Merge branch 'master' of [email protected]:ontos-lds.git

Conflicts:
	src/main/resources/framework-components.ttl

Author: jj

.gitignore

@@ -1,3 +1,7 @@
+#Framework configuration files
+/src/main/webapp/WEB-INF/web.xml
+/src/main/resources/framework-configuration.ttl
+
 #Mac
 .DS_Store
 

README.md

@@ -16,7 +16,9 @@ These option will not install any integrated component from the stack and you re
 
 1. Make a copy of the `src/main/resources/framework-configuration-template.ttl` to `src/main/resources/framework-configuration.ttl` and provide the ***REMOVED*** data.
 
-1. Make a copy of the `src/main/webapp/WEB-INF/web-template.xml` to `src/main/webapp/WEB-INF/web.xml` and provide the ***REMOVED*** data.
+2. Have a clean triple store and make sure to have a user create in the lds:StorageService, the lds:SecuredSPARQLEndPointService user will be automatically created
+
+3. Make a copy of the `src/main/webapp/WEB-INF/web-template.xml` to `src/main/webapp/WEB-INF/web.xml` and provide the ***REMOVED*** data.
 
 
 Note that the endpoint has to support [UPDATE](http://www.w3.org/TR/2013/REC-sparql11-update-20130321/) service and [Graph Store HTTP Protocol](http://www.w3.org/TR/2013/REC-sparql11-http-rdf-update-20130321/) 

src/main/java/accounts/VirtuosoUserManager.java

@@ -13,8 +13,7 @@ public class VirtuosoUserManager implements UserManager {
   private Connection connection;
 
   /**
-   * This class manages the User creation in virtuoso for authentication and
-   * graph access control
+   * This class manages the User creation in virtuoso for authentication and graph access control
    * 
    * @param connectionString
    *          Connection string to Virtuoso
@@ -30,46 +29,62 @@ public VirtuosoUserManager(String connectionString, String user, String password
   }
 
   @Override
-  public void createUser(String name, String password) throws Exception {
+  public void createUser(String name, String password) throws ClassNotFoundException, SQLException {
     executeUpdate(getConnection(), "DB.DBA.USER_CREATE('" + name + "', '" + password + "')");
     // executeUpdate(getConnection(), "USER_SET_OPTION('" + name +
     // "', 'DAV_ENABLE', 1)");
   }
 
   @Override
-  public void dropUser(String name) throws Exception {
+  public void dropUser(String name) throws ClassNotFoundException, SQLException {
     executeUpdate(getConnection(), "USER_DROP('" + name + "', 1)");
   }
 
   @Override
-  public void grantRole(String user, String role) throws Exception {
+  public void grantRole(String user, String role) throws ClassNotFoundException, SQLException {
     executeUpdate(getConnection(), "GRANT " + role + " TO \"" + user + "\"");
   }
 
   @Override
-  public void setDefaultRdfPermissions(String user, int permissions) throws Exception {
+  public void setDefaultRdfPermissions(String user, int permissions) throws ClassNotFoundException,
+      SQLException {
     executeUpdate(getConnection(), "DB.DBA.RDF_DEFAULT_USER_PERMS_SET ('" + user + "', "
         + permissions + ")");
   }
 
   @Override
-  public void setRdfGraphPermissions(String user, String graph, int permissions) throws Exception {
+  public void setRdfGraphPermissions(String user, String graph, int permissions)
+      throws ClassNotFoundException, SQLException {
     executeUpdate(getConnection(), "DB.DBA.RDF_GRAPH_USER_PERMS_SET ('" + graph + "', '" + user
         + "', " + permissions + ")");
   }
 
   @Override
-  public void deleteRdfGraphPermissions(String user, String graph) throws Exception {
+  public void deleteRdfGraphPermissions(String user, String graph) throws ClassNotFoundException,
+      SQLException {
     executeUpdate(getConnection(), "DB.DBA.RDF_GRAPH_USER_PERMS_DEL ('" + graph + "', '" + user
         + "')");
   }
 
