more verbose reports and demo VamsasDocument testing

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@130 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java
index ca3d90d..0bc3db5 100644 (file)
--- a/src/org/vamsas/test/objects/Core.java
+++ b/src/org/vamsas/test/objects/Core.java
@@ -3,24 +3,27 @@
  */
 package org.vamsas.test.objects;
 
-import org.vamsas.objects.core.Alignment;
-import org.vamsas.objects.core.AlignmentSequence;
-import org.vamsas.objects.core.DataSet;
-import org.vamsas.objects.core.Sequence;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.utils.Seq;
-import org.vamsas.objects.utils.SymbolDictionary;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.vamsas.objects.core.*;
+import org.vamsas.objects.utils.*;
+import org.vamsas.objects.utils.document.*;
+import org.vamsas.test.simpleclient.ArchiveReports;
 
 /**
  * @author jim
  * test XSD-Java binding classes in org.vamsas.objects.core
  */
 public class Core {
+  static Log log = LogFactory.getLog("org.vamsas.test.objects.Core");
+
   /**
    * 
    * complete any automatically completable entries in the dataset
    * @param ds
    */
+  public static String user = "org.vamsas.test.objects.Core";
+  
   public static void complete(DataSet ds) {
     Sequence[] q = ds.getSequence();
     for (int i=0,j=q.length; i<j; i++) {
@@ -33,19 +36,30 @@ public class Core {
      VAMSAS v=new VAMSAS();
      DataSet ds = new DataSet();
      ds.addSequence(Seq.newSequence("Dummy1","ASDFLEQ",SymbolDictionary.STANDARD_AA, 5, 11));
+     ds.addSequence(Seq.newSequence("Dummy2","ASFLEQ",SymbolDictionary.STANDARD_AA, 5, 10));
+     ds.addSequence(Seq.newSequence("Dummy3","ADFEQ",SymbolDictionary.STANDARD_AA, 3, 7));
+     ds.setProvenance(ProvenanceStuff.newProvenance(user, "constructed some dummy sequences"));
      complete(ds);
      v.addDataSet(ds);
      Alignment al = new Alignment();
-     
-     al.addAlignmentSequence(new AlignmentSequence());
+     al.setProvenance(ProvenanceStuff.newProvenance(user, "Created dummy alignment"));
+     //   rely on newAlignmentSequence to set start/end correctly
+     al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned1", "ASDFLEQ", ds.getSequence(0), -1, -1)); 
+     al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned2", "AS-FLEQ", ds.getSequence(1), -1, -1)); 
+     al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned3", "A-DF-EQ", ds.getSequence(2), -1, -1)); 
+     al.setGapChar("-");
+     ds.addAlignment(al);
+     // TODO: create annotations
+     // TODO: create tree
      return v;
    }
   /**
    * @param args
    */
   public static void main(String[] args) {
-    // TODO Auto-generated method stub
-
+    VamsasDocument doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { getDemoVamsas() }, 
+        ProvenanceStuff.newProvenance("org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
+        VersionEntries.latestVersion());
+    ArchiveReports.reportDocument(doc, null, true);
   }
-
 }

diff --git a/src/org/vamsas/test/simpleclient/ArchiveReports.java b/src/org/vamsas/test/simpleclient/ArchiveReports.java
index 7ff04b3..20c433b 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveReports.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReports.java
@@ -3,10 +3,22 @@ package org.vamsas.test.simpleclient;
 import java.io.InputStream;
 
 import org.vamsas.client.simpleclient.VamsasArchiveReader;
+import org.vamsas.objects.core.Alignment;
 import org.vamsas.objects.core.ApplicationData;
+import org.vamsas.objects.core.DataSet;
+import org.vamsas.objects.core.Entry;
+import org.vamsas.objects.core.Provenance;
+import org.vamsas.objects.core.Tree;
 import org.vamsas.objects.core.VAMSAS;
 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
+ * @author jimp
+ *
+ */
 public class ArchiveReports {
     /**
      * print an informative summary on a VamsasDocument
@@ -14,10 +26,23 @@ public class ArchiveReports {
      * @param archive - document source archive for resolving any appData refs
      * @return
      */
-  public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive) {
+  public static boolean reportProvenance(Provenance p) {
+    if (p==null) {
+      System.out.println("No Provenance");
+      return false;
+    }
+    Entry[] pe = p.getEntry();
+    for (int i=0; i<pe.length; i++)
+      System.out.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getAction());
+    return true;
+  }
+  public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade) {
     if (document!=null) {
-      System.out.print("Vamsas Document version '"+document.getVersion()+"'");
+      System.out.println("Vamsas Document version '"+document.getVersion()+"'");
+      reportProvenance(document.getProvenance());
       System.out.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" elements.\n");
+      if (document.getVAMSASCount()>0 && cascade)
+        rootReport(document.getVAMSAS(), true);
       if (document.getApplicationDataCount()>0) {
         System.out.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
         ApplicationData appd[] = document.getApplicationData();
@@ -54,20 +79,62 @@ public class ArchiveReports {
   /**
    * summarises all the datasets in a vamsas document.
    * @param roots
+   * @param cascade TODO
    * @return
    */
-  public static boolean rootReport(VAMSAS[] roots) {
+  public static boolean rootReport(VAMSAS[] roots, boolean cascade) {
     if (roots!=null) {
       for (int i=0; i<roots.length; i++) {
         VAMSAS r = roots[i];
+        int ds, tr;
         System.out.print("Vamsas Root "+i+" (id="
             +((r.getId()!=null) ? r.getId():"<none>")
-            +") contains "+r.getDataSetCount()+" DataSets, "
-            + r.getTreeCount()+" Global trees");
+            +") contains "+(ds=r.getDataSetCount())+" DataSets, "
+            + (tr=r.getTreeCount())+" Global trees\n");
+        if (cascade) {
+          for (int j=0; j<ds; j++) {
+            System.out.println("Dataset "+j);
+            cascade = datasetReport(r.getDataSet(j), true) && cascade ;
+          }
+          for (int j=0; j<tr; j++) {
+            System.out.println("Global tree "+j);
+            cascade = treeReport(r.getTree(j), true) && cascade;
+          }
+        }
       }
       return true;
     }
     return false;
   }
+  public static boolean datasetReport(DataSet ds, boolean cascade) {
+    if (cascade)
+      reportProvenance(ds.getProvenance());
+    System.out.println("Dataset contains : "+ds.getSequenceCount()
+        +" sequences, "+ds.getAlignmentCount()+" alignments and "+ds.getTreeCount()+" trees.");
+    if (cascade)
+      alignmentReport(ds.getAlignment(), true);
+    return true;
+  }
+  public static boolean alignmentReport(Alignment[] al, boolean cascade) {
+    boolean val=true;
+    if (al!=null && al.length>0) {
+      for (int i=0; i<al.length; i++) {
+        System.out.println("Alignment "+i);
+        if (cascade)
+          reportProvenance(al[i].getProvenance());
+        System.out.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
+            +al[i].getAlignmentAnnotationsCount()+" annotations and "+al[i].getTreeCount()+" trees.");
+        if (cascade) {
+          for (int t=0; t<al[i].getTreeCount(); t++)
+            treeReport(al[i].getTree(t), true);
+        }
+      }
+    }
+    return val;
+  }
+  public static boolean treeReport(Tree t, boolean cascade) {
+    System.out.println("Tree: '"+t.getTitle()+"'");
+    return !cascade || reportProvenance(t.getProvenance());
+  }
 
 }