X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Ftest%2Fsimpleclient%2FVamsasArchive.java;h=09ddf347801959d979ccb2a675359331c44722c1;hb=7700d838b129db99edacb208b3153546795a33c7;hp=112a4b234c20c77500473f1f65c4c7661347edf1;hpb=277d50147b238cbf89038d96187304285a3df516;p=vamsas.git

diff --git a/src/org/vamsas/test/simpleclient/VamsasArchive.java b/src/org/vamsas/test/simpleclient/VamsasArchive.java
index 112a4b2..09ddf34 100644
--- a/src/org/vamsas/test/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/test/simpleclient/VamsasArchive.java
@@ -79,7 +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);
@@ -125,12 +125,18 @@ public class VamsasArchive {
         }
         while (newf.exists()); 
       } */
+      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.
-        va = new org.vamsas.client.simpleclient.VamsasArchive(newf, true, true); // , sfile);
+        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");
@@ -146,9 +152,11 @@ public class VamsasArchive {
       {
         Lock lock=sfile.getLock();
         if (lock==null)
-          while ((lock=sfile.getLock())==null)
+          while ((lock=sfile.getLock())==null) {
             log.info("Waiting for lock.");
-        VamsasArchiveReader vreader = new VamsasArchiveReader(newf);
+            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();
@@ -180,9 +188,15 @@ public class VamsasArchive {
         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");
-        ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out);
+        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);