Rename MeatadataType as MedataProfile

Added metadatatype attribute also to MedataProfile


git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/gcubedatacatalogue-metadata-discovery@146329 82a268e6-3cf1-43bd-a215-b396298e98cf

.classpath

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry including="**/*.java" kind="src" output="target/gcubedatacatalogue-metadata-discovery-1.0.0-SNAPSHOT/WEB-INF/classes" path="src/main/java">
+	<classpathentry including="**/*.java" kind="src" output="target/gcubedatacatalogue-metadata-discovery-3.0.0-SNAPSHOT/WEB-INF/classes" path="src/main/java">
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
@@ -27,5 +27,5 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="output" path="target/gcubedatacatalogue-metadata-discovery-1.0.0-SNAPSHOT/WEB-INF/classes"/>
+	<classpathentry kind="output" path="target/gcubedatacatalogue-metadata-discovery-3.0.0-SNAPSHOT/WEB-INF/classes"/>
 </classpath>

src/main/java/org/gcube/datacatalogue/metadatadiscovery/DataCalogueMetadataFormatReader.java

@@ -6,7 +6,7 @@ import java.util.Map;
 
 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.MetadataProfile;
 import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
 import org.gcube.datacatalogue.metadatadiscovery.reader.MetadataFormatDiscovery;
 import org.gcube.datacatalogue.metadatadiscovery.reader.MetadataFormatReader;
@@ -44,9 +44,12 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 
 		scope  = new ScopeBean(scopeString);
 		medataFormatDiscovery = new MetadataFormatDiscovery(scope);
-		logger.info("MedataFormatDiscovery has retrieved: "+medataFormatDiscovery.getMetadataTypes().size() +" metadata type/s");
+		logger.info("MedataFormatDiscovery has retrieved: "+medataFormatDiscovery.getMetadataProfiles().size() +" metadata type/s");
 		logger.debug("filling cache for MedataFormat");
-		for (MetadataType mT : medataFormatDiscovery.getMetadataTypes()) {
+		for (MetadataProfile mT : medataFormatDiscovery.getMetadataProfiles()) {
+			if(mT==null)
+				continue;
+
 			MetadataFormatReader reader = new MetadataFormatReader(scope, mT.getId());
 			hash.put(mT.getId(), reader.getMetadataFormat());
 			logger.debug("MetadataType id: "+mT.getId() +" cached as: "+reader.getMetadataFormat());
@@ -57,25 +60,25 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 	 * @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#getListOfMetadataTypes()
 	 */
 	@Override
-	public List<MetadataType> getListOfMetadataTypes() throws Exception {
+	public List<MetadataProfile> getListOfMetadataProfiles() throws Exception {
 
-		return medataFormatDiscovery.getMetadataTypes();
+		return medataFormatDiscovery.getMetadataProfiles();
 	}
 
 	/* (non-Javadoc)
 	 * @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#getMetadataFormatForMetadataType(org.gcube.datacatalogue.metadatadiscovery.bean.MetadataType)
 	 */
 	@Override
-	public MetadataFormat getMetadataFormatForMetadataType(MetadataType type) throws Exception {
+	public MetadataFormat getMetadataFormatForMetadataProfile(MetadataProfile profile) throws Exception {
 
-		if(type==null)
+		if(profile==null)
-			throw new Exception("MetadataType is null");
+			throw new Exception("Input "+ MetadataProfile.class.getSimpleName() + " is null");
 
-		MetadataFormat format = hash.get(type.getId());
+		MetadataFormat format = hash.get(profile.getId());
 		if(format!=null)
 			return format;
 
-		MetadataFormatReader reader = new MetadataFormatReader(scope, type.getId());
+		MetadataFormatReader reader = new MetadataFormatReader(scope, profile.getId());
 		return reader.getMetadataFormat();
 	}
 

src/main/java/org/gcube/datacatalogue/metadatadiscovery/DataCatalogueMetadataDiscovery.java

@@ -5,16 +5,17 @@ package org.gcube.datacatalogue.metadatadiscovery;
 
 import java.util.List;
 
-import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataType;
+import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataProfile;
 import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
 
 
 
+
 /**
  * The Interface DataCatalogueMetadataDiscovery.
  *
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * Jun 8, 2016
+ * Mar 24, 2017
  */
 public interface DataCatalogueMetadataDiscovery {
 
@@ -23,9 +24,9 @@ public interface DataCatalogueMetadataDiscovery {
 	 * Gets the list of metadata types.
 	 *
 	 * @return the list of metadata types
-	 * @throws Exception
+	 * @throws Exception the exception
 	 */
-	List<MetadataType> getListOfMetadataTypes() throws Exception;
+	List<MetadataProfile> getListOfMetadataProfiles() throws Exception;
 
