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org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl Maven / Gradle / Ivy
/* This file is part of the OWL API.
* The contents of this file are subject to the LGPL License, Version 3.0.
* Copyright 2014, The University of Manchester
*
* 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.
* 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.manchestersyntax.parser;
import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntax.*;
import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxTokenizer.*;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.function.Function;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.inject.Inject;
import org.semanticweb.owlapi.expression.OWLEntityChecker;
import org.semanticweb.owlapi.expression.OWLOntologyChecker;
import org.semanticweb.owlapi.formats.ManchesterSyntaxDocumentFormat;
import org.semanticweb.owlapi.io.XMLUtils;
import org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxTokenizer.Token;
import org.semanticweb.owlapi.manchestersyntax.renderer.ParserException;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.semanticweb.owlapi.util.CollectionFactory;
import org.semanticweb.owlapi.util.DefaultPrefixManager;
import org.semanticweb.owlapi.util.NamespaceUtil;
import org.semanticweb.owlapi.util.OntologyAxiomPair;
import org.semanticweb.owlapi.util.RemappingIndividualProvider;
import org.semanticweb.owlapi.util.mansyntax.ManchesterOWLSyntaxParser;
import org.semanticweb.owlapi.vocab.DublinCoreVocabulary;
import org.semanticweb.owlapi.vocab.Namespaces;
import org.semanticweb.owlapi.vocab.OWL2Datatype;
import org.semanticweb.owlapi.vocab.OWLFacet;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
import org.semanticweb.owlapi.vocab.SWRLBuiltInsVocabulary;
import org.semanticweb.owlapi.vocab.XSDVocabulary;
/**
* A parser for the Manchester OWL Syntax. All properties must be defined before
* they are used. For example, consider the restriction hasPart some Leg. The
* parser must know in advance whether or not hasPart is an object property or a
* data property so that Leg gets parsed correctly. In a tool, such as an
* editor, it is expected that hasPart will already exists as either a data
* property or an object property. If a complete ontology is being parsed, it is
* expected that hasPart will have been defined at the top of the file before it
* is used in any class expressions or property assertions (e.g. ObjectProperty:
* hasPart)
*
* @author Matthew Horridge, The University Of Manchester, Bio-Health
* Informatics Group
* @since 2.2.0
*/
public class ManchesterOWLSyntaxParserImpl implements ManchesterOWLSyntaxParser {
private static final String INFINITY = "Infinity";
// This parser was built by hand! After struggling with terrible
// error messages produced by ANTLR (or JavaCC) I decides to construct
// this parser by hand. The error messages that this parser generates
// are specific to the Manchester OWL Syntax and are such that it should
// be easy to use this parser in tools such as editors.
@Nonnull private OWLOntologyLoaderConfiguration loaderConfig;
protected OWLDataFactory df;
private List tokens;
private int tokenIndex;
private OWLEntityChecker checker;
private OWLOntologyChecker owlOntologyChecker = name -> null;
private final Map> classFrameSections = new EnumMap<>(
ManchesterOWLSyntax.class);
@Nonnull protected final Set classNames = new HashSet<>();
@Nonnull protected final Set objectPropertyNames = new HashSet<>();
@Nonnull protected final Set dataPropertyNames = new HashSet<>();
@Nonnull protected final Set individualNames = new HashSet<>();
@Nonnull protected final Set dataTypeNames = new HashSet<>();
@Nonnull protected final Set annotationPropertyNames = new HashSet<>();
@Nonnull private final Map ruleBuiltIns = new TreeMap<>();
@Nonnull protected final DefaultPrefixManager pm = new DefaultPrefixManager();
@Nonnull protected final Set potentialKeywords = new HashSet<>();
private OWLOntology defaultOntology;
private static final boolean ALLOWEMPTYFRAMESECTIONS = false;
private final Map> dataPropertyFrameSections = new EnumMap<>(
ManchesterOWLSyntax.class);
private final Map> objectPropertyFrameSections = new EnumMap<>(
ManchesterOWLSyntax.class);
private final Map> annotationPropertyFrameSections = new EnumMap<>(
ManchesterOWLSyntax.class);
private final Map> individualFrameSections = new EnumMap<>(
ManchesterOWLSyntax.class);
protected RemappingIndividualProvider anonProvider;
private final Map nameIRIMap = new HashMap<>();
/**
