import java.sql.*;
import java.io.*;
import java.util.*;

interface Constants
{
    public static final int NUM_ARGS = 2;
    public static final int INPUT_FILE_ARG = 0;
    public static final int OUTPUT_FILE_ARG = 1;
    public static final String DB_USER = "root";
    public static final String DB_PASS = "*_*lotuSMysql1";
    public static final String DB_URL = "jdbc:mysql:///umls?socketFactory=com.mysql.jdbc.NamedPipeSocketFactory&namedPipePath=\\\\.\\Pipe\\mysql.sock ";
}

I2B2Relation TeRP = new I2B2Relation();
I2B2Relation TeCP = new I2B2Relation();
I2B2Relation TrIP = new I2B2Relation();
I2B2Relation TrWP = new I2B2Relation();
I2B2Relation TrCP = new I2B2Relation();
I2B2Relation TrAP = new I2B2Relation();
I2B2Relation TrNAP = new I2B2Relation();
I2B2Relation PIP = new I2B2Relation();

public class Connect implements Constants
{

  public static void main (String[] args)
  {
    Connection conn = null;
    String phrase;
    ResultSet rs,rsConcept1,rsConcept2;

    PIP.UMLSInteresting.add("associated_with");
    PIP.UMLSInteresting.add("co-occurs_with");
    PIP.UMLSInteresting.add("diagnoses");
    PIP.UMLSInteresting.add("result_of");
    PIP.UMLSInteresting.add("manifestation_of");
    PIP.UMLSInteresting.add("causes");

    TeCP.UMLSInteresting.add("associated_with");
    TeCP.UMLSInteresting.add("assesses_effect_of");
    TeCP.UMLSInteresting.add("measures");

    TeRP.UMLSInteresting.add("indicates");
    TeRP.UMLSInteresting.add("diagnoses");

    TrIP.UMLSInteresting.add("treats");

    TrWP.UMLSInteresting.add("complicates");

    TrCP.UMLSInteresting.add("result_of");
    TrCP.UMLSInteresting.add("causes");

    TrAP.UMLSInteresting.add("associated_with");

    TrNAP.UMLSInteresting.add("complicates");

        // args.length is equivalent to argc in C
        if (args.length == NUM_ARGS)
        {
            try
            {
        // open record name file
        FileInputStream fstreamIn = new FileInputStream(args[INPUT_FILE_ARG]);

        // open mapping result file
                FileOutputStream fstreamOut = new FileOutputStream(args[OUTPUT_FILE_ARG]);

                // Convert to BufferedReader/Writer
                BufferedReader nameFile = new BufferedReader(new InputStreamReader(fstreamIn));
                BufferedWriter resultFile = new BufferedWriter(new OutputStreamWriter(fstreamOut));

        Class.forName ("com.mysql.jdbc.Driver").newInstance ();
        conn = DriverManager.getConnection (DB_URL, DB_USER, DB_PASS);
        System.out.println ("Database connection established");
        Statement statement = conn.createStatement();
      }
      catch (Exception e)
      {
        System.err.println("Caught Exception: "
                                 + e.getMessage());
      }
      // We are now connected and the record name file is open
      // read in names of record files to be processed
      while (nameFile.available() != 0)
      { // each line is a record name
        String recordName = nameFile.readLine();

        try
        { // open this record file
          FileInputStream fstreamIn = new FileInputStream(recordName);

          // get BufferedReader
          BufferedReader recordFile = new BufferedReader(new InputStreamReader(fstreamIn));
        }
        catch (Exception e)
        {
          System.err.println("Caught Exception: "
                                   + e.getMessage());
        } // record open

        // read in pairs of concepts
        while (recordFile.available() != 0)
        { // each line is a concept pair
          String relation = recordFile.readLine();
          String[] relationParts = relation.split("||");

          // First Concept
          String[] concept1 = relationParts[0].split("\\s");

          // I2B2 Relation
          String I2B2Relation = relationParts[1];

          // Second Concept
          String[] concept2 = relationParts[2].split("\\s");

