com.generalbioinformatics.rdf.AbstractTripleStore.java Source code

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Here is the source code for com.generalbioinformatics.rdf.AbstractTripleStore.java

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/**
* Copyright (c) 2015 General Bioinformatics Limited
* Distributed under the GNU GPL v2. For full terms see the file LICENSE.
*/
package com.generalbioinformatics.rdf;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.zip.GZIPOutputStream;

import nl.helixsoft.recordstream.RecordStream;
import nl.helixsoft.recordstream.StreamException;
import nl.helixsoft.recordstream.TsvRecordStream;
import nl.helixsoft.stats.DataFrame;
import nl.helixsoft.stats.DataFrameOperation;
import nl.helixsoft.util.HFileUtils;

/**
 * An abstract base class for TripleStores, 
 * providing a simple implementation of the caching feature.
 */
public abstract class AbstractTripleStore implements TripleStore {
    private File cacheDir = null;

    /** {@inheritDoc} */
    @Override
    public void setCacheDir(File dir) {
        this.cacheDir = dir;
    }

    @Override
    public DataFrame sparqlSelectDF(String query) throws StreamException {
        return DataFrameOperation.createFromRecordStream(sparqlSelect(query));
    }

    public RecordStream sparqlSelect(String query) throws StreamException {
        try {
            RecordStream rs;

            long start = System.currentTimeMillis();

            if (cacheDir == null) {
                rs = _sparqlSelectDirect(query);
                long delta = System.currentTimeMillis() - start;
                fireQueryPerformed(query, delta);
            } else {
                if (!cacheDir.exists()) {
                    if (!cacheDir.mkdirs())
                        throw new IOException("Could not create cache directory");
                }

                int hashCode = query.hashCode() + 3 * this.hashCode();
                String hashCodeString = String.format("%08x", hashCode);
                File cacheSubdir = new File(cacheDir, hashCodeString.substring(0, 2));
                File out = new File(cacheSubdir, hashCodeString + ".txt.gz");

                if (out.exists()) {
                    // merely "touch" the file, so we know the cached file was used recently.
                    org.apache.commons.io.FileUtils.touch(out);
                } else {
                    // make subdir if it doesn't exist.
                    if (!cacheSubdir.exists()) {
                        if (!cacheSubdir.mkdir())
                            throw new IOException("Couldn't create directory " + cacheSubdir);
                    }

                    File tmp = File.createTempFile(hashCodeString + "-", ".tmp", cacheSubdir);
                    try {
                        OutputStream os = new FileOutputStream(tmp);
                        GZIPOutputStream gos = new GZIPOutputStream(os);
                        RecordStream rsx = _sparqlSelectDirect(query);
                        long delta = System.currentTimeMillis() - start;
                        Utils.queryResultsToFile(this, delta, rsx, query, gos);
                        gos.finish();
                        os.close();
                        fireQueryPerformed(query, delta);
                    } catch (RuntimeException e) {
                        tmp.delete();
                        throw (e);
                    } catch (StreamException e) {
                        tmp.delete();
                        throw (e);
                    }
                    tmp.renameTo(out);
                }

                InputStream is = HFileUtils.openZipStream(out);
                rs = TsvRecordStream.open(is).filterComments().get();
            }

            return rs;
        } catch (IOException ex) {
            throw new StreamException(ex);
        }
    }

    protected void fireQueryPerformed(String query, long delta) {
        for (TripleStoreListener l : listeners) {
            l.queryPerformed(query, delta);
        }
    }

    private NS namespaces = new NS();

    public NamespaceMap getNamespaces() {
        return namespaces;
    }

    private List<TripleStoreListener> listeners = new ArrayList<TripleStoreListener>();

    @Override
    public void addListener(TripleStoreListener l) {
        listeners.add(l);
    }

    @Override
    public void removeListener(TripleStoreListener l) {
        listeners.remove(l);
    }
}