* @param configurationProvider
* configuration provider
* @param dataFactory
* dataFactory
*/
@Inject
public ManchesterOWLSyntaxParserImpl(OntologyConfigurator configurationProvider, OWLDataFactory dataFactory) {
loaderConfig = configurationProvider.buildLoaderConfiguration();
df = dataFactory;
anonProvider = new RemappingIndividualProvider(configurationProvider, df);
pm.setPrefix("rdf:", Namespaces.RDF.toString());
pm.setPrefix("rdfs:", Namespaces.RDFS.toString());
pm.setPrefix("owl:", Namespaces.OWL.toString());
pm.setPrefix("dc:", DublinCoreVocabulary.NAME_SPACE);
NamespaceUtil u = new NamespaceUtil();
initialiseClassFrameSections();
initialiseObjectPropertyFrameSections();
initialiseDataPropertyFrameSections();
initialiseAnnotationPropertyFrameSections();
initialiseIndividualFrameSections();
for (XSDVocabulary v : XSDVocabulary.values()) {
dataTypeNames.add(v.getIRI().toString());
dataTypeNames.add(v.getIRI().toQuotedString());
dataTypeNames.add(v.getPrefixedName());
}
for (OWL2Datatype v : OWL2Datatype.values()) {
dataTypeNames.add(v.getIRI().toString());
dataTypeNames.add(v.getIRI().toQuotedString());
dataTypeNames.add(v.getPrefixedName());
}
dataTypeNames.add(OWLRDFVocabulary.RDFS_LITERAL.getPrefixedName());
dataTypeNames.add(OWLRDFVocabulary.RDF_XML_LITERAL.getShortForm());
dataTypeNames.add(OWLRDFVocabulary.RDF_XML_LITERAL.getPrefixedName());
for (IRI iri : OWLRDFVocabulary.BUILT_IN_AP_IRIS) {
String string = iri.toString();
String ns = XMLUtils.getNCNamePrefix(string);
String fragment = XMLUtils.getNCNameSuffix(string);
annotationPropertyNames.add(u.getPrefix(ns) + ':' + (fragment != null ? fragment : ""));
}
checker = new DefaultEntityChecker();
for (SWRLBuiltInsVocabulary v : SWRLBuiltInsVocabulary.values()) {
ruleBuiltIns.put(v.getShortForm(), v);
ruleBuiltIns.put(v.getIRI().toQuotedString(), v);
}
}
/**@return the prefix manager used by this parser*/
//XXX add this method to the interface in next release
public PrefixManager getPrefixManager() {
return pm;
}
@Override
public OWLOntologyLoaderConfiguration getOntologyLoaderConfiguration() {
return loaderConfig;
}
@Override
public void setOntologyLoaderConfiguration(OWLOntologyLoaderConfiguration conf) {
loaderConfig = conf;
}
@Override
public void setStringToParse(String s) {
tokens = new ArrayList<>();
tokens.addAll(getTokenizer(s).tokenize());
tokenIndex = 0;
}
protected static ManchesterOWLSyntaxTokenizer getTokenizer(String s) {
return new ManchesterOWLSyntaxTokenizer(s);
}
private void initialiseClassFrameSections() {
//@formatter:off
initialiseSection(new AnnAxiom(x -> parseAnnotation(), ANNOTATIONS, (s, o, anns) -> df.getOWLAnnotationAssertionAxiom(s.getIRI(), o, anns)), classFrameSections);
initialiseSection(new AnnAxiom(x -> parseUnion(), SUBCLASS_OF, (s, o, anns) -> df.getOWLSubClassOfAxiom(s, o, anns)), classFrameSections);
initialiseSection(new AnnAxiom(x -> parseUnion(), EQUIVALENT_TO, (s, o, anns) -> df.getOWLEquivalentClassesAxiom(s, o, anns)), classFrameSections);
initialiseSection(new AnnAxiom(x -> parseUnion(), DISJOINT_WITH, (s, o, anns) -> df.getOWLDisjointClassesAxiom(s, o, anns)), classFrameSections);
initialiseSection(new AnnAxiom>(x -> parsePropertyList(), HAS_KEY, (s, o, anns) -> df.getOWLHasKeyAxiom(s, o, anns)), classFrameSections);
initialiseSection(new AnnAxiom>(x -> parseClassExpressionList(), DISJOINT_UNION_OF, (s, o, anns) -> df.getOWLDisjointUnionAxiom(s, o, anns)), classFrameSections);
// Extensions
initialiseSection(new AnnAxiom(x -> parseUnion(), SUPERCLASS_OF, (s, o, anns) -> df.getOWLSubClassOfAxiom(o, s, anns)), classFrameSections);
initialiseSection(new AnnAxiom>(x -> parseClassExpressionList(), DISJOINT_CLASSES, (s, o, anns) -> df.getOWLDisjointClassesAxiom(o, anns)), classFrameSections);
initialiseSection(new AnnAxiom(x -> parseIndividual(), INDIVIDUALS, (s, o, anns) -> df.getOWLClassAssertionAxiom(s, o, anns)), classFrameSections);
//@formatter:on
}
private void initialiseObjectPropertyFrameSections() {
//@formatter:off
