Merge branch 'dev'

src/main/java/pt/ua/bioinformatics/coeus/actions/ManagerActionBean.java

@@ -0,0 +1,108 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package pt.ua.bioinformatics.coeus.actions;
+
+import net.sourceforge.stripes.action.ActionBean;
+import net.sourceforge.stripes.action.ActionBeanContext;
+import net.sourceforge.stripes.action.DefaultHandler;
+import net.sourceforge.stripes.action.ForwardResolution;
+import net.sourceforge.stripes.action.Resolution;
+import net.sourceforge.stripes.action.UrlBinding;
+
+/**
+ *
+ * @author sernadela
+ */
+@UrlBinding("/manager/{$model}/{method}")
+public class ManagerActionBean implements ActionBean {
+
+    private static final String INDEX_VIEW = "/setup/index.jsp";
+    private static final String SEEDS_VIEW = "/setup/seeds.jsp";
+    //private static final String SEEDS_ADD_VIEW = "/setup/addseed.jsp";
+    //private static final String ENTITY_ADD_VIEW = "/setup/addentity.jsp";
+    private static final String ENTITIES_VIEW = "/setup/entities.jsp";
+    //private static final String CONCEPT_ADD_VIEW = "/setup/addconcept.jsp";
+    private static final String CONCEPTS_VIEW = "/setup/concepts.jsp";
+    //private static final String RESOURCE_ADD_VIEW = "/setup/addresource.jsp";
+    private static final String RESOURCES_VIEW = "/setup/resources.jsp";
+    private static final String SELECTORS_VIEW = "/setup/selectors.jsp";
+    private static final String ENVIRONMENTS_VIEW = "/setup/environments.jsp";
+    private static final String ENVIRONMENTS_EDIT_VIEW = "/setup/editenvironment.jsp";
+    private static final String NOTFOUND_VIEW = "/setup/404.jsp";
+    private static final String GRAPH_VIEW = "/setup/graph.jsp";
+    private String method;
+    private String model;
+    private ActionBeanContext context;
+
+    @DefaultHandler
+    public Resolution handle() {
+        return new ForwardResolution(NOTFOUND_VIEW);
+    }
+
+    public Resolution config() {
+        return new ForwardResolution("/setup/config.jsp");
+    }
+
+    public Resolution graph() {
+        return new ForwardResolution(GRAPH_VIEW);
+    }
+
+    public Resolution environments() {
+        if (method != null && method.startsWith("edit")) {
+            return new ForwardResolution(ENVIRONMENTS_EDIT_VIEW);
+        } else {
+            return new ForwardResolution(ENVIRONMENTS_VIEW);
+        }
+    }
+
+    public Resolution seed() {
+        if (method == null) {
+            return new ForwardResolution(SEEDS_VIEW);
+        } else {
+            return new ForwardResolution(INDEX_VIEW);
+        }
+    }
+
+    public Resolution entity() {
+        return new ForwardResolution(ENTITIES_VIEW);
+    }
+
+    public Resolution concept() {
+        return new ForwardResolution(CONCEPTS_VIEW);
+    }
+
+    public Resolution resource() {
+        return new ForwardResolution(RESOURCES_VIEW);
+    }
+    public Resolution selector() {
+        return new ForwardResolution(SELECTORS_VIEW);
+    }
+
+    public String getModel() {
+        return model;
+    }
+
+    public void setModel(String model) {
+        this.model = model;
+    }
+
+    public String getMethod() {
+        return method;
+    }
+
+    public void setMethod(String method) {
+        this.method = method;
+    }
+
+    @Override
+    public void setContext(ActionBeanContext actionBeanContext) {
+        this.context = actionBeanContext;
+    }
+
+    @Override
+    public ActionBeanContext getContext() {
+        return context;
+    }
+}

src/main/java/pt/ua/bioinformatics/coeus/actions/UpdateActionBean.java

@@ -108,7 +108,7 @@ public Resolution handle() {
                 if (sub.indexOf(":") > 1) {
                     try {
                         if (pred.indexOf(":") > 1) {
-
+                            System.err.println(old_obj+" , "+new_obj);
                             // test old_obj
                             String xsd = "http://www.w3.org/2001/XMLSchema#";
                             Statement statToRemove = null;
@@ -142,8 +142,9 @@ public Resolution handle() {
 
                             if (Boot.getAPI().containsStatement(statToRemove)) {
 
-                                Boot.getAPI().addStatement(statToAdd);
                                 Boot.getAPI().removeStatement(statToRemove);
+                                Boot.getAPI().addStatement(statToAdd);
+
 
                                 result.put("status", 100);
                                 result.put("message", "[COEUS][API][Update] Triples updated in the knowledge base.");

src/main/java/pt/ua/bioinformatics/coeus/actions/WriteActionBean.java

@@ -92,6 +92,7 @@ public Resolution handle() {
                             //verify if is a xsd type
                             if (obj.startsWith("xsd:")) {
                                 String[] old = obj.split(":", 3);
+                                System.err.println(obj);
                                 Literal l = Boot.getAPI().getModel().createTypedLiteral(old[2], xsd + old[1]);
                                 statToAdd = Boot.getAPI().getModel().createLiteralStatement(Boot.getAPI().createResource(PrefixFactory.decode(sub)), Predicate.get(pred), l);
                             } else if (obj.indexOf(":") > 1) {

src/main/java/pt/ua/bioinformatics/coeus/api/DB.java

@@ -1,5 +1,9 @@
 package pt.ua.bioinformatics.coeus.api;
 
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
 import java.sql.Connection;
 import java.sql.DriverManager;
 import java.sql.PreparedStatement;
@@ -239,4 +243,53 @@ public ResultSet getData(String query) {
         }
 
     }
+
+     /**
+     * Create the DB and it table structure if not exists according to the giving parameters
+     * 
+     * @param url
+     * @param user
+     * @param pass
+     * @throws ClassNotFoundException
+     * @throws SQLException
+     * @throws IOException 
+     */
+    public void createDB(String url, String user, String pass) throws ClassNotFoundException, SQLException, IOException {
+
+            Class.forName("com.mysql.jdbc.Driver");
+            url=url.replace("?autoReconnect=true","");
+            String[] urlSplited=url.split("/");
+            String db=urlSplited[urlSplited.length-1];
+            //System.out.println(db);
+            String jdbc=url.replace("/"+db, "") + "?allowMultiQueries=true&user=" + user + "&password=" + pass;
+            System.out.println(jdbc);
+            connection = DriverManager.getConnection(jdbc);
+            String script=readScript().replaceAll("coeusdb", db);
+            pStatement = connection.prepareStatement(script);
+            pStatement.execute();
+            pStatement.close();
+            connection.close();
+    }
+
+    /**
+     * Read the coeus.sql file and convert it to String
+     *
+     * @return
+     * @throws FileNotFoundException
+     * @throws IOException
+     */
+    public String readScript() throws FileNotFoundException, IOException {
+        StringBuilder sb = new StringBuilder();
+
+        BufferedReader br = new BufferedReader(new FileReader(DB.class.getResource("/").getPath() + "coeus.sql"));
+        String line = br.readLine();
+
+        while (line != null) {
+            sb.append(line);
+            sb.append('\n');
+            line = br.readLine();
+        }
+        br.close();
+        return sb.toString();
+    }
 }