show vamsasId for aligments.

[vamsas.git] / src / org / vamsas / test / simpleclient / VamsasArchive.java

diff --git a/src/org/vamsas/test/simpleclient/VamsasArchive.java b/src/org/vamsas/test/simpleclient/VamsasArchive.java
index 94d702b..09ddf34 100644 (file)
--- a/src/org/vamsas/test/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/test/simpleclient/VamsasArchive.java
@@ -5,8 +5,11 @@ import java.io.ObjectOutputStream;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.vamsas.client.simpleclient.Lock;
+import org.vamsas.client.simpleclient.SessionFile;
 import org.vamsas.client.simpleclient.SimpleDocument;
 import org.vamsas.client.simpleclient.VamsasArchiveReader;
+import org.vamsas.client.simpleclient.VamsasFile;
 import org.vamsas.objects.core.ApplicationData;
 import org.vamsas.objects.core.User;
 import org.vamsas.objects.core.VAMSAS;
@@ -76,7 +79,7 @@ public class VamsasArchive {
     apuser.setDataReference(appdata_ref);
     appdata.addUser(apuser);
     appdata.setVersion("noggin");
-    appdata.setUrn("program:/the.nog/");
+    //TODO: write instance appdata  appdata.setUrn("program:/the.nog/");
     try {
       ObjectOutputStream ost = new ObjectOutputStream(va.getAppDataStream(appdata_ref));
       ost.writeObject(appdata);
@@ -114,32 +117,50 @@ public class VamsasArchive {
       else 
         log.info(av+" has been backed up as "+backup);
       File newf=new File(av.getAbsolutePath()+"_new.zip");
-      if (newf.exists()) {
+      VamsasFile sfile = new VamsasFile(newf);
+      /* if (newf.exists()) {
         int q=1;
         do {
           newf=new File(av.getAbsolutePath()+"_"+q+++"_new.zip");
         }
         while (newf.exists()); 
-      } 
-      log.info("Now writing new Archive "+newf.getAbsolutePath());
-      org.vamsas.client.simpleclient.VamsasArchive va = new org.vamsas.client.simpleclient.VamsasArchive(newf, true);
-      // open another and...
-      ApplicationData appdata = makeDemoAppdata(va, 
-          "org.vamsas.test.simpleclient.VamsasArchive", "arnold Bugger esq", "disOrganised");
-      log.info("Preparing to write new document.");
-      doc.addApplicationData(appdata);
-      doc.addVAMSAS(Core.getDemoVamsas());
-      // TODO: ensure all jar entries are transferred over (at least those that are referenced - make a flag for 'tidy zip manifest'.
-      va.putVamsasDocument(doc); // gets stream and puts it.
-      // TODO: verify that the vxml stream close method overridden ?
-      va.closeArchive();
-      
+      } */
+      if (newf.exists()) {
+        log.info("Removing existing "+newf);
+        newf.delete();
+      }
+        
+      log.info("Now writing new Archive into "+newf.getAbsolutePath());
+      org.vamsas.client.simpleclient.VamsasArchive va=null;
+      { // hold lock over deletion and write of new archive.
+        //Lock wlock = sfile.getLock();
+        //newf.delete(); // clear out old file.
+        sfile.getLock();
+        va = new org.vamsas.client.simpleclient.VamsasArchive(newf, true, true, sfile);
+        // open another and...
+        ApplicationData appdata = makeDemoAppdata(va, 
+            "org.vamsas.test.simpleclient.VamsasArchive", "arnold Bugger esq", "disOrganised");
+        log.info("Preparing to write new document.");
+        doc.addApplicationData(appdata);
+        doc.addVAMSAS(Core.getDemoVamsas());
+        va.putVamsasDocument(doc); // gets stream and puts it.
+        va.closeArchive();
+        sfile.unLock();
+      }
       log.info("Dump of new vamsas document :");
       log.info("Testing update: ");
-      VamsasArchiveReader vreader = new VamsasArchiveReader(newf);
-      SimpleDocument sdoc = new SimpleDocument("testing new vamsas write");
-      ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out);
-      
+      {
+        Lock lock=sfile.getLock();
+        if (lock==null)
+          while ((lock=sfile.getLock())==null) {
+            log.info("Waiting for lock.");
+            Thread.sleep(100);
+          }
+        VamsasArchiveReader vreader = new VamsasArchiveReader(sfile.getVamsasFile());// lock); // cannot do new JarFile on a locked file. // newf);
+        SimpleDocument sdoc = new SimpleDocument("testing new vamsas write");
+        ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out);
+        sfile.unLock();
+      }
       // backup.delete(); // tidy up
       
       log.info("Now Cancelling write to original archive "+av);
@@ -147,9 +168,9 @@ public class VamsasArchive {
         log.info("Successfully cancelled.");
       else
         log.info("Didn't cancel.");
-      
+      long t=System.currentTimeMillis()+200; while (t>System.currentTimeMillis());
       log.info("Now testing archive update.");
-      va = new org.vamsas.client.simpleclient.VamsasArchive(newf, true); // TODO - refactor Reader class to have deserializing helpers
+      va = new org.vamsas.client.simpleclient.VamsasArchive(newf, false, true, sfile);
       doc = va.getVamsasDocument();
       doc.addVAMSAS(Core.getDemoVamsas());
       doc.addApplicationData(makeDemoAppdata(va, 
@@ -160,10 +181,23 @@ public class VamsasArchive {
         log.warn("No appdatas were transferred. This is wrong.");
       va.putVamsasDocument(doc);
       va.closeArchive();
+      sfile.unLock();
       log.info("Testing update: ");
-      vreader = new VamsasArchiveReader(newf);
-      sdoc = new SimpleDocument("testing vamsas update");
-      ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out);
+      {
+        Lock lock=sfile.getLock();
+        if (lock==null)
+          while ((lock=sfile.getLock())==null)
+            log.info("Waiting for lock.");
+        // VamsasArchiveReader vreader = new VamsasArchiveReader(lock);
+        VamsasArchiveReader vreader = new VamsasArchiveReader(newf);
+        
+        SimpleDocument sdoc = new SimpleDocument("testing vamsas update");
+        VamsasDocument finaldoc = sdoc.getVamsasDocument(vreader);
+        if (finaldoc!=null)
+          ArchiveReports.reportDocument(finaldoc, vreader, true, System.out);
+        else 
+          log.error("Null Document Read from "+newf);
+      }
     } catch (Exception e) {
       e.printStackTrace(System.err);
     }