          // this nested loop structure grabs adjacent words in the concept
          // -- for example: "Her Left Arm Pain" might return nothing
          // -- but: "Pain" would return 'Sign or Symptom' which is what we want
          // -- Similarly, : "Blood Pressure High" might not return anything,
          // -- but: "Blood Pressure" returns "Finding"
          for (int i = 0; i < concept1.length; i++)
          {
            for (int p = 0; (p - i) <= 0; p++)
            {
              for (int c = p; c <= (concept1.length - (p + i)); c++)
              {
                if (concept1[c].compareTo("") != 0)
                {
                  phrase = phrase.concat(" ").concat(concept1[c]);
                }
              }
              // pull all unique CUIds for phrase
              String CUIdQuery = "select distinct cui as type from mrxns_eng where mrxns_eng.nstr LIKE \""+phrase+"\"";
              rs = statement.executeQuery(CUIdQuery);

              // this query pulls all unique semantic types for this phrase
              // *Note* we use WHERE cui = "C###" OR cui = "C###" OR ...
              // and then strip off the last 3 characters
              String semanticTypeQuery = "select distinct sty as type from mrsty where";
              while (rs.next())
              {
                semanticTypeQuery.concat(" cui = ").concat(rs.getInt("cui")).concat(" OR");
              }
              semanticTypeQuery = semanticTypeQuery.substring(0,(semanticTypeQuery.length() - 3));

              // add all types to concept1 Types list
              rsConcept1 = statement.executeQuery(CUIdQuery);
            }
          }

          // this nested loop structure grabs adjacent words in the concept
          // -- for example: "Her Left Arm Pain" might return nothing
          // -- but: "Pain" would return 'Sign or Symptom' which is what we want
          // -- Similarly, : "Blood Pressure High" might not return anything,
          // -- but: "Blood Pressure" returns "Finding"
          for (int i = 0; i < concept2.length; i++)
          {
            for (int p = 0; (p - i) <= 0; p++)
            {
              for (int c = p; c <= (concept2.length - (p + i)); c++)
              {
                if (concept2[c].compareTo("") != 0)
                {
                  phrase = phrase.concat(" ").concat(concept2[c]);
                }
              }
              // pull all unique CUIds for phrase
              String CUIdQuery = "select distinct cui as type from mrxns_eng where mrxns_eng.nstr LIKE \""+phrase+"\"";
              rs = statement.executeQuery(CUIdQuery);

              // this query pulls all unique semantic types for this phrase
              // *Note* we use WHERE cui = "C###" OR cui = "C###" OR ...
              // and then strip off the last 3 characters
              String semanticTypeQuery = "select distinct sty as type from mrsty where";
              while (rs.next())
              {
                semanticTypeQuery.concat(" cui = ").concat(rs.getInt("cui")).concat(" OR");
              }
              semanticTypeQuery = semanticTypeQuery.substring(0,(semanticTypeQuery.length() - 3));

              // add all types to concept2 Types list
              rsConcept2 = statement.executeQuery(CUIdQuery);
            }
          }

          // Build query for UMLS relations
          String relationQuery = "Select * from srstre2 where";
          while (rsConcept1.next())
          {
            while (rsConcept2.next())
            {
              relationQuery.concat(" (STY1 = \""+ rsConcept1.getString("type") +"\"");
              relationQuery.concat(" AND ");
              relationQuery.concat("STY2 = \""+ rsConcept2.getString("type") +"\")");
              relationQuery.concat(" OR ");
              relationQuery.concat("(STY1 = \""+ rsConcept2.getString("type") +"\"");
              relationQuery.concat(" AND ");
              relationQuery.concat("STY2 = \""+ rsConcept1.getString("type") +"\")");
              relationQuery.concat(" OR");
            }
            rsConcept2.beforeFirst();
          }
          relationQuery = relationQuery.substring(0,(relationQuery.length() - 3));

          // run query
          rs = statement.executeQuery(relationQuery);
          String UMLSRelation;
          while (rs.next())
          {
            // build string from query result
            UMLSRelation = rs.getString("STY1");
            UMLSRelation.concat(rs.getString("RL"));
            UMLSRelation.concat(rs.getString("STY2"));

