sparql functionalities improved

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>es.upm.fi.oeg</groupId>
 	<artifactId>wothive</artifactId>
-	<version>0.2.0</version>
+	<version>0.2.1</version>
 	<name>Directory for the Web of Things</name>
 
 	<properties>

src/main/java/directory/Utils.java

@@ -46,7 +46,7 @@ public class Utils {
 	public static final String METHOD_PUT = "PUT";
 
 	public static final String MIME_DIRECTORY_ERROR = "application/problem+json";
-	protected static final String DIRECTORY_VERSION = "WoTHive/0.2.0";
+	protected static final String DIRECTORY_VERSION = "WoTHive/0.2.1";
 	protected static final String WOT_DIRECTORY_LOGO = "\n"+
 			"██╗    ██╗ ██████╗ ████████╗\n" + 
 			"██║    ██║██╔═══██╗╚══██╔══╝\n" + 

src/main/java/directory/configuration/DirectoryConfiguration.java

@@ -67,10 +67,9 @@ public void setValidation(ValidationConfiguration validation) {
 
 	public DirectoryConfiguration createDefault() {
 		try {
-			this.triplestore = new TriplestoreConfiguration(DEFAULT_TRIPLESTORE_ENDPOINT, DEFAULT_TRIPLESTORE_ENDPOINT,
-					true);
+			this.triplestore = new TriplestoreConfiguration(DEFAULT_TRIPLESTORE_ENDPOINT, DEFAULT_TRIPLESTORE_ENDPOINT);
 			this.service = new ServiceConfiguration("https://oeg.fi.upm.es/wothive/", 9000, 200, 2, 30000, 100, "./events.json");
-			this.validation = new ValidationConfiguration(true, true, "./schema.json", "./shape.ttl");
+			this.validation = new ValidationConfiguration(false, true, "./schema.json", "./shape.ttl");
 		} catch (Exception e) {
 			Directory.LOGGER.error(e.toString());
 		}

src/main/java/directory/configuration/TriplestoreConfiguration.java

@@ -4,35 +4,37 @@
 import java.net.URISyntaxException;
 
 import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
 import com.google.gson.JsonObject;
 
+import directory.Directory;
 import directory.exceptions.ConfigurationException;
 
 public class TriplestoreConfiguration extends AbstractConfiguration{
 
 	// -- Attributes
 	private URI updateEnpoint = null;
 	private URI queryEnpoint = null;
-	private Boolean queryUsingGET = true;
+	private String username = null;
+	private String password = null;
 
 	// -- Constructors
 
 	public TriplestoreConfiguration() {
 		super();
 	}
 
-	public TriplestoreConfiguration( String queryEnpoint, String updateEnpoint, Boolean queryUsingGET) throws URISyntaxException {
+	public TriplestoreConfiguration( String queryEnpoint, String updateEnpoint) throws URISyntaxException {
 		super();
 		this.updateEnpoint = new URI(updateEnpoint);
 		this.queryEnpoint = new URI(queryEnpoint);
-		this.queryUsingGET = queryUsingGET;
+
 	}
 
-	public TriplestoreConfiguration( URI queryEnpoint, URI updateEnpoint, Boolean queryUsingGET) {
+	public TriplestoreConfiguration( URI queryEnpoint, URI updateEnpoint) {
 		super();
 		this.updateEnpoint = updateEnpoint;
 		this.queryEnpoint = queryEnpoint;
-		this.queryUsingGET = queryUsingGET;
 	}
 
 	// -- Getters & Setters
@@ -52,17 +54,25 @@ public URI getQueryEnpoint() {
 	public void setQueryEnpoint(URI queryEnpoint) {
 		this.queryEnpoint = queryEnpoint;
 	}
+
+	public String getUsername() {
+		return username;
+	}
 
-	public Boolean getQueryUsingGET() {
-		return queryUsingGET;
+	public void setUsername(String username) {
+		this.username = username;
 	}
 
-	public void setQueryUsingGET(Boolean queryUsingGET) {
-		this.queryUsingGET = queryUsingGET;
+	public String getPassword() {
+		return password;
+	}
+
+	public void setPassword(String password) {
+		this.password = password;
 	}
 
