Merge branch 'ontos-geoknow'

Author: alegrm

.gitignore

@@ -18,3 +18,4 @@
 /src/main/webapp/VAADIN/gwt-unitCache
 /src/main/webapp/VAADIN/widgetsets
 /target
+/bin

src/main/java/ImportRDF.java

@@ -146,7 +146,7 @@ private int httpUpdate(String endpoint, String graph, Model model) throws Except
     RdfStoreManager rdfStoreManager = null;
     if (username != null && !username.isEmpty() && token != null && !token.isEmpty()) {
       FrameworkUserManager frameworkUserManager = FrameworkConfiguration.getInstance(
-          getServletContext(), false).getFrameworkUserManager();
+          getServletContext()).getFrameworkUserManager();
       if (frameworkUserManager.checkToken(username, token))
         rdfStoreManager = frameworkUserManager.getRdfStoreManager(username);
     }

src/main/java/accounts/FrameworkUserManager.java

@@ -8,4 +8,5 @@ public interface UserManager {
     public void setRdfGraphPermissions(String user, String graph, int permissions) throws Exception;
     public void deleteRdfGraphPermissions(String user, String graph) throws Exception;
     public void setDefaultGraphPermissions(String graph, int permissions) throws Exception;
+    public boolean checkUserExists(String username, String email) throws Exception;
 }

src/main/java/accounts/UserManager.java

@@ -5,7 +5,7 @@ public class UserProfile {
     private String settingsGraph;
     private String accountURI;
     private String email;
-    private boolean admin;
+    private UserRole role;
 
     public String getUsername() {
         return username;
@@ -39,12 +39,12 @@ public void setEmail(String email) {
         this.email = email;
     }
 
-    public boolean isAdmin() {
-        return admin;
+    public UserRole getRole() {
+        return role;
     }
 
-    public void setAdmin(boolean admin) {
-        this.admin = admin;
+    public void setRole(UserRole role) {
+        this.role = role;
     }
 
     @Override

src/main/java/accounts/UserProfile.java

@@ -0,0 +1,36 @@
+package accounts;
+
+import java.util.Collection;
+
+/**
+ * Created by taleksaschina on 24.06.2014.
+ */
+public class UserRole {
+    private String uri;
+    private String name;
+    private Collection<String> services;
+
+    public String getUri() {
+        return uri;
+    }
+
+    public void setUri(String uri) {
+        this.uri = uri;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public Collection<String> getServices() {
+        return services;
+    }
+
+    public void setServices(Collection<String> services) {
+        this.services = services;
+    }
+}

src/main/java/accounts/UserRole.java

@@ -1,9 +1,6 @@
 package accounts;
 
-import java.sql.Connection;
-import java.sql.DriverManager;
-import java.sql.SQLException;
-import java.sql.Statement;
+import java.sql.*;
 
 public class VirtuosoUserManager implements UserManager {
   private static final String jdbcDriver = "virtuoso.jdbc4.Driver";
@@ -29,8 +26,10 @@ public VirtuosoUserManager(String connectionString, String user, String password
   }
 
   @Override
-  public void createUser(String name, String password) throws ClassNotFoundException, SQLException {
-    executeUpdate(getConnection(), "DB.DBA.USER_CREATE('" + name + "', '" + password + "')");
+  public void createUser(String name, String password) throws Exception {
+    if (checkUserExists(name, null))
+        throw new Exception("User " + name + " already exists");
+    executeUpdate(getConnection(), "DB.DBA.USER_CREATE('" + name + "', '" + password + "')");  //NB! this function doesn't throw exception if user already exists
     // executeUpdate(getConnection(), "USER_SET_OPTION('" + name +
     // "', 'DAV_ENABLE', 1)");
   }
@@ -42,7 +41,7 @@ public void dropUser(String name) throws ClassNotFoundException, SQLException {
 
   @Override
   public void grantRole(String user, String role) throws ClassNotFoundException, SQLException {
-    executeUpdate(getConnection(), "GRANT " + role + " TO \"" + user + "\"");
+    executeUpdate(getConnection(), "GRANT " + role + " TO \"" + user + "\""); //NB! this function throws exception if the role is already granted
   }
 
