edu.harvard.i2b2.Icd9.BinResourceFromIcd9Data.java Source code

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Here is the source code for edu.harvard.i2b2.Icd9.BinResourceFromIcd9Data.java

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/*
 * Copyright (c) 2006-2007 Massachusetts General Hospital 
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the i2b2 Software License v1.0 
 * which accompanies this distribution. 
 * 
 * Contributors:
 *       Kavishwar Wagholikar (kavi)
 *       July 17, 2015
 */
package edu.harvard.i2b2.Icd9;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Reader;
import java.io.StringReader;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.Arrays;

import javax.xml.bind.JAXBException;

import org.apache.commons.csv.CSVFormat;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import au.com.bytecode.opencsv.CSV;
import au.com.bytecode.opencsv.CSVParser;
import au.com.bytecode.opencsv.CSVReadProc;
import au.com.bytecode.opencsv.CSVReader;

/*
Download data from http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html
    
to get codes from metathesaurus!
*/
public class BinResourceFromIcd9Data {
    static Logger logger = LoggerFactory.getLogger(BinResourceFromIcd9Data.class);

    HashMap<String, String> Icd9CodeToNameMap;
    String inputDataFolder;

    public BinResourceFromIcd9Data(String inputDataFolder) throws IOException {

        this.inputDataFolder = inputDataFolder;
        Icd9CodeToNameMap = new HashMap<String, String>();
        initIcd9CodeToNameMap();
        serializeIcd9CodeToNameMap();

    }

    private static final CSV csv = CSV.separator(';').quote('\'').skipLines(1).charset("UTF-8").create();

    /*
    public void toDoinitIcd9CodeToNameMap() throws IOException, TikaException {
       String inputFilePath = "/Users/kbw19/Downloads/Dindex12.rtf";
       FileInputStream is=new FileInputStream(inputFilePath);
           
           
        
        
       File tmpFile= File.createTempFile("Dindex12",".txt.tmp");
       FileOutputStream os=new FileOutputStream(tmpFile);
        
       Tika tika = new Tika();
        String txtFormat=null;
       try {
       txtFormat=tika.parseToString(is);
        } finally {
       is.close();
        }
           
        os.write(txtFormat.getBytes());
        os.close();
        logger.info("created:"+tmpFile.getAbsolutePath());
            
       final int maxLines = Utils.countLines(tmpFile.getAbsolutePath());
       try (BufferedReader br = new BufferedReader(new FileReader(tmpFile)))
       {
        
     String sCurrentLine;
        
     while ((sCurrentLine = br.readLine()) != null) {
        System.out.println(sCurrentLine);
     }
        
       } catch (IOException e) {
     e.printStackTrace();
       } 
        
           
           
    }
    */

    public void initIcd9CodeToNameMap() throws IOException {
        String inputFilePath = inputDataFolder + "CMS31_DESC_LONG_DX.txt";
        final int maxLines = Utils.countLines(inputFilePath);
        CSV csv = CSV.separator(',') // delimiter of fields
                .quote('"') // quote character
                .create(); // new instance is immutable
        //File csvData = new File(inputFilePath);
        csv.read(inputFilePath, new CSVReadProc() {
            public void procRow(int rowIndex, String... values) {
                List<String> arr = Arrays.asList(values);
                //logger.trace(rowIndex+""+Arrays.asList(values).get(0));
                if (rowIndex > 1) {
                    int sep = arr.get(0).indexOf(" ");
                    String num = arr.get(0).substring(0, sep).trim();
                    String name = arr.get(0).substring(sep + 1).trim();
                    if (num.contains("37993") || num.contains("V902"))
                        logger.trace("<" + num + ">-><" + name + ">");
                    //logger.trace(num+"->"+name);
                    Icd9CodeToNameMap.put(num, name);
                }
                if (rowIndex % 1000 == 0)
                    System.out.println((rowIndex * 100) / maxLines + "%-" + Icd9CodeToNameMap.size());
            }
        });
    }

    public void serializeIcd9CodeToNameMap() throws IOException {

        FileOutputStream fos = null;
        ObjectOutputStream oos = null;

        try {
            fos = new FileOutputStream("Icd9CodeToNameMap.bin");

            oos = new ObjectOutputStream(fos);
            oos.writeObject(Icd9CodeToNameMap);

        } catch (Exception e) {
            logger.error(e.getMessage(), e);
        } finally {
            fos.close();
            oos.close();
        }
    }

    public static HashMap<String, String> deSerializeIcd9CodeToNameMap() throws IOException {

        HashMap<String, String> map = null;
        ObjectInputStream ois = null;
        InputStream fis = null;

        try {
            fis = BinResourceFromIcd9Data.class.getResourceAsStream("/icd9/Icd9CodeToNameMap.bin");
            ois = new ObjectInputStream(fis);
            map = (HashMap<String, String>) ois.readObject();

        } catch (Exception e) {
            logger.error(e.getMessage(), e);
        } finally {
            ois.close();
            fis.close();
        }

        return map;
    }

    public static void main(String[] args) {

        try {
            new BinResourceFromIcd9Data(//"/Users/kbw19/Downloads/");
                    "/Users/kbw19/Downloads/cmsv31-master-descriptions/");
        } catch (IOException e) {
            // TODO Auto-generated catch block
            System.out.println(e.getMessage());

            e.printStackTrace();
        }
    }

    static String readFile(String path, Charset encoding) throws IOException {
        byte[] encoded = Files.readAllBytes(Paths.get(path));
        return new String(encoded, encoding);
    }
}