com.apelon.akcds.loinc.CSVFileReader.java Source code

Introduction

Here is the source code for com.apelon.akcds.loinc.CSVFileReader.java

Source

/**
 * Copyright Notice
 *
 * This is a work of the U.S. Government and is not subject to copyright
 * protection in the United States. Foreign copyrights may apply.
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package com.apelon.akcds.loinc;

import gov.va.oia.terminology.converters.sharedUtils.ConsoleUtil;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.Arrays;
import org.apache.commons.io.input.BOMInputStream;
import au.com.bytecode.opencsv.CSVReader;

/**
 * 
 * {@link CSVFileReader}
 *
 * Reads the CSV formatted release files of LOINC, and the custom release notes file
 * to extract the date and time information.
 * 
 * @author <a href="mailto:daniel.armbrust.list@gmail.com">Dan Armbrust</a>
 */
public class CSVFileReader extends LOINCReader {
    String[] header;
    CSVReader reader;
    String version = null;
    String release = null;

    public CSVFileReader(File f) throws IOException {
        ConsoleUtil.println("Using the data file " + f.getAbsolutePath());
        //Their new format includes the (optional) UTF-8 BOM, which chokes java for stupid legacy reasons.
        reader = new CSVReader(
                new BufferedReader(new InputStreamReader(new BOMInputStream(new FileInputStream(f)))));
        header = readLine();

        readReleaseNotes(f.getParentFile());
    }

    private void readReleaseNotes(File dataFolder) throws IOException {
        File relNotes = null;
        for (File f : dataFolder.listFiles()) {
            if (f.getName().toLowerCase().equals("loinc_releasenotes.txt")) {
                relNotes = f;
                break;
            }
        }
        if (relNotes.exists()) {
            BufferedReader br = new BufferedReader(new FileReader(relNotes));
            String line = br.readLine();
            while (line != null) {
                if (line.contains("Version")) {
                    String temp = line.substring(line.indexOf("Version") + "Version ".length());
                    temp = temp.replace('|', ' ');
                    version = temp.trim();

                }
                if (line.contains("Released")) {
                    String temp = line.substring(line.indexOf("Released") + "Released ".length());
                    temp = temp.replace('|', ' ');
                    release = temp.trim();
                    break;
                }
                line = br.readLine();
            }
            br.close();
        } else {
            ConsoleUtil.printErrorln("Couldn't find release notes file - can't read version or release date!");
        }
    }

    @Override
    public String getVersion() {
        return version;
    }

    @Override
    public String getReleaseDate() {
        return release;
    }

    @Override
    public String[] getHeader() {
        return header;
    }

    @Override
    public String[] readLine() throws IOException {
        String[] temp = reader.readNext();
        if (temp != null) {
            if (fieldCount_ == 0) {
                fieldCount_ = temp.length;
                int i = 0;
                for (String s : temp) {
                    fieldMapInverse_.put(i, s);
                    fieldMap_.put(s, i++);
                }
            } else if (temp.length < fieldCount_) {
                temp = Arrays.copyOf(temp, fieldCount_);
            } else if (temp.length > fieldCount_) {
                throw new RuntimeException("Data error - to many fields found on line: " + Arrays.toString(temp));
            }
        }
        return temp;
    }

    @Override
    public void close() throws IOException {
        reader.close();
    }

}