remove old ebi packages

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

diff --git a/src/org/vamsas/test/simpleclient/ArchiveReports.java b/src/org/vamsas/test/simpleclient/ArchiveReports.java
index b38f87a..4a3a284 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveReports.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReports.java
@@ -4,13 +4,15 @@ import java.io.InputStream;
 import java.io.PrintStream;
 import java.io.PrintWriter;
 
-import org.vamsas.client.object;
+import org.vamsas.client.ClientDocument;
+import org.vamsas.client.Vobject;
 import org.vamsas.client.simpleclient.VamsasArchiveReader;
 import org.vamsas.objects.core.Alignment;
 import org.vamsas.objects.core.AppData;
 import org.vamsas.objects.core.ApplicationData;
 import org.vamsas.objects.core.DataSet;
 import org.vamsas.objects.core.Entry;
+import org.vamsas.objects.core.Instance;
 import org.vamsas.objects.core.Provenance;
 import org.vamsas.objects.core.Tree;
 import org.vamsas.objects.core.User;
@@ -19,8 +21,8 @@ import org.vamsas.objects.core.VamsasDocument;
 /**
  * this class contains static methods for writing info to stdout about a vamsas document
  * Methods have a 'cascade' switch to indicate if sub-objects should have info printed on them.
- * Methods return true or false - indicating if the object was valid or not
- * TODO: LATER: propagate true/false return so that an invalid vamsas object invalidates the whole document
+ * Methods return true or false - indicating if the Vobject was valid or not
+ * TODO: LATER: propagate true/false return so that an invalid vamsas Vobject invalidates the whole document
  * @author jimp
  *
  */
@@ -39,7 +41,7 @@ public class ArchiveReports {
     }
     Entry[] pe = p.getEntry();
     for (int i=0; i<pe.length; i++)
-      outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getAction());
+      outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getApp()+"\t'"+pe[i].getAction()+"'");
     return true;
   }
   public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
@@ -77,6 +79,13 @@ public class ArchiveReports {
     if (appD!=null) {
       // Report on root appData
       appDataEntryReport(appD, archive, cascade, outstr);
+      if (appD.getInstanceCount()>0) {
+        Instance inst[] = appD.getInstance();
+        for (int i=0,j=inst.hashCode(); i<j; i++) {
+          outstr.println("Data for App Instance URN: '"+inst[i].getUrn());
+          appDataEntryReport(inst[i],archive,cascade,outstr);
+        }
+      }
       if (appD.getUserCount()>0) {
         User users[] = appD.getUser();
         for (int i=0,j=users.length; i<j; i++) {
@@ -99,7 +108,7 @@ public class ArchiveReports {
         outstr.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
         ApplicationData appd[] = document.getApplicationData();
         for (int i=0,j=appd.length; i<j; i++) {
-          outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\nURN: '"+appd[i].getUrn()+"'\n");
+          outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\n");
           outstr.print("AppData is :");
           appDataReport(appd[i], archive, cascade, outstr);
         }
@@ -107,7 +116,7 @@ public class ArchiveReports {
       }
       return true;
     } else {
-      outstr.print("Document Object is null");
+      outstr.println("Document Object is null");
     }
     return false;
   }
@@ -156,11 +165,11 @@ public class ArchiveReports {
     boolean val=true;
     if (al!=null && al.length>0) {
       for (int i=0; i<al.length; i++) {
-        outstr.println("Alignment "+i);
+        outstr.println("Alignment "+i+(al[i].isRegistered() ? " ("+al[i].getVorbaId()+")" : " (unregistered)"));
         if (cascade)
           reportProvenance(al[i].getProvenance(), outstr);
         outstr.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
-            +al[i].getAlignmentAnnotationsCount()+" annotations and "+al[i].getTreeCount()+" trees.");
+            +al[i].getAlignmentAnnotationCount()+" annotations and "+al[i].getTreeCount()+" trees.");
         if (cascade) {
           for (int t=0; t<al[i].getTreeCount(); t++)
             treeReport(al[i].getTree(t), true, outstr);