Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@633 348d0f76-0448-11de-a6fe-93d51630548a

ivy.xml

@@ -12,7 +12,5 @@
       
     <!-- The following are all castor dependencies. Remove when transitive dependencies are working -->
     <dependency org="commons-logging" name="commons-logging" rev="latest.integration" />
-    <dependency org="org.codehaus.castor" name="castor-core" rev="1.3" />
-    <dependency org="org.codehaus.castor" name="castor-xml" rev="1.3" />
   </dependencies>
 </ivy-module>

java/src/org/broadinstitute/sting/playground/samples/SampleXmlMarshaller.java

@@ -1,12 +1,13 @@
 package org.broadinstitute.sting.playground.samples;
 
-import org.exolab.castor.xml.*;
 import org.apache.log4j.BasicConfigurator;
+import org.broadinstitute.sting.utils.StingException;
+import org.simpleframework.xml.Element;
+import org.simpleframework.xml.Root;
+import org.simpleframework.xml.Serializer;
+import org.simpleframework.xml.core.Persister;
 
-import java.io.FileWriter;
+import java.io.File;
-import java.io.IOException;
-import java.io.FileReader;
-import java.io.FileNotFoundException;
 
 /**
  * Created by IntelliJ IDEA.
@@ -15,11 +16,18 @@ import java.io.FileNotFoundException;
  * Time: 2:16:43 PM
  * To change this template use File | Settings | File Templates.
  */
+
+@Root // this is a root output object for simpleXML
 public class SampleXmlMarshaller {
     public enum RMDType { HapMap };
 
+    @Element // simpleXML tag to say make it an element, you could also specifiy Attribute
     private RMDType type;
+
+    @Element
     private String fileVersion;
+
+    @Element
     private String fileName;
 
     public SampleXmlMarshaller() {
@@ -59,55 +67,59 @@ public class SampleXmlMarshaller {
         return String.format("Type = %s, Name = %s, Version = %s%n", type, fileName, fileVersion );
     }
 
-    public static void main( String argv[] ) {
+    public boolean equals(SampleXmlMarshaller other) {
-        if( argv.length == 0 || (!argv[0].equalsIgnoreCase("marshal") && !argv[0].equalsIgnoreCase("unmarshal")) ) {
+        if (other == null) { return false; }
-            System.out.println( "USAGE: java org.broadinstitute.sting.playground.samples.SampleXmlMarshaller {marshal | unmarshal}");
+        if (other.getType() == this.getType() &&
-            System.exit(-1);
+                other.getFileVersion().equals(this.getFileVersion()) &&
+                other.getFileName().equals(this.getFileName())) {
+            return true;
         }
+        return false;
+    }
+
+    public static void main( String argv[] ) {
+        if (argv.length != 1) {
+            System.err.println("You must specify a filename for the XML output.");
+            System.err.println("\nUsage: SampleXmlMarshaller outputfile\n");       
+        }
+        // our SampleXmlMarshallers
+        SampleXmlMarshaller startWith = new SampleXmlMarshaller(RMDType.HapMap, "testFile.xml", "0.1");
+        SampleXmlMarshaller endWith = null;
+
+        // where to read and write to
+        String writeTo = argv[0];
 
         BasicConfigurator.configure();
 
-        if( argv[0].equalsIgnoreCase("marshal") )
+        marshal(startWith, writeTo);
-            marshal();
+        endWith = unmarshal(writeTo);
-        else if( argv[0].equalsIgnoreCase("unmarshal") )
+
-            unmarshal();
+        if (startWith.equals(endWith)) {
+            System.out.println("they're equal, check " + writeTo.toString() + " for the output");
+        } else {
+            System.out.println("they're NOT equal, check " + writeTo.toString() + " for the output.  Something must of gone wrong");
+        }
+
     }
 
-    public static void marshal() {
+    public static void marshal(SampleXmlMarshaller sample, String filename) {
-        SampleXmlMarshaller descriptor = new SampleXmlMarshaller( RMDType.HapMap, "foo.hapmap", "1.0" );
+       Serializer serializer = new Persister();
-        System.out.printf( "Marshalling descriptor = %s%n", descriptor );
+        File out = new File(filename);
         try {
-            FileWriter writer = new FileWriter( "foo.xml" );
+            serializer.write(sample, out);
-            Marshaller.marshal( descriptor, writer );
+        } catch (Exception e) {
-        }
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-        catch( IOException ex ) {
-            System.out.println("Unable to open writer:" + ex);
-        }
-        catch( MarshalException ex ) {
-            System.out.println("Unable to marshal data:" + ex);
-        }
-        catch( ValidationException ex ) {
-            System.out.println("Unable to validate data: " + ex);
         }
     }
 
-    public static void unmarshal() {
+    public static SampleXmlMarshaller unmarshal(String filename) {
-        SampleXmlMarshaller descriptor = null;
+        Serializer serializer = new Persister();
+        File source = new File(filename);
         try {
-            FileReader reader = new FileReader( "foo.xml" );
+            SampleXmlMarshaller example = serializer.read(SampleXmlMarshaller.class, source);
-            descriptor = (SampleXmlMarshaller)Unmarshaller.unmarshal( SampleXmlMarshaller.class, reader );
+            return example;
+        } catch (Exception e) {
+            throw new StingException("Failed to marshal the data to file " + filename,e);
         }
-        catch( FileNotFoundException ex ) {
-            System.out.println("Unable to open reader:" + ex);
-        }
-        catch( MarshalException ex ) {
-            System.out.println("Unable to unmarshal data:" + ex);
-        }
-        catch( ValidationException ex ) {
-            System.out.println("Unable to validate data: " + ex);
-        }
-
-        System.out.printf( "Unmarshalled descriptor = %s%n", descriptor );
-
     }
 }