4184: Create datacatalogue-metadata-discovery library

Task-Url: https://support.d4science.org/issues/4184

Added MetadataFormatDiscovery
Added MetadataFormatReader

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/gcubedatacatalogue-metadata-discovery@129013 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/datacatalogue/metadatadiscovery/bean/MetadataType.java

@@ -7,9 +7,10 @@ import java.io.Serializable;
 
 
 /**
+ * The Class MetadataType.
  *
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * Jun 7, 2016
+ * Jun 8, 2016
  */
 public class MetadataType implements Serializable{
 
@@ -23,16 +24,18 @@ public class MetadataType implements Serializable{
 	private String description;
 
 	/**
-	 *
+	 * Instantiates a new metadata type.
 	 */
 	public MetadataType() {
 
 	}
 
 	/**
-	 * @param id
+	 * Instantiates a new metadata type.
-	 * @param name
+	 *
-	 * @param description
+	 * @param id the id
+	 * @param name the name
+	 * @param description the description
 	 */
 	public MetadataType(String id, String name, String description) {
 
@@ -44,6 +47,8 @@ public class MetadataType implements Serializable{
 
 
 	/**
+	 * Gets the id.
+	 *
 	 * @return the id
 	 */
 	public String getId() {
@@ -53,6 +58,8 @@ public class MetadataType implements Serializable{
 
 
 	/**
+	 * Gets the name.
+	 *
 	 * @return the name
 	 */
 	public String getName() {
@@ -62,6 +69,8 @@ public class MetadataType implements Serializable{
 
 
 	/**
+	 * Gets the description.
+	 *
 	 * @return the description
 	 */
 	public String getDescription() {
@@ -71,6 +80,8 @@ public class MetadataType implements Serializable{
 
 
 	/**
+	 * Sets the id.
+	 *
 	 * @param id the id to set
 	 */
 	public void setId(String id) {
@@ -80,6 +91,8 @@ public class MetadataType implements Serializable{
 
 
 	/**
+	 * Sets the name.
+	 *
 	 * @param name the name to set
 	 */
 	public void setName(String name) {
@@ -89,6 +102,8 @@ public class MetadataType implements Serializable{
 
 
 	/**
+	 * Sets the description.
+	 *
 	 * @param description the description to set
 	 */
 	public void setDescription(String description) {

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

@@ -9,10 +9,12 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 
 
+
 /**
+ * The Class MetadataField.
  *
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * May 27, 2016
+ * Jun 8, 2016
  */
 @XmlRootElement(name="metadatafield")
 @XmlAccessorType(XmlAccessType.FIELD)
@@ -32,20 +34,22 @@ public class MetadataField {
 	private MetadataValidator validator;
 
 	/**
-	 *
+	 * Instantiates a new metadata field.
 	 */
 	public MetadataField() {
 	}
 
 
 	/**
-	 * @param fieldName
+	 * Instantiates a new metadata field.
-	 * @param mandatory
+	 *
-	 * @param isBoolean
+	 * @param fieldName the field name
-	 * @param defaulValue
+	 * @param mandatory the mandatory
-	 * @param note
+	 * @param isBoolean the is boolean
-	 * @param vocabulary
+	 * @param defaulValue the defaul value
-	 * @param validator
+	 * @param note the note
+	 * @param vocabulary the vocabulary
+	 * @param validator the validator
 	 */
 	public MetadataField(
 		String fieldName, Boolean mandatory, Boolean isBoolean,
@@ -64,6 +68,8 @@ public class MetadataField {
 
 
 	/**
+	 * Gets the field name.
+	 *
 	 * @return the fieldName
 	 */
 	public String getFieldName() {
@@ -74,6 +80,8 @@ public class MetadataField {
 
 
 	/**
+	 * Gets the mandatory.
+	 *
 	 * @return the mandatory
 	 */
 	public Boolean getMandatory() {
@@ -84,6 +92,8 @@ public class MetadataField {
 
 
 	/**
+	 * Gets the checks if is boolean.
+	 *
 	 * @return the isBoolean
 	 */
 	public Boolean getIsBoolean() {
@@ -94,6 +104,8 @@ public class MetadataField {
 
 
 	/**
+	 * Gets the defaul value.
+	 *
 	 * @return the defaulValue
 	 */
 	public String getDefaulValue() {
@@ -104,6 +116,8 @@ public class MetadataField {
 
