EDIT

/**

 * 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.query;

import java.io.File;

import java.io.FileInputStream;

import java.io.FileOutputStream;

import java.io.IOException;

import java.io.InputStream;

import java.net.URI;

import java.net.URISyntaxException;

import java.util.NoSuchElementException;

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.atlas.web.HttpException;

import org.apache.jena.query.Dataset;

import org.apache.jena.query.Query;

import org.apache.jena.query.QueryExecution;

import org.apache.jena.query.QueryExecutionFactory;

import org.apache.jena.query.QueryFactory;

import org.apache.jena.query.ReadWrite;

import org.apache.jena.query.ResultSet;

import org.apache.jena.query.ResultSetFormatter;

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

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

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

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

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

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

import org.apache.jena.tdb.TDBFactory;

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

import org.bgbm.biovel.drf.checklist.DRFChecklistException;

import org.bgbm.biovel.drf.checklist.EEA_BDC_Client.RdfSchema;

import org.slf4j.Logger;

import org.slf4j.LoggerFactory;

/**

 * @author a.kohlbecker

 * @date Sep 30, 2015

 *

 */

public class SparqlClient implements IQueryClient {

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

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

    private Opmode opmode = null;

    private final String baseUri;

    private File rdfFile = null;

    private Dataset dataset = null;

    public enum Opmode{

        SPARCLE_ENDPOINT, RDF_ARCHIVE;

    }

    /**

     *

     */

    public SparqlClient(String baseUri, Opmode opmode) {

        this.baseUri = baseUri;

        this.opmode = opmode;

        if(opmode.equals(Opmode.RDF_ARCHIVE)) {

            if(baseUri != null) {

                this.rdfFile = downloadAndExtract();

            }

            try {

                createStore();

            } catch (IOException e) {

                // TODO Auto-generated catch block

                e.printStackTrace();

            }

        }

    }

    /**

     *

     */

    private File downloadAndExtract() {

        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 " + baseUri);

            HttpGet httpGet = new HttpGet(baseUri);

            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;

    }

    /**

     * 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(tmpDir, "drf_tnb_store" + 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.dataset = dataset;

    }

    public String select(String queryString) throws DRFChecklistException {

        QueryExecution qe = executionFor(queryString);

        try {

            ResultSet results = qe.execSelect();

            System.err.println(ResultSetFormatter.asText(results));

        } catch (HttpException e) {

            switch(e.getResponseCode()) {

                // interpretation based on

                // http://image.slidesharecdn.com/swtss1006sparql-100614020655-phpapp02/95/semantic-web-technologies-ss-2010-06-sparql-46-728.jpg?cb=1276481316

                case 400:

                    throw new DRFChecklistException("Malformed Query ?", e);

                case 500:

                    throw new DRFChecklistException("Query Request Refused ?", e);

                default:

                    throw e;

            }

        } finally {

            // Important - free up resources used running the query

            qe.close();

        }

        return null;

    }

    public Model describe(String queryString) throws DRFChecklistException {

        QueryExecution qe = executionFor(queryString);

        Model result = null;

        try {

            if(dataset != null) {

                dataset.begin(ReadWrite.READ) ;

            }

            result = qe.execDescribe();

            if(logger.isDebugEnabled()) {

                result.write(System.err);

            }

        } catch (HttpException e) {

            switch(e.getResponseCode()) {

                // interpretation based on

                // http://image.slidesharecdn.com/swtss1006sparql-100614020655-phpapp02/95/semantic-web-technologies-ss-2010-06-sparql-46-728.jpg?cb=1276481316

                case 400:

                    throw new DRFChecklistException("Malformed Query ?", e);

                case 500:

                    throw new DRFChecklistException("Query Request Refused ?", e);

                default:

                    throw e;

            }

        } finally {

            // Important - free up resources used running the query

            qe.close();

