X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fclient%2Fsimpleclient%2FVamsasArchive.java;h=e697861fca9fb8590875f9e9cdb94040a17409b8;hb=30801ef84cde704404d052f00c70ae129820bb0b;hp=f065d04848e7158b68d7b23f6959a454386cf71c;hpb=4f11373ddecd53546b3b22e0358f3df01b24a6e6;p=vamsas.git

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index f065d04..e697861 100644
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchive.java
@@ -154,7 +154,7 @@ public class VamsasArchive {
    */
   File originalBackup = null;
   
-  boolean donotdeletebackup=false;
+  boolean donotdeletebackup=true;
   private final int _TRANSFER_BUFFER=4096*4;
   protected SimpleDocument vorba = null;
   /**
@@ -216,7 +216,7 @@ public class VamsasArchive {
    */
   public VamsasArchive(File archive, boolean overwrite, boolean vamsasdocument, SessionFile extantLock) throws IOException {
     super();
-    if (archive==null || (archive!=null && !(archive.getParentFile().canWrite() && (!archive.exists() || archive.canWrite())))) {
+    if (archive==null || (archive!=null && !(archive.getAbsoluteFile().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"));
       return;
@@ -248,9 +248,9 @@ public class VamsasArchive {
       else
         rchive = new SessionFile(archive);
       rchive.lockFile();
-      if (rchive.fileLock==null || rchive.fileLock.rafile==null || !rchive.fileLock.isLocked())
+      if (rchive.fileLock==null || !rchive.fileLock.isLocked())
         throw new IOException("Lock failed for new archive"+archive);
-      rchive.fileLock.rafile.setLength(0); // empty the archive.
+      rchive.fileLock.getRaFile().setLength(0); // empty the archive.
       virginArchive = true;
     }
     this.openArchive(); // open archive
@@ -383,7 +383,9 @@ public class VamsasArchive {
       newarchive.closeEntry();
       if (!isDocumentWritten())
         log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
-      newarchive.close(); // use newarchive.finish(); for a stream IO
+      newarchive.finish();// close(); // use newarchive.finish(); for a stream IO
+      newarchive.flush();
+      //
       updateOriginal();
       closeAndReset();
     } else {
@@ -563,9 +565,9 @@ public class VamsasArchive {
     if (!rchive.lockFile()) 
       throw new IOException("Failed to get lock on file "+archive);
     // LATER: locked IO stream based access.
-    //Manifest newmanifest = new Manifest();
-    //newarchive = new JarOutputStream(rchive.fileLock.getBufferedOutputStream(true), newmanifest);  
-    newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));  
+    Manifest newmanifest = new Manifest();
+    newarchive = new JarOutputStream(rchive.fileLock.getBufferedOutputStream(true), newmanifest);  
+    //newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));  
     entries = new Hashtable();
   }
   public void putVamsasDocument(VamsasDocument doc) throws IOException, 
@@ -781,14 +783,19 @@ public class VamsasArchive {
         odoclock.updateFrom(null, rchive);
       }
       catch (IOException e) {
-        // LATER: decide if leaving nastily named backup files around is necessary. 
-        log.error("Problem updating archive from temporary file! - backup left in '"
+        // LATER: decide if leaving nastily named backup files around is necessary.
+        File backupFile=backupFile();
+        if (backupFile!=null)
+          log.error("Problem updating archive from temporary file! - backup left in '"
             +backupFile().getAbsolutePath()+"'",e);
+        else
+          log.error("Problems updating, and failed to even make a backup file. Ooops!", e);
       }
       // Tidy up if necessary.
       removeBackup();
     } else {
       
+      
     }
   }
 }