 
 	/**
+	 * Gets the note.
+	 *
 	 * @return the note
 	 */
 	public String getNote() {
@@ -114,6 +128,8 @@ public class MetadataField {
 
 
 	/**
+	 * Gets the vocabulary.
+	 *
 	 * @return the vocabulary
 	 */
 	public MetadataVocabulary getVocabulary() {
@@ -124,6 +140,8 @@ public class MetadataField {
 
 
 	/**
+	 * Gets the validator.
+	 *
 	 * @return the validator
 	 */
 	public MetadataValidator getValidator() {
@@ -134,6 +152,8 @@ public class MetadataField {
 
 
 	/**
+	 * Sets the field name.
+	 *
 	 * @param fieldName the fieldName to set
 	 */
 	public void setFieldName(String fieldName) {
@@ -144,6 +164,8 @@ public class MetadataField {
 
 
 	/**
+	 * Sets the mandatory.
+	 *
 	 * @param mandatory the mandatory to set
 	 */
 	public void setMandatory(Boolean mandatory) {
@@ -154,6 +176,8 @@ public class MetadataField {
 
 
 	/**
+	 * Sets the checks if is boolean.
+	 *
 	 * @param isBoolean the isBoolean to set
 	 */
 	public void setIsBoolean(Boolean isBoolean) {
@@ -164,6 +188,8 @@ public class MetadataField {
 
 
 	/**
+	 * Sets the defaul value.
+	 *
 	 * @param defaulValue the defaulValue to set
 	 */
 	public void setDefaulValue(String defaulValue) {
@@ -174,6 +200,8 @@ public class MetadataField {
 
 
 	/**
+	 * Sets the note.
+	 *
 	 * @param note the note to set
 	 */
 	public void setNote(String note) {
@@ -184,6 +212,8 @@ public class MetadataField {
 
 
 	/**
+	 * Sets the vocabulary.
+	 *
 	 * @param vocabulary the vocabulary to set
 	 */
 	public void setVocabulary(MetadataVocabulary vocabulary) {
@@ -194,6 +224,8 @@ public class MetadataField {
 
 
 	/**
+	 * Sets the validator.
+	 *
 	 * @param validator the validator to set
 	 */
 	public void setValidator(MetadataValidator validator) {

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

@@ -12,11 +12,12 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 
 
+
 /**
  * The Class MetadataFormat.
  *
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * May 27, 2016
+ * Jun 8, 2016
  */
 @XmlRootElement(name="metadataformat")
 @XmlAccessorType(XmlAccessType.FIELD)
@@ -27,6 +28,8 @@ public class MetadataFormat {
 
 
 	/**
+	 * Gets the metadata fields.
+	 *
 	 * @return the metadataFields
 	 */
 	public List<MetadataField> getMetadataFields() {
@@ -36,6 +39,8 @@ public class MetadataFormat {
 
 
 	/**
+	 * Sets the metadata fields.
+	 *
 	 * @param metadataFields the metadataFields to set
 	 */
 	public void setMetadataFields(List<MetadataField> metadataFields) {

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

@@ -9,9 +9,10 @@ import javax.xml.bind.annotation.XmlRootElement;
 
 
 /**
+ * The Class MetadataValidator.
  *
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * May 27, 2016
+ * Jun 8, 2016
  */
 @XmlRootElement(name = "metadatavalidator")
 @XmlAccessorType (XmlAccessType.FIELD)
@@ -21,7 +22,7 @@ public class MetadataValidator {
 
 
 	/**
-	 *
+	 * Instantiates a new metadata validator.
 	 */
 	public MetadataValidator() {
 
@@ -30,7 +31,9 @@ public class MetadataValidator {
 
 
 	/**
-	 * @param regularExpression
+	 * Instantiates a new metadata validator.
+	 *
+	 * @param regularExpression the regular expression
 	 */
 	public MetadataValidator(String regularExpression) {
 
@@ -40,6 +43,8 @@ public class MetadataValidator {
 
 
 	/**
+	 * Gets the regular expression.
+	 *
 	 * @return the regularExpression
 	 */
 	public String getRegularExpression() {
@@ -49,6 +54,8 @@ public class MetadataValidator {
 
