Refactored and added method 'toMetadataFormat'

.classpath

@@ -6,7 +6,17 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" path="src/main/resources"/>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
 		<attributes>
 			<attribute name="test" value="true"/>

.settings/org.eclipse.core.resources.prefs

@@ -1,4 +1,6 @@
 eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
 encoding/<project>=UTF-8

README.md

@@ -2,9 +2,9 @@
 
 The metadata-profile-discovery library is able to build java objects parsing the 'gCube Metadata Profiles' models:
 
-- defined in the contexts (scopes) of the D4Science Infrastructure;
+* defined in the contexts (scopes) of the D4Science Infrastructure;
 
-- passed as an input stream; 
+* passed as an input stream; 
 
 ## Built With
 

src/main/java/org/gcube/common/metadataprofilediscovery/MetadataProfileDiscovery.java

@@ -11,13 +11,13 @@ import org.gcube.common.metadataprofilediscovery.jaxb.NamespaceCategory;
 
 
 /**
- * The Interface DataCatalogueMetadataDiscovery.
+ * The Interface MetadataProfileDiscovery.
  *
  * @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
  * 
  * Sep 30, 2020
  */
-public interface DataCatalogueMetadataDiscovery {
+public interface MetadataProfileDiscovery {
 
 	/**
 	 * Gets the list of metadata types.

src/main/java/org/gcube/common/metadataprofilediscovery/MetadataProfileReader.java

@@ -13,6 +13,9 @@ import java.util.Map;
 import java.util.stream.Collectors;
 
 import javax.xml.XMLConstants;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
@@ -37,12 +40,17 @@ import org.w3c.dom.Document;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
+
 /**
- * The Class DataCalogueMetadataReader.
+ * The Class MetadataProfileReader.
  *
- * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it Jun 8, 2016
+ * @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
+ * 
+ * Sep 30, 2020
  */
-public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDiscovery {
+public class MetadataProfileReader implements MetadataProfileDiscovery {
+
+	public static final String URL_OF_GCDCMETADATAPROFILEV3_XSD = "https://wiki.gcube-system.org/images_gcube/e/e8/Gcdcmetadataprofilev3.xsd";
 
 	private static String SCHEMA_FILENAME = "Gdcmetadataprofilev3.xsd";
 
@@ -53,14 +61,23 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 
 	private String profileSchema = null;
 
-	private static Logger logger = LoggerFactory.getLogger(DataCalogueMetadataFormatReader.class);
+	private String grMetadataProfileSecondaryType;
+
+	private static Logger logger = LoggerFactory.getLogger(MetadataProfileReader.class);
+	
 	
 	/**
-	 * Instantiates a new data calogue metadata format reader.
+	 * Instantiates a new metadata profile reader.
 	 *
+	 * @param grMetadataProfileSecondaryType the SecondaryType that must be used to discover the "gCube Metadata Profiles" from Information System
 	 * @throws Exception the exception
 	 */
-	public DataCalogueMetadataFormatReader() throws Exception {
+	public MetadataProfileReader(String grMetadataProfileSecondaryType) throws Exception {
+		
+		if(grMetadataProfileSecondaryType==null || grMetadataProfileSecondaryType.isEmpty())
+			throw new NullPointerException("Invalid input parameter");
+		
+		this.grMetadataProfileSecondaryType = grMetadataProfileSecondaryType;
 		
 		String scopeString = ScopeProvider.instance.get();
 		logger.debug("Read scope " + scopeString + " from ScopeProvider");
@@ -70,7 +87,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 
 		scope = new ScopeBean(scopeString);
 		readNamespaces();
-		readMetadaFormats();
+		readMetadataFormats();
 	}
 	
 	/**
@@ -78,9 +95,12 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 	 *
 	 * @throws Exception the exception
 	 */
-	private void readMetadaFormats() throws Exception {
+	private void readMetadataFormats() throws Exception {
+		
+		//reading from Generic Resource for Secondary Type
+		if(grMetadataProfileSecondaryType!=null) {
+			medataFormatDiscovery = new MetadataFormatDiscovery(scope, grMetadataProfileSecondaryType);
 	
