X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2Fsimpleclient%2FVamsasArchive.java;h=c01ac26743d49604023aa3e6ac8fb2b8401dbd77;hb=f5306591821b5f6d4e381ff30b647bd149d51f43;hp=b6854cf6a8230f88e31261b7fe35694d4b312622;hpb=63b0b269c333a317ddd018c70a336c4cf839a2ee;p=vamsas.git

diff --git a/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java b/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java
index b6854cf..c01ac26 100644
--- a/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java
@@ -19,11 +19,8 @@ import java.util.jar.Manifest;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.AppDataReference;
-import org.vamsas.objects.utils.DocumentStuff;
-import org.vamsas.objects.utils.ProvenanceStuff;
-import org.vamsas.objects.utils.document.VersionEntries;
 
+import uk.ac.vamsas.client.AppDataOutputStream;
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.IVorbaIdFactory;
 import uk.ac.vamsas.client.SessionHandle;
@@ -34,6 +31,10 @@ import uk.ac.vamsas.client.VorbaXmlBinder;
 import uk.ac.vamsas.objects.core.ApplicationData;
 import uk.ac.vamsas.objects.core.VAMSAS;
 import uk.ac.vamsas.objects.core.VamsasDocument;
+import uk.ac.vamsas.objects.utils.AppDataReference;
+import uk.ac.vamsas.objects.utils.DocumentStuff;
+import uk.ac.vamsas.objects.utils.ProvenanceStuff;
+import uk.ac.vamsas.objects.utils.document.VersionEntries;
 
 /**
  * Class for high-level io and Jar manipulation involved in creating 
@@ -138,7 +139,7 @@ public class VamsasArchive {
   /**
    * Output stream for archived data
    */
-  JarOutputStream newarchive=null;
+  org.apache.tools.zip.ZipOutputStream newarchive=null;
   /**
    * JarEntries written to archive
    */
@@ -277,8 +278,12 @@ public class VamsasArchive {
    * @return true if entry was unique and was added.
    */
   private boolean addEntry(String entry) {
-    if (entries!=null)
+    if (entries==null)
       entries=new Hashtable();
+    if (log.isDebugEnabled())
+    {   
+      log.debug("validating '"+entry+"' in hash for "+this);
+    }
     if (entries.containsKey(entry))
       return false;
     entries.put(entry, new Integer(entries.size()));
@@ -291,7 +296,8 @@ public class VamsasArchive {
    * @throws IOException if entry name was invalid or a new entry could not be made on newarchive
    */
   private boolean addValidEntry(String entry) throws IOException {
-    JarEntry je = new JarEntry(entry);
+    org.apache.tools.zip.ZipEntry je = new org.apache.tools.zip.ZipEntry(entry);
+    // je.setExsetExtra(null);
     if (!addEntry(entry))
       return false;
     newarchive.flush();
@@ -307,7 +313,7 @@ public class VamsasArchive {
     
     if (!virginArchive) {
       makeBackup();
-      donotdeletebackup=false; // external reference has been made.
+      donotdeletebackup=true; // external reference has been made.
       return ((original!=null) ? originalBackup : null);
     }
     return null;
@@ -321,7 +327,7 @@ public class VamsasArchive {
     if (newarchive!=null) {
       try { 
         newarchive.closeEntry();
-        newarchive.putNextEntry(new JarEntry("deleted"));
+        newarchive.putNextEntry(new org.apache.tools.zip.ZipEntry("deleted"));
         newarchive.closeEntry();
         newarchive.close();
         
@@ -566,8 +572,8 @@ 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);  
+    // Manifest newmanifest = new Manifest();
+    newarchive = new org.apache.tools.zip.ZipOutputStream(rchive.fileLock.getBufferedOutputStream(true));// , newmanifest);  
     //newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));  
     entries = new Hashtable();
   }