Refs #13079: Add the create/update/delete operation in Profile Collection in gCat

Task-Url: https://support.d4science.org/issues/13079

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/gcubedatacatalogue-metadata-discovery@176268 82a268e6-3cf1-43bd-a215-b396298e98cf

.classpath

@@ -1,11 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry including="**/*.java" kind="src" output="target/gcubedatacatalogue-metadata-discovery-3.1.0-SNAPSHOT/WEB-INF/classes" path="src/main/java">
+	<classpathentry including="**/*.java" kind="src" output="target/gcubedatacatalogue-metadata-discovery-3.4.0-SNAPSHOT/WEB-INF/classes" path="src/main/java">
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="src" path="src/main/resources"/>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
 		<attributes>
 			<attribute name="optional" value="true"/>
@@ -27,5 +28,5 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="output" path="target/gcubedatacatalogue-metadata-discovery-3.1.0-SNAPSHOT/WEB-INF/classes"/>
+	<classpathentry kind="output" path="target/gcubedatacatalogue-metadata-discovery-3.4.0-SNAPSHOT/WEB-INF/classes"/>
 </classpath>

pom.xml

@@ -13,7 +13,7 @@
 	<groupId>org.gcube.data-catalogue</groupId>
 	<artifactId>gcubedatacatalogue-metadata-discovery</artifactId>
 	<packaging>jar</packaging>
-	<version>3.3.0-SNAPSHOT</version>
+	<version>3.4.0-SNAPSHOT</version>
 	<name>The gCube data catalogue metadata discovery library</name>
 	<description>The gCube data catalogue metadata discovery library</description>
 	<scm>
@@ -112,6 +112,14 @@
 			<version>4.8.1</version>
 			<scope>test</scope>
 		</dependency>
+		
+		<!-- Required to log on tests -->
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<version>1.0.13</version>
+			<scope>test</scope>
+		</dependency>
 
 	</dependencies>
 

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

@@ -1,9 +1,21 @@
 package org.gcube.datacatalogue.metadatadiscovery;
 
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.StringReader;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
+
+import javax.xml.XMLConstants;
+import javax.xml.transform.stream.StreamSource;
+import javax.xml.validation.Schema;
+import javax.xml.validation.SchemaFactory;
+import javax.xml.validation.Validator;
 
 import org.gcube.common.scope.api.ScopeProvider;
 import org.gcube.common.scope.impl.ScopeBean;
@@ -15,8 +27,7 @@ import org.gcube.datacatalogue.metadatadiscovery.reader.MetadataFormatReader;
 import org.gcube.datacatalogue.metadatadiscovery.reader.NamespaceCategoryReader;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
-
+import org.xml.sax.SAXException;
 
 /**
  * The Class DataCalogueMetadataReader.
@@ -24,135 +35,167 @@ import org.slf4j.LoggerFactory;
  * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
  * Jun 8, 2016
  */
-public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDiscovery{
-
+public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDiscovery {
+	
+	private static String SCHEMA_FILENAME = "Gdcmetadataprofilev3.xsd";
+	
 	private MetadataFormatDiscovery medataFormatDiscovery;
 	private ScopeBean scope;
-	private Map<String, MetadataFormat> hashMetadataFormats = null;
+	private Map<String,MetadataFormat> hashMetadataFormats = null;
 	private List<NamespaceCategory> namespaceCategories = null;
 