-		medataFormatDiscovery = new MetadataFormatDiscovery(scope);
 			logger.info("MedataFormatDiscovery has retrieved: " + medataFormatDiscovery.getMetadataProfiles().size()
 					+ " metadata type/s");
 			logger.debug("filling cache for MedataFormat");
@@ -94,6 +114,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 				logger.debug("MetadataType id: " + mT.getId() + " cached as: " + reader.getMetadataFormat());
 			}
 		}
+	}
 
 	/**
 	 * Read namespaces.
@@ -120,7 +141,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 	 * @return the profile schema string
 	 */
 	public static String getProfileSchemaString() {
-		InputStream inputStream = DataCalogueMetadataFormatReader.getProfileSchemaInputStream();
+		InputStream inputStream = MetadataProfileReader.getProfileSchemaInputStream();
 		return new BufferedReader(new InputStreamReader(inputStream)).lines().collect(Collectors.joining("\n"));
 	}
 
@@ -130,7 +151,15 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 	 * @return the profile schema input stream
 	 */
 	public static InputStream getProfileSchemaInputStream() {
-		return DataCalogueMetadataFormatReader.class.getResourceAsStream(SCHEMA_FILENAME);
+		try {
+			logger.info("Trying to return the URL resource: "+URL_OF_GCDCMETADATAPROFILEV3_XSD);
+			return new URL(URL_OF_GCDCMETADATAPROFILEV3_XSD).openStream();
+			
+		} catch (Exception e) {
+			logger.warn("Error on reading the URL: "+URL_OF_GCDCMETADATAPROFILEV3_XSD);
+		}
+		logger.info("Returning local resource: "+SCHEMA_FILENAME);
+		return MetadataProfileReader.class.getResourceAsStream(SCHEMA_FILENAME);
 	}
 
 	/**
@@ -139,7 +168,15 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 	 * @return the profile schema URL
 	 */
 	public static URL getProfileSchemaURL() {
-		return DataCalogueMetadataFormatReader.class.getResource(SCHEMA_FILENAME);
+		try {
+			logger.info("Trying to return the URL object: "+URL_OF_GCDCMETADATAPROFILEV3_XSD);
+			return new URL(URL_OF_GCDCMETADATAPROFILEV3_XSD);
+			
+		} catch (Exception e) {
+			logger.warn("Error on reading the URL: "+URL_OF_GCDCMETADATAPROFILEV3_XSD);
+		}
+		logger.info("Returning local URL of: "+SCHEMA_FILENAME);
+		return MetadataProfileReader.class.getResource(SCHEMA_FILENAME);
 	}
 
 	/**
@@ -198,7 +235,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 	public List<MetadataProfile> getListOfMetadataProfiles() throws Exception {
 
 		if (medataFormatDiscovery == null)
-			readMetadaFormats();
+			readMetadataFormats();
 
 		return medataFormatDiscovery.getMetadataProfiles();
 	}
@@ -252,7 +289,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 	 */
 	public String getProfileSchema() {
 		if (profileSchema == null) {
-			profileSchema = DataCalogueMetadataFormatReader.getProfileSchemaString();
+			profileSchema = MetadataProfileReader.getProfileSchemaString();
 		}
 		return profileSchema;
 
@@ -272,4 +309,22 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
 		validateAgainstXSD(source, getProfileSchemaURL());
 	}
 	
+	/**
+	 * Utility method to get a metadata format from a "gCube Metadata Profiles" model (XML-based)
+	 *
+	 * @param metadataProfileStream the metadata profile stream
+	 * @return the metadata format
+	 * @throws JAXBException the JAXB exception
+	 */
+	public MetadataFormat toMetadataFormat(InputStream metadataProfileStream) throws JAXBException{
+		
+		if(metadataProfileStream==null)
+			throw new NullPointerException("Invalid input parameter");
+		
+		JAXBContext jaxbContext = JAXBContext.newInstance(MetadataFormat.class);
+	    Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
+	    return (MetadataFormat) jaxbUnmarshaller.unmarshal(metadataProfileStream);
+	}
+
+
 }

src/main/java/org/gcube/common/metadataprofilediscovery/reader/MetadataFormatDiscovery.java