   @Override
-  public void setDefaultGraphPermissions(String graph, int permissions) throws Exception {
+  public void setDefaultGraphPermissions(String graph, int permissions)
+      throws ClassNotFoundException, SQLException {
     executeUpdate(getConnection(), "DB.DBA.RDF_GRAPH_USER_PERMS_SET ('" + graph + "', 'nobody', "
         + permissions + ")");
   }
 
+  /**
+   * This function grant L_O_LOOK in virtuoso which was required to solve the error: Virtuoso 42000
+   * Error SR186: No permission to execute dpipe DB.DBA.L_O_LOOK with user ID 106, group ID 106
+   * 
+   * @param user
+   * @throws ClassNotFoundException
+   * @throws SQLException
+   */
+  public void grantLOLook(String user) throws ClassNotFoundException, SQLException {
+    executeUpdate(getConnection(), "GRANT EXECUTE ON DB.DBA.L_O_LOOK TO '" + user + "'");
+  }
+
   private Connection getConnection() throws ClassNotFoundException, SQLException {
     if (connection == null || connection.isClosed()) {
       Class.forName(jdbcDriver);

src/main/java/authentication/FrameworkConfiguration.java

@@ -48,6 +48,7 @@ public class FrameworkConfiguration {
   private String settingsGraph = "";
   private String initialSettingsGraph = "";
   private String groupsGraph = "";
+  private String frameworkUri;
 
   private static FrameworkConfiguration instance;
 
@@ -75,7 +76,7 @@ public static synchronized FrameworkConfiguration getInstance(ServletContext con
       String accountsOntologyFile = "framework-accounts-ontology.ttl";
 
       // initialize parameters from context
-      String frameworkUri = context.getInitParameter("framework-uri");
+      instance.frameworkUri = context.getInitParameter("framework-uri");
 
       instance.setFrameworkOntologyNS(context.getInitParameter("framework-ontology-ns"));
       instance.setAccountsOntologyNamespace(context.getInitParameter("accounts-ns"));
@@ -96,11 +97,10 @@ public static synchronized FrameworkConfiguration getInstance(ServletContext con
       } catch (RiotException e) {
         throw new IOException("Malformed " + configurationFile + " file");
       }
-      // get and set the properties framework configuration (endpoints and
-      // credentials)
+      // get the endpoint URL to use for the framework
       String query = "PREFIX lds: <http://stack.linkeddata.org/ldis-schema/> "
-          + " SELECT ?endpoint WHERE {" + " <" + frameworkUri + ">  lds:integrates ?component ."
-          + " ?component lds:providesService ?service ."
+          + " SELECT ?endpoint WHERE {" + " <" + instance.getFrameworkUri()
+          + ">  lds:integrates ?component ." + " ?component lds:providesService ?service ."
           + " ?service a lds:SPARQLEndPointService ." + " ?service lds:serviceUrl ?endpoint  }";
 
       QueryExecution qexec = QueryExecutionFactory.create(query, configurationModel);
@@ -113,8 +113,9 @@ public static synchronized FrameworkConfiguration getInstance(ServletContext con
       }
       qexec.close();
 
+      // get the endpoint for authenticated users, and user and password of the system framework
       query = "PREFIX lds: <http://stack.linkeddata.org/ldis-schema/>"
-          + " SELECT ?endpoint ?user ?password WHERE {" + " <" + frameworkUri
+          + " SELECT ?endpoint ?user ?password WHERE {" + " <" + instance.getFrameworkUri()
           + ">  lds:integrates ?component ." + " ?component lds:providesService ?service ."
           + " ?service a lds:SecuredSPARQLEndPointService ."
           + " ?service lds:serviceUrl ?endpoint ." + " ?service lds:user ?user ."
@@ -134,7 +135,7 @@ public static synchronized FrameworkConfiguration getInstance(ServletContext con
 
