org.tridas.io.formats.lipd.LiPDFile.java Source code

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Here is the source code for org.tridas.io.formats.lipd.LiPDFile.java

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/**
 * Copyright 2010 Peter Brewer and Daniel Murphy
 * 
 * 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.tridas.io.formats.lipd;

import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.StringWriter;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;

import jxl.write.WriteException;

import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.tridas.interfaces.ITridasSeries;
import org.tridas.io.I18n;
import org.tridas.io.defaults.IMetadataFieldSet;
import org.tridas.io.formats.lipd.TridasToLiPDDefaults.DefaultFields;
import org.tridas.io.formats.lipdmetadata.LiPDMetadataFile;
import org.tridas.io.util.TridasUtils;
import org.tridas.schema.TridasValues;

import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;

/**
 * LiPD format is used to describe a wide range of paleoclimate data.  
 * 
 * @author pbrewer
 *
 */
public class LiPDFile extends LiPDMetadataFile {

    public LiPDFile(TridasToLiPDDefaults argDefaults, List<TridasValues> values) {
        super(argDefaults, values);
    }

    @Override
    public String[] saveToString() {

        throw new UnsupportedOperationException(I18n.getText("fileio.binaryAsStringUnsupported"));

    }

    /**
     * An alternative to the normal saveToString() as this is a binary format
     * 
     * @param os
     * @throws IOException
     * @throws WriteException
     */
    public void saveToDisk(OutputStream os) throws IOException, WriteException {

        // Create a buffer for reading the files
        byte[] buf = new byte[1024];

        // Create the ZIP file
        ZipOutputStream out = new ZipOutputStream(os);

        // Compress the files

        // Create JSON File
        out.putNextEntry(new ZipEntry("LiPD.jsonld"));
        String json = getJSONFileString();
        ByteArrayInputStream in = new ByteArrayInputStream(json.getBytes(StandardCharsets.UTF_8));
        // Transfer bytes from the file to the ZIP file
        int len;
        while ((len = in.read(buf)) > 0) {
            out.write(buf, 0, len);
        }
        // Complete the entry
        out.closeEntry();
        in.close();

        // Create CSV File
        out.putNextEntry(new ZipEntry("lipd-data.csv"));
        String[] matrix = flipMatrix();
        String data = "";

        // Remove header
        for (int i = 1; i < matrix.length; i++) {
            data += matrix[i] + "\n";
        }
        in = new ByteArrayInputStream(data.getBytes(StandardCharsets.UTF_8));
        // Transfer bytes from the file to the ZIP file
        while ((len = in.read(buf)) > 0) {
            out.write(buf, 0, len);
        }
        // Complete the entry
        out.closeEntry();
        in.close();

        // Complete the ZIP file
        out.close();

    }

    private String[] flipMatrix() {

        String[] lines = new String[fileYearRange.span() + 1];

        ArrayList<String[]> matrix = getMatrix();

        for (int i = 0; i < lines.length; i++) {
            String line = "";
            for (String[] column : matrix) {
                if (column[i] == null) {
                    line += ",";
                } else {
                    line += column[i] + ",";
                }
            }
            lines[i] = line.substring(0, line.length() - 1);
        }

        return lines;
    }

    /**
     * @see org.tridas.io.IDendroFile#getExtension()
     */
    @Override
    public String getExtension() {
        return "lpd";
    }

    /**
     * @see org.tridas.io.IDendroFile#getSeries()
     */
    @Override
    public ITridasSeries[] getSeries() {
        return null;
    }

    /**
     * @see org.tridas.io.IDendroFile#getDefaults()
     */
    @Override
    public IMetadataFieldSet getDefaults() {
        return defaults;
    }

}