 
 	/**
+	 * Sets the regular expression.
+	 *
 	 * @param regularExpression the regularExpression to set
 	 */
 	public void setRegularExpression(String regularExpression) {

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

@@ -10,11 +10,12 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
 
 
+
 /**
  * The Class MetadataVocabulary.
  *
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * May 27, 2016
+ * Jun 8, 2016
  */
 @XmlRootElement(name = "metadatavocabulary")
 @XmlAccessorType (XmlAccessType.FIELD)

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

@@ -21,11 +21,12 @@ import org.slf4j.LoggerFactory;
 import org.w3c.dom.Node;
 import org.xml.sax.InputSource;
 
+
 /**
- * The Class MedataFormatReader.
+ * The Class MedataFormatDiscovery.
  *
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * @Jul 26, 2013
+ * Jun 8, 2016
  */
 public class MedataFormatDiscovery {
 
@@ -150,77 +151,11 @@ public class MedataFormatDiscovery {
 	}
 
 	/**
-	 * Gets the metadata type from resource.
+	 * Gets the gcube generic query string.
 	 *
 	 * @param secondaryType the secondary type
-	 * @return the metadata type from resource
+	 * @return the gcube generic query string
 	 */
-	/*private MetadataType getMetadataTypeFromResource(XPathHelper helper) throws ApplicationProfileNotFoundException{
-
-		List<String> metadataformat;
-
-		List<GeoexplorerDefaultLayer> listGeoexplorerDefaultLayer = new ArrayList<GeoexplorerDefaultLayer>();
-
-		try {
-
-			metadataformat = helper.evaluate("/Resource/Profile/Body/metadataformat");
-
-			if (metadataformat != null && metadataformat.size() > 0) {
-
-				List<String> metadatafields = helper.evaluate("/Resource/Profile/Body/metadataformat/metadatafield/text()");
-
-				List<String> currValue = null;
-
-				for (String metafield : metadatafields) {
-					logger.trace("found metafield : "+metafield);
-					GeoexplorerDefaultLayer geoDefLayer = new GeoexplorerDefaultLayer();
-					geoDefLayer.setUUID(uuid);
-					geoDefLayer.setScope(scope.toString());
-
-//					currValue = helper.evaluate("/Resource/Profile/Body/DefaultLayers/DefaultLayer[UUID='"+uuid+"']/@isBaseLayer");
-					currValue = helper.evaluate("/Resource/Profile/Body/DefaultLayers/DefaultLayer[UUID='"+uuid+"']/IsBaseLayer/text()");
-
-					logger.trace("is base layer?" +currValue);
-					if (currValue != null && currValue.size() > 0){
-						boolean isBase = Boolean.parseBoolean(currValue.get(0));
-						geoDefLayer.setBaseLayer(isBase);
-//						logger.trace("isBaseLayer : "+isBase);
-					}
-
-					currValue = helper.evaluate("/Resource/Profile/Body/DefaultLayers/DefaultLayer[UUID='"+uuid+"']/Description/text()");
-
-					String descr = "";
-					if (currValue != null && currValue.size() > 0) {
-						descr = currValue.get(0);
-						geoDefLayer.setDescription(descr);
-//						logger.trace("description: "+descr+" for UUID: "+uuid);
-					}
-
-					currValue = helper.evaluate("/Resource/Profile/Body/DefaultLayers/DefaultLayer[UUID='"+uuid+"']/Name/text()");
-					descr = "";
-					if (currValue != null && currValue.size() > 0) {
-						descr = currValue.get(0);
-						geoDefLayer.setName(descr);
-//						logger.trace("name: "+descr+" for UUID: "+uuid);
-					}
-
-					logger.trace("Filled object: "+geoDefLayer);
-					listGeoexplorerDefaultLayer.add(geoDefLayer);
-				}
-
-			}
-
-			else throw new ApplicationProfileNotFoundException("Your applicationProfile with scope "+scope.toString()+" is wrong, consider adding <DefaultLayer><UUID> element in <Body>");
-
-		} catch (Exception e) {
-			logger.error("An error occurred in getListDefaultLayerFromNode ", e);
-			return listGeoexplorerDefaultLayer;
-		}
-
-		return listGeoexplorerDefaultLayer;
-	}*/
-
-
 	public synchronized String getGcubeGenericQueryString(String secondaryType){
 
 		return "for $profile in collection('/db/Profiles/GenericResource')//Resource" +

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

@@ -2,17 +2,22 @@ package org.gcube.datacatalogue.metadatadiscovery.reader;
 
 import static org.gcube.resources.discovery.icclient.ICFactory.client;
 