@@ -28,28 +28,30 @@ import org.xml.sax.InputSource;
 
 
 /**
- * The Class MedataFormatDiscovery.
+ * The Class MetadataFormatDiscovery.
  *
- * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
+ * @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
- * Jun 8, 2016
+ * 
+ * Sep 30, 2020
  */
 public class MetadataFormatDiscovery {
 
 	private static Logger logger = LoggerFactory.getLogger(MetadataFormatDiscovery.class);
-	public static final String DATA_CATALOGUE_METADATA_SECONDARY_TYPE = "DataCatalogueMetadata";
 	private String secondaryType;
 	private ScopeBean scope;
 	private List<MetadataProfile> metadataProfiles;
 
+
 	/**
-	 * Instantiates a new medata format reader.
+	 * Instantiates a new metadata format discovery.
 	 *
-	 * @param scope - the scope to be searched
+	 * @param scope the scope
+	 * @param secondaryType the secondary type
 	 * @throws Exception the exception
 	 */
-	public MetadataFormatDiscovery(ScopeBean scope) throws Exception {
+	public MetadataFormatDiscovery(ScopeBean scope, String secondaryType) throws Exception {
 		this.scope = scope;
-		this.secondaryType = DATA_CATALOGUE_METADATA_SECONDARY_TYPE;
+		this.secondaryType = secondaryType;
 		this.metadataProfiles = readMetadataProfilesFromInfrastrucure();
 	}
 
@@ -115,6 +117,7 @@ public class MetadataFormatDiscovery {
 	/**
 	 * Gets the metadata type from resource.
 	 *
+	 * @param doc the doc
 	 * @param helper the helper
 	 * @return the metadata type from resource
 	 * @throws MetadataProfileNotFoundException the application profile not found exception

src/test/.gitignore

@@ -0,0 +1 @@
+/resources/

src/test/java/org/gcube/common/metadataprofilediscovery/TestDataCatalogueMetadataFormatReader.java

@@ -28,12 +28,13 @@ public class TestDataCatalogueMetadataFormatReader {
 	/**
 	 * Test.
 	 */
-//	@Test
+	@Test
 	public void test() {
 		try {
 			String scopeString = "/gcube/devsec/devVRE";
+			String grMetadataProfileSecondaryType = "DataCatalogueMetadata";
 			ScopeProvider.instance.set(scopeString);
-			DataCalogueMetadataFormatReader reader = new DataCalogueMetadataFormatReader();
+			MetadataProfileReader reader = new MetadataProfileReader(grMetadataProfileSecondaryType);
 			int i = 0;
 
 			List<NamespaceCategory> categs = reader.getListOfNamespaceCategories();
@@ -63,7 +64,7 @@ public class TestDataCatalogueMetadataFormatReader {
 //	@Test
 	public void validateAgainstProfileSchema() throws Exception {
 		InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream(PROFILE_EXAMPLE_FILENAME);
-		DataCalogueMetadataFormatReader.validateProfile(inputStream);
+		MetadataProfileReader.validateProfile(inputStream);
 	}
 }
 

src/test/java/org/gcube/common/metadataprofilediscovery/TestMetadataFormatDiscovery.java

@@ -21,15 +21,16 @@ public class TestMetadataFormatDiscovery {
 	/**
 	 * Test.
 	 */
-//	@Test
+	@Test
 	public void test() {
 
 		String scopeString = "/gcube/devsec/devVRE";
+		String grMetadataProfileSecondaryType = "DataCatalogueMetadata";
 		final ScopeBean scope  = new ScopeBean(scopeString);
 		MetadataFormatDiscovery reader;
 		try {
 			ScopeProvider.instance.set(scopeString);
-			reader = new MetadataFormatDiscovery(scope);
+			reader = new MetadataFormatDiscovery(scope, grMetadataProfileSecondaryType);
 			//System.out.println(reader.getMetadataProfiles());
 
 			for (MetadataProfile metaProfile : reader.getMetadataProfiles()) {