSAS();
     if (roots == null) {
-      // Make a new one to return to client : TODO: Decide if this is correct
+      // Make a new one to return to client to get filled. 
       _VamsasRoots = new VAMSAS[] { new VAMSAS() };
+      // Do provenance now. just in case.
+      doc.getProvenance().addEntry(sclient.getProvenanceEntry("Created new document root [id="+_VamsasRoots[0].getId()+"]"));
+      doc.addVAMSAS(_VamsasRoots[0]);
     } else {
       _VamsasRoots = new VAMSAS[roots.length];
       for (int r=0;r<roots.length; r++)
@@ -244,6 +263,10 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @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.");
@@ -271,6 +294,10 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
    */
   public void addVamsasRoot(VAMSAS newroot) {
+    if (doc==null) {
+      log.debug("addVamsasRoots called on null document.");
+      return;
+    }
     VAMSAS[] newroots = _combineRoots(new VAMSAS[] {newroot}, _VamsasRoots, this);
     _VamsasRoots = newroots;  
   }
@@ -281,6 +308,14 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#registerObjects(org.vamsas.client.Vobject[])
    */
   public VorbaId[] registerObjects(Vobject[] unregistered) {
+    if (doc==null) {
+      log.warn("registerObjects[] called on null document.");
+      return null;
+    }
+    if (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++)
@@ -299,6 +334,14 @@ 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 (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 id = _registerObject(unregistered);
       log.debug("Registered object - total of "+objrefs.size()+" ids.");
@@ -315,6 +358,10 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
    * @see org.vamsas.client.IClientDocument#getClientAppdata()
    */
   public IClientAppdata getClientAppdata() {
+    if (doc==null) {
+      log.warn("getClientAppdata called on null document.");
+      return null;
+    }
     if (scappd==null) {
       log.debug("Creating new SimpleClientAppdata instance for "+sclient.getSessionHandle());
       scappd = new SimpleClientAppdata(this);
@@ -350,6 +397,15 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
   }
   protected boolean updateSessionDocument() throws java.io.IOException {
     boolean docupdate = true; // 'non-serious' problems below set this false
+    if (doc==null) {
+      log.warn("updateSessionDocument called on null document.");
+      throw new java.io.IOException("Document is closed.");
+    }
+    if (archive==null) {
+      log.warn("updateSessionDocument called document archive handler.");
+      throw new java.io.IOException("Document is closed.");
+    }
+    
     if (!isModified() && !scappd.isModified()) {
       log.debug("Document update not necessary. returning false.");
       return false;
@@ -426,7 +482,6 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
       log.debug("No remaining appdatas were transferred. (Correct?)");
     archive.closeArchive();
     log.debug("...successully finished and closed.");
-
     return docupdate; // no errors ?
   }
   /* (non-Javadoc)
@@ -438,7 +493,13 @@ public class ClientDocument extends org.vamsas.client.ClientDocument implements
       scappd.finalize();
       scappd = null;
     }
-    // TODO local garbage collection
+    if (doc!=null) {
+      doc = null;
+    }
+    // disengage from client
+    if (sclient!=null)
+      sclient.cdocument = null;
+    sclient=null;
     
     super.finalize();
   }
diff --git a/src/org/vamsas/client/simpleclient/SessionFile.java b/src/org/vamsas/client/simpleclient/SessionFile.java
index 0ff306e..0eabf6d 100644
--- a/src/org/vamsas/client/simpleclient/SessionFile.java
+++ b/src/org/vamsas/client/simpleclient/SessionFile.java
@@ -46,17 +46,27 @@ public class SessionFile {
         fileLock.release();
     fileLock = null;
     if (sessionFile != null) {
-      if (sessionFile.exists()) {
-        // TODO: see if we need to loop-wait for locks or they just block until
-        // lock is made...
-        do {
-          if (fileLock!=null)
-            fileLock.release();
-          fileLock = new Lock(sessionFile); // TODO: wait around if we can't get the lock.
-        } while (!fileLock.isLocked());
-        // fileLock = new Lock(sessionFile);
-        return fileLock.isLocked();
+      if (!sessionFile.exists()) {
+        // create new file
+        try {
+          if (!sessionFile.createNewFile()) {
+            log.error("Failed to create file prior to locking: "+sessionFile);
+            return false;
+          }
+        } catch (IOException e) {
+          log.error("Exception when trying to create file "+sessionFile, e);
+          return false;
+        }
       }
+      // TODO: see if we need to loop-wait for locks or they just block until
+      // lock is made...
+      do {
+        if (fileLock!=null)
+          fileLock.release();
+          fileLock = new Lock(sessionFile); // TODO: wait around if we can't get the lock.
+      } while (!fileLock.isLocked());
+      // fileLock = new Lock(sessionFile);
+      return fileLock.isLocked();    
     } else
       log.error("lockFile called for non-initialised SessionFile!");
   
diff --git a/src/org/vamsas/client/simpleclient/SimpleClient.java b/src/org/vamsas/client/simpleclient/SimpleClient.java
index 970bcfa..e824549 100644
--- a/src/org/vamsas/client/simpleclient/SimpleClient.java
+++ b/src/org/vamsas/client/simpleclient/SimpleClient.java
@@ -288,10 +288,11 @@ public class SimpleClient implements IClient {
     // 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;
+    cdocument = null; // this is probably done by finalize
   }
   
   /*
@@ -341,7 +342,7 @@ public class SimpleClient implements IClient {
     }
     
     if (!evgen.isAlive()) {
-      log.warn("pollUpdate called before joinSession()");
+      log.warn("pollUpdate called before joinSession() - trying to do this.");
       try {
         joinSession();
       } catch (Exception e) {
@@ -386,6 +387,6 @@ public class SimpleClient implements IClient {
    */
   public void importDocument(File location) {
     // TODO LATER: implement SimpleClient.importDocument()
-    log.error("importDocument is not implemented for a SimpleClient Session.");
+    log.error("importDocument is not yet implemented for a SimpleClient Session.");
   }
 }
diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index d510d51..c485124 100644
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchive.java
@@ -225,6 +225,8 @@ public class VamsasArchive {
       else
         rchive = new SessionFile(archive);
       rchive.lockFile();
+      if (rchive.fileLock==null || rchive.fileLock.rafile==null)
+        throw new IOException("Lock failed for new archive"+archive);
       rchive.fileLock.rafile.setLength(0); // empty the archive.
       virginArchive = true;
     }
-- 
1.7.10.2