X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fclient%2Fsimpleclient%2FVamsasArchive.java;h=4c4fbfd21c7c5e7157ab3b1dc639a12300fe179f;hb=d2cb3f9a881f6b937adb5c54a4b20a08eb2e99db;hp=c58c5f36b762d90393b303b22c6af5cc13a7d4d0;hpb=d3c6dfdbb5e6d268c45ddf261f941af1309649ba;p=vamsas.git

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index c58c5f3..4c4fbfd 100644
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchive.java
@@ -15,6 +15,7 @@ import java.util.Iterator;
 import java.util.Vector;
 import java.util.jar.JarEntry;
 import java.util.jar.JarOutputStream;
+import java.util.jar.Manifest;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -187,6 +188,16 @@ public class VamsasArchive {
     this(archive, overwrite, vamsasdocument, null);
   }
   /**
+   * Constructor for accessing Files under file-lock management (ie a session file)
+   * @param archive
+   * @param vamsasdocument
+   * @param overwrite
+   * @throws IOException
+   */
+  public VamsasArchive(VamsasFile archive, boolean vamsasdocument, boolean overwrite) throws IOException {
+    this(archive.sessionFile, overwrite, vamsasdocument, archive);
+  }
+  /**
    * 
    * @param archive file to write
    * @param overwrite true if original contents should be deleted
@@ -205,10 +216,13 @@ public class VamsasArchive {
     this.vamsasdocument = vamsasdocument;
     if (archive.exists() && !overwrite) {
       this.original = archive;
-      if (extantLock!=null)
+      if (extantLock!=null) {
         this.odoclock = extantLock;
-      else 
-        this.odoclock = new SessionFile(archive); 
+        if (odoclock.fileLock==null || !odoclock.fileLock.isLocked())
+          odoclock.lockFile();
+      } else { 
+        this.odoclock = new SessionFile(archive);
+      }
       odoclock.lockFile(); // lock the file *immediatly*
       this.archive = null;       // archive will be a temp file when the open method is called
       virginArchive=false;
@@ -225,7 +239,7 @@ public class VamsasArchive {
       else
         rchive = new SessionFile(archive);
       rchive.lockFile();
-      if (rchive.fileLock==null || rchive.fileLock.rafile==null)
+      if (rchive.fileLock==null || rchive.fileLock.rafile==null || !rchive.fileLock.isLocked())
         throw new IOException("Lock failed for new archive"+archive);
       rchive.fileLock.rafile.setLength(0); // empty the archive.
       virginArchive = true;
@@ -269,6 +283,7 @@ public class VamsasArchive {
     JarEntry je = new JarEntry(entry);
     if (!addEntry(entry))
       return false;
+    newarchive.flush();
     newarchive.putNextEntry(je);
     return true;
   }
@@ -294,6 +309,9 @@ public class VamsasArchive {
   public boolean cancelArchive() {
     if (newarchive!=null) {
       try { 
+        newarchive.closeEntry();
+        newarchive.putNextEntry(new JarEntry("deleted"));
+        newarchive.closeEntry();
         newarchive.close();
         
       } catch (Exception e) {
@@ -351,10 +369,11 @@ public class VamsasArchive {
    */
   public void closeArchive() throws IOException {
     if (newarchive!=null) {
+      newarchive.flush();
       newarchive.closeEntry();
       if (!isDocumentWritten())
         log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
-      newarchive.close();
+      newarchive.finish();
       updateOriginal();
       closeAndReset();
     } else {
@@ -533,7 +552,8 @@ public class VamsasArchive {
       rchive = new SessionFile(archive);
     if (!rchive.lockFile()) 
       throw new IOException("Failed to get lock on file "+archive);
-    newarchive = new JarOutputStream(rchive.fileLock.getBufferedOutputStream(true));  
+    Manifest newmanifest = new Manifest();
+    newarchive = new JarOutputStream(rchive.fileLock.getBufferedOutputStream(true), newmanifest);  
     entries = new Hashtable();
   }
   public void putVamsasDocument(VamsasDocument doc) throws IOException, 
@@ -543,6 +563,8 @@ public class VamsasArchive {
   
   public void putVamsasDocument(VamsasDocument doc, VorbaIdFactory vorba) throws IOException, 
   org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+    if (vamsasdocument)
+      doc.setVersion(VersionEntries.latestVersion()); // LATER: ensure this does the correct thing.
     VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);
   }