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
 import java.io.StringReader;
 import java.util.ArrayList;
 import java.util.List;
 
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Unmarshaller;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 
 import org.gcube.common.resources.gcore.utils.XPathHelper;
 import org.gcube.common.scope.api.ScopeProvider;
 import org.gcube.common.scope.impl.ScopeBean;
-import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataType;
+import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataField;
+import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
 import org.gcube.resources.discovery.client.api.DiscoveryClient;
 import org.gcube.resources.discovery.client.queries.api.Query;
 import org.gcube.resources.discovery.client.queries.impl.QueryBox;
@@ -30,32 +35,34 @@ import org.xml.sax.InputSource;
 public class MedataFormatReader {
 
 	public static Logger logger = LoggerFactory.getLogger(MedataFormatReader.class);
-	protected static final String DATA_CATALOGUE_METADATA_SECONDARY_TYPE = "DataCatalogueMetadata";
-	private String secondaryType;
 	private ScopeBean scope;
-	private List<MetadataType> metadataTypes;
+	private MetadataFormat metadataFormat;
 	private String resourceID;
 
+
 	/**
 	 * Instantiates a new medata format reader.
 	 *
-	 * @param scope - the scope to be searched
+	 * @param scope the scope
+	 * @param resourceID the resource id
 	 * @throws Exception the exception
 	 */
 	public MedataFormatReader(ScopeBean scope, String resourceID) throws Exception {
 		this.scope = scope;
 		this.resourceID = resourceID;
-		this.metadataTypes = getMedataFormatByID();
+		this.metadataFormat = getMedataFormatByID(resourceID);
 	}
 
+
 	/**
-	 * this method looks up the applicationProfile profile among the ones available in the infrastructure.
+	 * Gets the medata format by id.
 	 *
-	 * @return the applicationProfile profile
+	 * @param resourceID the resource id
+	 * @return the medata format by id
 	 * @throws Exception the exception
 	 */
-	private List<MetadataType> getMedataFormatByID() throws Exception {
+	private MetadataFormat getMedataFormatByID(String resourceID) throws Exception {
-		logger.trace("read secondary type: "+secondaryType);
+		logger.trace("Get MedataFormat with resourceID: "+resourceID);
 
 		if(this.scope==null)
 			throw new Exception("Scope is null");
@@ -63,14 +70,14 @@ public class MedataFormatReader {
 		String scopeString = this.scope.toString();
 		logger.trace("read scope: "+scopeString);
 
-		List<MetadataType> list = new ArrayList<MetadataType>();
+		MetadataFormat mf = new MetadataFormat();
 
 		try {
 
 			ScopeProvider.instance.set(scopeString);
 			logger.info("scope provider set instance: "+scopeString);
 
-			String queryString = getGcubeGenericQueryString(secondaryType);
+			String queryString = getQuesryStringForGenericResourceById(resourceID);
 			logger.trace("queryString: " +queryString);
 			Query q = new QueryBox(queryString);
 
@@ -78,70 +85,71 @@ public class MedataFormatReader {
 		 	List<String> appProfile = client.submit(q);
 
 			if (appProfile == null || appProfile.size() == 0)
-				throw new ApplicationProfileNotFoundException("Your applicationProfile is not registered in the infrastructure, the scope is "+scopeString);
+				throw new ApplicationProfileNotFoundException("Your resourceID "+resourceID+" is not registered in the infrastructure, the scope is "+scopeString);
 			else {
-
+				String theResource = null;
-				for (String elem : appProfile) {
+				try{
-					try{
+					theResource = appProfile.get(0);
-						DocumentBuilder docBuilder =  DocumentBuilderFactory.newInstance().newDocumentBuilder();
+//					logger.trace("Resource with resourceID "+resourceID+" matched "+theResource);
-						Node node = docBuilder.parse(new InputSource(new StringReader(elem))).getDocumentElement();
+					logger.trace("Resource with resourceID "+resourceID+" found ");
-						XPathHelper helper = new XPathHelper(node);
+					DocumentBuilder docBuilder =  DocumentBuilderFactory.newInstance().newDocumentBuilder();
-						MetadataType meta = getMetadataTypeFromResource(helper);
+					Node node = docBuilder.parse(new InputSource(new StringReader(theResource))).getDocumentElement();
-						list.add(meta);
+					XPathHelper helper = new XPathHelper(node);
-					}catch(Exception e){
+					List<MetadataField> fields = getMetadataFieldsFromResource(helper);
-						logger.error("Error while trying to fetch applicationProfile "+secondaryType+" from the infrastructure, ",e);
+					mf.setMetadataFields(fields);
-					}
+				}catch(Exception e){
+					logger.error("Error while parsing Resource "+theResource+" from the infrastructure, the scope is "+scopeString,e);
 				}
 			}
 
