Framework configuration refactoring major changes

src/main/java/accounts/FrameworkUserManager.java
- minor changes of some get functions
- added a rollback of virtuoso user creation if the graph insert has an error
- added a missing prefix to  getPrefixes() (I was having an error because a default prefix : was missing)

src/main/java/authentication/FrameworkConfiguration.java
- this file changed a lot to be able to read configuration from web.xml and from ttl files

src/main/java/accounts/VirtuosoUserManager.java
- irrelevant formatting changes

src/main/java/authentication/web/AuthenticationServlet.java
src/main/java/authentication/web/GraphManagerServlet.java
src/main/java/authentication/web/HttpRequestManager.java
src/main/java/authentication/web/UserManagerServlet.java
src/main/java/authentication/web/VirtuosoProxy.java
- added a exception handle
- added the context parameter to the Framework configuration

src/main/java/authentication/web/RdfStoreProxy.java
- added the context parameter to the Framework configuration
- I started checking how to do here the exception in order that the webapp provides more information about errors.. but not finished
- do some formatting

src/main/webapp/WEB-INF/web.xml
- lots of changes.. some configuration is to be handled here : namespaces, Uris, and email settings

src/main/resources/*
- replaced all configuration files
- these files are copied to classes directory when the application is deployed, and then, they can be read by the configuration class

src/main/webapp/js/config.js

- these file should not hava anymore any configuration for the endopoints

- I have to still change it to be able to take namespaces form the server.. thus some configuration is still there

src/main/java/accounts/FrameworkUserManager.java

@@ -10,6 +10,7 @@
 import util.ObjectPair;
 import util.RandomStringGenerator;
 
+import java.io.IOException;
 import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -61,13 +62,13 @@ public void createUser(String name, String password, String email) throws Except
             counter++;
         } while (error && counter<10);
         //grant SPARQL_UPDATE role to created Virtuoso user
-        // todo users with only read access?
+        //TODO: users with only read access?
         rdfStoreUserManager.grantRole(rdfStoreUser, "SPARQL_UPDATE");
 
         //create setting graph for user
         String userSettingsGraphURI = frameworkConfig.getResourceNamespace() + URLEncoder.encode(name, "UTF-8") + "/settingsGraph";
         // grant write permissions to framework - otherwise framework fails to create graph
-        rdfStoreUserManager.setRdfGraphPermissions(frameworkConfig.getSparqlFrameworkLogin(), userSettingsGraphURI, 3);
+        rdfStoreUserManager.setRdfGraphPermissions(frameworkConfig.getAuthSparqlUser(), userSettingsGraphURI, 3);
         rdfStoreManager.createGraph(userSettingsGraphURI);
         //grant write permissions to user
         rdfStoreUserManager.setRdfGraphPermissions(rdfStoreUser, userSettingsGraphURI, 3); // todo deny access for user?
@@ -76,8 +77,15 @@ public void createUser(String name, String password, String email) throws Except
         String query = getPrefixes() + "\n"
                 + "INSERT INTO <" + userSettingsGraphURI + "> {?s ?p ?o} "
                 + "WHERE {GRAPH <" + frameworkConfig.getInitialSettingsGraph() + "> {?s ?p ?o} }";
-        rdfStoreManager.execute(query, jsonResponseFormat);
-
+        try{
+        	rdfStoreManager.execute(query, jsonResponseFormat);
+        }
+        catch(IOException e)
+        {	// failed to write user graph 
+        	// rollback actions:
+            rdfStoreUserManager.dropUser(rdfStoreUser);
+            throw e;
+        }
         // write user account to accounts graph
         query = getPrefixes() + "\n"
                 + "INSERT DATA { GRAPH <" + frameworkConfig.getAccountsGraph() + "> {\n"
@@ -90,8 +98,17 @@ public void createUser(String name, String password, String email) throws Except
                 + " :" + name + " foaf:mbox <mailto:" + email + "> .\n"
                 + " :" + name + " dcterms:created \"" + ISO8601Utils.format(new Date()) + "\"^^xsd:date .\n"
                 + "} }";
-        rdfStoreManager.execute(query, jsonResponseFormat);
-
+
+        try{
+        	rdfStoreManager.execute(query, jsonResponseFormat);
+        }
+        catch(IOException e)
+        {	// failed to register user in to the accounts graph
+        	// rollback actions:
+            rdfStoreUserManager.dropUser(rdfStoreUser);
+            rdfStoreManager.dropGraph(userSettingsGraphURI);
+            throw e;
+        }
         //todo delete Virtuoso user if failed to write account triples
     }
 
@@ -623,12 +640,12 @@ public String getDescribedIn(String graph) throws Exception {
 
     private String getPrefixes() {
         if (prefixes==null) {
-            prefixes = "PREFIX : <" + frameworkConfig.getAccountsNamespace() + ">\n"
-                    + "PREFIX ao: <" + frameworkConfig.getAccountsOntologyNamespace() + ">\n"
+            prefixes ="PREFIX : <" + frameworkConfig.getResourceNamespace() + ">\n" 
+            		+ "PREFIX ao: <" + frameworkConfig.getAccountsOntologyNamespace() + ">\n"
+            		+ "PREFIX gkg: <"+ frameworkConfig.getFrameworkOntologyNS() +">\n"
                     + "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
                     + "PREFIX user: <http://schemas.talis.com/2005/user/schema#>\n"
                     + "PREFIX sd: <http://www.w3.org/ns/sparql-service-description#>\n"
-                    + "PREFIX gkg: <http://generator.geoknow.eu/ontology/>\n"
                     + "PREFIX acl: <http://www.w3.org/ns/auth/acl#>\n"
                     + "PREFIX foaf: <http://xmlns.com/foaf/0.1/>\n"
                     + "PREFIX dcterms: <http://purl.org/dc/terms/>";
@@ -662,7 +679,7 @@ private boolean checkUserExists(String username, String email) throws Exception
 
     private Collection<String> getSettingsGraphs() throws Exception {
         Collection<String> settingsGraphList = new ArrayList<String>();
-        settingsGraphList.add(frameworkConfig.getDefaultSettingsGraph());
+        settingsGraphList.add(frameworkConfig.getSettingsGraph());
         String query = getPrefixes() + "\n"
                 + " SELECT DISTINCT ?sg FROM <" + frameworkConfig.getAccountsGraph() + "> "
                 + " WHERE { ?account ao:settingsGraph ?sg }";

src/main/java/accounts/VirtuosoUserManager.java

@@ -12,6 +12,12 @@ public class VirtuosoUserManager implements UserManager {
     private String password;
     private Connection connection;
 
+    /**
+     * This class manages the User creation in virtuoso for authentication and graph access control
+     * @param connectionString 	Connection string to Virtuoso
+     * @param user 				Virtuoso user
+     * @param password 			Virtuoso password
+     */
     public VirtuosoUserManager(String connectionString, String user, String password) {
         this.connectionString = connectionString;
         this.user = user;
@@ -31,7 +37,7 @@ public void dropUser(String name) throws Exception {
 
     @Override
     public void grantRole(String user, String role) throws Exception {
-        executeUpdate(getConnection(), "GRANT " + role + " TO \"" + user + "\"");
+        	executeUpdate(getConnection(), "GRANT " + role + " TO \"" + user + "\"");
     }
 
     @Override