initialiseSection(new AnnAxiom(x -> parseAnnotation(), ANNOTATIONS, (s, o, anns) -> df.getOWLAnnotationAssertionAxiom(s.getIRI(), o, anns)), objectPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseObjectPropertyExpression(false), SUB_PROPERTY_OF, (s, o, anns) -> df.getOWLSubObjectPropertyOfAxiom(s, o, anns)), objectPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseObjectPropertyExpression(false), EQUIVALENT_TO, (s, o, anns) -> df.getOWLEquivalentObjectPropertiesAxiom(s, o, anns)), objectPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseObjectPropertyExpression(false), DISJOINT_WITH, (s, o, anns) -> df.getOWLDisjointObjectPropertiesAxiom(s, o, anns)), objectPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseUnion(), DOMAIN, (s, o, anns) -> df.getOWLObjectPropertyDomainAxiom(s, o, anns)), objectPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseUnion(), RANGE, (s, o, anns) -> df.getOWLObjectPropertyRangeAxiom(s, o, anns)), objectPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseObjectPropertyExpression(false), INVERSE_OF, (s, o, anns) -> df.getOWLInverseObjectPropertiesAxiom(s, o, anns)), objectPropertyFrameSections);
initialiseSection(new AnnAxiom(this::parseObjectPropertyCharacteristic, CHARACTERISTICS, (s, o, anns) -> o.getAnnotatedAxiom(anns)), objectPropertyFrameSections);
initialiseSection(new AnnAxiom>(x -> parseObjectPropertyChain(), SUB_PROPERTY_CHAIN, (s, o, anns) -> df.getOWLSubPropertyChainOfAxiom(o, s, anns)), objectPropertyFrameSections);
// Extensions
initialiseSection(new AnnAxiom(x -> parseObjectPropertyExpression(false), SUPER_PROPERTY_OF, (s, o, anns) -> df.getOWLSubObjectPropertyOfAxiom(o, s, anns)), objectPropertyFrameSections);
//@formatter:on
}
private void initialiseDataPropertyFrameSections() {
//@formatter:off
initialiseSection(new AnnAxiom(x -> parseDataProperty(), SUB_PROPERTY_OF, (s, o, anns) -> df.getOWLSubDataPropertyOfAxiom(s, o, anns)), dataPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseDataProperty(), EQUIVALENT_TO, (s, o, anns) -> df.getOWLEquivalentDataPropertiesAxiom(s,o, anns)), dataPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseDataProperty(), DISJOINT_WITH, (s, o, anns) -> df.getOWLDisjointDataPropertiesAxiom(s,o, anns)), dataPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseUnion(), DOMAIN, (s, o, anns) -> df.getOWLDataPropertyDomainAxiom(s, o, anns)), dataPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseDataRange(), RANGE, (s, o, anns) -> df.getOWLDataPropertyRangeAxiom(s, o, anns)), dataPropertyFrameSections);
initialiseSection(new AnnAxiom(this::parseDataPropertyCharacteristic, CHARACTERISTICS, (s, o, anns) -> o.getAnnotatedAxiom(anns)), dataPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseAnnotation(), ANNOTATIONS, (s, o, anns) -> df.getOWLAnnotationAssertionAxiom(s.getIRI(), o, anns)), dataPropertyFrameSections);
//@formatter:on
}
private void initialiseAnnotationPropertyFrameSections() {
//@formatter:off
initialiseSection(new AnnAxiom(x -> parseAnnotationProperty(), SUB_PROPERTY_OF, (s, o, anns) -> df.getOWLSubAnnotationPropertyOfAxiom(s, o, anns)), annotationPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseIRI(), DOMAIN, (s, o, anns) -> df.getOWLAnnotationPropertyDomainAxiom(s, o, anns)), annotationPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseIRI(), RANGE, (s, o, anns) -> df.getOWLAnnotationPropertyRangeAxiom(s, o, anns)), annotationPropertyFrameSections);
initialiseSection(new AnnAxiom(x -> parseAnnotation(), ANNOTATIONS, (s, o, anns) -> df.getOWLAnnotationAssertionAxiom(s.getIRI(), o, anns)), annotationPropertyFrameSections);
//@formatter:on
}
private void initialiseIndividualFrameSections() {
//@formatter:off
initialiseSection(new AnnAxiom(x -> parseAnnotation(), ANNOTATIONS, (s, o, anns) -> create(df, s, o, anns)), individualFrameSections);
initialiseSection(new AnnAxiom(x -> parseUnion(), TYPES, (s, o, anns) -> df.getOWLClassAssertionAxiom(o, s, anns)), individualFrameSections);
initialiseSection(new AnnAxiom<>(this::parseFact, FACTS, (s, o, anns) -> o.getAnnotatedAxiom(anns)), individualFrameSections);
initialiseSection(new AnnAxiom(x -> parseIndividual(), SAME_AS, (s, o, anns) -> df.getOWLSameIndividualAxiom(s, o, anns)), individualFrameSections);
initialiseSection(new AnnAxiom(x -> parseIndividual(), DIFFERENT_FROM, (s, o, anns) -> df.getOWLDifferentIndividualsAxiom(s, o, anns)), individualFrameSections);
// Extensions
initialiseSection(new AnnAxiom>(x -> parseIndividualList(), DIFFERENT_INDIVIDUALS, (s, o, anns) -> create(df, s, o, anns)), individualFrameSections);
//@formatter:on
}
@Override
public void setOWLEntityChecker(OWLEntityChecker owlEntityChecker) {
checker = owlEntityChecker;
}
private boolean isOntologyName(String name) {
return owlOntologyChecker.getOntology(name) != null;
}
private boolean isClassName(String name) {
return classNames.contains(name) || checker != null && checker.getOWLClass(name) != null;
}
@Nullable
private OWLOntology getOntology(@Nullable String name) {
return owlOntologyChecker.getOntology(name);
}
@Override
public void setOWLOntologyChecker(OWLOntologyChecker owlOntologyChecker) {
