merged and updated stuff with new configuration

Author: alegrm

src/main/java/authentication/web/HttpRequestManager.java

@@ -14,8 +14,6 @@
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.log4j.Logger;
 
-import util.UnsupportedAuthenticationSchema;
-
 public class HttpRequestManager {
 
     private static final Logger log = Logger
@@ -38,7 +36,7 @@ public static String executePost(String url, String urlParameters)
     }
 
     public static String executePost(String url, String urlParameters,
-	    String username, String password) throws IOException {
+	    String username, String password) throws Exception {
 	// TODO: May be try to do Authorized post by default first ??? to avoid
 	// doing two queries? are all the queries made by the generator will use
 	// the
@@ -73,10 +71,8 @@ public static String executePost(String url, String urlParameters,
 		    throw new HTTPException(responseCode);
 		}
 	    } else
-		throw new UnsupportedAuthenticationSchema(
-			"Unsupported authentication type: "
-				+ wwwAuthenticateHeader
-					.getAuthenticationScheme());
+		throw new Exception("Unsupported authentication type: "
+			+ wwwAuthenticateHeader.getAuthenticationScheme());
 	case 400: // bad request
 	    log.error(connection.getResponseCode() + "\n\t "
 		    + connection.getResponseMessage() + "\n\t url:" + url
@@ -119,8 +115,7 @@ private static HttpURLConnection sendPost(String url, String urlParameters)
 
     private static HttpURLConnection sendAuthorizedPost(String url,
 	    String urlParameters, WWWAuthenticateHeader wwwAuthenticateHeader,
-	    String username, String password) throws IOException,
-	    UnsupportedAuthenticationSchema {
+	    String username, String password) throws Exception {
 	log.debug("Execute authorized POST to " + url);
 	URL targetURL = new URL(url);
 	HttpURLConnection connection = (HttpURLConnection) targetURL
@@ -178,13 +173,11 @@ private static WWWAuthenticateHeader getWWWAuthenticationHeader(
 
     private static String getDigestAuthorizationProperty(String endpoint,
 	    WWWAuthenticateHeader wwwAuthenticateHeader, String username,
-	    String password, String requestMethod)
-	    throws UnsupportedAuthenticationSchema {
+	    String password, String requestMethod) throws Exception {
 	if (!wwwAuthenticateHeader.isDigest())
-	    throw new UnsupportedAuthenticationSchema(
-		    "Unexpected authentication scheme "
-			    + wwwAuthenticateHeader.getAuthenticationScheme()
-			    + ", Digest expected");
+	    throw new Exception("Unexpected authentication scheme "
+		    + wwwAuthenticateHeader.getAuthenticationScheme()
+		    + ", Digest expected");
 	String nc = "00000001";
 	String cnonce = DigestUtils.md5Hex(Long.toString(System
 		.currentTimeMillis()));

src/main/java/rest/Configuration.java

@@ -53,6 +53,8 @@ public Response getConfiguration(@Context ServletContext context) {
 		    frameworkConf.getPublicSparqlEndpoint());
 	    config.addProperty("authSparqlEndpoint",
 		    frameworkConf.getAuthSparqlEndpoint());
+	    config.addProperty("flagPath",
+		    context.getInitParameter("framework-setup-path"));
 
 	} catch (IOException e) {
 	    log.error(e);

src/main/java/rest/WorkbenchSetup.java

@@ -25,6 +25,9 @@ public class WorkbenchSetup {
 
     private static final Logger log = Logger.getLogger(WorkbenchSetup.class);
 
+    private @Context
+    ServletContext context;
+
     /**
      * Get the status of the setup
      * 
@@ -33,7 +36,8 @@ public class WorkbenchSetup {
     @GET
     @Produces(MediaType.TEXT_PLAIN)
     public Response isSetuUp() {
-	RDFStoreSetupManager setupManager = new RDFStoreSetupManager();
+	RDFStoreSetupManager setupManager = new RDFStoreSetupManager(
+		context.getInitParameter("framework-setup-path"));
 	return Response.ok(setupManager.isSetUp(), MediaType.TEXT_PLAIN)
 		.build();
     }
@@ -46,7 +50,8 @@ public Response isSetuUp() {
      */
     @POST
     public Response reset(@Context ServletContext context) {
-	RDFStoreSetupManager setupManager = new RDFStoreSetupManager();
+	RDFStoreSetupManager setupManager = new RDFStoreSetupManager(
+		context.getInitParameter("framework-setup-path"));
 	FrameworkConfiguration frameworkConfiguration = null;
 	try {
 	    frameworkConfiguration = FrameworkConfiguration
@@ -75,7 +80,8 @@ public Response reset(@Context ServletContext context) {
      */
     @PUT
     public Response initialize(@Context ServletContext context) {
-	RDFStoreSetupManager setupManager = new RDFStoreSetupManager();
+	RDFStoreSetupManager setupManager = new RDFStoreSetupManager(
+		context.getInitParameter("framework-setup-path"));
 
 	if (setupManager.isSetUp()) {
 	    log.info("System is already set up. To reset system use PUT method");

src/main/java/setup/RDFStoreSetupManager.java

@@ -33,11 +33,11 @@ public class RDFStoreSetupManager {
     private static final Logger log = Logger
 	    .getLogger(RDFStoreSetupManager.class);
 
