import java.util.*;

import java.io.*;

import gov.nih.nlm.nls.skr.*;

public class metamappdr {

  static GenericObject gj = new GenericObject();

  public static void main(String[] args) throws Exception {

    Scanner in = new Scanner(new File("cleaned_pdr_data.csv"));

    PrintWriter out = new PrintWriter(new File("outputpdr.csv"));

    while (in.hasNext()) {

      String line = in.nextLine();

      boolean inQuotes = false;

      boolean inApos = false;

      ArrayList<String> terms = new ArrayList<String>();

      String term = "";

      for (int i = 0; i < line.length(); i++) {

        if (line.charAt(i) != ',' || inQuotes) {

          if (line.charAt(i) == '\"') inQuotes = !inQuotes;

          else term = term + line.charAt(i);

        }

        else {

          if (!inQuotes) {terms.add(term); term = "";}

        }

      }

      terms.add(term);

      out.print(terms.get(0) + "," + terms.get(1) + "," + terms.get(2) + ",\"[");

      ArrayList<String> indications = new ArrayList<String>();

      String indication = "";

      for (int i = 1; i < terms.get(3).length()-1; i++) {

        if (terms.get(3).charAt(i) != ',' || inApos) {

          if (terms.get(3).charAt(i) == '\'') inApos = !inApos;

          else indication = indication + terms.get(3).charAt(i);

        }

        else {

          if (!inApos) {indications.add(indication); indication = "";}

        }

      }

      indications.add(indication);

      for (String ind : indications) {

        PrintWriter tmp = new PrintWriter(new File("input.txt"));

        tmp.print(ind);

        tmp.close();

        out.print('\'' + getMetamap() + "\',");

      }

      out.print("]\",\"[");

      inApos = false;

      ArrayList<String> contrainds = new ArrayList<String>();

      String contraind = "";

      for (int i = 1; i < terms.get(4).length()-1; i++) {

        if (terms.get(4).charAt(i) != ',' || inApos) {

          if (terms.get(4).charAt(i) == '\'') inApos = !inApos;

          else contraind = contraind + terms.get(4).charAt(i);

        }

        else {

          if (!inApos) {contrainds.add(contraind); contraind = "";}

        }

      }

      contrainds.add(contraind);

      for (int i = 0; i < contrainds.size(); i++) {

        PrintWriter tmp = new PrintWriter(new File("input.txt"));

        tmp.print(contrainds.get(i));

        tmp.close();

        out.print('\'' + getMetamap() + "\'");

        if (i < contrainds.size() - 1) out.print(",");

      }

      out.print("]\"");

      out.println();

    }

    in.close();

    out.close();

  }

  static String getMetamap() {

    gj.setField("Email_Address", "neilmalur@hotmail.com");

    gj.setFileField("UpLoad_File", "./input.txt");

    //gj.setField("APIText", input);

    //gj.setField("Batch_Command", "MTI -opt1L_DCMS -E");

    gj.setField("Batch_Command", "metamap -pcI");

    gj.setField("BatchNotes", "SKR Web API test");

    gj.setField("SilentEmail", true);

    return gj.handleSubmission();

  }

}