owlapi-version5/rio/src/main/java/org/semanticweb/owlapi/rio/RioParserImpl.java
/*
 * This file is part of the OWL API.
 * 
 * The contents of this file are subject to the LGPL License, Version 3.0.
 * 
 * Copyright (C) 2011, The University of Queensland
 * 
 * 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/.
 * 
 * 
 * Alternatively, the contents of this file may be used under the terms of the Apache License,
 * Version 2.0 in which case, the provisions of the Apache License Version 2.0 are applicable
 * instead of those above.
 * 
 * Copyright 2011, The University of Queensland
 * 
 * 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 org.semanticweb.owlapi.rio;

import static org.semanticweb.owlapi.io.DocumentSources.wrapInputAsReader;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.checkNotNull;

import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.io.Serializable;
import java.net.MalformedURLException;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Map;
import java.util.Optional;
import java.util.Set;

import javax.annotation.Nullable;

import org.eclipse.rdf4j.model.Resource;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.RDF;
import org.eclipse.rdf4j.rio.RDFHandler;
import org.eclipse.rdf4j.rio.RDFHandlerException;
import org.eclipse.rdf4j.rio.RDFParseException;
import org.eclipse.rdf4j.rio.RDFParser;
import org.eclipse.rdf4j.rio.Rio;
import org.eclipse.rdf4j.rio.RioSetting;
import org.eclipse.rdf4j.rio.UnsupportedRDFormatException;
import org.eclipse.rdf4j.rio.helpers.BasicParserSettings;
import org.eclipse.rdf4j.rio.helpers.StatementCollector;
import org.eclipse.rdf4j.rio.helpers.XMLParserSettings;
import org.semanticweb.owlapi.annotations.HasPriority;
import org.semanticweb.owlapi.formats.RioRDFDocumentFormatFactory;
import org.semanticweb.owlapi.io.AbstractOWLParser;
import org.semanticweb.owlapi.io.DocumentSources;
import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
import org.semanticweb.owlapi.io.OWLOntologyInputSourceException;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLDocumentFormat;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
import org.semanticweb.owlapi.model.UnloadableImportException;
import org.semanticweb.owlapi.util.AnonymousNodeChecker;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 */
@HasPriority(7)
public class RioParserImpl extends AbstractOWLParser implements RioParser {

    protected static final Logger LOGGER = LoggerFactory.getLogger(RioParserImpl.class);
    private static final RIOAnonymousNodeChecker CHECKER = new RIOAnonymousNodeChecker();
    private final RioRDFDocumentFormatFactory owlFormatFactory;

    /**
     * @param nextFormat format factory
     */
    public RioParserImpl(RioRDFDocumentFormatFactory nextFormat) {
        owlFormatFactory = checkNotNull(nextFormat, "nextFormat cannot be null");
    }

    @Override
    public RioRDFDocumentFormatFactory getSupportedFormat() {
        return owlFormatFactory;
    }

    @Override
    public OWLDocumentFormat parse(final OWLOntologyDocumentSource documentSource,
        final OWLOntology ontology, final OWLOntologyLoaderConfiguration configuration) {
        try {
            RioOWLRDFConsumerAdapter consumer =
                new RioOWLRDFConsumerAdapter(ontology, CHECKER, configuration);
            consumer.setOntologyFormat(owlFormatFactory.createFormat());
            String baseUri = "urn:default:baseUri:";
            // Override the default baseUri for non-anonymous ontologies
            if (!ontology.getOntologyID().isAnonymous()
                && ontology.getOntologyID().getDefaultDocumentIRI().isPresent()) {
                baseUri = ontology.getOntologyID().getDefaultDocumentIRI().get().toString();
            } else {
                baseUri = documentSource.getDocumentIRI().toString();
            }
            RioParserRDFHandler handler = new RioParserRDFHandler(consumer);
            if (documentSource instanceof RioMemoryTripleSource) {
                RioMemoryTripleSource tripleSource = (RioMemoryTripleSource) documentSource;
                Map<String, String> namespaces = tripleSource.getNamespaces();
                Iterator<Statement> statementsIterator = tripleSource.getStatementIterator();
                handler.startRDF();
                namespaces.forEach(handler::handleNamespace);
                while (statementsIterator.hasNext()) {
                    handler.handleStatement(statementsIterator.next());
                }
                handler.endRDF();
            } else {
                parseDocumentSource(documentSource, baseUri, handler, configuration);
            }
            return consumer.getOntologyFormat();
        } catch (final RDFHandlerException e) {
            // See sourceforge bug 3566820 for more information about this
            // branch
            if (e.getCause() != null && e.getCause().getCause() != null
                && e.getCause().getCause() instanceof UnloadableImportException) {
                throw (UnloadableImportException) e.getCause().getCause();
            } else {
                throw new OWLParserException(e);
            }
        } catch (RDFParseException | UnsupportedRDFormatException | OWLOntologyInputSourceException
            | IOException e) {
            throw new OWLParserException(e);
        }
    }

