From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 16 Jan 2006 09:37:30 +0000 (+0000)
Subject: debug as far as test marshalling - a vorbaIdFactory is now required.
X-Git-Tag: Release_0.2~386
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7cd19d45b73dd3b862cc0c67d18ce976240ac636;p=vamsas.git

debug as far as test marshalling - a vorbaIdFactory is now required.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@134 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index fab9ef2..ec42a33 100644
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchive.java
@@ -155,7 +155,6 @@ public class VamsasArchive {
     if (!virginArchive) {
       makeBackup();
       return ((original!=null) ? originalBackup : null);
-      
     }
     return null;
   }
@@ -174,7 +173,7 @@ public class VamsasArchive {
    */
   protected boolean isDocumentWritten() {
     if (newarchive==null)
-      log.warn("isDocumentWritten called for unopened archive.");
+      log.warn("isDocumentWritten() called for unopened archive.");
     if (entries!=null) {
       if (entries.containsKey(getDocumentJarEntry()))
         return true;
@@ -266,7 +265,7 @@ public class VamsasArchive {
    * @throws IOException
    */
   public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
-    if (newarchive!=null)
+    if (newarchive==null)
       openArchive();
     if (addValidEntry(appdataReference)) {
       return new AppDataOutputStream(newarchive);
@@ -276,7 +275,7 @@ public class VamsasArchive {
   
   /**
    * Stops any current write to archive, and reverts to the backup if it exists.
-   * All existing locks on the original will be released.
+   * All existing locks on the original will be released. All backup files are removed.
    */
   public boolean cancelArchive() {
     if (newarchive!=null) {
@@ -306,15 +305,11 @@ public class VamsasArchive {
             return false;
           }
         }
-        // original is untouched
-        // just delete temp files
-        
-        
       }
     } else {
       log.info("cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
     }
-    closeAndReset();
+    closeAndReset(); // tidy up and release locks.
     return true;
   }
   
@@ -420,6 +415,8 @@ public class VamsasArchive {
   /**
    * Tidies up and closes archive, removing any backups that were created.
    * NOTE: It is up to the caller to delete the original archive backup obtained from backupFile()
+   * TODO: ensure all extant AppDataReference jar entries are transferred to new Jar
+   * TODO: provide convenient mechanism for generating new unique AppDataReferences and adding them to the document
    */
   public void closeArchive() throws IOException {
     if (newarchive!=null) {
diff --git a/src/org/vamsas/objects/utils/Seq.java b/src/org/vamsas/objects/utils/Seq.java
index ca83223..7564f1d 100644
--- a/src/org/vamsas/objects/utils/Seq.java
+++ b/src/org/vamsas/objects/utils/Seq.java
@@ -87,6 +87,7 @@ public class Seq {
        if ((start-end)!=Sequence.length())
          seq.setEnd(end+Sequence.length());
      }
+     seq.getVorbaId();
      return seq;
   }
   public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, int start, int end) {
diff --git a/src/org/vamsas/test/simpleclient/VamsasArchive.java b/src/org/vamsas/test/simpleclient/VamsasArchive.java
index 1e96cc9..e820c52 100644
--- a/src/org/vamsas/test/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/test/simpleclient/VamsasArchive.java
@@ -4,21 +4,28 @@ import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.ObjectOutputStream;
+import java.io.PrintWriter;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.vamsas.client.SimpleClient;
 import org.vamsas.client.simpleclient.*;
+import org.vamsas.objects.core.AppDataChoice;
+import org.vamsas.objects.core.ApplicationData;
+import org.vamsas.objects.core.User;
 import org.vamsas.objects.core.VAMSAS;
 import org.vamsas.objects.core.VamsasDocument;
+import org.vamsas.test.objects.Core;
 
 public class VamsasArchive {
   /**
    * test the org.vamsas.simpleclient.vamsasArchive class
    */
   static Log log = LogFactory.getLog("org.vamsas.test.simpleclient.vamsasArchive");
-
+  
   public static void main(String args[]) {
-
+    
     try {
       File av;
       if (args.length>0)
@@ -44,12 +51,48 @@ public class VamsasArchive {
         log.info(av+" is a New Archive.");
       else 
         log.info(av+" has been backed up as "+backup);
-      varchive.cancelArchive();
       if (backup!=null) {
-        log.info("Backup "+backup+" is being deleted.");
+        log.info("Backup "+backup+" is being written to.");
+        // open another and...
+        ApplicationData appdata = new ApplicationData();
+        appdata.setName("org.vamsas.test.simpleclient.VamsasArchive");
+        appdata.setAppDataChoice(new AppDataChoice());
+        appdata.getAppDataChoice().setData(new String("this is some test data.").getBytes());
+        User apuser = new User();
+        apuser.setFullname("arnold Bugger esq");
+        apuser.setOrganization("disOrganised");
+        String appdata_ref = "vamsas:org.vamsas.test.simpleclient.VamsasArchive/"+apuser.getOrganization()+"/"+apuser.getFullname();
+        org.vamsas.client.simpleclient.VamsasArchive va = new org.vamsas.client.simpleclient.VamsasArchive(backup, true);
+        VamsasArchiveReader vread = va.getOriginalArchiveReader();
+        if (vread.getAppdataStream(appdata_ref)!=null) {
+          int i=0;
+          while (vread.getAppdataStream(appdata_ref+"/"+Integer.toString(++i))!=null)
+              ;
+          appdata_ref+="/"+Integer.toString(i);
+        }
+        log.info("Writing an apdata reference using AppDataStream interface.");
+        apuser.setAppDataChoice(new AppDataChoice());
+        apuser.getAppDataChoice().setDataReference(appdata_ref);
+        ObjectOutputStream apdos = new ObjectOutputStream(va.getAppDataStream(appdata_ref));
+        apdos.writeObject(appdata_ref);
+        apdos.writeObject(apuser); // some random content
+        apdos.close(); // this should *not* close the archive!
+        log.info("Preparing to write new document.");
+        doc.addApplicationData(appdata);
+        doc.addVAMSAS(Core.getDemoVamsas());
+        PrintWriter vxml = varchive.getDocumentOutputStream();
+        doc.marshal(vxml);
+        // TODO: verify that the vxml stream close method overridden ?
+        va.closeArchive();
+        log.info("Dump of new vamsas document :");
+        va = new org.vamsas.client.simpleclient.VamsasArchive(backup, true); // TODO - refactor Reader class to have deserializing helpers
+        ArchiveReports.reportDocument(va.getVamsasDocument(), va.getOriginalArchiveReader(), true);
         backup.delete(); // tidy up
       }
-      } catch (Exception e) {
+      log.info("Cancelling write to original archive "+av);
+      varchive.cancelArchive();
+
+    } catch (Exception e) {
       e.printStackTrace(System.err);
     }
   }