From 88c78c876c6de96c25cb49e818d8c75ed6a1a7df Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 13 Jan 2006 14:53:22 +0000
Subject: [PATCH] synchronizing commit

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@109 be28352e-c001-0410-b1a7-c7978e42abec
---
 .../vamsas/test/simpleclient/ArchiveReader.java    |    4 ++
 .../vamsas/test/simpleclient/ArchiveWriter.java    |   44 ++++++++++++++++----
 2 files changed, 39 insertions(+), 9 deletions(-)

diff --git a/src/org/vamsas/test/simpleclient/ArchiveReader.java b/src/org/vamsas/test/simpleclient/ArchiveReader.java
index 5f7fd6a..8f461c3 100644
--- a/src/org/vamsas/test/simpleclient/ArchiveReader.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReader.java
@@ -10,6 +10,10 @@ import org.vamsas.objects.core.VAMSAS;
 import org.vamsas.objects.core.VamsasDocument;
 
 public class ArchiveReader {
+  /**
+   * tests VamsasArchiveReader archive reader on a vamsas jar file
+   * @param args
+   */
   public static void main(String args[]) {
     
     try {
diff --git a/src/org/vamsas/test/simpleclient/ArchiveWriter.java b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
index 7f45d5c..a4b2255 100644
--- a/src/org/vamsas/test/simpleclient/ArchiveWriter.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
@@ -30,6 +30,7 @@ public class ArchiveWriter {
    * @param action
    *          text for action entry
    * @return new Provenance entry for ArchiveWriter created docs.
+   * TODO: Verify and move to SimpleClient class for provenance handling
    */
   public static Entry newProvenanceEntry(String user, String action) { 
     log.debug("Adding ProvenanceEntry("+user+","+action+")");
@@ -45,6 +46,7 @@ public class ArchiveWriter {
     list.addEntry(newProvenanceEntry("ArchiveWriter", "Created new Vamsas Document"));
     return list;
   }
+  
   private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) {
     int i;
     for (i=0; i<svec1.length; i++)
@@ -72,6 +74,13 @@ public class ArchiveWriter {
     }
     return ht;
   }
+  /**
+   * safely copies an appData from one archive to another.
+   * @param darc destination archive
+   * @param dest destination document object
+   * @param sarc source archive reader
+   * @param entry application data to be copied from source archive
+   */
   public static void addAppDataEntry(VamsasArchive darc, VamsasDocument dest,  VamsasArchiveReader sarc, ApplicationData entry) {
     
     // check uniqueness of entry.urn amongst dest.ApplicationData[].urn
@@ -94,14 +103,26 @@ public class ArchiveWriter {
       // 
     }
   }
+  /**
+   * Copy new datasets and appdatas from one vamsas document to another.
+   * @param darc
+   * @param dest
+   * @param sarc
+   * @param source
+   * @return true if merge was successful.
+   */
   public static boolean mergeDocs(VamsasArchive darc, VamsasDocument dest,  VamsasArchiveReader sarc, VamsasDocument source) {
     log.debug("mergeDocs entered.");
     // search for appDatas in cdoc
     VAMSAS[] newr = new VAMSAS[dest.getVAMSASCount()+source.getVAMSASCount()];
     mergeVecs(newr, dest.getVAMSAS(), source.getVAMSAS());
     dest.setVAMSAS(newr);
-    // TODO: should verify that all ids really are unique in newly merged document. If not then what ?
-    
+    /** TODO: LATER: should verify that all ids really are unique in newly merged document. If not then what ?
+     *  investigate possibility of having an id translation between appDatas and the core document - 
+     *  the mapping is stored when an external application performs a merge, but when the owning 
+     *  Application accesses the object, the vorba_id is updated to the new one when it writes its 
+     *  references in to its appdata again
+     */
     if (source.getApplicationDataCount()>0) {
       ApplicationData[] newdat = new ApplicationData[source.getApplicationDataCount()+dest.getApplicationDataCount()];
       ApplicationData[] sappd = source.getApplicationData();
@@ -117,6 +138,9 @@ public class ArchiveWriter {
   
   
   public static void main(String argv[]) {
+    /**
+     * TODO: switches for setting user identities for writing to vamsas document
+     */ 
     if (argv.length<1) {
       log.fatal("Usage : <archive to create> [(commands)]");
       return;
@@ -131,26 +155,28 @@ public class ArchiveWriter {
       docroot.setProvenance(newProvenance());
       while (++argpos<argv.length) {
         File archive = new File(argv[argpos]);
+        InputStream istream;
         if (archive.exists()) {
           VamsasArchiveReader vdoc = new VamsasArchiveReader(archive);
           if (vdoc.isValid()) {
-            InputStream istream = vdoc.getVamsasDocumentStream(); 
+            istream = vdoc.getVamsasDocumentStream(); 
             if (istream!=null) {
               VamsasDocument cdocroot = VamsasDocument.unmarshal(new InputStreamReader(istream));
               if (cdocroot!=null) 
                 mergeDocs(varc, docroot, vdoc, cdocroot);
-            } else {
+            } else 
+              log.warn("Unexpectedly null document stream from existing document "+archive);
+          } else {
+              // updating an oldformat stream ?
               if ((istream = vdoc.getVamsasXmlStream())!=null) {
                 // make a new vamsas document from the vamsas.xml entry
-                VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream));
+                VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream)); // TODO: verify only one VAMSAS element per vamsas.xml entry.
                 docroot.getProvenance().addEntry(newProvenanceEntry("user", "added vamsas.xml from "+argv[argpos-1]));
                 docroot.addVAMSAS(root);
               }
-            }
-            
           }
-          // Write a dummy vamsas document
-        
+        } else {
+          // Begin a new vamsas document
           PrintWriter docwriter = varc.getDocumentOutputStream();
         }
       }
-- 
1.7.10.2