this.owlOntologyChecker = owlOntologyChecker;
}
private boolean isObjectPropertyName(String name) {
return objectPropertyNames.contains(name) || checker != null && checker.getOWLObjectProperty(name) != null;
}
private boolean isAnnotationPropertyName(String name) {
return annotationPropertyNames.contains(name) || checker != null && checker.getOWLAnnotationProperty(
name) != null;
}
private boolean isDataPropertyName(String name) {
return dataPropertyNames.contains(name) || checker != null && checker.getOWLDataProperty(name) != null;
}
private boolean isIndividualName(String name) {
return individualNames.contains(name) || checker != null && checker.getOWLIndividual(name) != null;
}
private boolean isDatatypeName(String name) {
return dataTypeNames.contains(name) || checker != null && checker.getOWLDatatype(name) != null;
}
private boolean isSWRLBuiltin(String name) {
return ruleBuiltIns.containsKey(name);
}
private OWLClass getOWLClass(String name) {
OWLClass cls = checker.getOWLClass(name);
if (cls == null && classNames.contains(name)) {
cls = df.getOWLClass(getIRI(name));
}
if (cls == null) {
throw new ExceptionBuilder().withKeyword(potentialKeywords).withClass().build();
}
return cls;
}
private OWLObjectProperty getOWLObjectProperty(String name) {
OWLObjectProperty prop = checker.getOWLObjectProperty(name);
if (prop == null && objectPropertyNames.contains(name)) {
prop = df.getOWLObjectProperty(getIRI(name));
}
if (prop == null) {
throw new ExceptionBuilder().withObject().build();
}
return prop;
}
private OWLIndividual getOWLIndividual(String name) {
if (name.startsWith("_:")) {
return anonProvider.getOWLAnonymousIndividual(name);
}
return getOWLNamedIndividual(name);
}
private OWLNamedIndividual getOWLNamedIndividual(String name) {
OWLNamedIndividual ind = checker.getOWLIndividual(name);
if (ind == null && individualNames.contains(name)) {
ind = df.getOWLNamedIndividual(getIRI(name));
}
if (ind == null) {
throw new ExceptionBuilder().withInd().build();
}
return ind;
}
private OWLDataProperty getOWLDataProperty(String name) {
OWLDataProperty prop = checker.getOWLDataProperty(name);
if (prop == null && dataPropertyNames.contains(name)) {
prop = df.getOWLDataProperty(getIRI(name));
}
if (prop == null) {
throw new ExceptionBuilder().withData().build();
}
return prop;
}
private OWLDatatype getOWLDatatype(String name) {
OWLDatatype dt = checker.getOWLDatatype(name);
if (dt == null && dataTypeNames.contains(name)) {
dt = df.getOWLDatatype(getIRI(name));
}
if (dt == null) {
throw new ExceptionBuilder().withDt().build();
}
return dt;
}
private OWLAnnotationProperty getOWLAnnotationProperty(String name) {
OWLAnnotationProperty prop = checker.getOWLAnnotationProperty(name);
if (prop == null && annotationPropertyNames.contains(name)) {
prop = df.getOWLAnnotationProperty(getIRI(name));
}
if (prop == null) {
throw new ExceptionBuilder().withAnn().build();
}
return prop;
}
protected Token getLastToken() {
if (tokenIndex - 1 > -1) {
return tokens.get(tokenIndex - 1);
} else {
return tokens.get(0);
}
}
private String peekToken() {
return getToken().getToken();
}
private String consumeToken() {
String token = getToken().getToken();
if (tokenIndex < tokens.size()) {
tokenIndex++;
}
return token;
}
private void consumeToken(String expected) {
String tok = consumeToken();
if (!tok.equals(expected)) {
throw new ExceptionBuilder().withKeyword(expected).build();
}
}
private void consumeToken(ManchesterOWLSyntax expected) {
String tok = consumeToken();
if (!expected.matches(tok)) {
throw new ExceptionBuilder().withKeyword(expected).build();
}
}
private Token getToken() {
return tokens.get(tokenIndex < tokens.size() ? tokenIndex : tokenIndex - 1);
}
/* Parser */
@Override
public OWLClassExpression parseClassExpression() {
OWLClassExpression desc = parseUnion();
if (!eof(consumeToken())) {
throw new ExceptionBuilder().withKeyword(EOFTOKEN).build();
}
return desc;
}
protected OWLClassExpression parseIntersection() {
Set ops = new HashSet<>();
String kw = AND.keyword();
while (AND.matches(kw)) {
potentialKeywords.remove(AND);
ops.add(parseNonNaryClassExpression());
potentialKeywords.add(AND);
kw = peekToken();
if (AND.matches(kw)) {
kw = consumeToken();
} else if (THAT.matches(kw)) {
consumeToken();
kw = AND.keyword();
}
}
if (ops.size() == 1) {
return ops.iterator().next();
} else {
return df.getOWLObjectIntersectionOf(ops);
}
}
protected OWLClassExpression parseUnion() {
Set ops = new HashSet<>();
String kw = OR.keyword();
while (OR.matches(kw)) {
potentialKeywords.remove(OR);
ops.add(parseIntersection());
