SiLeBAT/FSK-Lab

/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Department Biological Safety - BfR
 *******************************************************************************/
package de.bund.bfr.knime.pmm.combaseio.lib;

import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.UnsupportedEncodingException;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.List;

import de.bund.bfr.knime.pmm.common.KnimeUtils;
import de.bund.bfr.knime.pmm.common.MiscXml;
import de.bund.bfr.knime.pmm.common.PmmException;
import de.bund.bfr.knime.pmm.common.PmmTimeSeries;
import de.bund.bfr.knime.pmm.common.PmmXmlDoc;
import de.bund.bfr.knime.pmm.common.PmmXmlElementConvertable;
import de.bund.bfr.knime.pmm.common.TimeSeriesXml;
import de.bund.bfr.knime.pmm.common.pmmtablemodel.AttributeUtilities;

public class CombaseWriter {

    private LinkedList<PmmTimeSeries> buffer;
    private String filename;
    private MiscConversion conversion;

    public CombaseWriter(final String filename) {
        conversion = new MiscConversion();
        this.filename = filename;
        buffer = new LinkedList<>();
    }

    public void add(final PmmTimeSeries candidate) throws PmmException {

        if (candidate == null)
            throw new PmmException("Candidate must not be null.");

        buffer.add(candidate);
    }

    public void flush() throws UnsupportedEncodingException, FileNotFoundException, IOException, PmmException {
        flush16le(); // "UTF-16LE"
    }

    public void flush16le() throws UnsupportedEncodingException, FileNotFoundException, IOException, PmmException {
        StringBuffer buf = new StringBuffer();
        for (PmmTimeSeries candidate : buffer) {
            String organism = "";
            String matrix = "";

            if (candidate.getAgentName() != null) {
                organism = candidate.getAgentName();
            } else if (candidate.getAgentDetail() != null) {
                organism = candidate.getAgentDetail();
            }

            if (candidate.getMatrixName() != null) {
                matrix = candidate.getMatrixName();
            } else if (candidate.getMatrixDetail() != null) {
                matrix = candidate.getMatrixDetail();
            }

            if (candidate.hasCombaseId()) {
                buf.append("\"RecordID\"\t\"" + candidate.getCombaseId() + "\"\n");
            }

            if (candidate.hasAgent()) {
                buf.append("\"Organism\"\t\"" + organism + "\"\n");
            }

            if (candidate.hasMatrix()) {
                buf.append("\"Environment\"\t\"" + matrix + "\"\n");
            }

            if (candidate.hasTemperature()) {
                buf.append("\"Temperature\"\t\"" + candidate.getTemperature() + " °C\"\n");
            }

            if (candidate.hasPh()) {
                buf.append("\"pH\"\t\"" + candidate.getPh() + "\"\n");
            }

            if (candidate.hasWaterActivity()) {
                buf.append("\"Water Activity\"\t\"" + candidate.getWaterActivity() + "\"\n");
            }

            if (candidate.hasMisc()) {
                PmmXmlDoc doc = candidate.getMisc();
                if (doc != null) {
                    // String xmlStr = doc.toXmlString();
                    String cb = xml2Combase(doc);
                    if (cb != null)
                        buf.append("\"Conditions\"\t\"" + cb + "\"\n");
                }
            }

            /*
             * if( candidate.hasMaximumRate() ) { buf.append(
             * "\"Maximum Rate\"\t\""+candidate.getMaximumRate()+"\"\n" ); }
             * 
             * if( candidate.hasDoublingTime() ) { buf.append(
             * "\"Doubling Time (h)\"\t\""+candidate.getDoublingTime()+"\"\n" );
             * }
             */

            buf.append("\"Time (h)\"\t\"logc\"\n");

            if (!candidate.isEmpty()) {
                PmmXmlDoc tsXmlDoc = candidate.getTimeSeries();
                for (PmmXmlElementConvertable el : tsXmlDoc.getElementSet()) {
                    if (el instanceof TimeSeriesXml) {
                        TimeSeriesXml tsx = (TimeSeriesXml) el;
                        buf.append("\"" + tsx.time + "\"\t\"" + tsx.concentration + "\"\n");
                    }
                }
            }

            buf.append("\n\n\n");
        }
        OutputStream out = new FileOutputStream(KnimeUtils.getFile(filename));
        out.write(encodeString(buf.toString()));
        out.close();
    }

    public static byte[] encodeString(final String message) {

        byte[] tmp = null;
        try {
            tmp = message.getBytes("UTF-16LE");
        } catch (UnsupportedEncodingException e) {
            // should not possible
            AssertionError ae = new AssertionError("Could not encode UTF-16LE");
            ae.initCause(e);
            throw ae;
        }

        // use brute force method to add BOM
        byte[] utf16lemessage = new byte[2 + tmp.length];
        utf16lemessage[0] = (byte) 0xFF;
        utf16lemessage[1] = (byte) 0xFE;
        System.arraycopy(tmp, 0, utf16lemessage, 2, tmp.length);
        return utf16lemessage;
    }

    private String xml2Combase(PmmXmlDoc misc) {
        List<Integer> tempPhAwIds = Arrays.asList(AttributeUtilities.ATT_TEMPERATURE_ID, AttributeUtilities.ATT_PH_ID,
                AttributeUtilities.ATT_AW_ID);
        String result = null;
        if (misc != null) {
            result = "";
            for (PmmXmlElementConvertable el : misc.getElementSet()) {
                if (el instanceof MiscXml) {
                    MiscXml mx = (MiscXml) el;

                    if (tempPhAwIds.contains(mx.id)) {
                        continue;
                    }

                    if (!result.isEmpty())
                        result += ", ";
                    result += conversion.pmmToCombase(mx);
                    if (mx.unit != null && !mx.unit.isEmpty())
                        result += " (" + mx.unit + ")";
                    if (mx.value != null && !Double.isNaN(mx.value))
                        result += ":" + mx.value;
                }
            }
        }
        return result;
    }
}