 
 	/**
@@ -33,8 +34,8 @@ public interface DataCatalogueMetadataDiscovery {
 	 *
 	 * @param type the type
 	 * @return the metadata format for metadata type
-	 * @throws Exception
+	 * @throws Exception the exception
 	 */
-	MetadataFormat getMetadataFormatForMetadataType(MetadataType type) throws Exception;
+	MetadataFormat getMetadataFormatForMetadataProfile(MetadataProfile type) throws Exception;
 
 }

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

@@ -6,27 +6,29 @@ package org.gcube.datacatalogue.metadatadiscovery.bean;
 import java.io.Serializable;
 
 
+
 /**
- * The Class MetadataType.
+ * The Class MetadataProfile.
  *
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
- * Jun 8, 2016
+ * Mar 24, 2017
  */
-public class MetadataType implements Serializable{
+public class MetadataProfile implements Serializable{
+
 
 	/**
 	 *
 	 */
-	private static final long serialVersionUID = -975360133066572549L;
+	private static final long serialVersionUID = 8829173012445264057L;
-
 	private String id;
 	private String name;
 	private String description;
+	private String metadataType;
 
 	/**
 	 * Instantiates a new metadata type.
 	 */
-	public MetadataType() {
+	public MetadataProfile() {
 
 	}
 
@@ -37,12 +39,13 @@ public class MetadataType implements Serializable{
 	 * @param name the name
 	 * @param description the description
 	 */
-	public MetadataType(String id, String name, String description) {
+	public MetadataProfile(String id, String name, String description, String metadataType) {
 
 		super();
 		this.id = id;
 		this.name = name;
 		this.description = description;
+		this.metadataType = metadataType;
 	}
 
 
@@ -111,6 +114,23 @@ public class MetadataType implements Serializable{
 		this.description = description;
 	}
 
+	/**
+	 * @return the metadataType
+	 */
+	public String getMetadataType() {
+
+		return metadataType;
+	}
+
+
+	/**
+	 * @param metadataType the metadataType to set
+	 */
+	public void setMetadataType(String metadataType) {
+
+		this.metadataType = metadataType;
+	}
+
 	/* (non-Javadoc)
 	 * @see java.lang.Object#toString()
 	 */
@@ -118,14 +138,17 @@ public class MetadataType implements Serializable{
 	public String toString() {
 
 		StringBuilder builder = new StringBuilder();
-		builder.append("MetadataType [id=");
+		builder.append("MetadataProfile [id=");
 		builder.append(id);
 		builder.append(", name=");
 		builder.append(name);
 		builder.append(", description=");
 		builder.append(description);
+		builder.append(", metadataType=");
+		builder.append(metadataType);
 		builder.append("]");
 		return builder.toString();
 	}
 
+
 }

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

@@ -31,6 +31,10 @@ public class MetadataFormat implements Serializable{
 	 */
 	private static final long serialVersionUID = -5881074882343424963L;
 
+	public static final String LOCAL_NAME_METADATA_TYPE = "metadatatype";
+
+	public static final String LOCAL_NAME_METADATA_FORMAT = "metadataformat";
+
 	/**
 	 * Instantiates a new metadata format.
 	 */
@@ -44,7 +48,7 @@ public class MetadataFormat implements Serializable{
 	@XmlElement(name = "metadatafield")
 	private List<MetadataField> metadataFields;
 
-	@XmlAttribute(name = "metadatatype", required=true)
+	@XmlAttribute(name = LOCAL_NAME_METADATA_TYPE, required=true)
 	private String metadataType = "";
 
 	@XmlTransient

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

@@ -8,15 +8,21 @@ import java.util.List;
 
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpression;
+import javax.xml.xpath.XPathFactory;
 
 import org.gcube.common.resources.gcore.utils.XPathHelper;
 import org.gcube.common.scope.impl.ScopeBean;
-import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataType;
+import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataProfile;
+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;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.xml.sax.InputSource;
 
@@ -33,7 +39,7 @@ public class MetadataFormatDiscovery {
 	protected static final String DATA_CATALOGUE_METADATA_SECONDARY_TYPE = "DataCatalogueMetadata";
 	private String secondaryType;
 	private ScopeBean scope;
-	private List<MetadataType> metadataTypes;
+	private List<MetadataProfile> metadataProfiles;
 