 		} catch (Exception e) {
-			logger.error("Error while trying to fetch applicationProfile "+secondaryType+" from the infrastructure, "+e);
+			logger.error("Error while trying to fetch resourceID "+resourceID+" from the infrastructure, the scope is "+scopeString,e);
-			return list;
+			return mf;
 		} finally{
 			ScopeProvider.instance.reset();
 		}
 
-		return list;
+		return mf;
-
 	}
 
 	/**
-	 * Gets the metadata type from resource.
+	 * Gets the metadata fields from resource.
 	 *
 	 * @param helper the helper
-	 * @return the metadata type from resource
+	 * @return the metadata fields from resource
 	 * @throws ApplicationProfileNotFoundException the application profile not found exception
 	 */
-	private MetadataType getMetadataTypeFromResource(XPathHelper helper) throws ApplicationProfileNotFoundException{
+	private List<MetadataField> getMetadataFieldsFromResource(XPathHelper helper) throws Exception{
-
 
 		try {
 
-			MetadataType metaType = new MetadataType();
+			List<String> metadatafields = helper.evaluate("/Resource/Profile/Body/metadataformat/metadatafield");
 
-			List<String> id = helper.evaluate("/Resource/ID/text()");
+			if(metadatafields==null || metadatafields.isEmpty())
+				throw new Exception("Metadata fields not found");
 
-			if(id==null || id.isEmpty())
+			JAXBContext jaxbContext = JAXBContext.newInstance(MetadataField.class);
-				throw new ApplicationProfileNotFoundException("Resource ID not found for "+helper.toString());
+		    Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
-			else{
+
-				metaType.setId(id.get(0));
+//		    for (String string : metadatafields) {
+//		    	logger.debug("mf "+string);
+//			}
+
+		    List<MetadataField> mfs = new ArrayList<MetadataField>();
+		    logger.debug("MetadataFields are: "+metadatafields.size());
+
+		    for (String mfield : metadatafields) {
+		    	try{
+		    	InputStream stream = new ByteArrayInputStream(mfield.getBytes());
+		    	MetadataField mtdf = (MetadataField) jaxbUnmarshaller.unmarshal(stream);
+		    	logger.debug("Unmarshalled: "+mtdf);
+				mfs.add(mtdf);
+		    	}catch(Exception e){
+		    		logger.error("An error occurred during unmarshall performing on "+mfield+", skipping this metadatafield");
+		    	}
 			}
 
-			List<String> name = helper.evaluate("/Resource/Profile/Name/text()");
+			return mfs;
-
-			if(name==null || name.isEmpty())
-				throw new ApplicationProfileNotFoundException("Resource Name not found for "+helper.toString());
-			else
-				metaType.setName(name.get(0));
-
-			List<String> description = helper.evaluate("/Resource/Profile/Description/text()");
-
-			if(description==null || description.isEmpty())
-				throw new ApplicationProfileNotFoundException("Resource Name not found for "+helper.toString());
-			else
-				metaType.setDescription(description.get(0));
-
-			return metaType;
 
 		} catch (Exception e) {
 			logger.error("An error occurred in getListDefaultLayerFromNode ", e);
@@ -150,114 +158,42 @@ public class MedataFormatReader {
 
 	}
 
-	/**
+	public synchronized String getQuesryStringForGenericResourceById(String resourceId){
-	 * Gets the metadata type from resource.
-	 *
-	 * @param secondaryType the secondary type
-	 * @return the metadata type from resource
-	 */
-	/*private MetadataType getMetadataTypeFromResource(XPathHelper helper) throws ApplicationProfileNotFoundException{
 