   @Override
@@ -82,9 +81,23 @@ public void setDefaultGraphPermissions(String graph, int permissions)
    * @throws SQLException
    */
   public void grantLOLook(String user) throws ClassNotFoundException, SQLException {
-    executeUpdate(getConnection(), "GRANT EXECUTE ON DB.DBA.L_O_LOOK TO '" + user + "'");
+    executeUpdate(getConnection(), "GRANT EXECUTE ON DB.DBA.L_O_LOOK TO \"" + user + "\"");
   }
 
+    @Override
+    public boolean checkUserExists(String username, String email) throws Exception {
+        //todo is there any simpler way to check if the user exists? some function?
+        String query = "select * from DB.DBA.SYS_USERS where U_NAME='" + username + "'";
+        Connection conn = getConnection();
+        Statement stmt = conn.createStatement();
+        try {
+            ResultSet resultSet = stmt.executeQuery(query);
+            return resultSet.next();
+        } finally {
+            stmt.close();
+        }
+    }
+
   private Connection getConnection() throws ClassNotFoundException, SQLException {
     if (connection == null || connection.isClosed()) {
       Class.forName(jdbcDriver);

src/main/java/accounts/VirtuosoUserManager.java

@@ -1,6 +1,5 @@
 package authentication;
 
-import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 
 import javax.servlet.ServletContext;
@@ -31,7 +30,6 @@ public class FrameworkConfiguration {
   private String emailUsername = "";
   private String emailPassword = "";
 
-  private String accountsOntologyNS = "";
   private String resourceNS = "";
   private String frameworkOntologyNS = "";
 
@@ -55,31 +53,21 @@ public class FrameworkConfiguration {
   /**
    * 
    * @param context
-   * @param reset
    * @return
    * @throws Exception
    */
-  // TODO: replace System.out.println with a logging implementation
-  public static synchronized FrameworkConfiguration getInstance(ServletContext context,
-      boolean reset) throws Exception {
+  public static synchronized FrameworkConfiguration getInstance(ServletContext context) throws Exception {
 
     if (instance == null) {
 
-      System.out.println("[INFO] System Initialization ");
-
       instance = new FrameworkConfiguration();
 
       String configurationFile = "framework-configuration.ttl";
-      String datasetsFile = "framework-datasets.ttl";
-      String componentsFile = "framework-components.ttl";
-      String ontologyFile = "framework-ontology.ttl";
-      String accountsOntologyFile = "framework-accounts-ontology.ttl";
 
       // initialize parameters from context
       instance.frameworkUri = context.getInitParameter("framework-uri");
 
       instance.setFrameworkOntologyNS(context.getInitParameter("framework-ontology-ns"));
-      instance.setAccountsOntologyNamespace(context.getInitParameter("accounts-ns"));
       instance.setResourceNamespace(context.getInitParameter("framework-ns"));
 