potentialKeywords.add(OR);
kw = peekToken();
if (OR.matches(kw)) {
kw = consumeToken();
}
}
if (ops.size() == 1) {
return ops.iterator().next();
} else {
return df.getOWLObjectUnionOf(ops);
}
}
protected OWLObjectPropertyExpression parseObjectPropertyExpression(boolean allowUndeclared) {
String tok = consumeToken();
if (INVERSE.matches(tok)) {
String open = peekToken();
boolean brackets = false;
if (OPEN.matches(open)) {
consumeToken();
brackets = true;
}
OWLObjectPropertyExpression prop = parseObjectPropertyExpression(false);
if (prop.isAnonymous()) {
throw new ExceptionBuilder().withKeyword(
"Inverse construct uses nested object property expression, but object property only is allowed")
.build();
}
if (brackets) {
String close = consumeToken();
if (!CLOSE.matches(close)) {
throw new ExceptionBuilder().withKeyword(CLOSE).build();
}
}
return df.getOWLObjectInverseOf(prop.asOWLObjectProperty());
} else {
if (!allowUndeclared && !isObjectPropertyName(tok)) {
throw new ExceptionBuilder().withObject().build();
}
return getOWLObjectProperty(tok);
}
}
private OWLPropertyExpression parsePropertyExpression() {
String tok = peekToken();
if (isObjectPropertyName(tok)) {
return parseObjectPropertyExpression(false);
} else if (INVERSE.matches(tok)) {
return parseObjectPropertyExpression(false);
} else if (isDataPropertyName(tok)) {
return parseDataProperty();
} else {
consumeToken();
throw new ExceptionBuilder().withObject().withData().build();
}
}
/**
* Parses all class expressions except ObjectIntersectionOf and
* ObjectUnionOf.
*
* @return The class expression which was parsed @ * if a non-nary class
* expression could not be parsed
*/
private OWLClassExpression parseNonNaryClassExpression() {
String tok = peekToken();
if (NOT.matches(tok)) {
consumeToken();
OWLClassExpression complemented = parseNestedClassExpression(false);
return df.getOWLObjectComplementOf(complemented);
} else if (isClassName(tok)) {
consumeToken();
return getOWLClass(tok);
} else if (isObjectPropertyName(tok) || INVERSE.matches(tok)) {
return parseObjectRestriction();
} else if (isDataPropertyName(tok)) {
// Data restriction
return parseDataRestriction();
} else if (OPENBRACE.matches(tok)) {
return parseObjectOneOf();
} else if (OPEN.matches(tok)) {
return parseNestedClassExpression(false);
}
// Add option for strict class name checking
else {
consumeToken();
throw new ExceptionBuilder().withClass().withObject().withData().withKeyword(OPEN, OPENBRACE, NOT, INVERSE)
.build();
}
}
private OWLClassExpression parseObjectRestriction() {
OWLObjectPropertyExpression prop = parseObjectPropertyExpression(false);
String kw = consumeToken();
if (SOME.matches(kw)) {
String possSelfToken = peekToken();
if (SELF.matches(possSelfToken)) {
consumeToken();
return df.getOWLObjectHasSelf(prop);
} else {
OWLClassExpression filler = null;
try {
filler = parseNestedClassExpression(false);
} catch (ParserException e) {
e.getExpectedKeywords().add(SELF.keyword());
throw e;
}
return df.getOWLObjectSomeValuesFrom(prop, filler);
}
} else if (ONLY.matches(kw)) {
OWLClassExpression filler = parseNestedClassExpression(false);
return df.getOWLObjectAllValuesFrom(prop, filler);
} else if (VALUE.matches(kw)) {
String indName = consumeToken();
if (!isIndividualName(indName)) {
throw new ExceptionBuilder().withInd().build();
}
return df.getOWLObjectHasValue(prop, getOWLIndividual(indName));
} else if (MIN.matches(kw)) {
int card = parseInteger();
OWLClassExpression filler = parseNestedClassExpression(true);
return df.getOWLObjectMinCardinality(card, prop, filler);
} else if (MAX.matches(kw)) {
int card = parseInteger();
OWLClassExpression filler = parseNestedClassExpression(true);
return df.getOWLObjectMaxCardinality(card, prop, filler);
} else if (EXACTLY.matches(kw)) {
int card = parseInteger();
OWLClassExpression filler = parseNestedClassExpression(true);
return df.getOWLObjectExactCardinality(card, prop, filler);
} else if (ONLYSOME.matches(kw)) {
String tok = peekToken();
Set descs = new HashSet<>();
if (!OPENBRACKET.matches(tok)) {
descs.add(parseUnion());
} else {
descs.addAll(parseClassExpressionList(OPENBRACKET, CLOSEBRACKET));
}
Set ops = new HashSet<>();
descs.forEach(d -> ops.add(df.getOWLObjectSomeValuesFrom(prop, d)));
OWLClassExpression filler;
if (descs.size() == 1) {
filler = descs.iterator().next();
} else {
filler = df.getOWLObjectUnionOf(descs);
}
ops.add(df.getOWLObjectAllValuesFrom(prop, filler));
return df.getOWLObjectIntersectionOf(ops);
} else if (SELF.matches(kw)) {
return df.getOWLObjectHasSelf(prop);
} else {
// Error!