    /**
     * Parse the given document source and return a {@link StatementCollector} containing the RDF
     * statements found in the source.
     *
     * @param source An {@link OWLOntologyDocumentSource} containing RDF statements.
     * @param baseUri The base URI to use when parsing the document source.
     * @param handler RDF handler
     * @param config loading configuration
     * @throws OWLOntologyInputSourceException if the source cannot be accessed
     * @throws UnsupportedRDFormatException If the document contains a format which is currently
     *         unsupported, based on the parsers that are currently available.
     * @throws IOException If there is an input/output exception while accessing the document
     *         source.
     * @throws RDFParseException If there is an error while parsing the document source.
     * @throws RDFHandlerException If there is an error related to the processing of the RDF
     *         statements after parsing.
     * @throws MalformedURLException If there are malformed URLs.
     */
    protected void parseDocumentSource(final OWLOntologyDocumentSource source, final String baseUri,
        final RDFHandler handler, OWLOntologyLoaderConfiguration config)
        throws OWLOntologyInputSourceException, IOException {
        final RDFParser createParser = Rio.createParser(owlFormatFactory.getRioFormat());
        createParser.getParserConfig().addNonFatalError(BasicParserSettings.VERIFY_DATATYPE_VALUES);
        createParser.getParserConfig().addNonFatalError(BasicParserSettings.VERIFY_LANGUAGE_TAGS);
        createParser.getParserConfig().addNonFatalError(BasicParserSettings.VERIFY_URI_SYNTAX);
        createParser.getParserConfig().addNonFatalError(XMLParserSettings.DISALLOW_DOCTYPE_DECL);
        createParser.getParserConfig().set(XMLParserSettings.DISALLOW_DOCTYPE_DECL, Boolean.FALSE);
        createParser.getParserConfig().set(BasicParserSettings.VERIFY_URI_SYNTAX, Boolean.FALSE);
        addParametersIfPresent(source, createParser);
        createParser.setRDFHandler(handler);
        long rioParseStart = System.currentTimeMillis();
        try {
            if (owlFormatFactory.isTextual()) {
                try (Reader wrappedInput = wrapInputAsReader(source, config)) {
                    createParser.parse(wrappedInput, baseUri);
                }
                return;
            }
            // if the format is not textual, but the source is a String based
            // source,
            // the following call can fail with an OWLOntologyInputSource
            // exception without
            // there being an actual I/O error. This should be considered a
            // parser error
            // and further parsing attempted.
            try (InputStream wrappedInput = DocumentSources.wrapInput(source, config)) {
                createParser.parse(wrappedInput, baseUri);
            } catch (OWLOntologyInputSourceException e) {
                throw new OWLParserException(e.getMessage(), e);
            }
        } finally {
            if (LOGGER.isDebugEnabled()) {
                LOGGER.debug("rioParse: timing={}",
                    Long.valueOf(System.currentTimeMillis() - rioParseStart));
            }
        }
    }

    // These warnings are suppressed because the types cannot be easily determined here without
    // forcing constraints that might need to be updated when Rio introduces new settings.
    @SuppressWarnings({"null", "rawtypes", "unchecked"})
    protected void addParametersIfPresent(OWLOntologyDocumentSource documentSource,
        RDFParser createParser) {
        Collection<RioSetting<?>> supportedSettings = createParser.getSupportedSettings();
        Optional<OWLDocumentFormat> format = documentSource.getFormat();
        if (format.isPresent() && !supportedSettings.isEmpty()) {
            for (RioSetting r : supportedSettings) {
                Serializable v = format.get().getParameter(r, null);
                if (v != null) {
                    createParser.getParserConfig().set(r, v);
                }
            }
        }
    }

