partially implemented ArchiveWriter test class (routines will form basis of Get/Set...

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@104 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/test/simpleclient/ArchiveWriter.java b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
new file mode 100644 (file)
index 0000000..7f45d5c
--- /dev/null
+++ b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
@@ -0,0 +1,161 @@
+package org.vamsas.test.simpleclient;
+
+import java.io.File;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.text.DateFormat;
+import java.util.Date;
+import java.util.Hashtable;
+
+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.ApplicationData;
+import org.vamsas.objects.core.Entry;
+import org.vamsas.objects.core.Provenance;
+import org.vamsas.objects.core.VAMSAS;
+import org.vamsas.objects.core.VamsasDocument;
+
+public class ArchiveWriter {
+  
+  /**
+   * Test program for writing archive files.
+   */
+  
+  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;
+  }
+  private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) {
+    int i;
+    for (i=0; i<svec1.length; i++)
+      destvec[i] = svec1[i];
+    for (int j=0; j<svec2.length; i++, j++)
+      destvec[i] = svec2[j];
+  }
+  // Merge appDataReferences require transfer of jar entries, perhaps with a renaming of the entry.
+  // Merge appDatas require eventually unique URNS
+  
+  public static Hashtable hashOfAppDatas(Hashtable ht, ApplicationData[] 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());
+      } else {
+        // ensure urns and references are unique
+        
+        
+      }
+          
+    }
+    return ht;
+  }
+  public static void addAppDataEntry(VamsasArchive darc, VamsasDocument dest,  VamsasArchiveReader sarc, ApplicationData entry) {
+    
+    // check uniqueness of entry.urn amongst dest.ApplicationData[].urn
+    //  check uniqueness of entry.user[].urn amongst dest.ApplicationData[].user[].urn
+    // check uniqueness of entry.user
+    // entry.getAppDataChoice().getData() or getDataReference is unique
+    ApplicationData newo = new ApplicationData();
+    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();
+      int v = 1;
+      while (o.getUrn().equals(urn)) {
+        urn = entry.getUrn()+v++;      
+      }
+      // uniqueness of urn
+      // check each user ApplicationData
+      // uniqueness (again)
+      // copy over valid objects
+      // 
+    }
+  }
+  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 ?
+    
+    if (source.getApplicationDataCount()>0) {
+      ApplicationData[] newdat = new ApplicationData[source.getApplicationDataCount()+dest.getApplicationDataCount()];
+      ApplicationData[] sappd = source.getApplicationData();
+      // check refs and update/modify if necessary
+      for (int i=0; i<sappd.length; i++) {
+        addAppDataEntry(darc, dest, sarc, sappd[i]);
+      }
+      
+    }
+    
+    return true; // success    
+  }
+  
+  
+  public static void main(String argv[]) {
+    if (argv.length<1) {
+      log.fatal("Usage : <archive to create> [(commands)]");
+      return;
+    }
+    File newarch = new File(argv[0]);
+    int argpos = 0;
+    try {
+      // test fully fledged doc construction
+      VamsasArchive varc = new VamsasArchive(newarch, true);
+      VamsasDocument docroot;
+      docroot = new VamsasDocument();
+      docroot.setProvenance(newProvenance());
+      while (++argpos<argv.length) {
+        File archive = new File(argv[argpos]);
+        if (archive.exists()) {
+          VamsasArchiveReader vdoc = new VamsasArchiveReader(archive);
+          if (vdoc.isValid()) {
+            InputStream istream = vdoc.getVamsasDocumentStream(); 
+            if (istream!=null) {
+              VamsasDocument cdocroot = VamsasDocument.unmarshal(new InputStreamReader(istream));
+              if (cdocroot!=null) 
+                mergeDocs(varc, docroot, vdoc, cdocroot);
+            } else {
+              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]));
+                docroot.addVAMSAS(root);
+              }
+            }
+            
+          }
+          // Write a dummy vamsas document
+        
+          PrintWriter docwriter = varc.getDocumentOutputStream();
+        }
+      }
+    } catch (Exception e) {
+      log.error("Whilst manipulating "+argv[0], e);
+    }
+  }
+}