 	/**
 	 * Instantiates a new medata format reader.
@@ -44,7 +50,7 @@ public class MetadataFormatDiscovery {
 	public MetadataFormatDiscovery(ScopeBean scope) throws Exception {
 		this.scope = scope;
 		this.secondaryType = DATA_CATALOGUE_METADATA_SECONDARY_TYPE;
-		this.metadataTypes = readProfileFromInfrastrucure();
+		this.metadataProfiles = readMetadataProfilesFromInfrastrucure();
 	}
 
 	/**
@@ -53,7 +59,7 @@ public class MetadataFormatDiscovery {
 	 * @return the applicationProfile profile
 	 * @throws Exception the exception
 	 */
-	private List<MetadataType> readProfileFromInfrastrucure() throws Exception {
+	private List<MetadataProfile> readMetadataProfilesFromInfrastrucure() throws Exception {
 		logger.trace("read secondary type: "+secondaryType);
 
 		if(this.scope==null)
@@ -62,7 +68,7 @@ public class MetadataFormatDiscovery {
 		String scopeString = this.scope.toString();
 		logger.trace("read scope: "+scopeString);
 
-		List<MetadataType> list = new ArrayList<MetadataType>();
+		List<MetadataProfile> list = new ArrayList<MetadataProfile>();
 
 		try {
 
@@ -77,21 +83,22 @@ public class MetadataFormatDiscovery {
 			Query q = new QueryBox(queryString);
 
 			DiscoveryClient<String> client = client();
-		 	List<String> appProfile = client.submit(q);
+		 	List<String> metaProfile = client.submit(q);
 
-			if (appProfile == null || appProfile.size() == 0)
+			if (metaProfile == null || metaProfile.size() == 0)
-				throw new ApplicationProfileNotFoundException("ApplicationProfile with secondaryType: "+secondaryType+" is not registered in the scope: "+scopeString);
+				throw new MetadataProfileNotFoundException("Resource/s with secondaryType: "+secondaryType+" is/are not registered in the scope: "+scopeString);
 			else {
 
-				for (String elem : appProfile) {
+				for (String elem : metaProfile) {
 					try{
 						DocumentBuilder docBuilder =  DocumentBuilderFactory.newInstance().newDocumentBuilder();
-						Node node = docBuilder.parse(new InputSource(new StringReader(elem))).getDocumentElement();
+						Document doc = docBuilder.parse(new InputSource(new StringReader(elem)));
+						Node node = doc.getDocumentElement();
 						XPathHelper helper = new XPathHelper(node);
-						MetadataType meta = getMetadataTypeFromResource(helper);
+						MetadataProfile meta = getMetadataProfileFromResource(doc, helper);
 						list.add(meta);
 					}catch(Exception e){
-						logger.error("Error while trying to fetch applicationProfile "+secondaryType+" from the infrastructure, ",e);
+						logger.error("Error while trying to fetch resource with secondary type "+secondaryType+" from the infrastructure, scope: "+scopeString,e);
 					}
 				}
 			}
@@ -110,41 +117,51 @@ public class MetadataFormatDiscovery {
 	 *
 	 * @param helper the helper
 	 * @return the metadata type from resource
-	 * @throws ApplicationProfileNotFoundException the application profile not found exception
+	 * @throws MetadataProfileNotFoundException the application profile not found exception
 	 */
-	private MetadataType getMetadataTypeFromResource(XPathHelper helper) throws ApplicationProfileNotFoundException{
+	private MetadataProfile getMetadataProfileFromResource(Document doc, XPathHelper helper) throws MetadataProfileNotFoundException{
 
 
 		try {
 
-			MetadataType metaType = new MetadataType();
+			MetadataProfile metadataProfile = new MetadataProfile();
 
 			List<String> id = helper.evaluate("/Resource/ID/text()");
 
 			if(id==null || id.isEmpty())
-				throw new ApplicationProfileNotFoundException("Resource ID not found for "+helper.toString());
+				throw new MetadataProfileNotFoundException("Resource ID not found for "+helper.toString());
 			else{
-				metaType.setId(id.get(0));
+				metadataProfile.setId(id.get(0));
 			}
 
 			List<String> name = helper.evaluate("/Resource/Profile/Name/text()");
 
 			if(name==null || name.isEmpty())
-				throw new ApplicationProfileNotFoundException("Resource Name not found for "+helper.toString());
+				throw new MetadataProfileNotFoundException("Resource Name not found for Resource Id: "+metadataProfile.getId());
 			else
-				metaType.setName(name.get(0));
+				metadataProfile.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());
+				logger.info("Description not found for Resource ID: "+metadataProfile.getId()+", continuing.. ");
 			else
-				metaType.setDescription(description.get(0));
+				metadataProfile.setDescription(description.get(0));
 