 	// Serialization methods
-		
+
 	public static TriplestoreConfiguration serialiseFromJson(String rawJson) {
 		JsonObject body = null;
 		try {
@@ -75,9 +85,14 @@ public static TriplestoreConfiguration serialiseFromJson(String rawJson) {
 
 		validatePayload( body, "updateEnpoint", ConfigurationException.EXCEPTION_CODE_2, "Provided JSON lacks of mandatory key \"updateEnpoint\" with the triplestore endpoint for updating data");
 		validatePayload( body, "queryEnpoint", ConfigurationException.EXCEPTION_CODE_2, "Provided JSON lacks of mandatory key \"queryEnpoint\" with the triplestore endpoint for querying data");
-		validatePayload( body, "queryUsingGET", ConfigurationException.EXCEPTION_CODE_2, "Provided JSON lacks of mandatory key \"queryUsingGET\" with a boolean value indicating if the communication with the triplestore shuld be done using the GET method. If false the directory will use POST.");
+		if((!body.has("username") && body.has("password")) ||(body.has("username") && !body.has("password")))
+			throw new ConfigurationException(ConfigurationException.EXCEPTION_CODE_2, "Provided JSON must have both optional keywords \"username\" and \"passwords\" in order to connect to a remote triple store");
+		if(!body.has("username"))
+			Directory.LOGGER.info("No 'username' has been provided for the remote triple store");
+		if(!body.has("password"))
+			Directory.LOGGER.info("No 'password' has been provided for the remote triple store");
 
-		return (new Gson()).fromJson(body, TriplestoreConfiguration.class);
+		return (new GsonBuilder().serializeNulls().create()).fromJson(body, TriplestoreConfiguration.class);
 	}
 
 

src/main/java/directory/things/Things.java

@@ -39,12 +39,13 @@ public class Things {
 
 	public static String TDD_RAW_CONTEXT = "https://raw.githubusercontent.com/oeg-upm/wot-hive/AndreaCimminoArriaga-tdd-context/tdd.jsonld";
 
-	protected static String inject(JsonElement value, String injection) {
+	protected static String inject(JsonObject json, String key, String injection) {
+		JsonElement value = json.deepCopy().get(key);
 		JsonArray values = new JsonArray();
 		if(value instanceof JsonArray) {
 			values = value.getAsJsonArray();
 		}else if(value instanceof JsonPrimitive) {
-			values.add(value.toString());
+			values.add(value);
 		}
 		values.add(injection);
 		return values.toString();

src/main/java/directory/things/ThingsService.java

@@ -6,6 +6,9 @@
 import java.util.List;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.sparql.resultset.ResultsFormat;
+
+import com.google.gson.Gson;
+import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
 import directory.Utils;
 import directory.events.DirectoryEvent;
@@ -93,20 +96,20 @@ private static String prepareManagementInformation(JsonObject td, String graphId
 
 		String rawContext = td.get("@context").toString();
 		if(Utils.InjectRegistrationInfo)
-			rawContext = Things.inject(td.get("@context"), Things.TDD_RAW_CONTEXT);
+			rawContext = Things.inject(td, "@context", Things.TDD_RAW_CONTEXT).toString();
 
 		String frame = Utils.buildEncoded(" { \"@context\" : ",rawContext , ", \"@type\" : \"Thing\" }");
 		if(td.has("@type") && hasTypeThing) {
 			frame = Utils.buildEncoded(" { \"@context\" : ",rawContext, ", \"@type\" : ",td.get("@type").toString()," }");
 		}else if(td.has("@type") && !hasTypeThing) {
-			frame = Utils.buildEncoded(" { \"@context\" : ",rawContext , ", \"@type\" : ",Things.inject(td.get("@type"), "Thing")," }");
+			frame = Utils.buildEncoded(" { \"@context\" : ",rawContext , ", \"@type\" : ",Things.inject(td, "@type", "Thing").toString()," }");
 		}
 		return Utils.buildMessage("GRAPH <",MANAGEMENT_GRAPH,"> { <",graphId,"> <hive:b64:security> \"",security,"\" . <",graphId,"> <hive:b64:frame> \"",frame,"\" . <",graphId,"> <hive:b64:type> \"",hasTypeThing.toString(),"\"}");
 	}
 
 	private static void enrichTd(JsonObject td) {
 		if(!Things.hasThingType(td))
-			Things.inject(td.get("@type"), "Thing");
+			td.add("@type", (new Gson()).fromJson( Things.inject(td, "@type", "Thing"), JsonElement.class));
 		if(Utils.InjectRegistrationInfo) {
 			//TODO:
 		}
@@ -118,14 +121,18 @@ private static void enrichTd(JsonObject td) {
 	 * @return returns a JSON-LD 1.1 representation of the Thing
 	 */
 	protected static final JsonObject retrieveThing(String id) {
+		System.out.println(id);
 		String graphId = createGraphId(id);
 		if(!exists(graphId))
 			throw new ThingException(Utils.buildMessage("Requested Thing not found"));
 
