Added MetaMapAnnotator to the repository

Author: nikolamilosevic86

src/Annotation/MetaMapAnnotatorMain.java

@@ -0,0 +1,104 @@
+package Annotation;
+
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Statement;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.LinkedList;
+
+import DataBase.DataBaseAnnotationSaver;
+import Main.MarvinSemAnnotator;
+import Main.Word;
+import Main.WordMeaningOutputElement;
+
+
+public class MetaMapAnnotatorMain {
+
+	public static void main(String[] args) {
+		// TODO Auto-generated method stub
+		DataBaseAnnotationSaver dbas = new DataBaseAnnotationSaver();
+		try {
+			Statement stmt = dbas.conn.createStatement();
+			String insertTableSQL = "SELECT * FROM Cell where idCell > 489245"; // change this to be idCell that was available before running the last TableAnnotator load. Currently 489245.
+			ResultSet rs = stmt.executeQuery(insertTableSQL);
+			MarvinSemAnnotator marvin = new MarvinSemAnnotator();
+			while (rs.next()) {
+				int idCell = rs.getInt("idCell");
+				String CellID = rs.getString("CellID");
+				String CellType = rs.getString("CellType");
+				int Table_idTable  = rs.getInt("Table_idTable");
+				int RowN = rs.getInt("RowN");
+				int ColumnN = rs.getInt("ColumnN");
+				String Content = rs.getString("Content");
+				System.out.println("Processing cell record - \n\tidCell: " + idCell + "\n\tCellID: " + CellID + "\n\tCellType: " + CellType + "\n\tTable_idTable: " + Table_idTable + "\n\tRowN: " + RowN + "\n\tColumnN: " + ColumnN);
+				System.out.println("Cell content:" + Content);
+				if(Content==null)
+				{
+					Content = "";
+				}
+				int mathTypeIndex = Content.indexOf("MathType@");
+				if(mathTypeIndex>0)
+				{
+					Content = Content.substring(0, mathTypeIndex);
+				}
+				LinkedList<Word> words = null;
+				if(Content!=null){
+					Content = Content.trim();
+					words = marvin.annotate(Content);
+					if(words == null){
+					    System.out.println("ERROR: Marvin returned NULL when annotating content (see above) - this cell will be skipped for now ");
+					    System.out.println("ERROR: letting process rest and then initiating a new marvin metamap annotation connection....");
+					    try {
+						Thread.sleep(1000);                 //1000 milliseconds is one second.
+					    } catch(InterruptedException ex) {
+						Thread.currentThread().interrupt();
+					    }
+					    marvin = new MarvinSemAnnotator();
+					    continue;
+					}
+					
+					for(Word w:words)
+					{
+						
+						for(WordMeaningOutputElement wm: w.wordmeanings)
+						{
+							System.out.println(wm.AgentName);
+							Statement stmt8 = dbas.conn.createStatement();
+		        	  		String insertTableSQL8 = "INSERT INTO Annotation (Content,Start,End,AnnotationID,AgentType,AgentName,AnnotationURL,EnvironmentDescription,Cell_idCell,AnnotationDescription,AnnotationSchemaVersion,DateOfAction, Location) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?)";
+		        	  		PreparedStatement preparedStatement8 = dbas.conn.prepareStatement(insertTableSQL8,Statement.RETURN_GENERATED_KEYS);
+		        	  		preparedStatement8.setString(1,wm.appearingWord);
+		        	  		preparedStatement8.setInt(2,wm.startAt);
+		        	  		preparedStatement8.setInt(3,wm.endAt);
+		        	  		preparedStatement8.setString(4,wm.id);
+		        	  		preparedStatement8.setString(5,"Software");
+		        	  		preparedStatement8.setString(6,wm.AgentName);
+		        	  		preparedStatement8.setString(7,wm.URL);
+		        	  		preparedStatement8.setString(8,wm.EnvironmentDesc); 
+		        	  		preparedStatement8.setInt(9,idCell);
+		        	  		preparedStatement8.setString(10,wm.Description);
+		        	  		preparedStatement8.setString(11,wm.AgentVersion);// Should be version
+		        	  		//DateFormat dateFormat = new SimpleDateFormat("dd/MM/yyyy");
+						DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
+		        	  		Date date = new Date();
+		        	  		preparedStatement8.setString(12,dateFormat.format(date));
+		        	  		preparedStatement8.setString(13,wm.Location); // Should be location
+		        	  		// execute insert SQL stetement
+		        	  		preparedStatement8.executeUpdate();
+						}
+					}
+				} 
+			  }
+			
+			dbas.CloseDBConnection();
+			
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+
+	}
+
+}

src/DataBase/DataBaseAnnotationSaver.java

@@ -21,7 +21,7 @@
 import tablInEx.Table;
 
 public class DataBaseAnnotationSaver {
-	Connection conn = null;
+	public Connection conn = null;
 	Statement stmt = null;
 	ResultSet rs = null;