org.gbif.occurrence.util.CSVReader.java Source code

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Here is the source code for org.gbif.occurrence.util.CSVReader.java

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/***************************************************************************
 * Copyright 2010 Global Biodiversity Information Facility Secretariat
 * 
 * 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 org.gbif.occurrence.util;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.zip.GZIPInputStream;

import org.apache.commons.lang.text.StrTokenizer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * @author markus
 *
 */
public class CSVReader implements ClosableIterator<String[]>, Iterable<String[]> {
    private static final Logger LOG = LoggerFactory.getLogger(CSVReader.class);
    public final int headerRows;
    public final String encoding;
    public final String delimiter;
    public final Character quoteChar;
    public final String[] header;
    private final StrTokenizer tokenizer;
    private String row;
    private final BufferedReader br;

    public CSVReader(File source, String encoding, String delimiter, Character quotes, Integer headerRows)
            throws IOException {
        this.delimiter = delimiter;
        this.encoding = encoding;
        this.quoteChar = quotes;
        if (headerRows == null || headerRows < 0) {
            this.headerRows = 0;
        } else {
            this.headerRows = headerRows;
        }
        tokenizer = new StrTokenizer();
        tokenizer.setDelimiterString(delimiter);
        if (quotes != null) {
            tokenizer.setQuoteChar(quotes);
        }
        tokenizer.setIgnoreEmptyTokens(false);
        tokenizer.reset();
        InputStream fis = null;
        if (source.getName().endsWith(".gz")) {
            fis = new GZIPInputStream(new FileInputStream(source));
        } else {
            fis = new FileInputStream(source);
        }
        InputStreamReader reader = new InputStreamReader(fis, encoding);
        br = new BufferedReader(reader);
        row = br.readLine();
        // parse header row
        if (row == null) {
            header = null;
        } else {
            tokenizer.reset(row);
            header = tokenizer.getTokenArray();
        }
        // skip initial header rows?
        while (headerRows > 0) {
            headerRows--;
            row = br.readLine();
        }
    }

    /* (non-Javadoc)
     * @see org.gbif.file.ClosableIterator#close()
     */
    public void close() {
        try {
            br.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    /* (non-Javadoc)
     * @see java.util.Iterator#hasNext()
     */
    public boolean hasNext() {
        return row != null;
    }

    /* (non-Javadoc)
     * @see java.lang.Iterable#iterator()
     */
    public ClosableIterator<String[]> iterator() {
        return this;
    }

    /* (non-Javadoc)
     * @see java.util.Iterator#next()
     */
    public String[] next() {
        if (row == null) {
            return null;
        }
        tokenizer.reset(row);
        try {
            row = br.readLine();
            // skip empty lines
            while (row != null && row.equals("")) {
                row = br.readLine();
            }
        } catch (IOException e) {
            row = null;
            e.printStackTrace();
        }
        return tokenizer.getTokenArray();
    }

    /* (non-Javadoc)
     * @see java.util.Iterator#remove()
     */
    public void remove() {
        throw new UnsupportedOperationException("Remove not supported");
    }
}