-			return metaType;
+			XPathFactory xpathFactory = XPathFactory.newInstance();
+			XPath xpath = xpathFactory.newXPath();
+			XPathExpression expr = xpath.compile("/Resource/Profile/Body/metadataformat/@"+MetadataFormat.LOCAL_NAME_METADATA_TYPE);
+			String metadataType = (String) expr.evaluate(doc, XPathConstants.STRING);
+
+			if(metadataType==null || metadataType.isEmpty())
+				throw new MetadataProfileNotFoundException("Required attribute '"+MetadataFormat.LOCAL_NAME_METADATA_TYPE+"' not found in the element '"+MetadataFormat.LOCAL_NAME_METADATA_FORMAT+"' for Metadata Profile (with Resource) Id: "+metadataProfile.getId());
+			else
+				metadataProfile.setMetadataType(metadataType);
+
+			return metadataProfile;
 
 		} catch (Exception e) {
-			logger.error("An error occurred in getListDefaultLayerFromNode ", e);
+			logger.error("An error occurred in getMetadataProfileFromResource ", e);
 			return null;
 		}
 
@@ -186,8 +203,8 @@ public class MetadataFormatDiscovery {
 	 *
 	 * @return the metadataTypes
 	 */
-	public List<MetadataType> getMetadataTypes() {
+	public List<MetadataProfile> getMetadataProfiles() {
 
-		return metadataTypes;
+		return metadataProfiles;
 	}
 }

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

@@ -84,7 +84,7 @@ public class MetadataFormatReader {
 		 	List<String> appProfile = client.submit(q);
 
 			if (appProfile == null || appProfile.size() == 0)
-				throw new ApplicationProfileNotFoundException("Your resourceID "+resourceID+" is not registered in the infrastructure, the scope is "+scopeString);
+				throw new MetadataProfileNotFoundException("Your resourceID "+resourceID+" is not registered in the infrastructure, the scope is "+scopeString);
 			else {
 				String theResource = null;
 				try{

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

@@ -7,14 +7,14 @@ package org.gcube.datacatalogue.metadatadiscovery.reader;
  * Jun 7, 2016
  */
 @SuppressWarnings("serial")
-public class ApplicationProfileNotFoundException extends Exception {
+public class MetadataProfileNotFoundException extends Exception {
 
  	/**
  	 * Instantiates a new application profile not found exception.
  	 *
  	 * @param message the message
  	 */
- 	public ApplicationProfileNotFoundException(String message) {
+ 	public MetadataProfileNotFoundException(String message) {
 	    super(message);
 	  }
 }

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

@@ -4,7 +4,7 @@
 package org.gcube.datacatalogue.metadatadiscovery;
 
 import org.gcube.common.scope.api.ScopeProvider;
-import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataType;
+import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataProfile;
 import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
 import org.junit.Test;
 import org.slf4j.Logger;
@@ -31,8 +31,12 @@ public class TestDataCatalogueMetadataFormatReader {
 			ScopeProvider.instance.set(scopeString);
 			DataCalogueMetadataFormatReader reader = new DataCalogueMetadataFormatReader();
 			int i = 0;
-			for (MetadataType mt : reader.getListOfMetadataTypes()) {
+			for (MetadataProfile mt : reader.getListOfMetadataProfiles()) {
-				MetadataFormat metadataFormat = reader.getMetadataFormatForMetadataType(mt);
+
+				if(mt==null)
+					continue;
+
+				MetadataFormat metadataFormat = reader.getMetadataFormatForMetadataProfile(mt);
 				logger.trace("\n\n "+ ++i +".) Metadata source: "+metadataFormat.getMetadataSource().substring(0, 100));
 			}
 

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

@@ -5,7 +5,7 @@ package org.gcube.datacatalogue.metadatadiscovery;
 
 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.MetadataProfile;
 import org.gcube.datacatalogue.metadatadiscovery.reader.MetadataFormatDiscovery;
 import org.junit.Test;
 
@@ -30,10 +30,10 @@ public class TestMetadataFormatDiscovery {
 		try {
 			ScopeProvider.instance.set(scopeString);
 			reader = new MetadataFormatDiscovery(scope);
-			System.out.println(reader.getMetadataTypes());
+			//System.out.println(reader.getMetadataProfiles());
 
-			for (MetadataType type : reader.getMetadataTypes()) {
+			for (MetadataProfile metaProfile : reader.getMetadataProfiles()) {
-				System.out.println(type);
+				System.out.println(metaProfile.getId() +" name: "+metaProfile.getName() +" type: "+metaProfile.getMetadataType());
 			}
 
 		} catch (Exception e) {