    @Override
    public String toString() {
        return getClass().getName() + " : " + owlFormatFactory;
    }

    private static class RIOAnonymousNodeChecker implements AnonymousNodeChecker {

        RIOAnonymousNodeChecker() {}

        @Override
        public boolean isAnonymousNode(final IRI iri) {
            // HACK: FIXME: When the mess of having blank nodes
            // represented as IRIs is
            // finished remove the genid hack below
            if (anon(iri.toString())) {
                LOGGER.trace("isAnonymousNode(IRI {})", iri);
                return true;
            } else {
                LOGGER.trace("NOT isAnonymousNode(IRI {})", iri);
                return false;
            }
        }

        @Override
        public boolean isAnonymousNode(final String iri) {
            // HACK: FIXME: When the mess of having blank nodes
            // represented as IRIs is
            // finished remove the genid hack below
            if (anon(iri)) {
                LOGGER.trace("isAnonymousNode(String {})", iri);
                return true;
            } else {
                LOGGER.trace("NOT isAnonymousNode(String {})", iri);
                return false;
            }
        }

        // TODO: apparently we should be tracking whether they
        // gave a name to the blank
        // node themselves
        @Override
        public boolean isAnonymousSharedNode(final String iri) {
            // HACK: FIXME: When the mess of having blank nodes
            // represented as IRIs is
            // finished remove the genid hack below
            if (anon(iri)) {
                LOGGER.trace("isAnonymousSharedNode(String {})", iri);
                return true;
            } else {
                LOGGER.trace("NOT isAnonymousSharedNode(String {})", iri);
                return false;
            }
        }

        boolean anon(final String iri) {
            return iri.startsWith("_:") || iri.contains("genid");
        }
    }

    private static class RioParserRDFHandler implements RDFHandler {

        private static final Logger LOG = LoggerFactory.getLogger(RioParserRDFHandler.class);
        private final RDFHandler consumer;
        private final Set<Resource> typedLists = new HashSet<>();
        private final ValueFactory vf = SimpleValueFactory.getInstance();
        private long owlParseStart;

        RioParserRDFHandler(RDFHandler consumer) {
            this.consumer = consumer;
        }

        @Override
        public void startRDF() {
            owlParseStart = System.currentTimeMillis();
            try {
                consumer.startRDF();
            } catch (RDFHandlerException e) {
                throw new OWLParserException(e);
            }
        }

        @Override
        public void endRDF() {
            try {
                consumer.endRDF();
                if (LOG.isDebugEnabled()) {
                    LOG.debug("owlParse: timing={}",
                        Long.valueOf(System.currentTimeMillis() - owlParseStart));
                }
            } catch (RDFHandlerException e) {
                throw new OWLParserException(e);
            }
        }

        @Override
        public void handleNamespace(@Nullable String prefix, @Nullable String uri) {
            try {
                consumer.handleNamespace(prefix, uri);
            } catch (RDFHandlerException e) {
                throw new OWLParserException(e);
            }
        }

        @Override
        public void handleStatement(@Nullable Statement nextStatement) {
            checkNotNull(nextStatement);
            assert nextStatement != null;
            if (nextStatement.getPredicate().equals(RDF.FIRST)
                || nextStatement.getPredicate().equals(RDF.REST)) {
                if (!typedLists.contains(nextStatement.getSubject())) {
                    typedLists.add(nextStatement.getSubject());
                    try {
                        consumer.handleStatement(
                            vf.createStatement(nextStatement.getSubject(), RDF.TYPE, RDF.LIST));
                    } catch (RDFHandlerException e) {
                        throw new OWLParserException(e);
                    }
                    LOG.debug("Implicitly typing list={}", nextStatement);
                }
            } else if (nextStatement.getPredicate().equals(RDF.TYPE)
                && nextStatement.getObject().equals(RDF.LIST)) {
                if (!typedLists.contains(nextStatement.getSubject())) {
                    LOG.debug("Explicit list type found={}", nextStatement);
                    typedLists.add(nextStatement.getSubject());
                } else {
                    LOG.debug("duplicate rdf:type rdf:List statements found={}", nextStatement);
                }
            }
            try {
                consumer.handleStatement(nextStatement);
            } catch (RDFHandlerException e) {
                throw new OWLParserException(e);
            }
        }

        @Override
        public void handleComment(@Nullable String comment) {
            // do nothing
        }
    }
}
