From 58ced019430c430493a13d2a75dae6f604a4a78a Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 24 Mar 2006 19:16:26 +0000
Subject: [PATCH] fixed (hopefully) locking/read problems in
 test.simpleclient.VamsasArchive/Watcher classes and
 commented out the RandomAccess based reading/writing for
 mo.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@212 be28352e-c001-0410-b1a7-c7978e42abec
---
 .../vamsas/client/simpleclient/VamsasArchive.java  |   12 ++++++----
 .../client/simpleclient/VamsasArchiveReader.java   |   25 ++++++++++++--------
 2 files changed, 23 insertions(+), 14 deletions(-)

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index 6e8138b..d769a5c 100644
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchive.java
@@ -196,6 +196,7 @@ public class VamsasArchive {
    */
   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");
   }
   /**
    * 
@@ -256,7 +257,8 @@ public class VamsasArchive {
         odoclock = new SessionFile(original);
       odoclock.lockFile();
       if (odoc == null) 
-        odoc = new VamsasArchiveReader(odoclock.fileLock);
+        odoc = new VamsasArchiveReader(original);
+        // this constructor is not implemented yet odoc = new VamsasArchiveReader(odoclock.fileLock);
     }
   }
   
@@ -373,7 +375,7 @@ public class VamsasArchive {
       newarchive.closeEntry();
       if (!isDocumentWritten())
         log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
-      newarchive.finish();
+      newarchive.close(); // use newarchive.finish(); for a stream IO
       updateOriginal();
       closeAndReset();
     } else {
@@ -552,8 +554,10 @@ public class VamsasArchive {
       rchive = new SessionFile(archive);
     if (!rchive.lockFile()) 
       throw new IOException("Failed to get lock on file "+archive);
-    Manifest newmanifest = new Manifest();
-    newarchive = new JarOutputStream(rchive.fileLock.getBufferedOutputStream(true), newmanifest);  
+    // 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, 
diff --git a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java b/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
index d0476cd..b4455ac 100644
--- a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
@@ -35,7 +35,8 @@ public class VamsasArchiveReader {
   ZipInputStream jstream=null;
   Hashtable strmentries = null;
   private void streamInit() {
-    if (!stream) {
+    throw new Error("VamsasArchiveReader(Stream) Not implemented!");
+    /* if (!stream) {
       log.debug("Skipping init for Jar Stream input.");
       return;
     }
@@ -48,13 +49,13 @@ public class VamsasArchiveReader {
       if (jstream.available()==0)
         log.warn("Can't read from JarInputStream (Locked stream!)");
       ZipEntry entry=null;
+      long pos=0;
       do {
-        long pos = rfile.getFilePointer();
         if ((entry=jstream.getNextEntry())!=null) {
           if (strmentries.containsKey(entry.getName())) {
             log.info("Only recording last of duplicate entries '"+entry.getName()+"'");
           } 
-          strmentries.put(entry.getName(), new Long(pos));
+          strmentries.put(entry.getName(), new Long(pos++));
           jstream.closeEntry();
         }
       } while (entry!=null);
@@ -62,7 +63,7 @@ public class VamsasArchiveReader {
     catch (Exception e) {
       log.warn("Exceptions during init!",e);
       jstream=null;
-    }
+    }*/
   }
   
   public VamsasArchiveReader(File vamsasfile) {
@@ -85,11 +86,13 @@ public class VamsasArchiveReader {
    * @param vamsaslock
    */
   public VamsasArchiveReader(Lock vamsaslock) {
-    rfile = vamsaslock.rafile;
-    stream = true;
-    streamInit();
-    if (jstream==null)
-      throw new Error("Failed to open archive from Locked random access stream.");
+    // LATER: implement or remove
+    throw new Error("VamsasArchiveReading from locked IO stream not yet implemented.");
+    //rfile = vamsaslock.rafile;
+    //stream = true;
+    //streamInit();
+    //if (jstream==null)
+    //  throw new Error("Failed to open archive from Locked random access stream.");
   }
   
   /**
@@ -124,7 +127,9 @@ public class VamsasArchiveReader {
       return null;
     }
     try {
-      jstream.reset();
+      jstream=null;
+      rfile.seek(0);
+      jstream = new ZipInputStream(new FileInputStream(rfile.getFD()));
       ZipEntry entry = null;
       long epos = entrypos.longValue();
       do {
-- 
1.7.10.2