       instance.setSmtpHost(context.getInitParameter("smtp-host"));
@@ -174,145 +162,6 @@ else if ("groups".equals(soln.get("label").asLiteral().getString()))
           instance.setGroupsGraph(soln.get("name").toString());
       }
       qexec.close();
-
-      // creates the system user exist for the application in virtuoso
-      VirtuosoUserManager userManager = instance.getVirtuosoUserManager();
-
-      // if the flag to reinstall is true
-      if (reset) {
-        try {
-          userManager.dropUser(instance.getAuthSparqlUser());
-        } catch (Exception e) {
-          // catches the error in case the user do not exist
-        }
-        // TODO: we may need to delete all users before to clean the store?
-      }
-
-      try {
-
-        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) {
-        if ("virtuoso.jdbc4.VirtuosoException".equals(e.getClass().getCanonicalName()))
-          // TODO: replace with a logging implementation
-          System.out.println("Seems that the user is already there");
-        else
-          throw e;
-      }
-
-      SecureRdfStoreManagerImpl frameworkRdfStoreManager = new SecureRdfStoreManagerImpl(instance
-          .getAuthSparqlEndpoint(), instance.getAuthSparqlUser(), instance.getAuthSparqlPassword());
-      // delete all graphs if reinstall is requested
-      if (reset) {
-        try {
-          frameworkRdfStoreManager.dropGraph(instance.getSettingsGraph());
-          frameworkRdfStoreManager.dropGraph(instance.getAccountsGraph());
-          frameworkRdfStoreManager.dropGraph(instance.getGroupsGraph());
-          frameworkRdfStoreManager.dropGraph(instance.getInitialSettingsGraph());
-        } catch (Exception e) {
-        }
-      }
-
-      // check if settingsGraph exist do not overwrite
-      String queryString = " ASK { GRAPH <" + instance.getSettingsGraph() + "> {?s a ?o} }";
-      String response = frameworkRdfStoreManager.execute(queryString, "text/plain");
-      if (response.toLowerCase().indexOf("true") < 0) {
-
-        // TODO: replace with a logging implementation
-        System.out.println("[INFO] Default Graphs creation/configuration ");
-
-        // Read configuration files
-        Model datasetModel = ModelFactory.createDefaultModel();
-        Model componentsModel = ModelFactory.createDefaultModel();
-        Model ontologyModel = ModelFactory.createDefaultModel();
-        Model ontologyAccountsModel = ModelFactory.createDefaultModel();
-
-        try {
-          datasetModel.read(datasetsFile);
-          componentsModel.read(componentsFile);
-          ontologyModel.read(ontologyFile);
-          ontologyAccountsModel.read(accountsOntologyFile);
-        } catch (RiotException e) {
-          throw new IOException("Malformed configuration files");
-        }
-
-        // create required named graphs and load the configuration files
-        // using framework default user
-        frameworkRdfStoreManager.createGraph(instance.getSettingsGraph());
-        frameworkRdfStoreManager.createGraph(instance.getAccountsGraph());
-        frameworkRdfStoreManager.createGraph(instance.getGroupsGraph());
-        frameworkRdfStoreManager.createGraph(instance.getInitialSettingsGraph());
-
-        // Make graphs accessible to framework user only
-        userManager.setDefaultRdfPermissions("nobody", 0);
-        userManager.setRdfGraphPermissions(instance.getAuthSparqlUser(), instance
-            .getSettingsGraph(), 3);
-        userManager.setRdfGraphPermissions(instance.getAuthSparqlUser(), instance
-            .getAccountsGraph(), 3);
-        userManager.setRdfGraphPermissions(instance.getAuthSparqlUser(), instance.getGroupsGraph(),
-            3);
-        userManager.setRdfGraphPermissions(instance.getAuthSparqlUser(), instance
-            .getInitialSettingsGraph(), 3);
-
-        // join the settings files
-        Model settingsModel = ModelFactory.createDefaultModel();
-        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();
-        settingsModel.write(os, "N-TRIPLES");
-        queryString = "INSERT DATA { GRAPH <" + instance.getInitialSettingsGraph() + "> { "
-            + os.toString() + " } }";
-        os.close();
-        frameworkRdfStoreManager.execute(queryString, null);
-
-        // write the system settings model (include system graphs data)
-        // settingsModel.add(graphsModel);
-        os = new ByteArrayOutputStream();
-        settingsModel.write(os, "N-TRIPLES");
-        queryString = "INSERT DATA { GRAPH <" + instance.getSettingsGraph() + "> { "
-            + os.toString() + " } }";
-        os.close();
-        frameworkRdfStoreManager.execute(queryString, null);
-
-        // create and add accounts ontology to the accounts graph
-        os = new ByteArrayOutputStream();
-        ontologyAccountsModel.write(os, "N-TRIPLES");
-        queryString = "INSERT DATA { GRAPH <" + instance.getAccountsGraph() + "> { "
-            + os.toString() + " } }";
-        os.close();
-        frameworkRdfStoreManager.execute(queryString, null);
-      }
     }
 
     return instance;
@@ -439,14 +288,6 @@ public void setAuthSparqlPassword(String authSparqlPassword) {
   // this.accountsNamespace = accountsNamespace;
   // }
 
-  public String getAccountsOntologyNamespace() {
-    return accountsOntologyNS;
-  }
-
-  public void setAccountsOntologyNamespace(String accountsNamespace) {
-    this.accountsOntologyNS = accountsNamespace;
-  }
-
   public String getAccountsGraph() {
     return accountsGraph;
   }