From c513d5195afea00b40a8d157e26df71c2277d68b Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 19 Jan 2006 11:51:36 +0000
Subject: [PATCH] generalised ArchiveReports functions to output on any
 stream.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@144 be28352e-c001-0410-b1a7-c7978e42abec
---
 src/org/vamsas/test/objects/Core.java              |    2 +-
 .../vamsas/test/simpleclient/ArchiveReader.java    |    4 +-
 .../vamsas/test/simpleclient/ArchiveReports.java   |   90 ++++++++++----------
 .../vamsas/test/simpleclient/VamsasArchive.java    |   10 +--
 4 files changed, 55 insertions(+), 51 deletions(-)

diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java
index 8a24e95..f606a19 100644
--- a/src/org/vamsas/test/objects/Core.java
+++ b/src/org/vamsas/test/objects/Core.java
@@ -76,6 +76,6 @@ public class Core {
     VamsasDocument doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { getDemoVamsas() }, 
         ProvenanceStuff.newProvenance("org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
         VersionEntries.latestVersion());
-    ArchiveReports.reportDocument(doc, null, true);
+    ArchiveReports.reportDocument(doc, null, true, System.out);
   }
 }
diff --git a/src/org/vamsas/test/simpleclient/ArchiveReader.java b/src/org/vamsas/test/simpleclient/ArchiveReader.java
index f99bed8..d7959b4 100644
--- a/src/org/vamsas/test/simpleclient/ArchiveReader.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReader.java
@@ -23,7 +23,7 @@ public class ArchiveReader {
       if (var.isValid()) {
         InputStreamReader vdoc = new InputStreamReader(var.getVamsasDocumentStream());
         VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
-        if (ArchiveReports.reportDocument(doc, var, true)) {
+        if (ArchiveReports.reportDocument(doc, var, true, System.out)) {
           roots = doc.getVAMSAS();
         }
       } else {
@@ -41,7 +41,7 @@ public class ArchiveReader {
           }
         }
       }
-      if (!ArchiveReports.rootReport(roots, true))
+      if (!ArchiveReports.rootReport(roots, true, System.out))
         System.err.print(args[0]+" is not a valid vamsas archive.");
     } catch (Exception e) {
       e.printStackTrace(System.err);
diff --git a/src/org/vamsas/test/simpleclient/ArchiveReports.java b/src/org/vamsas/test/simpleclient/ArchiveReports.java
index 998191f..b38f87a 100644
--- a/src/org/vamsas/test/simpleclient/ArchiveReports.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReports.java
@@ -1,6 +1,8 @@
 package org.vamsas.test.simpleclient;
 
 import java.io.InputStream;
+import java.io.PrintStream;
+import java.io.PrintWriter;
 
 import org.vamsas.client.object;
 import org.vamsas.client.simpleclient.VamsasArchiveReader;
@@ -25,35 +27,36 @@ import org.vamsas.objects.core.VamsasDocument;
 public class ArchiveReports {
     /**
      * print an informative summary on a VamsasDocument
+     * @param outstr TODO
      * @param document - the document itself
      * @param archive - document source archive for resolving any appData refs
      * @return
      */
-  public static boolean reportProvenance(Provenance p) {
+  public static boolean reportProvenance(Provenance p, PrintStream outstr) {
     if (p==null) {
-      System.out.println("No Provenance");
+      outstr.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());
+      outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getAction());
     return true;
   }
-  public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade) {
+  public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
     if (appD!=null) {
       boolean nulldata=false;
       if (appD.getDataReference()!=null) {
         String appData=appD.getDataReference();
-        if (appData==null) { System.out.println("Empty DataReference - not valid ?"); } 
+        if (appData==null) { outstr.println("Empty DataReference - not valid ?"); } 
         else 
           if (appData.length()>1) {
-          System.out.print("a reference ("+appData+")");
+          outstr.print("a reference ("+appData+")");
           InputStream jstrm;
           if ((jstrm=archive.getAppdataStream(appData))!=null)
-            System.out.println(" which resolves to a JarEntry.");
+            outstr.println(" which resolves to a JarEntry.");
           else {
-            System.out.println(" which does not resolve to a JarEntry.");
-            System.err.println("Unresolved appdata reference '"+appData+"'");
+            outstr.println(" which does not resolve to a JarEntry.");
+            outstr.println("Unresolved appdata reference '"+appData+"'");
           }
         } else {
           nulldata=true;
@@ -62,49 +65,49 @@ public class ArchiveReports {
         if (appD.getData()==null)
           nulldata &= true;
           else
-          System.out.println("an embedded chunk of "+appD.getData().length+" bytes.");
+          outstr.println("an embedded chunk of "+appD.getData().length+" bytes.");
       }
       if (nulldata)
-        System.out.println("Null AppData reference/data chunk.");
+        outstr.println("Null AppData reference/data chunk.");
     }
     return true;
   }
   
