import java.util.*;

import java.io.*;

import java.net.*;

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

public class ctmetamaptest {

  static GenericObject gj = new GenericObject();

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

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

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

    String useless = in.nextLine();

    while(in.hasNext()) {

      String[] terms = in.nextLine().split(",");

      String source = getURLSource(terms[2]);

      int index = source.indexOf("display_order");

      if (index > 0) {

        ArrayList<Integer> indices = new ArrayList<Integer>();

        ArrayList<Integer> startinds = new ArrayList<Integer>();

        ArrayList<Integer> endinds = new ArrayList<Integer>();

        while (index > 0) {

          indices.add(index);

          startinds.add(source.indexOf("description", index));

          endinds.add(source.indexOf("}", index));

          index = source.indexOf("display_order", index+1);

        }

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

        for (int i = 0; i < startinds.size(); i++) strings.add(source.substring(startinds.get(i) + 14, endinds.get(i)-1));

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

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

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

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

          tmp.close();

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

          if (i < strings.size() - 1) 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();

  }

  public static String getURLSource(String url) throws IOException

    {

        URL urlObject = new URL(url);

        URLConnection urlConnection = urlObject.openConnection();

        urlConnection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11");

        try {

        return toString(urlConnection.getInputStream());}catch(Exception e) {return "";}

    }

  private static String toString(InputStream inputStream) throws IOException

    {

        try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream, "UTF-8")))

        {

            String inputLine;

            StringBuilder stringBuilder = new StringBuilder();

            while ((inputLine = bufferedReader.readLine()) != null)

            {

                stringBuilder.append(inputLine);

            }

            return stringBuilder.toString();

        }

    }

}