X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Ftest%2Fsimpleclient%2FClientDoc.java;h=da05e0090027c26f51c20a4b59522a36ae1e1947;hb=7700d838b129db99edacb208b3153546795a33c7;hp=f15eec5ebd532def9751fa0baf881768a3696643;hpb=c48e7dc90f1cc593738404dcf83a8a36e1b9a3b0;p=vamsas.git

diff --git a/src/org/vamsas/test/simpleclient/ClientDoc.java b/src/org/vamsas/test/simpleclient/ClientDoc.java
index f15eec5..da05e00 100644
--- a/src/org/vamsas/test/simpleclient/ClientDoc.java
+++ b/src/org/vamsas/test/simpleclient/ClientDoc.java
@@ -5,6 +5,7 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.vamsas.client.IClientAppdata;
 import org.vamsas.client.Vobject;
 import org.vamsas.client.VorbaId;
 import org.vamsas.client.simpleclient.ClientDocument;
@@ -16,7 +17,13 @@ import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.objects.utils.ProvenanceStuff;
 
 // simple holder to pass to client.
-public class ClientDoc {
+public class ClientDoc extends org.vamsas.client.ClientDocument {
+  /* (non-Javadoc)
+   * @see org.vamsas.client.IClientDocument#getClientAppdata()
+   */
+  public IClientAppdata getClientAppdata() {
+    throw new Error("Appdata access is not implemented in the test.simpleclient.ClientDoc instance."); // TODO Auto-generated method stub
+  }
   protected boolean isModified=false;
   private Log log = LogFactory.getLog(ClientDoc.class);
   protected VamsasDocument doc;
@@ -24,18 +31,21 @@ public class ClientDoc {
   protected VamsasArchive iohandler=null;
   protected VamsasArchiveReader reader=null;
   private String user=null;
+  private String app=null;
   
   /**
    * @param doc
    * @param iohandler
    * @param reader
+   * @param app
    * @param user
    */
-  public ClientDoc(VamsasDocument doc, VamsasArchive iohandler, VamsasArchiveReader reader, String user, Hashtable objrefs) {
-    super();
+  public ClientDoc(VamsasDocument doc, VamsasArchive iohandler, VamsasArchiveReader reader, String app, String user, Hashtable objrefs) {
+    super(objrefs, (iohandler!=null) ? iohandler.getVorba() : null);
     this.doc = doc;
     this.iohandler = iohandler;
     this.reader = reader;
+    this.app = app;
     this.user = user;
     this.objrefs = objrefs;
     _VamsasRoots = doc.getVAMSAS();
@@ -47,7 +57,7 @@ public class ClientDoc {
    */
   protected Entry getProvenanceEntry(String action) {
     // VAMSAS: modify schema to allow referencing of user field (plus other issues, ClientUrn field, machine readable action, input parameters, additional data generated notes
-    Entry prov = ProvenanceStuff.newProvenanceEntry(user, action);
+    Entry prov = ProvenanceStuff.newProvenanceEntry(app, user, action);
     return prov;
   }
   public VAMSAS[] getVamsasRoots() {
@@ -206,14 +216,32 @@ public class ClientDoc {
   public VamsasArchiveReader getReader() {
     return reader;
   }
+  private void _finalize() {
+    log.debug("finalizing clientDoc");
+    if (doc!=null) {
+      doc = null;
+    }
+    if (_VamsasRoots!=null) {
+      for (int i=0; i<_VamsasRoots.length; i++)
+        _VamsasRoots[i]=null;
+      _VamsasRoots=null;
+       
+    }
+      
+    if (reader!=null) {
+      log.debug("Closing and removing reader reference");
+      reader.close();
+      reader=null;
+    }
+    if (iohandler!=null) {
+      log.debug("Removing ioHandler reference.");
+      iohandler.cancelArchive();
+      iohandler=null;
+    }
+  }
   protected void finalize() throws Throwable {
+    _finalize();
     super.finalize();
-    //if (reader!=null)
-    //  reader.close();
-    //reader=null;
-//    if (iohandler!=null) {
-//      iohandler.cancelArchive(); // otherwise the original may be overwritten.
-//    }
   }
   private java.util.Hashtable objrefs=null;
   
@@ -258,14 +286,13 @@ public class ClientDoc {
     }
     
     if (unregistered!=null) {
-      VorbaId id = iohandler.getVorba().makeVorbaId(unregistered);
+      VorbaId id = this._registerObject(unregistered);
       log.debug("Registered object - total of "+objrefs.size()+" ids.");
       return id;
     }
     log.warn("Null Vobject passed to registerObject.");
     return null;
   }
-
   /*
    * (non-Javadoc)
    * 
@@ -276,8 +303,8 @@ public class ClientDoc {
       log.debug("getObject called on null objrefs list.");
       return null;
     }
-    if (objrefs.containsKey(id))
-      return (Vobject) objrefs.get(id);
+    if (objrefs.containsKey(id.getId()))
+      return (Vobject) objrefs.get(id.getId());
     log.debug("Returning null Vobject reference for id "+id.getId());
     return null;
   }
@@ -300,5 +327,29 @@ public class ClientDoc {
         log.debug("Returning null Vobject reference for id "+ids[i].getId());
     return vo;
   }
+  protected void updateDocumentRoots() {
+    if (doc==null) {
+      log.error("updateDocumentRoots called on null document. Probably an implementation error.");
+      return;
+    }
+    if (isModified) {
+      if (_VamsasRoots!=null) {
+        doc.setVAMSAS(_VamsasRoots);
+        _VamsasRoots=null;
+      }
+    }
+  }
+  /**
+   * tell vamsas client to close the document and reset the object. Once closed, nothing can be done with the object.
+   *
+   */
+  public void closeDoc() {
+    if (doc!=null) {
+      log.debug("Closing open document.");
+      _finalize();
+    } else {
+      log.warn("Ignoring closeDoc on invalid document.");
+    }
+  }
   
 }
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