       // get and set the database configuration (Virtuoso)
       query = "PREFIX lds: <http://stack.linkeddata.org/ldis-schema/>"
-          + " SELECT ?connectionString ?user ?password WHERE {" + " <" + frameworkUri
+          + " SELECT ?connectionString ?user ?password WHERE {" + " <" + instance.getFrameworkUri()
           + ">  lds:integrates ?component ." + " ?component lds:providesService ?service ."
           + " ?service a lds:StorageService ."
           + " ?service lds:connectionString ?connectionString ." + " ?service lds:user ?user ."
@@ -151,12 +152,11 @@ public static synchronized FrameworkConfiguration getInstance(ServletContext con
       }
       qexec.close();
 
-      // get and set the named graphs
+      // get and set the system named graphs
       query = "PREFIX  sd:    <http://www.w3.org/ns/sparql-service-description#> "
           + "PREFIX  rdfs:  <http://www.w3.org/2000/01/rdf-schema#> " + "SELECT ?name ?label  "
           + "WHERE "
           + "{ ?s sd:namedGraph  ?o .  ?o sd:name ?name . ?o sd:graph ?g . ?g rdfs:label ?label } ";
-
       qexec = QueryExecutionFactory.create(query, configurationModel);
       results = qexec.execSelect();
       if (!results.hasNext())
@@ -193,7 +193,10 @@ else if ("groups".equals(soln.get("label").asLiteral().getString()))
         userManager.createUser(instance.getAuthSparqlUser(), instance.getAuthSparqlPassword());
         userManager.setDefaultRdfPermissions(instance.getAuthSparqlUser(), 3);
         userManager.grantRole(instance.getAuthSparqlUser(), "SPARQL_UPDATE");
+        userManager.grantLOLook(instance.getAuthSparqlUser());
+        // TODO: check if we still need to grant these to SPARQL user
         userManager.grantRole("SPARQL", "SPARQL_UPDATE");
+        userManager.grantLOLook("SPARQL");
 
         System.out.println("[INFO] System User was created ");
       } catch (Exception e) {
@@ -226,13 +229,13 @@ else if ("groups".equals(soln.get("label").asLiteral().getString()))
         System.out.println("[INFO] Default Graphs creation/configuration ");
 
         // Read configuration files
-        Model datrasetModel = ModelFactory.createDefaultModel();
+        Model datasetModel = ModelFactory.createDefaultModel();
         Model componentsModel = ModelFactory.createDefaultModel();
         Model ontologyModel = ModelFactory.createDefaultModel();
         Model ontologyAccountsModel = ModelFactory.createDefaultModel();
 
         try {
-          datrasetModel.read(datasetsFile);
+          datasetModel.read(datasetsFile);
           componentsModel.read(componentsFile);
           ontologyModel.read(ontologyFile);
           ontologyAccountsModel.read(accountsOntologyFile);
@@ -258,10 +261,32 @@ else if ("groups".equals(soln.get("label").asLiteral().getString()))
         userManager.setRdfGraphPermissions(instance.getAuthSparqlUser(), instance
             .getInitialSettingsGraph(), 3);
 
+        // join the settings files
         Model settingsModel = ModelFactory.createDefaultModel();
-        settingsModel.add(datrasetModel);
+        settingsModel.add(datasetModel);
         settingsModel.add(componentsModel);
         settingsModel.add(ontologyModel);
+
+        // add to settings virtuoso component without users/passwords
+        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 lds:<http://stack.linkeddata.org/ldis-schema/>" + " CONSTRUCT   { <"
+            + instance.getFrameworkUri() + "> ?p ?o . " + "<" + instance.getFrameworkUri()
+            + "> lds:integrates ?component ."
+            + "?component rdfs:label ?label . ?component rdf:type ?type . "
+            + "?component lds:providesService ?service . ?service rdf:type ?servicetype ."
+            + "?service lds:serviceUrl ?serviceUrl .} " + " WHERE  { <"
+            + instance.getFrameworkUri() + "> ?p ?o ." + "<" + instance.getFrameworkUri()
+            + "> lds:integrates ?component ."
+            + "?component rdfs:label ?label . ?component rdf:type ?type . "
+            + "?component lds:providesService ?service . ?service rdf:type ?servicetype ."
+            + "?service lds:serviceUrl ?serviceUrl .}";
+        qexec = QueryExecutionFactory.create(queryString, configurationModel);
+        Model triples = qexec.execConstruct();
+        settingsModel.add(triples);
+        qexec.close();
+
         // write the initial settings model (default settings for new
         // users)
         ByteArrayOutputStream os = new ByteArrayOutputStream();
@@ -485,4 +510,13 @@ public String getFrameworkOntologyNS() {
   public void setFrameworkOntologyNS(String frameworkOntologyNS) {
     this.frameworkOntologyNS = frameworkOntologyNS;
   }
+
+  public String getFrameworkUri() {
+    return frameworkUri;
+  }
+
+  public void setFrameworkUri(String frameworkUri) {
+    this.frameworkUri = frameworkUri;
+  }
+
 }

