SE-146 Schema validation for quantML files added

SVN: 12910

rtd_yeastx/build/build.xml

@@ -27,6 +27,7 @@
 			</fileset>
 			<fileset dir="source">
 				<include name="**/*.sql" />
+				<include name="**/*.xsd" />
 			</fileset>	
 		</recursive-jar>
 	</target>

rtd_yeastx/resource/examples/allFields.quantML

@@ -2,8 +2,8 @@
 <quantML>
    <msQuantification>
       <source>msSoft</source>
-      <valid>true</valid>
       <comment>no comment</comment>
+      <valid>true</valid>
       <registrationDate>04-Apr-1980 12:00:21</registrationDate>
       <registrator>John Doe</registrator>
       <concentration>

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java

@@ -17,16 +17,23 @@
 package ch.systemsx.cisd.yeastx.quant;
 
 import java.io.File;
+import java.io.FileReader;
 import java.io.IOException;
 
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.SchemaOutputResolver;
 import javax.xml.bind.Unmarshaller;
+import javax.xml.bind.UnmarshallerHandler;
 import javax.xml.transform.Result;
 import javax.xml.transform.stream.StreamResult;
 
+import org.xml.sax.EntityResolver;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
 import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.utilities.XMLInfraStructure;
 import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationsDTO;
 
 /**
@@ -46,6 +53,9 @@ class QuantMLParser
     private QuantMLParser()
     {
         this.unmarshaller = createUnmarshaller();
+        unmarshaller.setSchema(XMLInfraStructure.createSchema("/"
+                + QuantMLParser.class.getPackage().getName().replace('.', '/')
+                + "/quantml-schema.xsd"));
     }
 
     private static Unmarshaller createUnmarshaller()
@@ -90,7 +100,7 @@ class QuantMLParser
                 throw new IllegalArgumentException("Wrong type: " + object);
             }
             return (MSQuantificationsDTO) object;
-        } catch (JAXBException ex)
+        } catch (Exception ex)
         {
             throw CheckedExceptionTunnel.wrapIfNecessary(ex);
         }