-  public static boolean appDataReport(ApplicationData appD, VamsasArchiveReader archive, boolean cascade) {
+  public static boolean appDataReport(ApplicationData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
     if (appD!=null) {
       // Report on root appData
-      appDataEntryReport(appD, archive, cascade);
+      appDataEntryReport(appD, archive, cascade, outstr);
       if (appD.getUserCount()>0) {
         User users[] = appD.getUser();
         for (int i=0,j=users.length; i<j; i++) {
-          System.out.println("Data for User '"+users[i].getFullname()+"' of '"+users[i].getOrganization()+"'");
-          appDataEntryReport(users[i], archive, cascade);
+          outstr.println("Data for User '"+users[i].getFullname()+"' of '"+users[i].getOrganization()+"'");
+          appDataEntryReport(users[i], archive, cascade, outstr);
         }
       }
     }
 
     return true;
   }
-  public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade) {
+  public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
     if (document!=null) {
-      System.out.println("Vamsas Document version '"+document.getVersion()+"'");
-      reportProvenance(document.getProvenance());
-      System.out.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" Application data elements.\n");
+      outstr.println("Vamsas Document version '"+document.getVersion()+"'");
+      reportProvenance(document.getProvenance(), outstr);
+      outstr.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" Application data elements.\n");
       if (document.getVAMSASCount()>0 && cascade)
-        rootReport(document.getVAMSAS(), true);
+        rootReport(document.getVAMSAS(), true, outstr);
       if (document.getApplicationDataCount()>0) {
-        System.out.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
+        outstr.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
         ApplicationData appd[] = document.getApplicationData();
         for (int i=0,j=appd.length; i<j; i++) {
-          System.out.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\nURN: '"+appd[i].getUrn()+"'\n");
-          System.out.print("AppData is :");
-          appDataReport(appd[i], archive, cascade);
+          outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\nURN: '"+appd[i].getUrn()+"'\n");
+          outstr.print("AppData is :");
+          appDataReport(appd[i], archive, cascade, outstr);
         }
           