            // add query to appropriate list
            if (I2B2Relation.compareTo("TeRP") == 0)
            {
              if (TeRP.UMLSInteresting.contains(rs.getString("RL"))) {
                TeRP.UMLSRelationsList.add(UMLSRelation);
              }
            }
            else if (I2B2Relation.compareTo("TeCP") == 0)
            {
              if (TeCP.UMLSInteresting.contains(rs.getString("RL"))) {
                TeCP.UMLSRelationsList.add(UMLSRelation);
              }
            }
            else if (I2B2Relation.compareTo("TrIP") == 0)
            {
              if (TrIP.UMLSInteresting.contains(rs.getString("RL"))) {
                TrRP.UMLSRelationsList.add(UMLSRelation);
              }
            }
            else if (I2B2Relation.compareTo("TrWP") == 0)
            {
              if (TrWP.UMLSInteresting.contains(rs.getString("RL"))) {
                TrWP.UMLSRelationsList.add(UMLSRelation);
              }
            }
            else if (I2B2Relation.compareTo("TrAP") == 0)
            {
              if (TrCP.UMLSInteresting.contains(rs.getString("RL"))) {
                TrCP.UMLSRelationsList.add(UMLSRelation);
              }
            }
            else if (I2B2Relation.compareTo("TrNAP") == 0)
            {
              if (TrAP.UMLSInteresting.contains(rs.getString("RL"))) {
                TraP.UMLSRelationsList.add(UMLSRelation);
              }
            }
            else if (I2B2Relation.compareTo("TrCP") == 0)
            {
              if (TrNAP.UMLSInteresting.contains(rs.getString("RL"))) {
                TrNAP.UMLSRelationsLisst.add(UMLSRelation);
              }
            }
            else if (I2B2Relation.compareTo("PIP") == 0)
            {
              if (PIP.contains(rs.getString("RL"))) {
                PIP.UMLSRelationsList.add(UMLSRelation);
              }
            }
          } // end of record queries
        } // end of recordFile

        recordFile.close();
      }// end of nameFile

      in.close();

      out.write("TeRP:",0,5);
      TeRP.printToWriter(out);
      out.newLine();

      out.write("TeRP:",0,5);
      TeCP.printToWriter(out);
      out.newLine();

      out.write("TeRP:",0,5);
      TrIP.printToWriter(out);
      out.newLine();

      out.write("TeRP:",0,5);
      TrWP.printToWriter(out);
      out.newLine();

      out.write("TeRP:",0,5);
      TrCP.printToWriter(out);
      out.newLine();

      out.write("TeRP:",0,5);
      TrAP.printToWriter(out);
      out.newLine();

      out.write("TeRP:",0,5);
      TrNAP.printToWriter(out);
      out.newLine();

      out.write("TeRP:",0,5);
      PIP.printToWriter(out);
      out.newLine();

      out.close();
      conn.close();
        } else {
      System.out.println("Invalid parameters");
    }
  }
}



--- I2B2Relation.java ---
import java.util.*;
import java.io.*;

public class I2B2Relation {
  private class UMLSRelationsList {
    private class UMLSRelationsNode {
      String name;
      int count;
      UMLSRelationsNode next;

      public UMLSRelationsNode(String n)
      {
        name = n;
        count= 0;
        next = null;
      }

    }
    UMLSRelationsNode head;
    UMLSRelationsNode tail;

    public void add(String n)
    {
      // search list for string matching N
      UMLSRelationsNode current = head;

      while (current != null)
      {
        // if string found, increment that node's count
        if (current.name.compareTo(n) == 0) {
          current.count++;
          return;
        }
        current = current.next;
      }

      // if string not found, add node to beginning of list
      current = new UMLSRelationsNode(n);
      current.next = head;
      head = current;
    }

    public void printToWriter(BufferedWriter out) throws IOException
    {
      UMLSRelationsNode current = head;

      while (current != null)
      {
        out.write(current.name,0,current.name.length());
        out.write(" ",0,1);
        out.write(current.count);
        out.newLine();
        current = current.next;
      }

      out.flush();
    }
  }

  List<String> UMLSInteresting;
  UMLSRelationsList UMLSRelations;

  public I2B2Relation ()
  {
    UMLSInteresting = null;
    UMLSRelations = null;
  }
}