throw new ExceptionBuilder().withKeyword(SOME, ONLY, VALUE, MIN, MAX, EXACTLY, SELF).build();
}
}
private OWLClassExpression parseDataRestriction() {
OWLDataPropertyExpression prop = parseDataProperty();
String kw = consumeToken();
if (SOME.matches(kw)) {
OWLDataRange rng = parseDataRange();
return df.getOWLDataSomeValuesFrom(prop, rng);
} else if (ONLY.matches(kw)) {
OWLDataRange rng = parseDataRange();
return df.getOWLDataAllValuesFrom(prop, rng);
} else if (VALUE.matches(kw)) {
OWLLiteral con = parseLiteral(null);
return df.getOWLDataHasValue(prop, con);
} else if (MIN.matches(kw)) {
int card = parseInteger();
OWLDataRange rng = parseDataRange();
return df.getOWLDataMinCardinality(card, prop, rng);
} else if (EXACTLY.matches(kw)) {
int card = parseInteger();
OWLDataRange rng = parseDataRange();
return df.getOWLDataExactCardinality(card, prop, rng);
} else if (MAX.matches(kw)) {
int card = parseInteger();
OWLDataRange rng = parseDataRange();
return df.getOWLDataMaxCardinality(card, prop, rng);
}
throw new ExceptionBuilder().withKeyword(SOME, ONLY, VALUE, MIN, EXACTLY, MAX).build();
}
@Nullable
private OWLFacet parseFacet() {
String facet = consumeToken();
if (MIN_INCLUSIVE_FACET.matches(facet, peekToken())) {
consumeToken();
return OWLFacet.MIN_INCLUSIVE;
}
if (MAX_INCLUSIVE_FACET.matches(facet, peekToken())) {
consumeToken();
return OWLFacet.MAX_INCLUSIVE;
}
if (MIN_EXCLUSIVE_FACET.matches(facet)) {
return OWLFacet.MIN_EXCLUSIVE;
}
if (MAX_EXCLUSIVE_FACET.matches(facet)) {
return OWLFacet.MAX_EXCLUSIVE;
}
return OWLFacet.getFacetBySymbolicName(facet);
}
private OWLDatatype parseDatatype() {
String name = consumeToken();
return getOWLDatatype(name);
}
@Override
public OWLDataRange parseDataRange() {
return parseDataIntersectionOf();
}
private OWLDataRange parseDataIntersectionOf() {
String sep = AND.keyword();
Set ranges = new HashSet<>();
while (AND.matches(sep)) {
ranges.add(parseDataUnionOf());
sep = peekToken();
if (AND.matches(sep)) {
consumeToken();
}
}
if (ranges.isEmpty()) {
return df.getTopDatatype();
}
if (ranges.size() == 1) {
return ranges.iterator().next();
}
return df.getOWLDataIntersectionOf(ranges);
}
private OWLDataRange parseDataUnionOf() {
String sep = OR.keyword();
Set ranges = new HashSet<>();
while (OR.matches(sep)) {
ranges.add(parseDataRangePrimary());
sep = peekToken();
if (OR.matches(sep)) {
consumeToken();
}
}
if (ranges.size() == 1) {
return ranges.iterator().next();
} else {
return df.getOWLDataUnionOf(ranges);
}
}
private OWLDataRange parseDataRangePrimary() {
String tok = peekToken();
if (isDatatypeName(tok)) {
consumeToken();
OWLDatatype datatype = getOWLDatatype(tok);
String next = peekToken();
if (OPENBRACKET.matches(next)) {
// Restricted data range
consumeToken();
String sep = COMMA.keyword();
Set facetRestrictions = new HashSet<>();
while (COMMA.matches(sep)) {
OWLFacet fv = parseFacet();
if (fv == null) {
throw new ExceptionBuilder().withKeyword(OWLFacet.getFacets()).build();
}
OWLLiteral con = parseLiteral(datatype);
facetRestrictions.add(df.getOWLFacetRestriction(fv, con));
sep = consumeToken();
}
if (!CLOSEBRACKET.matches(sep)) {
throw new ExceptionBuilder().withKeyword(CLOSEBRACKET).build();
}
return df.getOWLDatatypeRestriction(datatype, facetRestrictions);
} else {
return datatype;
}
} else if (NOT.matches(tok)) {
return parseDataComplementOf();
} else if (OPENBRACE.matches(tok)) {
return parseDataOneOf();
} else if (OPEN.matches(tok)) {
consumeToken();
OWLDataRange rng = parseDataRange();
consumeToken(CLOSE.keyword());
return rng;
} else {
consumeToken();
throw new ExceptionBuilder().withDt().withKeyword(OPENBRACE, NOT).build();
}
}
@Override
public Set parseDataRangeList() {
String sep = COMMA.keyword();
Set ranges = new HashSet<>();
while (COMMA.matches(sep)) {
potentialKeywords.remove(COMMA);