 		// Retrieve meta information of Thing
-		String query = Utils.buildMessage("SELECT ?security ?frame ?type WHERE { <",graphId,"> <hive:b64:security> ?security ; <hive:b64:frame> ?frame; <hive:b64:type> ?type . } ");
+		String query = Utils.buildMessage("SELECT ?security ?frame ?type WHERE { GRAPH <",MANAGEMENT_GRAPH, "> { <",graphId,"> <hive:b64:security> ?security ; <hive:b64:frame> ?frame; <hive:b64:type> ?type . } }");
 		ByteArrayOutputStream baos = Sparql.query(query, ResultsFormat.FMT_RS_CSV);
-		String[] rawResponse = baos.toString().replace("security,frame,type", "").trim().split(",");
+		String baosRaw = baos.toString().replace("security,frame,type", "").trim();
+		if(baosRaw.isEmpty())
+			throw new ThingException(Utils.buildMessage("Requested Thing not found"));
+		String[] rawResponse = baosRaw.split(",");
 		String security = new String(Base64.getDecoder().decode(rawResponse[0].getBytes()));
 		String frame = new String(Base64.getDecoder().decode(rawResponse[1].getBytes()));
 		Boolean type = Boolean.valueOf(new String(rawResponse[2]));
@@ -140,7 +147,7 @@ protected static final JsonObject retrieveThing(String id) {
 
 		if(!type) 
 			Things.cleanThingType(response);
-
+		System.out.println(response);
 		return response;
 	}
 

src/main/java/directory/triplestore/Sparql.java

@@ -2,6 +2,12 @@
 
 import java.io.ByteArrayOutputStream;
 
+import org.apache.http.auth.AuthScope;
+import org.apache.http.auth.Credentials;
+import org.apache.http.auth.UsernamePasswordCredentials;
+import org.apache.http.impl.client.BasicCredentialsProvider;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
 import org.apache.jena.query.Dataset;
 import org.apache.jena.query.DatasetFactory;
 import org.apache.jena.query.Query;
@@ -20,6 +26,7 @@
 import org.apache.jena.update.UpdateFactory;
 import org.apache.jena.update.UpdateProcessor;
 import org.apache.jena.update.UpdateRequest;
+import org.eclipse.jetty.client.HttpClient;
 
 import directory.Directory;
 import directory.Utils;
@@ -43,11 +50,20 @@ public static ResultsFormat guess(String str) {
 	// query methods
 
 	public static ByteArrayOutputStream query(String sparql, ResultsFormat format) {
+		return  query(sparql, format, Directory.getConfiguration().getTriplestore().getQueryEnpoint().toString(), Directory.getConfiguration().getTriplestore().getUsername(), Directory.getConfiguration().getTriplestore().getPassword());
+	}
+
+	public static ByteArrayOutputStream query(String sparql, ResultsFormat format, String endpoint, String username, String password) {
 
 		ByteArrayOutputStream stream = new ByteArrayOutputStream();
 		try {
 			Query query = QueryFactory.create(sparql) ;
-	        QueryExecution qexec = QueryExecutionFactory.sparqlService(Directory.getConfiguration().getTriplestore().getQueryEnpoint().toString(), query);        
+			QueryExecution qexec = QueryExecutionFactory.sparqlService(endpoint, query);
+			if(username!= null && password!=null) {
+				CloseableHttpClient client = connectPW(endpoint, username,password);
+				qexec = QueryExecutionFactory.sparqlService(Directory.getConfiguration().getTriplestore().getQueryEnpoint().toString(), query, client);        
+			}
+
 			if(query.isSelectType()) {
 				ResultSetFormatter.output(stream, qexec.execSelect(), format);
 	        }else if(query.isAskType()) {
@@ -81,12 +97,27 @@ public static ByteArrayOutputStream query(String sparql, ResultsFormat format) {
         return stream;
 	}
 
+	public static CloseableHttpClient connectPW(String URL, String user, String password) {
+		  BasicCredentialsProvider credsProvider = new BasicCredentialsProvider();
+		  Credentials credentials = new UsernamePasswordCredentials(user, password);
+		  credsProvider.setCredentials(AuthScope.ANY, credentials);
+		  return  HttpClients.custom().setDefaultCredentialsProvider(credsProvider).build();
+
+	}
 
+	public static void update(String sparql ) { 
+		update( sparql,  Directory.getConfiguration().getTriplestore().getUpdateEnpoint().toString(), Directory.getConfiguration().getTriplestore().getUsername(), Directory.getConfiguration().getTriplestore().getPassword());
+	}
 
-	public static void update(String sparql)  {
+	public static void update(String sparql, String endpoint, String username, String password)  {
 		try {
 			UpdateRequest updateRequest = UpdateFactory.create(sparql);
-			UpdateProcessor updateProcessor = UpdateExecutionFactory.createRemote(updateRequest, Directory.getConfiguration().getTriplestore().getUpdateEnpoint().toString());
+			UpdateProcessor updateProcessor = UpdateExecutionFactory.createRemote(updateRequest, endpoint);
+
+			if(username!=null && password!=null) {
+				CloseableHttpClient client = connectPW(endpoint,username, password);
+				updateProcessor = UpdateExecutionFactory.createRemote(updateRequest, endpoint, client);
+			}	
 			updateProcessor.execute();
 		 }catch(QueryException e){
 	        throw new RemoteSparqlEndpointException(e.toString()); // syntax error