updated test cases for spring 2006 schema, and major debug of locking system

[vamsas.git] / src / org / vamsas / client / simpleclient / VamsasArchive.java

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index c58c5f3..e697861 100644 (file)
--- 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;
@@ -153,7 +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;
   /**
@@ -187,6 +188,25 @@ 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);
+    // log.debug("using non-functional lock-IO stream jar access constructor");
+  }
+  /**
+   * read and write to archive - will not overwrite original contents, and will always write an up to date vamsas document structure.
+   * @param archive
+   * @throws IOException
+   */
+  public VamsasArchive(VamsasFile archive) throws IOException {
+    this(archive, true, false); 
+  }
+  /**
    * 
    * @param archive file to write
    * @param overwrite true if original contents should be deleted
@@ -196,7 +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;
@@ -205,10 +225,13 @@ 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;
@@ -225,9 +248,9 @@ public class VamsasArchive {
       else
         rchive = new SessionFile(archive);
       rchive.lockFile();
-      if (rchive.fileLock==null || rchive.fileLock.rafile==null)
+      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
@@ -243,6 +266,7 @@ public class VamsasArchive {
       odoclock.lockFile();
       if (odoc == null) 
         odoc = new VamsasArchiveReader(original);
+        // this constructor is not implemented yet odoc = new VamsasArchiveReader(odoclock.fileLock);
     }
   }
   
@@ -269,6 +293,7 @@ public class VamsasArchive {
     JarEntry je = new JarEntry(entry);
     if (!addEntry(entry))
       return false;
+    newarchive.flush();
     newarchive.putNextEntry(je);
     return true;
   }
@@ -294,6 +319,9 @@ 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 +379,13 @@ 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();// close(); // use newarchive.finish(); for a stream IO
+      newarchive.flush();
+      //
       updateOriginal();
       closeAndReset();
     } else {
@@ -533,7 +564,10 @@ 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));  
+    // 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)));  
     entries = new Hashtable();
   }
   public void putVamsasDocument(VamsasDocument doc) throws IOException, 
@@ -543,6 +577,8 @@ 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);
   }
   
@@ -747,14 +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 {
       
+      
     }
   }
 }