pt.ua.dicoogle.core.query.ExportToCSVQueryTask.java Source code

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Here is the source code for pt.ua.dicoogle.core.query.ExportToCSVQueryTask.java

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/**
 * Copyright (C) 2014  Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/
 *
 * This file is part of Dicoogle/dicoogle.
 *
 * Dicoogle/dicoogle 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.
 *
 * Dicoogle/dicoogle 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 Dicoogle.  If not, see <http://www.gnu.org/licenses/>.
 */
package pt.ua.dicoogle.core.query;

import java.io.OutputStream;
import java.io.PrintWriter;
import java.util.HashMap;
import java.util.List;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.ExecutionException;

import org.apache.commons.lang3.StringUtils;

import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

import pt.ua.dicoogle.sdk.datastructs.SearchResult;
import pt.ua.dicoogle.sdk.task.JointQueryTask;
import pt.ua.dicoogle.sdk.task.Task;

public class ExportToCSVQueryTask extends JointQueryTask {

    private static final Logger log = LogManager.getLogger(ExportToCSVQueryTask.class.getName());

    private static String[] searchChars = new String[] { "\n", ";" };
    private static String[] replaceChars = new String[] { "", "," };

    private List<String> tagsOrder;
    // private OutputStream outputStream;
    private PrintWriter writter;
    private CountDownLatch latch;

    private int nLines = 0;

    public ExportToCSVQueryTask(List<String> tagsOrder, OutputStream outputStream) {
        super();
        this.tagsOrder = tagsOrder;
        this.latch = new CountDownLatch(1);
        writter = new PrintWriter(outputStream);

        printFirstLine();
    }

    @Override
    public void onCompletion() {
        // TODO Auto-generated method stub
        writter.flush();
        writter.close();
        latch.countDown();

        log.info("Exported CSV Table: ", tagsOrder.toString(), nLines);
    }

    @Override
    public void onReceive(Task<Iterable<SearchResult>> e) {
        // TODO Auto-generated method stub

        try {
            Iterable<SearchResult> it = e.get();
            for (SearchResult result : it) {
                printLine(result);
            }
        } catch (InterruptedException | ExecutionException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }

    }

    /**
     * Print the first line of the .csv file
     * 
     */
    private void printFirstLine() {
        StringBuilder builder = new StringBuilder();

        log.debug("Started, Printing first line: ", tagsOrder);

        for (String tag : tagsOrder) {
            builder.append(tag).append(";");
        }

        this.writter.println(builder.toString());
    }

    private void printLine(SearchResult result) {
        StringBuilder builder = new StringBuilder();

        HashMap<String, Object> extraFields = result.getExtraData();

        for (String tag : tagsOrder) {
            Object temp1 = extraFields.get(tag);

            String s = StringUtils.trimToEmpty(temp1.toString());

            if (s.length() > 0) {
                String temp = StringUtils.replaceEach(s, searchChars, replaceChars);
                builder.append(temp).append(";");
            } else {
                builder.append(";");
            }
        }

        log.debug("Printing Line: ", builder.toString());
        nLines++;
        this.writter.println(builder.toString());
    }

    public void await() {
        // TODO Auto-generated method stub
        try {
            latch.await();
        } catch (InterruptedException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }

}