Merge remote-tracking branch 'remotes/origin/master' into ontos-ldiw-acc

taleksashina · taleksashina · commit 126bc0a74e4b · 2014-06-26T15:16:54.000+04:00
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,7 @@
+#Framework configuration files
+/src/main/webapp/WEB-INF/web.xml
+/src/main/resources/framework-configuration.ttl
+
 #Mac
 .DS_Store
 
diff --git a/README.md b/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/) 
diff --git a/src/main/java/accounts/VirtuosoUserManager.java b/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);
diff --git a/src/main/java/authentication/FrameworkConfiguration.java b/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;
+  }
+
 }
diff --git a/src/main/resources/framework-components.ttl b/src/main/resources/framework-components.ttl
@@ -50,29 +50,81 @@
   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
-  a       lds:StackComponent ;
-  rdfs:label "Service URL"^^xsd:string ;
-  dcterms:hasVersion "7.0"^^xsd:string ;
-  lds:providesService :VirtuosoConductor, :VirtuosoAutSPARQLEndpoint, :VirtuosoEndpoint;
-  foaf:homepage <http://virtuoso.openlinksw.com/> .
+:Sparqlify
+      a       lds:StackComponent ;
+      rdfs:label "Sparqlify"^^xsd:string ;
+      lds:providesService :SparqlifyService ;
+      lds:version "0.1-SNAPSHOT"^^xsd:string ;
+      foaf:homepage <http://aksw.org/Projects/Sparqlify.html> .
 
-:VirtuosoConductor 
-  a  lds:StorageService  ;
-  lds:serviceUrl <http://localhost:8890/conductor> .
+:SparqlifyService
+      a       lds:ExplorationService ;
+      lds:serviceUrl <http://localhost:8080/sparqlify/> .
 
-:VirtuosoAuthSPARQLEndpoint
-  a       lds:SecuredSPARQLEndPointService ;
-  lds:serviceUrl <http://localhost:8890/sparql-auth> .
+:Facete
+      a       lds:StackComponent ;
+      rdfs:label "Facete"^^xsd:string ;
+      lds:providesService :FaceteService ;
+      lds:version "0.1-SNAPSHOT"^^xsd:string ;
+      foaf:homepage <http://aksw.org/Projects/Facete.html> .
+:FaceteService 
+      a       lds:ExplorationService ;
+      lds:serviceUrl <http://cstadler.aksw.org/facete2/> .
 
-:VirtuosoEndpoint
-  a       lds:SPARQLEndPointService ;
-  lds:serviceUrl <http://localhost:8890/sparql> .
+:Limes
+      a       lds:StackComponent ;
+      rdfs:label "Limes Linking Service"^^xsd:string ;
+      lds:providesService :LimesService;
+      lds:version "0.6.4"^^xsd:string ;
+      foaf:homepage <http://aksw.org/Projects/LIMES.html> .
+:LimesService
+      a       lds:InterlinkingService ;
+      lds:serviceUrl <http://localhost:8080/Limes-Service> .
+
+:TripleGeo
+      a       lds:StackComponent ;
+      rdfs:label "TripleGeo"^^xsd:string ;
+      lds:providesService :TripleGeoService ;
+      lds:version "1.0"^^xsd:string ;
+      foaf:homepage <https://web.imis.athena-innovation.gr/redmine/projects/geoknow_public/wiki/TripleGeo> .
+:TripleGeoService 
+      a       lds:ExtractionService ;
+      lds:serviceUrl <http://localhost:8080/TripleGeo-Service> .
+
+:GeoLift
+      a       lds:StackComponent ;
+      rdfs:label "GeoLift"^^xsd:string ;
+      lds:providesService :GeoLiftService ;
+      lds:version "0.6.4"^^xsd:string ;
+      foaf:homepage <https://github.com/AKSW/GeoLift> .
+:GeoLiftService
+      a       lds:EnrichmentService ;
+      lds:serviceUrl <http://localhost:8080/GeoLift-Service> .
+
+:OntoWiki
+      a       lds:StackComponent ;
+      rdfs:label "OntoWiki"^^xsd:string ;
+      lds:providesService :OntoWikiService ;
+      lds:version "0.9.10-1"^^xsd:string ;
+      foaf:homepage <http://aksw.org/Projects/OntoWiki.html> .
+:OntoWikiService 
+      a       lds:AuthoringService ;
+      lds:serviceUrl <http://192.168.2.18/ontowiki> .
+
+:Mappify
+      a       lds:StackComponent ;
+      rdfs:label "Mappify"^^xsd:string ;
+      lds:providesService :MappifyService ;
+      lds:version "0.9.10-1"^^xsd:string ;
+      foaf:homepage <https://github.com/GeoKnow/Mappify> .
+:MappifyService
+      a       lds:ExplorationService ;
+      lds:serviceUrl <http://cstadler.aksw.org/mappify2/> .
 
- :D2RQ
+:D2RQ
       a       lds:StackComponent ;
       rdfs:label "D2RQ"^^xsd:string ;
       lds:providesService :D2RQService ;
diff --git a/src/main/resources/framework-configuration-template.ttl b/src/main/resources/framework-configuration-template.ttl
@@ -26,18 +26,18 @@
   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 :VirtuosoAutSPARQLEndpoint ;
+  gkg:authEndpoint :VirtuosoAuthSPARQLEndpoint ;
   lds:integrates :Virtuoso ;
   foaf:homepage <http://localhost:8080/generator> .
 
 :Virtuoso
   a       lds:StackComponent ;
   rdfs:label "Service URL"^^xsd:string ;
   dcterms:hasVersion "7.0"^^xsd:string ;
-  lds:providesService :VirtuosoConductor , :VirtuosoAutSPARQLEndpoint, :VirtuosoEndpoint;
+  lds:providesService :VirtuosoConductor , :VirtuosoAuthSPARQLEndpoint, :VirtuosoEndpoint;
   foaf:homepage <http://virtuoso.openlinksw.com/> .
 
 :VirtuosoConductor 
@@ -47,7 +47,7 @@
   lds:connectionString "jdbc:virtuoso://***REMOVED***:1111/"^^xsd:string;
   lds:user   "***REMOVED***""^^xsd:string . 
 
-:VirtuosoAutSPARQLEndpoint
+:VirtuosoAuthSPARQLEndpoint
   a       lds:SecuredSPARQLEndPointService ;
   lds:password "***REMOVED***"^^xsd:string ;
   lds:serviceUrl <http://***REMOVED***:8890/sparql-auth> ;
@@ -132,4 +132,3 @@
     dcterms:created "2014-04-12"^^xsd:date;
     void:sparqlEndpoint <http://10.0.0.63:8890/sparql> ]
   .
-
diff --git a/src/main/webapp/WEB-INF/web-template.xml b/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>
diff --git a/src/main/webapp/popup.html b/src/main/webapp/popup.html