src/main/resources/framework-components.ttl

@@ -50,7 +50,7 @@
   dcterms:hasVersion "2.0"^^xsd:string ;
   gkg:publicEndpoint :VirtuosoEndpoint ;
   gkg:authEndpoint :VirtuosoAuthSPARQLEndpoint ;
-  lds:integrates :Virtuoso, :Facete, :Limes, :Sparqlify, :TripleGeo, :GeoLift, :OntoWiki, :Mappify ;
+  lds:integrates :Facete, :Limes, :Sparqlify, :TripleGeo, :GeoLift, :OntoWiki, :Mappify ;
   foaf:homepage <http://localhost:8080/generator> .
 
 :Virtuoso
@@ -81,7 +81,7 @@
 
 :SparqlifyService
       a       lds:ExplorationService ;
-      lds:serviceUrl <http://144.76.166.111:8080/sparqlify/> .
+      lds:serviceUrl <http://localhost:8080/sparqlify/> .
 
 :Facete
       a       lds:StackComponent ;
@@ -131,7 +131,7 @@
       foaf:homepage <http://aksw.org/Projects/OntoWiki.html> .
 :OntoWikiService 
       a       lds:AuthoringService ;
-      lds:serviceUrl <http://144.76.166.111/ontowiki> .
+      lds:serviceUrl <http://localhost/ontowiki> .
 
 :Mappify
       a       lds:StackComponent ;

src/main/resources/framework-configuration-template.ttl

@@ -26,7 +26,7 @@
   rdfs:comment "This resource contains all the configuration required by the application"^^xsd:string ;
   rdfs:label "GeoKnowGeneator"^^xsd:string ;
   dcterms:hasVersion "2.0"^^xsd:string ;
-  lds:password "***REMOVED***""^^xsd:string ;         # an admin user for the webapp
+  lds:password "***REMOVED***""^^xsd:string ;         # an admin user for the webapp NOT IMPLEMENTED YET
   lds:user   "***REMOVED***""^^xsd:string ;
   gkg:publicEndpoint :VirtuosoEndpoint ;
   gkg:authEndpoint :VirtuosoAuthSPARQLEndpoint ;
@@ -132,4 +132,3 @@
     dcterms:created "2014-04-12"^^xsd:date;
     void:sparqlEndpoint <http://10.0.0.63:8890/sparql> ]
   .
-

src/main/webapp/WEB-INF/web-template.xml

@@ -179,4 +179,4 @@
     <mime-type>application/rdf+xml</mime-type>
   </mime-mapping>
 
-</web-app> 
+</web-app>

src/main/webapp/popup.html

@@ -49,7 +49,6 @@
     ================================================== -->
     <!-- Placed at the end of the document so the pages load faster -->
     <!-- <script src="lib/jquery/jquery-1.7.2.min.js"></script> -->
-    
     <script src="lib/jquery/jquery-1.9.1.js"></script>
     <script src="lib/jquery/jquery-ui-1.10.1.custom.min.js"></script>
 
@@ -59,6 +58,7 @@
     <script src="lib/angularjs/angular-route.js"></script>
     <script src="lib/modal-master/bootstrap-modal.js"></script>
     <script src="lib/modal-master/bootstrap-modalmanager.js"></script>
+    <script src="js/config.js"></script>
     <script src="js/app.js"></script>
     <!-- services for the different modules/pages -->
     <script src="js/services/config.js"></script>