edu.utah.bmi.ibiomes.lite.ExperimentIndex.java Source code

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Here is the source code for edu.utah.bmi.ibiomes.lite.ExperimentIndex.java

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/*
 * iBIOMES - Integrated Biomolecular Simulations
 * Copyright (C) 2014  Julien Thibault, University of Utah
 * 
 * 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/>.
 */

package edu.utah.bmi.ibiomes.lite;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;

import org.apache.commons.compress.compressors.CompressorException;

import edu.utah.bmi.ibiomes.io.IBIOMESFileReader;

/**
 * Index of experiments published in iBIOMES Lite. Each experiment is represented by an entry in a dedicated text file.
 * @author Julien Thibault, University of Utah
 *
 */
public class ExperimentIndex {

    private File file;

    private class IndexEntry {
        long timestamp;
        String experimentPath;

        public IndexEntry(String experimentPath) {
            this.experimentPath = experimentPath;
            this.timestamp = (new Date()).getTime();
        }

        public IndexEntry(long timestamp, String experimentPath) {
            this.experimentPath = experimentPath;
            this.timestamp = timestamp;
        }

        @Override
        public String toString() {
            return (this.timestamp + "\t" + this.experimentPath);
        }
    }

    /**
     * Create reference to index file
     * @param filePath Path to index file
     * @throws IOException 
     */
    public ExperimentIndex(String filePath) throws IOException {
        Path path = Paths.get(filePath);
        if (Files.exists(path)) {
            Files.createFile(path);
        }
        this.file = new File(filePath);
    }

    private HashMap<String, IndexEntry> loadIndexFromFile() throws IOException, CompressorException {
        HashMap<String, IndexEntry> index = new HashMap<String, IndexEntry>();
        IBIOMESFileReader br = null;
        try {
            br = new IBIOMESFileReader(this.file);
            String line = null;
            while ((line = br.readLine()) != null) {
                line = line.trim();
                if (line.length() > 0) {
                    String[] entryValues = line.split("\\t");
                    long timestamp = Long.parseLong(entryValues[0]);
                    String experiment = entryValues[1];
                    index.put(experiment, new IndexEntry(timestamp, experiment));
                }
            }
            return index;
        } finally {
            if (br != null)
                br.close();
        }
    }

    private void storeIndexToFile(HashMap<String, IndexEntry> index) throws IOException {
        BufferedWriter bw = new BufferedWriter(new FileWriter(this.file, false));
        Collection<IndexEntry> entries = index.values();
        for (IndexEntry entry : entries) {
            bw.append(entry.toString() + "\n");
        }
        bw.close();
    }

    /**
     * Add entry (experiment) to index
     * @param experimentPath Path to experiment
     * @throws IOException 
     */
    public void addEntry(String experimentPath) throws IOException {
        BufferedWriter bw = new BufferedWriter(new FileWriter(this.file, true));
        bw.append(new IndexEntry(experimentPath).toString() + "\n");
        bw.close();
    }

    /**
     * Remove entry (experiment) from index
     * @param experimentPath Path to experiment
     * @throws IOException 
     * @throws CompressorException 
     */
    public void removeEntry(String experimentPath) throws IOException, CompressorException {
        HashMap<String, IndexEntry> index = loadIndexFromFile();
        index.remove(experimentPath);
        storeIndexToFile(index);
    }

    /**
     * Remove all entries
     * @throws IOException 
     */
    public void clearAll() throws IOException {
        BufferedWriter bw = new BufferedWriter(new FileWriter(this.file, false));
        bw.write("");
        bw.close();
    }
}