-		List<String> metadataformat;
+		return String.format("declare namespace ic = 'http://gcube-system.org/namespaces/informationsystem/registry'; " +
-
+						"for $resource in collection('/db/Profiles')//Document/Data/ic:Profile/Resource " +
-		List<GeoexplorerDefaultLayer> listGeoexplorerDefaultLayer = new ArrayList<GeoexplorerDefaultLayer>();
+						"where ($resource/ID/text() eq '%s') return $resource", resourceId);
-
-		try {
-
-			metadataformat = helper.evaluate("/Resource/Profile/Body/metadataformat");
-
-			if (metadataformat != null && metadataformat.size() > 0) {
-
-				List<String> metadatafields = helper.evaluate("/Resource/Profile/Body/metadataformat/metadatafield/text()");
-
-				List<String> currValue = null;
-
-				for (String metafield : metadatafields) {
-					logger.trace("found metafield : "+metafield);
-					GeoexplorerDefaultLayer geoDefLayer = new GeoexplorerDefaultLayer();
-					geoDefLayer.setUUID(uuid);
-					geoDefLayer.setScope(scope.toString());
-
-//					currValue = helper.evaluate("/Resource/Profile/Body/DefaultLayers/DefaultLayer[UUID='"+uuid+"']/@isBaseLayer");
-					currValue = helper.evaluate("/Resource/Profile/Body/DefaultLayers/DefaultLayer[UUID='"+uuid+"']/IsBaseLayer/text()");
-
-					logger.trace("is base layer?" +currValue);
-					if (currValue != null && currValue.size() > 0){
-						boolean isBase = Boolean.parseBoolean(currValue.get(0));
-						geoDefLayer.setBaseLayer(isBase);
-//						logger.trace("isBaseLayer : "+isBase);
-					}
-
-					currValue = helper.evaluate("/Resource/Profile/Body/DefaultLayers/DefaultLayer[UUID='"+uuid+"']/Description/text()");
-
-					String descr = "";
-					if (currValue != null && currValue.size() > 0) {
-						descr = currValue.get(0);
-						geoDefLayer.setDescription(descr);
-//						logger.trace("description: "+descr+" for UUID: "+uuid);
-					}
-
-					currValue = helper.evaluate("/Resource/Profile/Body/DefaultLayers/DefaultLayer[UUID='"+uuid+"']/Name/text()");
-					descr = "";
-					if (currValue != null && currValue.size() > 0) {
-						descr = currValue.get(0);
-						geoDefLayer.setName(descr);
-//						logger.trace("name: "+descr+" for UUID: "+uuid);
-					}
-
-					logger.trace("Filled object: "+geoDefLayer);
-					listGeoexplorerDefaultLayer.add(geoDefLayer);
-				}
-
-			}
-
-			else throw new ApplicationProfileNotFoundException("Your applicationProfile with scope "+scope.toString()+" is wrong, consider adding <DefaultLayer><UUID> element in <Body>");
-
-		} catch (Exception e) {
-			logger.error("An error occurred in getListDefaultLayerFromNode ", e);
-			return listGeoexplorerDefaultLayer;
-		}
-
-		return listGeoexplorerDefaultLayer;
-	}*/
-
-
-	public synchronized String getGcubeGenericQueryString(String secondaryType){
-
-		return "for $profile in collection('/db/Profiles/GenericResource')//Resource" +
-				" where $profile/Profile/SecondaryType/string() eq '"+secondaryType+"'" +
-				" return $profile";
 	}
 
-	/**
-	 * Gets the secondary type.
-	 *
-	 * @return the secondary type
-	 */
-	public String getSecondaryType() {
-		return secondaryType;
-	}
 
 	/**
-	 * Gets the scope.
-	 *
 	 * @return the scope
 	 */
 	public ScopeBean getScope() {
+
 		return scope;
 	}
 
-	/**
-	 * Gets the metadata types.
-	 *
-	 * @return the metadataTypes
-	 */
-	public List<MetadataType> getMetadataTypes() {
 
-		return metadataTypes;
+	/**
+	 * @return the metadataFormat
+	 */
+	public MetadataFormat getMetadataFormat() {
+
+		return metadataFormat;
 	}
 