-    private File catalinaBase = new File(System.getProperty("catalina.base"))
-	    .getAbsoluteFile();
-    // TODO: move a file outside the application (i.e. /etc/ontos)
-    private File initFile = new File(catalinaBase.getAbsoluteFile(),
-	    "webapps/generator/WEB-INF/init.txt");
+    private File initFile;
+
+    public RDFStoreSetupManager(String path) {
+	initFile = new File(path, "init.txt");
+    }
 
     // set rdf store up using configuration; if reset==true than clear (using
     // config) rdf store and set up once again
@@ -165,6 +165,7 @@ public void setUp(FrameworkConfiguration config, boolean reset)
 	queryString = "PREFIX foaf:<http://xmlns.com/foaf/0.1/> "
 		+ "PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
 		+ "PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> "
+		+ "PREFIX void:    <http://rdfs.org/ns/void#> "
 		+ "PREFIX lds:<http://stack.linkeddata.org/ldis-schema/>"
 		+ " CONSTRUCT   { <"
 		+ config.getFrameworkUri()
@@ -173,17 +174,29 @@ public void setUp(FrameworkConfiguration config, boolean reset)
 		+ config.getFrameworkUri()
 		+ "> lds:integrates ?component ."
 		+ "?component rdfs:label ?label . ?component rdf:type ?type . "
-		+ "?component lds:providesService ?service . ?service rdf:type ?servicetype ."
-		+ "?service lds:serviceUrl ?serviceUrl .} "
+		+ "?component lds:providesService ?service . "
+		+ "?service rdf:type ?servicetype ."
+		+ "?service rdfs:label ?servicelabel ."
+		+ "?service void:sparqlEndpoint ?serviceendpoint ."
+		+ "?service lds:serviceUrl ?serviceUrl ."
+		+ "} "
 		+ " WHERE  { <"
 		+ config.getFrameworkUri()
 		+ "> ?p ?o ."
 		+ "<"
 		+ config.getFrameworkUri()
 		+ "> lds:integrates ?component ."
 		+ "?component rdfs:label ?label . ?component rdf:type ?type . "
-		+ "?component lds:providesService ?service . ?service rdf:type ?servicetype ."
-		+ "?service lds:serviceUrl ?serviceUrl .}";
+		+ "?component lds:providesService ?service . "
+		+ "?service rdf:type ?servicetype ."
+		+ "?service lds:serviceUrl ?serviceUrl ."
+		+ "OPTIONAL { "
+		+ "   ?service rdfs:label ?servicelabel ."
+		+ "   ?service void:sparqlEndpoint ?serviceendpoint "
+		+ "  }"
+		+ "}";
+
+	log.debug(queryString);
 	QueryExecution qexec = QueryExecutionFactory.create(queryString,
 		configurationModel);
 	Model triples = qexec.execConstruct();
@@ -239,10 +252,16 @@ public void setUp(FrameworkConfiguration config, boolean reset)
 	}
 	qexec.close();
 
-	boolean created = initFile.createNewFile();
-	if (!created)
-	    throw new Exception("Failed to create init flag file "
-		    + initFile.getPath());
+	try {
+	    boolean created = initFile.createNewFile();
+	    if (!created) {
+		log.error("Failed to create init flag file "
+			+ initFile.getPath());
+	    }
+	} catch (Exception e) {
+	    log.error("Failed to create init flag file " + initFile.getPath());
+	    throw new Exception(e);
+	}
 
 	log.info("System was initialized successfully.");
     }
@@ -290,6 +309,8 @@ public void clear(FrameworkConfiguration config) throws Exception {
     }
 
     public boolean isSetUp() {
+	log.info("Checking if " + initFile.getPath() + initFile.getName()
+		+ " exists");
 	return initFile.exists();
     }
 }

src/main/java/util/UnsupportedAuthenticationSchema.java

@@ -1,18 +1,13 @@
 @prefix :        <http://***PROJECT_URL***/resource/> .
-@prefix d2rq:    <http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#> .
-@prefix dcmit:   <http://purl.org/dc/dcmitype/> .
 @prefix dcterms:  <http://purl.org/dc/terms/> .
 @prefix lds:     <http://stack.linkeddata.org/ldis-schema/> .
-@prefix owl:     <http://www.w3.org/2002/07/owl#> .
 @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix schema:  <http://schema.org/> .
 @prefix sd:      <http://www.w3.org/ns/sparql-service-description#> .
 @prefix void:    <http://rdfs.org/ns/void#> .
 @prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
 @prefix foaf:    <http://xmlns.com/foaf/0.1/> .
 @prefix ontos:     <http://ldiw.ontos.com/ontology/> .
-@prefix acl:     <http://www.w3.org/ns/auth/acl#> .
 
 ########### ABOUT THIS FILE #############################################################
 # This file contains the default set-up of components in the framework;