       }
       return true;
     } else {
-      System.out.print("Document Object is null");
+      outstr.print("Document Object is null");
     }
     return false;
   }
@@ -113,25 +116,26 @@ public class ArchiveReports {
    * summarises all the datasets in a vamsas document.
    * @param roots
    * @param cascade TODO
+   * @param outstr TODO
    * @return
    */
-  public static boolean rootReport(VAMSAS[] roots, boolean cascade) {
+  public static boolean rootReport(VAMSAS[] roots, boolean cascade, PrintStream outstr) {
     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="
+        outstr.print("Vamsas Root "+i+" (id="
             +((r.getId()!=null) ? r.getId():"<none>")
             +") 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 ;
+            outstr.println("Dataset "+j);
+            cascade = datasetReport(r.getDataSet(j), true, outstr) && cascade ;
           }
           for (int j=0; j<tr; j++) {
-            System.out.println("Global tree "+j);
-            cascade = treeReport(r.getTree(j), true) && cascade;
+            outstr.println("Global tree "+j);
+            cascade = treeReport(r.getTree(j), true, outstr) && cascade;
           }
         }
       }
@@ -139,35 +143,35 @@ public class ArchiveReports {
     }
     return false;
   }
-  public static boolean datasetReport(DataSet ds, boolean cascade) {
+  public static boolean datasetReport(DataSet ds, boolean cascade, PrintStream outstr) {
     if (cascade)
-      reportProvenance(ds.getProvenance());
-    System.out.println("Dataset contains : "+ds.getSequenceCount()
+      reportProvenance(ds.getProvenance(), outstr);
+    outstr.println("Dataset contains : "+ds.getSequenceCount()
         +" sequences, "+ds.getAlignmentCount()+" alignments and "+ds.getTreeCount()+" trees.");
     if (cascade)
-      alignmentReport(ds.getAlignment(), true);
+      alignmentReport(ds.getAlignment(), true, outstr);
     return true;
   }
-  public static boolean alignmentReport(Alignment[] al, boolean cascade) {
+  public static boolean alignmentReport(Alignment[] al, boolean cascade, PrintStream outstr) {
     boolean val=true;
     if (al!=null && al.length>0) {
       for (int i=0; i<al.length; i++) {
-        System.out.println("Alignment "+i);
+        outstr.println("Alignment "+i);
         if (cascade)
-          reportProvenance(al[i].getProvenance());
-        System.out.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
+          reportProvenance(al[i].getProvenance(), outstr);
+        outstr.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);
+            treeReport(al[i].getTree(t), true, outstr);
         }
       }
     }
     return val;
   }
-  public static boolean treeReport(Tree t, boolean cascade) {
-    System.out.println("Tree: '"+t.getTitle()+"'");
-    return !cascade || reportProvenance(t.getProvenance());
+  public static boolean treeReport(Tree t, boolean cascade, PrintStream outstr) {
+    outstr.println("Tree: '"+t.getTitle()+"'");
+    return !cascade || reportProvenance(t.getProvenance(), outstr);
   }
 
 }
diff --git a/src/org/vamsas/test/simpleclient/VamsasArchive.java b/src/org/vamsas/test/simpleclient/VamsasArchive.java
index 3f0da4c..94d702b 100644
--- a/src/org/vamsas/test/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/test/simpleclient/VamsasArchive.java
@@ -43,7 +43,7 @@ public class VamsasArchive {
         orignalnew = sdoc.getVamsasDocument(vread);
         log.info("*** Dump follows ***");
         
-        ArchiveReports.reportDocument(orignalnew, vread, false);
+        ArchiveReports.reportDocument(orignalnew, vread, false, System.out);
         log.info("*** Dump precedes ***");
       } catch (Exception e) {
         log.info("makeDemoAppdata: Problems accessing original document");
@@ -101,11 +101,11 @@ public class VamsasArchive {
       
       if (roots!=null) {
         log.info("Report on Original roots in archive:");
-        ArchiveReports.rootReport(roots, true);
+        ArchiveReports.rootReport(roots, true, System.out);
       }
       log.info("Getting current vamsas document.");
       VamsasDocument doc = varchive.getVamsasDocument();
-      ArchiveReports.reportDocument(doc, varchive.getOriginalArchiveReader(), true); // not modified document so references will still be valid
+      ArchiveReports.reportDocument(doc, varchive.getOriginalArchiveReader(), true, System.out); // not modified document so references will still be valid
       // do some stuff
       log.info("Retrieving backup");
       File backup = varchive.backupFile();
@@ -138,7 +138,7 @@ public class VamsasArchive {
       log.info("Testing update: ");
       VamsasArchiveReader vreader = new VamsasArchiveReader(newf);
       SimpleDocument sdoc = new SimpleDocument("testing new vamsas write");
-      ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true);
+      ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out);
       
       // backup.delete(); // tidy up
       
@@ -163,7 +163,7 @@ public class VamsasArchive {
       log.info("Testing update: ");
       vreader = new VamsasArchiveReader(newf);
       sdoc = new SimpleDocument("testing vamsas update");
-      ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true);
+      ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out);
     } catch (Exception e) {
       e.printStackTrace(System.err);
     }
-- 
1.7.10.2