eu.annocultor.utils.SparqlQueryHelper.java Source code

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Here is the source code for eu.annocultor.utils.SparqlQueryHelper.java

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/*
 * Copyright 2005-2009 the original author or authors.
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *      http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package eu.annocultor.utils;

import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.apache.commons.lang.StringUtils;
import org.openrdf.model.Statement;
import org.openrdf.model.URI;
import org.openrdf.model.Value;
import org.openrdf.model.ValueFactory;
import org.openrdf.query.BindingSet;
import org.openrdf.query.QueryLanguage;
import org.openrdf.query.TupleQuery;
import org.openrdf.query.TupleQueryResult;
import org.openrdf.repository.Repository;
import org.openrdf.repository.RepositoryConnection;
import org.openrdf.rio.RDFHandlerException;

import eu.annocultor.common.Helper;
import eu.annocultor.common.Utils;
import eu.annocultor.context.Namespaces;
import eu.annocultor.utils.SesameWriter;

/**
 * Apply a SPARQL query to a set of RDF files, and save the results of this query to another file;
 * made as a convenience method to use in XML converters. 
 * 
 * @author Borys Omelayenko
 *
 */
public class SparqlQueryHelper {

    Repository rdf;
    RepositoryConnection connection;
    TupleQueryResult queryResult;
    final String namespacePrefix;

    public SparqlQueryHelper(String namespacePrefix) {
        this.namespacePrefix = namespacePrefix;
    }

    public static void filter(Namespaces namespaces, String namespacePrefix, String outputFilePrefix, String query,
            String... inputFilePattern) throws Exception {

        List<File> files = new ArrayList<File>();
        for (String pattern : inputFilePattern) {
            files.addAll(Utils.expandFileTemplateFrom(new File("."), pattern));
        }
        SparqlQueryHelper sqh = new SparqlQueryHelper(namespacePrefix);
        try {
            sqh.open();
            sqh.load(namespacePrefix, files.toArray(new File[] {}));
            sqh.query(query);
            sqh.save(namespaces, outputFilePrefix);
        } finally {
            sqh.close();
        }
    }

    private void open() throws Exception {
        rdf = Helper.createLocalRepository();
    }

    private void load(String namespace, File... files) throws Exception {
        Helper.importRDFXMLFile(rdf, namespace, files);
    }

    private void query(String query) throws Exception {
        connection = rdf.getConnection();
        TupleQuery preparedQuery = connection.prepareTupleQuery(QueryLanguage.SPARQL, query);
        preparedQuery.setIncludeInferred(false);
        queryResult = preparedQuery.evaluate();
    }

    private void save(Namespaces namespaces, String outputFilePrefix) throws Exception {

        SesameWriter writer = SesameWriter.createRDFXMLWriter(new File(outputFilePrefix + ".1.rdf"), namespaces,
                "id", "description", 1000, 1000);
        ValueFactory valueFactory = connection.getValueFactory();
        writer.startRDF();
        while (queryResult.hasNext()) {
            final BindingSet binding = queryResult.next();
            final URI subject = valueFactory.createURI(binding.getBinding("subject").getValue().stringValue());
            final URI property = valueFactory.createURI(binding.getBinding("property").getValue().stringValue());
            final Value value = binding.getValue("value");
            Statement statement = valueFactory.createStatement(subject, property, value);
            writer.handleStatement(statement);

            if (!subject.stringValue().startsWith(namespacePrefix)) {
                throw new Exception("Expected " + subject.stringValue() + " to start with " + namespacePrefix);
            }

            writeStatementIntoSeparateFileByNamespace(statement, outputFilePrefix, namespaces);
        }
        writer.endRDF();

        closeWritersByNamespace();
    }

    private void closeWritersByNamespace() throws RDFHandlerException {
        for (SesameWriter nsWriter : filesPerNamespace.values()) {
            nsWriter.endRDF();
        }
    }

    private void writeStatementIntoSeparateFileByNamespace(Statement statement, String outputFilePrefix,
            Namespaces namespaces) throws Exception {
        String subject = statement.getSubject().stringValue();
        String nsFull = subject.substring(namespacePrefix.length());
        String nss[] = nsFull.split("/");
        String first = nss[0];
        String second = nss[1];
        if (StringUtils.containsAny(second, "0123456789")) {
            second = "";
        } else {
            second = "_" + second;
        }
        String ns = first + second;
        if (!filesPerNamespace.containsKey(ns)) {
            File nsFile = new File(outputFilePrefix + "_" + ns + ".1.rdf");
            SesameWriter writer = SesameWriter.createRDFXMLWriter(nsFile, namespaces, "id",
                    "Exported items belonging to " + nsFull, 1000, 1000);
            writer.startRDF();
            filesPerNamespace.put(ns, writer);
        }

        SesameWriter writer = filesPerNamespace.get(ns);
        writer.handleStatement(statement);
    }

    Map<String, SesameWriter> filesPerNamespace = new HashMap<String, SesameWriter>();

    private void close() throws Exception {
        if (queryResult != null)
            queryResult.close();
        if (connection != null)
            connection.close();
        if (rdf != null)
            rdf.shutDown();
    }

}