        }

        if(result != null && logger.isDebugEnabled()) {

            StringBuilder msg = new StringBuilder();

            msg.append("subjects in response:\n");

            int i = 1;

            for(ResIterator it = result.listSubjects(); it.hasNext(); ++i) {

                Resource res = it.next();

                msg.append("    " + i + ": " + res.toString() + "\n");

            }

            logger.debug(msg.toString());

        }

        if(dataset != null) {

            dataset.end();

        }

        return result;

    }

    /**

     * @param queryString

     * @return

     */

    private QueryExecution executionFor(String queryString) {

        QueryExecution qe;

        if(opmode.equals(Opmode.SPARCLE_ENDPOINT)) {

            Query query = QueryFactory.create(queryString);

            qe = QueryExecutionFactory.sparqlService(baseUri, query);

        } else {

            // local TDB Store

            qe = QueryExecutionFactory.create(queryString, dataset);

        }

        return qe;

    }

    /**

     * @param subject

     * @param nameSpace

     * @param localName

     * @return

     */

    public RDFNode asSingleObject(Resource subject, RdfSchema nameSpace, String localName) {

        RDFNode node = null;

        Resource _subject = subject;

        try {

            boolean hasNoPropertiesInGraph = !_subject.listProperties().hasNext();

            if(_subject.isURIResource() && hasNoPropertiesInGraph ) {

                logger.debug("loading UriResource " + _subject.getURI());

                _subject = getFromUri(_subject.getURI());

            }

            Model _model = _subject.getModel();

            node = _subject.listProperties(_model.getProperty(nameSpace.schemaUri(), localName)).next().getObject();

        } catch (NoSuchElementException e) {

            if(logger.isTraceEnabled()) {

                logger.debug(_subject.getURI() + " " +  nameSpace + ":" + localName + " not found in current graph");

                printProperties(_subject);

            }

        }

        return node;

    }

    /**

     * @param subject

     * @param nameSpace

     * @param localName

     * @return

     */

    public String objectAsString(Resource subject, RdfSchema nameSpace, String localName) {

        String txt = null;

        RDFNode node = asSingleObject(subject, nameSpace, localName);

        if(node != null) {

            txt = node.toString();

        }

        return txt;

    }

    /**

     * @param subject

     * @param nameSpace

     * @param localName

     * @return

     */

    public Resource objectAsResource(Resource subject, RdfSchema nameSpace, String localName) {

        Resource resource = null;

        RDFNode node = asSingleObject(subject, nameSpace, localName);

        if(node != null) {

            node.isResource();

            resource  = node.asResource();

        }

        return resource;

    }

    /**

     * @param subject

     * @param nameSpace

     * @param localName

     * @return

     */

    public URI objectAsURI(Resource subject, RdfSchema nameSpace, String localName) {

        URI uri = null;

        RDFNode node = asSingleObject(subject, nameSpace, localName);

        if(node != null) {

            node.isURIResource();

            try {

                uri  = new URI(node.asResource().getURI());

            } catch (URISyntaxException e) {

                // this should actually never happen

                throw new RuntimeException(e);

            }

        }

        return uri;

    }

    /**

     * @param subject

     */

    private void printProperties(Resource subject) {

        for( StmtIterator it = subject.listProperties(); it.hasNext(); ) {

            System.err.println(it.next().toString());

        }

    }

    public Resource getFromUri(String uri) {

        Model model;

        if(dataset != null) {

            dataset.begin(ReadWrite.READ) ;

            model = dataset.getDefaultModel();

            dataset.end();

        } else {

            model = ModelFactory.createDefaultModel();

            model.read(uri);

            if(logger.isDebugEnabled()) {

                model.write(System.err);

            }

        }

        return model.getResource(uri);

    }

    /**

     * @param matchedResourceURI

     * @return

     * @throws DRFChecklistException

     */

    public Resource getFromUri(URI matchedResourceURI) {

        return getFromUri(matchedResourceURI.toString());

    }

    /**

     * @return the rdfFile

     */

    public File getRdfFile() {

        return rdfFile;

    }

}