 
+	/**
+	 * @return the resourceID
+	 */
+	public String getResourceID() {
+
+		return resourceID;
+	}
+
+
+
 	/**
 	 * The main method.
 	 *
@@ -270,8 +206,8 @@ public class MedataFormatReader {
 		final ScopeBean scope  = new ScopeBean(scopeString);
 		MedataFormatReader reader;
 		try {
-			reader = new MedataFormatReader(scope, "");
+			reader = new MedataFormatReader(scope, "78355412-b45a-4519-adce-679452583aa2");
-			System.out.println(reader.getMetadataTypes());
+			System.out.println(reader.getMetadataFormat());
 
 //			String value = "true";
 //			if (value != null){

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

@@ -1,111 +0,0 @@
-/**
- *
- */
-package org.gcube.datacatalogue.metadatadiscovery;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
-
-import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataField;
-import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
-import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataValidator;
-import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataVocabulary;
-import org.junit.Test;
-
-
-/**
- *
- * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * May 27, 2016
- */
-public class MainJaxb {
-
-	static MetadataField ckanMetadata;
-	static MetadataFormat metadatas;
-	static String tmpFileXML = "." + File.separator + "CkanMetadatas.xml";
-
-	@Test
-	public static void createMetadata() {
-
-		metadatas = new MetadataFormat();
-
-		ckanMetadata = new MetadataField();
-		ckanMetadata.setFieldName("Name");
-		ckanMetadata.setMandatory(true);
-		ckanMetadata.setDefaulValue("default value");
-		List<String> vocabulary = new ArrayList<String>();
-		vocabulary.add("field1");
-		vocabulary.add("field2");
-		vocabulary.add("field3");
-		MetadataVocabulary cvc = new MetadataVocabulary(vocabulary);
-		ckanMetadata.setVocabulary(cvc);
-		ckanMetadata.setNote("shown as suggestions in the insert/update metadata form of CKAN");
-		MetadataValidator validator = new MetadataValidator("a regular expression for validating values");
-		ckanMetadata.setValidator(validator);
-		metadatas.addMetadata(ckanMetadata);
-
-		ckanMetadata = new MetadataField();
-		ckanMetadata.setFieldName("Accessibility");
-		ckanMetadata.setMandatory(true);
-		ckanMetadata.setDefaulValue("virtual/public");
-		List<String> vocabulary2 = new ArrayList<String>();
-		vocabulary2.add("virtual/public");
-		vocabulary2.add("virtual/private");
-		vocabulary2.add("transactional");
-		MetadataVocabulary cvc2 = new MetadataVocabulary(vocabulary2);
-		ckanMetadata.setVocabulary(cvc2);
-		ckanMetadata.setNote("shown as suggestions in the insert metadata form of CKAN");
-		MetadataValidator validator2 = new MetadataValidator("a regular expression for validating values");
-		ckanMetadata.setValidator(validator2);
-
-		metadatas.addMetadata(ckanMetadata);
-
-		try {
-
-			marshalingExample();
-			unMarshalingExample();
-		}
-		catch (JAXBException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-	}
-
-
-	private static void marshalingExample() throws JAXBException
-	{
-	    JAXBContext jaxbContext = JAXBContext.newInstance(MetadataFormat.class);
-	    Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
-
-	    jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
-
-	    //Marshal the employees list in console
-//	    jaxbMarshaller.marshal(employees, System.out);
-
-	    //Marshal the employees list in file
-	    jaxbMarshaller.marshal(metadatas, new File(tmpFileXML));
-	}
-
-
-	private static void unMarshalingExample() throws JAXBException
-	{
-	    JAXBContext jaxbContext = JAXBContext.newInstance(MetadataFormat.class);
-	    Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
-
-	    //We had written this file in marshalling example
-	    MetadataFormat mtds = (MetadataFormat) jaxbUnmarshaller.unmarshal(new File(tmpFileXML));
-
-	    for(MetadataField mtd : mtds.getMetadataFields())
-	    {
-	        System.out.println(mtd);
-	    }
-	}
-}
-
-

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

@@ -24,7 +24,7 @@ import org.junit.Test;
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
  * Jun 7, 2016
  */
-public class TestMetadataDiscovery {
+public class TestJaxbMetadataMarshUnmarsh {
 
 	static MetadataField ckanMetadata;
 	static MetadataFormat metadatas;