OWLDataRange rng = parseDataRange();
ranges.add(rng);
potentialKeywords.add(COMMA);
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
return ranges;
}
private OWLDataRange parseDataOneOf() {
consumeToken();
Set cons = new HashSet<>();
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
OWLLiteral con = parseLiteral(null);
cons.add(con);
sep = consumeToken();
}
if (!CLOSEBRACE.matches(sep)) {
throw new ExceptionBuilder().withKeyword(COMMA, CLOSEBRACE).build();
}
return df.getOWLDataOneOf(cons);
}
private OWLDataRange parseDataComplementOf() {
String not = consumeToken();
if (!NOT.matches(not)) {
throw new ExceptionBuilder().withKeyword(NOT).build();
}
OWLDataRange complementedDataRange = parseDataRangePrimary();
return df.getOWLDataComplementOf(complementedDataRange);
}
@Override
public OWLLiteral parseLiteral(@Nullable OWLDatatype datatype) {
String tok = consumeToken();
if (tok.startsWith("\"")) {
String lit = unquoteLiteral(tok);
if ("^".equals(peekToken())) {
consumeToken();
if (!"^".equals(peekToken())) {
throw new ExceptionBuilder().withKeyword("^").build();
}
consumeToken();
return df.getOWLLiteral(lit, parseDatatype());
} else if (peekToken().startsWith("@")) {
// Plain literal with a language tag
String lang = consumeToken().substring(1);
return df.getOWLLiteral(lit, lang);
} else {
// Plain literal without a language tag
return df.getOWLLiteral(lit, "");
}
} else {
if (datatype != null) {
// datatype is known from context
return df.getOWLLiteral(tok, datatype);
}
try {
int i = Integer.parseInt(tok);
return df.getOWLLiteral(i);
} catch (@SuppressWarnings("unused") NumberFormatException e) {
// Ignore - not interested
}
if (tok.endsWith("f") || tok.endsWith("F")) {
try {
// this extra F might qualify as Float a Double INF/-INF
float f = Float.parseFloat(tok.replace("INF", INFINITY).replace("inf", INFINITY));
return df.getOWLLiteral(asFloat(f), OWL2Datatype.XSD_FLOAT);
} catch (@SuppressWarnings("unused") NumberFormatException e) {
// Ignore - not interested
}
}
try {
// ensure it's a valid double, or skip
Double.parseDouble(tok);
return df.getOWLLiteral(tok, OWL2Datatype.XSD_DECIMAL);
} catch (@SuppressWarnings("unused") NumberFormatException e) {
// Ignore - not interested
}
if (LITERAL_TRUE.matches(tok)) {
return df.getOWLLiteral(true);
} else if (LITERAL_FALSE.matches(tok)) {
return df.getOWLLiteral(false);
}
}
throw new ExceptionBuilder().withKeyword(LITERAL_TRUE, LITERAL_FALSE, LITERAL_INTEGER, LITERAL_FLOAT,
LITERAL_DOUBLE, LITERAL_LITERAL, LITERAL_LIT_DATATYPE, LITERAL_LIT_LANG).build();
}
private String unquoteLiteral(String tok) {
String lit = "";
if (!tok.endsWith("\"")) {
consumeToken();
throw new ExceptionBuilder().withKeyword("\"").build();
}
if (tok.length() > 2) {
lit = tok.substring(1, tok.length() - 1);
}
return verifyNotNull(lit);
}
private static String asFloat(float f) {
return Float.toString(f).replace(INFINITY, "INF");
}
private int parseInteger() {
String i = consumeToken();
try {
return Integer.parseInt(i);
} catch (@SuppressWarnings("unused") NumberFormatException e) {
throw new ExceptionBuilder().withInt().build();
}
}
private OWLClassExpression parseNestedClassExpression(boolean lookaheadCheck) {
String tok = peekToken();
if (OPEN.matches(tok)) {
consumeToken();
OWLClassExpression desc = parseUnion();
String closeBracket = consumeToken();
if (!CLOSE.matches(closeBracket)) {
// Error!
throw new ExceptionBuilder().withKeyword(CLOSE).build();
}
return desc;
} else if (OPENBRACE.matches(tok)) {
return parseObjectOneOf();
} else if (isClassName(tok)) {
String name = consumeToken();
return getOWLClass(name);
}
// XXX problem: if the class expression is missing, we should return
// owl:Thing. But there are many ways in which it could be missing. Hard
// to tell what sort of lookahead is needed.
// The next two checks should cover most cases.
