Temporary commit just to show current progress.

code/factorbase/src/main/java/ca/sfu/cs/factorbase/database/FactorBaseDataBase.java

@@ -0,0 +1,13 @@
+package ca.sfu.cs.factorbase.database;
+
+import java.util.List;
+
+import ca.sfu.cs.factorbase.graph.Edge;
+
+/**
+ * Methods expected to be implemented to enable the extraction of data from a database for FactorBase.
+ */
+public interface FactorBaseDataBase {
+    public List<Edge> getForbiddenEdges(String idName, String pvid);
+    public List<Edge> getRequiredEdges();
+}

code/factorbase/src/main/java/ca/sfu/cs/factorbase/database/MySQLFactorBaseDataBase.java

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+package ca.sfu.cs.factorbase.database;
+
+import java.sql.DriverManager;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Statement;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.mysql.jdbc.Connection;
+
+import ca.sfu.cs.factorbase.graph.Edge;
+
+public class MySQLFactorBaseDataBase implements FactorBaseDataBase {
+
+    private Connection baseConnection;
+    private Connection bnConnection;
+    private Connection ctConnection;
+
+
+    /**
+     * Create connections to the databases required by FactorBase to learn a Bayesian Network.
+     *
+     * @param connectionString - The string used to the database with the original data.
+     *                           e.g. jdbc:mysql://127.0.0.1/unielwin
+     * @param username - username to use when accessing the database.
+     * @param password - password to use when accessing the database.
+     * @throws SQLException - if there is a problem connecting to the required databases.
+     */
+    public MySQLFactorBaseDataBase(String connectionString, String username, String password) throws SQLException {
+        baseConnection = (Connection) DriverManager.getConnection(connectionString, username, password);
+        bnConnection = (Connection) DriverManager.getConnection(connectionString + "_BN", username, password);
+        ctConnection = (Connection) DriverManager.getConnection(connectionString + "_CT", username, password);
+    }
+
+    @Override
+    public List<Edge> getForbiddenEdges(String idName, String pvid) {
+        try {
+            Statement statement = bnConnection.createStatement(); // Will change this to prepared statement.
+            ResultSet result = statement.executeQuery("SELECT * FROM Path_Forbidden_Edges WHERE " + idName + " = \"" + pvid + "\"");
+            List<Edge> forbiddenEdges = new ArrayList<Edge>();
+
+            // Parse results, can retrieve from cached value.
+            while (result.next()) {
+                String child = result.getString("child"); //.replace("`","");
+                String parent = result.getString("parent"); // .replace("`","");
+                forbiddenEdges.add(new Edge(parent, child));
+            }
+
+            return forbiddenEdges;
+        } catch (SQLException e) {
+            return null;
+        }
+    }
+
+    @Override
+    public List<Edge> getRequiredEdges() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+}

code/factorbase/src/main/java/ca/sfu/cs/factorbase/graph/Edge.java

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+package ca.sfu.cs.factorbase.graph;
+
+/**
+ * Simple class to store information for an edge between a parent and a child node.
+ */
+public class Edge {
+
+    private String parent;
+    private String child;
+
+
+    /**
+     * Create an edge object that represents an edge between the given child and parent.
+     * @param parent - the parent node.
+     * @param child - the child node.
+     */
+    public Edge(String parent, String child) {
+        this.parent = parent;
+        this.child = child;
+    }
+
+    /**
+     * Retrieve the parent for the given edge.
+     * @return the parent for the given edge.
+     */
+    public String getParent() {
+        return this.parent;
+    }
+
+    /**
+     * Retrieve the child for the given edge.
+     * @return the child for the given edge.
+     */
+    public String getChild() {
+        return this.child;
+    }
+}