+	private String profileSchema = null;
+	
 	private static Logger logger = LoggerFactory.getLogger(DataCalogueMetadataFormatReader.class);
-
+	
 	/**
 	 * Instantiates a new data calogue metadata format reader.
 	 *
 	 * @throws Exception the exception
 	 */
 	public DataCalogueMetadataFormatReader() throws Exception {
-
+		
 		String scopeString = ScopeProvider.instance.get();
-		logger.debug("Read scope "+scopeString +" from ScopeProvider");
-
-		if(scopeString==null || scopeString.isEmpty())
+		logger.debug("Read scope " + scopeString + " from ScopeProvider");
+		
+		if(scopeString == null || scopeString.isEmpty())
 			throw new Exception("Please set a valid scope into ScopeProvider");
-
-		scope  = new ScopeBean(scopeString);
+		
+		scope = new ScopeBean(scopeString);
 		readNamespaces();
 		readMetadaFormats();
 	}
-
-
+	
 	/**
 	 * Read metada formats.
 	 *
 	 * @throws Exception the exception
 	 */
-	private void readMetadaFormats() throws Exception{
-
+	private void readMetadaFormats() throws Exception {
+		
 		medataFormatDiscovery = new MetadataFormatDiscovery(scope);
-		logger.info("MedataFormatDiscovery has retrieved: "+medataFormatDiscovery.getMetadataProfiles().size() +" metadata type/s");
+		logger.info("MedataFormatDiscovery has retrieved: " + medataFormatDiscovery.getMetadataProfiles().size()
+				+ " metadata type/s");
 		logger.debug("filling cache for MedataFormat");
-		hashMetadataFormats = new HashMap<String, MetadataFormat>(medataFormatDiscovery.getMetadataProfiles().size());
-		for (MetadataProfile mT : medataFormatDiscovery.getMetadataProfiles()) {
-			if(mT==null)
+		hashMetadataFormats = new HashMap<String,MetadataFormat>(medataFormatDiscovery.getMetadataProfiles().size());
+		for(MetadataProfile mT : medataFormatDiscovery.getMetadataProfiles()) {
+			if(mT == null)
 				continue;
-
+			
 			MetadataFormatReader reader = new MetadataFormatReader(scope, mT.getId());
 			hashMetadataFormats.put(mT.getId(), reader.getMetadataFormat());
-			logger.debug("MetadataType id: "+mT.getId() +" cached as: "+reader.getMetadataFormat());
+			logger.debug("MetadataType id: " + mT.getId() + " cached as: " + reader.getMetadataFormat());
 		}
 	}
-
-
+	
 	/**
 	 * Read namespaces.
 	 */
 	private void readNamespaces() {
-
-		try{
-			if(namespaceCategories == null || namespaceCategories.isEmpty()){
-
+		
+		try {
+			if(namespaceCategories == null || namespaceCategories.isEmpty()) {
+				
 				if(namespaceCategories == null)
 					namespaceCategories = new ArrayList<NamespaceCategory>();
-
+				
 				NamespaceCategoryReader rd = new NamespaceCategoryReader(scope);
 				namespaceCategories.addAll(rd.getNamespaces().getNamespaceCategories());
 			}
-		}catch(Exception e){
+		} catch(Exception e) {
 			logger.debug("An error occurred during read namespaces for categories: ", e);
 		}
 	}
-
+	
 	/* (non-Javadoc)
 	 * @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#getMetadataFormatForMetadataType(org.gcube.datacatalogue.metadatadiscovery.bean.MetadataType)
 	 */
 	@Override
 	public MetadataFormat getMetadataFormatForMetadataProfile(MetadataProfile profile) throws Exception {
-
-		if(profile==null)
-			throw new Exception("Input "+ MetadataProfile.class.getSimpleName() + " is null");
-
+		
+		if(profile == null)
+			throw new Exception("Input " + MetadataProfile.class.getSimpleName() + " is null");
+		
 		MetadataFormat format = hashMetadataFormats.get(profile.getId());
-		if(format!=null)
+		if(format != null)
 			return format;
-
+		
 		MetadataFormatReader reader = new MetadataFormatReader(scope, profile.getId());
 		return reader.getMetadataFormat();
 	}
-
+	
 	/* (non-Javadoc)
 	 * @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#getListOfMetadataTypes()
 	 */
 	@Override
 	public List<MetadataProfile> getListOfMetadataProfiles() throws Exception {
-
-		if(medataFormatDiscovery==null)
+		
+		if(medataFormatDiscovery == null)
 			readMetadaFormats();
-
+		
 		return medataFormatDiscovery.getMetadataProfiles();
 	}
-
+	
 	/* (non-Javadoc)
 	 * @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#getListOfNamespaceCategories()
 	 */
 	@Override
 	public List<NamespaceCategory> getListOfNamespaceCategories() throws Exception {
-
+		
 		if(namespaceCategories == null)
 			readNamespaces();
-
+		
 		return namespaceCategories;
 	}
-
-
+	
 	/* (non-Javadoc)
 	 * @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#resetMetadataProfile()
 	 */
 	@Override
 	public void resetMetadataProfile() {
-
+		
 		medataFormatDiscovery = null;
 		hashMetadataFormats = null;
 	}
-
-
+	
 	/* (non-Javadoc)
 	 * @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#resetNamespaceCategories()
 	 */
 	@Override
 	public void resetNamespaceCategories() {
-
+		
 		namespaceCategories = null;
 	}
-
+	
+	@Override
+	public String getProfileSchema() {
+		if(profileSchema == null) {
+			InputStream inputStream = getProfileSchemaInputStream();
+			profileSchema = new BufferedReader(new InputStreamReader(inputStream)).lines()
+					.collect(Collectors.joining("\n"));
+		}
+		return profileSchema;
+		
+	}
+	
+	static InputStream getProfileSchemaInputStream() {
+		return DataCalogueMetadataFormatReader.class.getClassLoader().getResourceAsStream(SCHEMA_FILENAME);
+	}
+	
+	static void validateAgainstXSD(StreamSource xml, StreamSource xsd) throws SAXException, IOException {
+		SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
+		Schema schema = factory.newSchema(xsd);
+		Validator validator = schema.newValidator();
+		validator.validate(xml);
+	}
+	
+	@Override
+	public void validateProfile(String xmlProfile) throws Exception {
+		validateAgainstXSD(new StreamSource(xmlProfile), new StreamSource(getProfileSchema()));
+	}
+	
+	public static void validateProfile(InputStream xml) throws Exception {
+		validateAgainstXSD(new StreamSource(xml), new StreamSource(getProfileSchemaInputStream()));
+	}
+	
 }

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

@@ -3,11 +3,13 @@
  */
 package org.gcube.datacatalogue.metadatadiscovery;
 
