org.gbif.file.CSVReader.java Source code

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Here is the source code for org.gbif.file.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.file;

import org.gbif.dwc.text.ArchiveFile;
import org.gbif.utils.file.ClosableReportingIterator;

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.Map;
import java.util.Set;

import com.google.common.base.Strings;
import com.google.common.cache.Cache;
import com.google.common.cache.CacheBuilder;
import org.apache.commons.lang3.text.StrTokenizer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class CSVReader implements ClosableReportingIterator<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 int rows;
    private int readRows;
    private final Map<Integer, String> emptyLines;
    private final BufferedReader br;
    private boolean rowError;
    private String errorMessage;
    private Exception exception;

    public CSVReader(File source, String encoding, String delimiter, Character quotes, Integer headerRows)
            throws IOException {
        this(new FileInputStream(source), encoding, delimiter, quotes, headerRows);
    }

    public CSVReader(InputStream stream, String encoding, String delimiter, Character quotes, Integer headerRows)
            throws IOException {
        Cache<Integer, String> cache = CacheBuilder.newBuilder().maximumSize(1000).build();
        this.emptyLines = cache.asMap();
        this.rows = 0;
        this.readRows = 0;
        this.delimiter = delimiter;
        this.encoding = encoding;
        this.quoteChar = quotes;
        this.headerRows = headerRows == null || headerRows < 0 ? 0 : headerRows;
        tokenizer = new StrTokenizer();
        tokenizer.setDelimiterString(delimiter);
        if (quotes != null) {
            tokenizer.setQuoteChar(quotes);
        }
        tokenizer.setIgnoreEmptyTokens(false);
        tokenizer.reset();
        InputStreamReader reader = new InputStreamReader(stream, 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();
        }
    }

    public static CSVReader build(ArchiveFile source) throws IOException {
        return CSVReaderFactory.build(source);
    }

    public static CSVReader build(File source) throws IOException {
        return CSVReaderFactory.build(source);
    }

    public static CSVReader build(File source, String delimiter, boolean header) throws IOException {
        return CSVReaderFactory.build(source, delimiter, header);
    }

    public static CSVReader build(File source, String encoding, String delimiter, Character quotes, int headerRows)
            throws IOException {
        return CSVReaderFactory.build(source, encoding, delimiter, quotes, headerRows);
    }

    public static CSVReader build(File source, String encoding, String delimiter, int headerRows)
            throws IOException {
        return CSVReaderFactory.build(source, encoding, delimiter, headerRows);
    }

    public void close() {
        try {
            br.close();
        } catch (IOException e) {
            LOG.debug("Exception caught", e);
        }
    }

    /**
     * @return the current line number of the String[] iterator
     */
    public int currLineNumber() {
        return rows;
    }

    /**
     * @return a set of the line numbers of the firsts empty rows found in the file
     */
    public Set<Integer> getEmptyLines() {
        return emptyLines.keySet();
    }

    /**
     * @return the number of rows of data that were correctly read from the file
     */
    public int getReadRows() {
        return readRows;
    }

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

    public ClosableReportingIterator<String[]> iterator() {
        return this;
    }

    /*
     * (non-Javadoc)
     * @see java.util.Iterator#next()
     */
    public String[] next() {
        if (row == null) {
            return null;
        }
        tokenizer.reset(row);
        resetReportingIterator();
        try {
            row = br.readLine();
            rows++;
            // skip empty lines
            while (row != null && row.length() == 0) {
                // save line number of empty line
                emptyLines.put(rows + headerRows + 1, "");
                row = br.readLine();
                rows++;
            }
            readRows++;
        } catch (IOException e) {
            LOG.debug("Exception caught", e);
            rowError = true;
            exception = e;

            // construct error message showing exception and problem row
            StringBuilder msg = new StringBuilder();
            msg.append("Exception caught: ");
            msg.append(e.getMessage());
            if (!Strings.isNullOrEmpty(row)) {
                msg.append("\n");
                msg.append("Row: ");
                msg.append(row);
            }
            errorMessage = msg.toString();

            // ensure iteration terminates
            row = null;
        }
        return tokenizer.getTokenArray();
    }

    /**
     * Reset all reporting parameters.
     */
    private void resetReportingIterator() {
        rowError = false;
        exception = null;
        errorMessage = null;
    }

    public void remove() {
        throw new UnsupportedOperationException("Remove not supported");
    }

    public boolean hasRowError() {
        return rowError;
    }

    public String getErrorMessage() {
        return errorMessage;
    }

    public Exception getException() {
        return exception;
    }
}