X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Ftest%2Fsimpleclient%2FArchiveWriter.java;h=d6f8ee941b0bf2d12172858c82eb416208e1d8b0;hb=7700d838b129db99edacb208b3153546795a33c7;hp=7f45d5c86dde9a7125445bbeb5119f51d0a72b87;hpb=7d5afac27ba7da96347589d79617deecb057ee75;p=vamsas.git

diff --git a/src/org/vamsas/test/simpleclient/ArchiveWriter.java b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
index 7f45d5c..d6f8ee9 100644
--- a/src/org/vamsas/test/simpleclient/ArchiveWriter.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
@@ -7,44 +7,30 @@ import java.io.PrintWriter;
 import java.text.DateFormat;
 import java.util.Date;
 import java.util.Hashtable;
+import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.vamsas.client.simpleclient.VamsasArchive;
 import org.vamsas.client.simpleclient.VamsasArchiveReader;
+import org.vamsas.objects.core.Alignment;
 import org.vamsas.objects.core.ApplicationData;
 import org.vamsas.objects.core.Entry;
+import org.vamsas.objects.core.Instance;
 import org.vamsas.objects.core.Provenance;
 import org.vamsas.objects.core.VAMSAS;
 import org.vamsas.objects.core.VamsasDocument;
+import org.vamsas.objects.utils.ProvenanceStuff;
 
 public class ArchiveWriter {
   
   /**
    * Test program for writing archive files.
+   * form is ArchiveWriter new/modified argive command list
    */
   
-  static Log log = LogFactory.getLog("org.vamsas.test.simpleclient.ArchiveWriter");
-  
-  /**
-   * @param action
-   *          text for action entry
-   * @return new Provenance entry for ArchiveWriter created docs.
-   */
-  public static Entry newProvenanceEntry(String user, String action) { 
-    log.debug("Adding ProvenanceEntry("+user+","+action+")");
-    Entry e = new Entry();
-    e.setAction(action);
-    e.setUser(user);
-    e.setDate(new org.exolab.castor.types.Date(new Date()));
-    return e;
-  }
-  
-  public static Provenance newProvenance() {
-    Provenance list = new Provenance();
-    list.addEntry(newProvenanceEntry("ArchiveWriter", "Created new Vamsas Document"));
-    return list;
-  }
+  static Log log = LogFactory.getLog(ArchiveWriter.class);
+    
   private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) {
     int i;
     for (i=0; i<svec1.length; i++)
@@ -54,15 +40,16 @@ public class ArchiveWriter {
   }
   // Merge appDataReferences require transfer of jar entries, perhaps with a renaming of the entry.
   // Merge appDatas require eventually unique URNS
+  // TODO: merging global appdata from different documents where same app has written them causes conflict
   
-  public static Hashtable hashOfAppDatas(Hashtable ht, ApplicationData[] appdatas) {
+  public static Hashtable hashOfAppDatas(Hashtable ht, Instance[] appdatas) {
     if (ht==null)
       ht = new Hashtable();
     for (int i=0, j=appdatas.length; i<j; i++) {
       if (!ht.containsKey(appdatas[i].getUrn())) {
         Hashtable aphash = new Hashtable();
         ht.put(appdatas[i].getUrn(), aphash);
-        aphash.put(appdatas[i], appdatas[i].getAppDataChoice().getDataReference());
+        aphash.put(appdatas[i], appdatas[i].getDataReference());
       } else {
         // ensure urns and references are unique
         
@@ -72,9 +59,16 @@ public class ArchiveWriter {
     }
     return ht;
   }
+  /**
+   * safely copies an appData from one archive to another.
+   * @param darc destination archive
+   * @param dest destination document Vobject
+   * @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
+    // TODO: fix instances
+    // check uniqueness of instance's[] entry.urn amongst dest.ApplicationData[].getInstances[].urn 
     //  check uniqueness of entry.user[].urn amongst dest.ApplicationData[].user[].urn
     // check uniqueness of entry.user
     // entry.getAppDataChoice().getData() or getDataReference is unique
@@ -82,11 +76,11 @@ public class ArchiveWriter {
     for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
       ApplicationData o = dest.getApplicationData()[i];
       // ensure new urn is really unique
-      String urn = entry.getUrn();
+      //String urn = entry.getUrn();
       int v = 1;
-      while (o.getUrn().equals(urn)) {
-        urn = entry.getUrn()+v++;      
-      }
+      //while (o.getUrn().equals(urn)) {
+      //  urn = entry.getUrn()+v++;      
+     // }
       // uniqueness of urn
       // check each user ApplicationData
       // uniqueness (again)
@@ -94,14 +88,26 @@ 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 Vobject, 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();
@@ -115,8 +121,19 @@ public class ArchiveWriter {
     return true; // success    
   }
   
+  private static CommandProcessor cproc;
+  static {
+    cproc.addCommand("new", 0, "no args");
+    cproc.addCommand("add", 1, "Need another vamsas document archive filename as argument.");    
+    cproc.addCommand("repair", 0, "no args");
+    cproc.addCommand("list", 0, "no args");    
+    cproc.addCommand("monitor", 0, "no args");    
+  }
   
   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;
@@ -128,29 +145,31 @@ public class ArchiveWriter {
       VamsasArchive varc = new VamsasArchive(newarch, true);
       VamsasDocument docroot;
       docroot = new VamsasDocument();
-      docroot.setProvenance(newProvenance());
+      docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "user", "Created new Vamsas Document"));
       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));
-                docroot.getProvenance().addEntry(newProvenanceEntry("user", "added vamsas.xml from "+argv[argpos-1]));
+                VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream)); // TODO: verify only one VAMSAS element per vamsas.xml entry.
+                docroot.getProvenance().addEntry(ProvenanceStuff.newProvenanceEntry("ArchiveWriter", "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();
         }
       }