+import java.io.IOException;
 import java.util.List;
 
 import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataProfile;
 import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
 import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.NamespaceCategory;
+import org.xml.sax.SAXException;
 
 
 
@@ -20,7 +22,6 @@ import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.NamespaceCategory;
  */
 public interface DataCatalogueMetadataDiscovery {
 
-
 	/**
 	 * Gets the list of metadata types.
 	 *
@@ -62,4 +63,19 @@ public interface DataCatalogueMetadataDiscovery {
 	 */
 	void resetNamespaceCategories();
 
+	/**
+	 * Return the XSD of the profile schema
+	 * @return the String representation of the XSD containing the schema for a profile 
+	 */
+	String getProfileSchema();
+	
+	/**
+	 * Validate the xml provided as argument
+	 * @param xmlProfile the string representation of the XML to validate again the schema 
+	 * @throws IOException 
+	 * @throws SAXException 
+	 */
+	void validateProfile(String xmlProfile) throws Exception;
+
+	
 }

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

@@ -3,7 +3,11 @@
  */
 package org.gcube.datacatalogue.metadatadiscovery;
 
+import java.io.BufferedReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import org.gcube.common.scope.api.ScopeProvider;
 import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataProfile;
@@ -55,4 +59,15 @@ public class TestDataCatalogueMetadataFormatReader {
 			e.printStackTrace();
 		}
 	}
+	
+	
+		public static String PROFILE_EXAMPLE_FILENAME = "profileExample.xml";
+	
+	@Test
+	public void validateAgainstProfileSchema() throws Exception {
+		InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream(PROFILE_EXAMPLE_FILENAME);
+		DataCalogueMetadataFormatReader.validateProfile(inputStream);
+	}
 }
+
+

src/test/resources/logback-test.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE xml>
+<configuration>
+
+  <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+   <encoder>
+      <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{0}: %msg%n</pattern>
+    </encoder>
+  </appender>
+  
+  
+  <logger name="org.gcube" level="ERROR" />
+  <logger name="org.gcube.datacatalogue" level="TRACE" />
+  
+  <root level="WARN">
+    <appender-ref ref="STDOUT" />
+  </root>
+  
+</configuration>

src/test/resources/profileExample.xml

@@ -0,0 +1,80 @@
+<metadataformat type="Dataset">
+	<metadatafield>
+		<fieldName>spatial</fieldName>
+		<mandatory>false</mandatory>
+		<dataType>GeoJSON</dataType>
+		<maxOccurs>1</maxOccurs>
+		<defaultValue />
+		<note>Insert a geoJSON characterising the spatial coverage of the
+			dataset.
+		</note>
+		<vocabulary />
+		<validator />
+		<tagging create="false" />
+		<grouping create="false" />
+	</metadatafield>
+	<metadatafield>
+		<fieldName>timeField</fieldName>
+		<mandatory>false</mandatory>
+		<dataType>Time</dataType>
+		<maxOccurs>1</maxOccurs>
+		<defaultValue />
+		<note>Insert a time value characterising the temporal coverage of the
+			dataset.
+		</note>
+		<vocabulary />
+		<validator />
+		<tagging create="false" />
+		<grouping create="false" />
+	</metadatafield>
+	<metadatafield>
+		<fieldName>timeIntervalField</fieldName>
+		<mandatory>false</mandatory>
+		<dataType>Time_Interval</dataType>
+		<maxOccurs>1</maxOccurs>
+		<defaultValue />
+		<note>Insert a time interval value characterising the temporal
+			coverage of the dataset.
+		</note>
+		<vocabulary />
+		<validator />
+		<tagging create="false" />
+		<grouping create="false" />
+	</metadatafield>
+	<metadatafield>
+		<fieldName>timeListField</fieldName>
+		<mandatory>false</mandatory>
+		<dataType>Times_ListOf</dataType>
+		<maxOccurs>1</maxOccurs>
+		<defaultValue />
+		<note>Insert a time list characterising the temporal coverage of the
+			dataset.
+		</note>
+		<vocabulary />
+		<validator />
+		<tagging create="false" />
+		<grouping create="false" />
+	</metadatafield>
+	<metadatafield>
+		<fieldName>GACSTerms</fieldName>
+		<mandatory>true</mandatory>
+		<dataType>String</dataType>
+		<maxOccurs>*</maxOccurs>
+		<defaultValue />
+		<note>Select one or more terms</note>
+		<vocabulary isMultiSelection="true">
+			<vocabularyField>GACS.Term1</vocabularyField>
+			<vocabularyField>GACS.Term2</vocabularyField>
+			<vocabularyField>GACS.Term3</vocabularyField>
+			<vocabularyField>GACS.Term4</vocabularyField>
+			<vocabularyField>GACS.Term5</vocabularyField>
+			<vocabularyField>GACS.Term6</vocabularyField>
+			<vocabularyField>GACS.Term7</vocabularyField>
+			<vocabularyField>GACS.Term8</vocabularyField>
+			<vocabularyField>GACS.Term9</vocabularyField>
+		</vocabulary>
+		<validator />
+		<tagging create="true">onValue</tagging>
+		<grouping create="false" />
+	</metadatafield>
+</metadataformat>