edu.harvard.i2b2.Icd9ToSnomedCT.BinResourceFromIcd9ToSnomedCTMap.java Source code

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Here is the source code for edu.harvard.i2b2.Icd9ToSnomedCT.BinResourceFromIcd9ToSnomedCTMap.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.Icd9ToSnomedCT;

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 https://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html
    
to get codes from metathesaurus!
*/
public class BinResourceFromIcd9ToSnomedCTMap {
    static Logger logger = LoggerFactory.getLogger(BinResourceFromIcd9ToSnomedCTMap.class);

    HashMap<String, String> Icd9ToSnomedCTMap;
    String inputDataFolder;
    final static String binFileName = "/Icd9ToSnomedCTMap.bin";

    public BinResourceFromIcd9ToSnomedCTMap(String inputDataFolder) throws IOException {

        this.inputDataFolder = inputDataFolder;
        Icd9ToSnomedCTMap = new HashMap<String, String>();
        initIcd9SnomedCTMap();
        serializeIcd9CodeToNameMap();

    }

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

    public void initIcd9SnomedCTMap() throws IOException {
        String inputFilePath = inputDataFolder + "ICD9CM_SNOMED_MAP_1TO1_201512.txt";
        final int maxLines = Utils.countLines(inputFilePath);
        CSV csv = CSV.separator('\t') // 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);
                //if(rowIndex==1)logger.trace(rowIndex+"->"+Arrays.asList(values).get(0)+"-"+Arrays.asList(values).get(7));
                if (rowIndex > 0) {
                    String icd = arr.get(0).trim();
                    String sno = arr.get(7).trim();
                    if (icd.contains("427.31"))
                        logger.trace("<" + icd + ">-><" + sno + ">");
                    //logger.trace(num+"->"+name);
                    Icd9ToSnomedCTMap.put(icd, sno);
                }
                if (rowIndex % 1000 == 0)
                    System.out.println((rowIndex * 100) / maxLines + "%-" + Icd9ToSnomedCTMap.size());
            }
        });
    }

    public void serializeIcd9CodeToNameMap() throws IOException {

        FileOutputStream fos = null;
        ObjectOutputStream oos = null;

        try {
            fos = new FileOutputStream(binFileName);

            oos = new ObjectOutputStream(fos);
            oos.writeObject(Icd9ToSnomedCTMap);

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

    public static HashMap<String, String> deSerializeIcd9CodeToNameMap() throws IOException {
        logger.debug("loading map..");
        HashMap<String, String> map = null;
        ObjectInputStream ois = null;
        InputStream fis = null;

        try {
            fis = BinResourceFromIcd9ToSnomedCTMap.class.getResourceAsStream(binFileName);
            if (fis == null)
                logger.error("mapping file not found:" + binFileName);
            ois = new ObjectInputStream(fis);
            map = (HashMap<String, String>) ois.readObject();

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

        logger.debug("..loaded");
        return map;
    }

    public static void main(String[] args) {

        try {
            new BinResourceFromIcd9ToSnomedCTMap("/Users/kbw19/Downloads/ICD9CM_SNOMEDCT_map_201512/");
        } catch (IOException e) {
            System.out.println(e.getMessage());
            e.printStackTrace();
            logger.error(e.getMessage(), e);
        }
    }

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