EDIT

// $Id$

/**

* Copyright (C) 2015 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package org.bgbm.biovel.drf.store;

import java.io.File;

import java.io.FileInputStream;

import java.io.FileOutputStream;

import java.io.IOException;

import java.io.InputStream;

import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;

import org.apache.commons.compress.compressors.gzip.GzipUtils;

import org.apache.commons.compress.utils.IOUtils;

import org.apache.commons.io.FileUtils;

import org.apache.commons.io.FilenameUtils;

import org.apache.http.client.ClientProtocolException;

import org.apache.http.client.methods.CloseableHttpResponse;

import org.apache.http.client.methods.HttpGet;

import org.apache.http.impl.client.CloseableHttpClient;

import org.apache.http.impl.client.HttpClients;

import org.apache.jena.query.Dataset;

import org.apache.jena.query.ReadWrite;

import org.apache.jena.rdf.model.Model;

import org.apache.jena.tdb.TDBFactory;

import org.apache.jena.tdb.base.file.Location;

import org.slf4j.Logger;

import org.slf4j.LoggerFactory;

/**

 * @author a.kohlbecker

 * @date Oct 19, 2015

 *

 */

public class TripleStore {

    protected Logger logger = LoggerFactory.getLogger(TripleStore.class);

    private static final File tmpDir = new File(System.getProperty("java.io.tmpdir"));

    private static final File userHomeDir = new File(System.getProperty("user.home"));

    private static final File utisHome = new File(userHomeDir, ".utis");

    private File rdfFile = null;

    private Dataset dataset = null;

    public TripleStore() {

    }

    /**

     *

     * @param rdfFileUri

     *  the location of the file to load the rdf triples from

     * @throws IOException

     */

    public void loadIntoStore(String rdfFileUri) throws IOException {

        this.rdfFile = downloadAndExtract(rdfFileUri);

        createStore();

    }

    /**

     * WARNING!!! This needs at least 1.5GB of heap space!!!

     * set -Xmx1500M

     *

     * NOTE: The bulkloader is a faster way to load data into an empty dataset than just using the Jena update operations.

     * the bulkloader also requires less memory

     * It is accessed through the command line utility tdbloader.

     *

     * rm /tmp/drf_tnb_store/*; bin/tdbloader2 -l /tmp/drf_tnb_store /tmp/species.rdf

     * @throws IOException

     */

    private void createStore() throws IOException {

        boolean doClearStoreLocation = rdfFile != null;

        boolean doLoadRdfFile = rdfFile != null;

        File tdbStoreFolder = new File(utisHome, "tdb" + File.separator);

        if(tdbStoreFolder.exists()) {

            if( doClearStoreLocation ) {

                FileUtils.cleanDirectory(tdbStoreFolder);

            }

        } else {

            tdbStoreFolder.mkdirs();

        }

        Location location = Location.create(tdbStoreFolder.toString());

        Dataset dataset = TDBFactory.createDataset(location);

        logger.info("Using TDB store at " + location);

        dataset.begin(ReadWrite.READ) ;

        // Get model inside the transaction

        Model model = dataset.getDefaultModel() ;

        logger.info("Dataset in TDB has " + dataset.asDatasetGraph().size() + " named graphs");

        logger.info("Model-size: " + model.size());

        dataset.end();

        if(doLoadRdfFile) {

            dataset.begin(ReadWrite.WRITE);

            model = dataset.getDefaultModel();

            // parse InputStream as RDF in Turtle format

            InputStream fin = new FileInputStream(rdfFile);

            logger.info("loading RDF/XML into TDB store");

            model.read(fin, null, "RDF/XML");

            logger.info("loading RDF/XML done");

            logger.info("Dataset in TDB has " + dataset.asDatasetGraph().size() + " named graphs");

            logger.info("Model-size: " + model.size());

            dataset.commit();

            dataset.end();

            logger.info("rdf loaded into TDB store at " + tdbStoreFolder);

        }

        this.setDataset(dataset);

    }

    /**

     * @param rdfFileUri

    *

    */

   private File downloadAndExtract(String rdfFileUri) {

       File expandedFile = null;

       CloseableHttpClient httpClient = HttpClients.createDefault();

       CloseableHttpResponse response;

       try {

           // 1. download and store in local filesystem in TMP

           logger.debug("downloading rdf file from " + rdfFileUri);

           HttpGet httpGet = new HttpGet(rdfFileUri);

           response = httpClient.execute(httpGet);

           String archiveFileName = FilenameUtils.getName(httpGet.getURI().getRawPath());

           File archiveFile = new File(tmpDir, archiveFileName);

           FileOutputStream fout = new FileOutputStream(archiveFile);

           IOUtils.copy(response.getEntity().getContent(), new FileOutputStream(archiveFile));

           fout.close();

           logger.debug(archiveFile.length() + " bytes downloaded to " + archiveFile.getCanonicalPath());

           // 2. extract the archive

           FileInputStream fin = new FileInputStream(archiveFile);

           InputStream ain = null;

           if(GzipUtils.isCompressedFilename(archiveFileName)) {

               logger.debug("Extracting GZIP file " + archiveFile.getCanonicalPath());

               ain = new GzipCompressorInputStream(fin);

           } else {

               // TO UNZIP

               //ArchiveInputStream ain = new ArchiveStreamFactory().createArchiveInputStream(ArchiveStreamFactory.ZIP, fin);

           }

           expandedFile = new File(tmpDir, GzipUtils.getUncompressedFilename(archiveFileName));

           fout = new FileOutputStream(expandedFile);

           IOUtils.copy(ain, fout);

           fout.close();

           fin.close();

           logger.debug("Extracted to " + expandedFile.getCanonicalPath());

       } catch (ClientProtocolException e) {

           // TODO Auto-generated catch block

           e.printStackTrace();

       } catch (IOException e) {

           // TODO Auto-generated catch block

           e.printStackTrace();

       }

       return expandedFile;

   }

    /**

     * @return the dataset

     */

    public Dataset getDataset() {

        return dataset;

    }

    /**

     * @param dataset the dataset to set

     */

    public void setDataset(Dataset dataset) {

        this.dataset = dataset;

    }

}