fixes on unmarshalling

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/gcubedatacatalogue-metadata-discovery@146303 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/datacatalogue/metadatadiscovery/bean/jaxb/MetadataFormat.java

@@ -9,6 +9,7 @@ import java.util.List;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlTransient;
@@ -43,7 +44,7 @@ public class MetadataFormat implements Serializable{
 	@XmlElement(name = "metadatafield")
 	private List<MetadataField> metadataFields;
 
-	@XmlElement(name = "metadatatype", required=true)
+	@XmlAttribute(name = "metadatatype", required=true)
 	private String metadataType = "";
 
 	@XmlTransient
@@ -82,8 +83,6 @@ public class MetadataFormat implements Serializable{
 	}
 
 
-
-
 	/**
 	 * Gets the metadata categories.
 	 *
@@ -94,8 +93,6 @@ public class MetadataFormat implements Serializable{
 		return metadataCategories;
 	}
 
-
-
 	/**
 	 * Sets the metadata categories.
 	 *
@@ -180,8 +177,6 @@ public class MetadataFormat implements Serializable{
 		builder.append(metadataFields);
 		builder.append(", metadataType=");
 		builder.append(metadataType);
-		builder.append(", metadataSource=");
-		builder.append(metadataSource);
 		builder.append("]");
 		return builder.toString();
 	}

src/main/java/org/gcube/datacatalogue/metadatadiscovery/bean/jaxb/TaggingGroupingValue.java

@@ -53,7 +53,6 @@ public enum TaggingGroupingValue {
 
     	try{
     		for (TaggingGroupingValue tgv : TaggingGroupingValue.values()) {
-    			System.out.println("Comparing input value: "+value +" with "+tgv.value );
     			if(tgv.value.equals(value))
     				return tgv;
 			}

src/main/java/org/gcube/datacatalogue/metadatadiscovery/reader/MedataFormatReader.java

@@ -49,19 +49,20 @@ public class MedataFormatReader {
 	public MedataFormatReader(ScopeBean scope, String resourceID) throws Exception {
 		this.scope = scope;
 		this.resourceID = resourceID;
-		this.metadataFormat = getMedataFormatByID(resourceID);
+		this.metadataFormat = getMetadataFormatByID(resourceID);
 	}
 
 
+
 	/**
-	 * Gets the medata format by id.
+	 * Gets the metadata format by id.
 	 *
 	 * @param resourceID the resource id
-	 * @return the medata format by id
+	 * @return the metadata format by id
 	 * @throws Exception the exception
 	 */
-	private MetadataFormat getMedataFormatByID(String resourceID) throws Exception {
+	private MetadataFormat getMetadataFormatByID(String resourceID) throws Exception {
-		logger.trace("Get MedataFormat with resourceID: "+resourceID);
+		logger.trace("Getting MedataFormat with resourceID: "+resourceID);
 
 		if(this.scope==null)
 			throw new Exception("Scope is null");
@@ -73,9 +74,6 @@ public class MedataFormatReader {
 
 		try {
 
-//			ScopeProvider.instance.set(scopeString);
-//			logger.info("scope provider set instance: "+scopeString);
-
 			logger.info("Using scope from ScopeProvider: "+scopeString);
 
 			String queryString = getQuesryStringForGenericResourceById(resourceID);
@@ -92,15 +90,16 @@ public class MedataFormatReader {
 				try{
 					theResource = appProfile.get(0);
 //					logger.trace("Resource with resourceID "+resourceID+" matched "+theResource);
-					logger.trace("Resource with resourceID "+resourceID+" found ");
+					logger.debug("Resource (Metadata Format) with resourceID "+resourceID+" found");
 					DocumentBuilder docBuilder =  DocumentBuilderFactory.newInstance().newDocumentBuilder();
 					Node node = docBuilder.parse(new InputSource(new StringReader(theResource))).getDocumentElement();
 					XPathHelper helper = new XPathHelper(node);
-					List<MetadataField> fields = getMetadataFieldsFromResource(helper);
+//					List<MetadataField> fields = getMetadataFieldsFromResource(helper);
-					mf.setMetadataFields(fields);
+//					mf.setMetadataFields(fields);
+					logger.debug("Unmarshalling it..");
+					mf = getMetadataFormatFromResource(helper);
 					String metadataSource = getMetadataFormatSourceFromResource(helper);
 					mf.setMetadataSource(metadataSource);
-
 				}catch(Exception e){
 					logger.error("Error while parsing Resource "+theResource+" from the infrastructure, the scope is "+scopeString,e);
 				}
@@ -141,6 +140,38 @@ public class MedataFormatReader {
 		}
 	}
 
+
+
+	/**
+	 * Gets the metadata format from resource.
+	 *
+	 * @param helper the helper
+	 * @return the metadata format from resource
+	 * @throws Exception the exception
+	 */
+	private MetadataFormat getMetadataFormatFromResource(XPathHelper helper) throws Exception{
+
+		try {
+
+			List<String> metadataFormatSource = helper.evaluate("/Resource/Profile/Body/metadataformat");
+
+			JAXBContext jaxbContext = JAXBContext.newInstance(MetadataFormat.class);
+		    Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
+
+		    if(metadataFormatSource==null || metadataFormatSource.size()==0)
+		    	throw new Exception("Resource does not contain <metadataformat> in the body");
+
+		    InputStream stream = new ByteArrayInputStream(metadataFormatSource.get(0).getBytes());
+		    MetadataFormat mtdf = (MetadataFormat) jaxbUnmarshaller.unmarshal(stream);
+		    logger.debug("returning metadata format with medata type: "+mtdf.getMetadataType());
+		    return mtdf;
+
+		}catch(Exception e){
+			logger.error("An error occurred in getMetadataFormatSourceFromResource ", e);
+			return null;
+		}
+	}
+
 	/**
 	 * Gets the metadata fields from resource.
 	 *

src/test/java/org/gcube/datacatalogue/metadatadiscovery/TestDataCatalogueMetadataFormatReader.java

@@ -35,7 +35,7 @@ public class TestDataCatalogueMetadataFormatReader {
 			int i = 0;
 			for (MetadataType mt : reader.getListOfMetadataTypes()) {
 				MetadataFormat metadataFormat = reader.getMetadataFormatForMetadataType(mt);
-				logger.trace("\n\n "+ ++i +".) Metadata Format: "+metadataFormat.toString());
+				//logger.trace("\n\n "+ ++i +".) Metadata Format: "+metadataFormat.toString());
 			}
 
 		} catch (Exception e) {

src/test/java/org/gcube/datacatalogue/metadatadiscovery/TestJaxbMetadataMarshUnmarsh.java

@@ -134,6 +134,9 @@ public class TestJaxbMetadataMarshUnmarsh {
 	    //We had written this file in marshalling example
 	    MetadataFormat mtds = (MetadataFormat) jaxbUnmarshaller.unmarshal(new File(tmpFileXML));
 
+	    System.out.println("Metadata Format");
+	    System.out.println(mtds);
+
 	    System.out.println("Metadata Categories");
 	    if(mtds.getMetadataCategories()!=null){
 		    for (MetadataCategory cat : mtds.getMetadataCategories()) {