for (ManchesterOWLSyntax x : values()) {
if (x.matches(tok)) {
return df.getOWLThing();
}
}
if (eof(tok)) {
return df.getOWLThing();
}
if (!eof(tok) || !lookaheadCheck) {
consumeToken();
throw new ExceptionBuilder().withKeyword(OPEN, OPENBRACE).withClass().build();
}
return df.getOWLThing();
}
private OWLClassExpression parseObjectOneOf() {
String open = consumeToken();
if (!OPENBRACE.matches(open)) {
throw new ExceptionBuilder().withKeyword(OPENBRACE).build();
}
String sep = COMMA.keyword();
Set inds = new HashSet<>();
while (COMMA.matches(sep)) {
inds.add(parseIndividual());
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
String close = consumeToken();
if (!CLOSEBRACE.matches(close)) {
throw new ExceptionBuilder().withKeyword(CLOSEBRACE, COMMA).build();
}
return df.getOWLObjectOneOf(inds);
}
private static void initialiseSection(AnnAxiom parser, Map> map,
ManchesterOWLSyntax... synonyms) {
map.put(parser.keyword, parser);
for (ManchesterOWLSyntax syn : synonyms) {
map.put(syn, parser);
}
}
@Override
public Set parseFrames() {
Set axioms = new HashSet<>();
Set possible = new HashSet<>();
resetPossible(possible);
while (true) {
String tok = peekToken();
if (CLASS.matches(tok)) {
potentialKeywords.clear();
resetPossible(possible);
axioms.addAll(parseClassFrame());
possible.addAll(classFrameSections.keySet());
} else if (OBJECT_PROPERTY.matches(tok)) {
potentialKeywords.clear();
resetPossible(possible);
axioms.addAll(parseObjectPropertyFrame());
possible.addAll(objectPropertyFrameSections.keySet());
} else if (DATA_PROPERTY.matches(tok)) {
potentialKeywords.clear();
resetPossible(possible);
axioms.addAll(parseDataPropertyFrame());
possible.addAll(dataPropertyFrameSections.keySet());
} else if (ANNOTATION_PROPERTY.matches(tok)) {
potentialKeywords.clear();
resetPossible(possible);
axioms.addAll(parseAnnotationPropertyFrame());
possible.addAll(Arrays.asList(SUB_PROPERTY_OF, DOMAIN, RANGE));
} else if (INDIVIDUAL.matches(tok)) {
potentialKeywords.clear();
resetPossible(possible);
axioms.addAll(parseIndividualFrame());
possible.addAll(Arrays.asList(TYPES, FACTS, DIFFERENT_FROM, SAME_AS));
} else if (DATATYPE.matches(tok)) {
potentialKeywords.clear();
resetPossible(possible);
axioms.addAll(parseDatatypeFrame());
possible.add(EQUIVALENT_TO);
} else if (VALUE_PARTITION.matches(tok)) {
potentialKeywords.clear();
resetPossible(possible);
parseValuePartitionFrame();
} else if (RULE.matches(tok)) {
potentialKeywords.clear();
resetPossible(possible);
axioms.addAll(parseRuleFrame());
} else {
if (eof(tok)) {
break;
} else {
consumeToken();
throw new ExceptionBuilder().withKeyword(possible).build();
}
}
}
return axioms;
}
@Override
public Set parseDatatypeFrame() {
String tok = consumeToken();
if (!DATATYPE.matches(tok)) {
throw new ExceptionBuilder().withKeyword(DATATYPE).build();
}
String subj = consumeToken();
OWLDatatype datatype = getOWLDatatype(subj);
Set axioms = new HashSet<>();
axioms.add(new OntologyAxiomPair(defaultOntology, df.getOWLDeclarationAxiom(datatype)));
while (true) {
String sect = peekToken();
if (EQUIVALENT_TO.matches(sect)) {
potentialKeywords.clear();
consumeToken();
Set onts = getOntologies();
Set drs = parseDataRangeList();
for (OWLOntology ont : onts) {
for (OWLDataRange dr : drs) {
axioms.add(new OntologyAxiomPair(ont, df.getOWLDatatypeDefinitionAxiom(datatype, dr)));
}
}
} else if (ANNOTATIONS.matches(sect)) {
potentialKeywords.clear();
axioms.addAll(parseAnnotations(datatype.getIRI()));
} else {
break;
}
}
return axioms;
}
private static void resetPossible(Set possible) {
possible.clear();
possible.add(ANNOTATIONS);
possible.add(ANNOTATION_PROPERTY);
possible.add(CLASS);
possible.add(OBJECT_PROPERTY);
possible.add(DATATYPE);
possible.add(DATA_PROPERTY);
possible.add(INDIVIDUAL);
possible.add(VALUE_PARTITION);
possible.add(RULE);
}
private Set parseNaryEquivalentClasses() {
String tok = consumeToken();
if (!EQUIVALENT_CLASSES.matches(tok)) {
throw new ExceptionBuilder().withKeyword(EQUIVALENT_CLASSES).build();
}
Set ontologies = getOntologies();
Set annotations = parseAnnotations();
Set classExpressions = parseClassExpressionList();
Set pairs = new HashSet<>();
for (OWLOntology ont : ontologies) {
pairs.add(new OntologyAxiomPair(ont, df.getOWLEquivalentClassesAxiom(classExpressions, annotations)));
}
return pairs;
}
private Set parseNaryEquivalentProperties() {
String tok = consumeToken();
if (!EQUIVALENT_PROPERTIES.matches(tok)) {
throw new ExceptionBuilder().withKeyword(EQUIVALENT_PROPERTIES).build();
}
Set ontologies = getOntologies();
Set annotations = parseAnnotations();
Set properties = parsePropertyList();
OWLAxiom propertyAxiom;
if (properties.iterator().next().isObjectPropertyExpression()) {
Set ope = new HashSet<>();
properties.forEach(pe -> ope.add(pe.asObjectPropertyExpression()));
propertyAxiom = df.getOWLEquivalentObjectPropertiesAxiom(ope, annotations);
} else {
Set dpe = new HashSet<>();
properties.forEach(pe -> dpe.add(pe.asDataPropertyExpression()));
propertyAxiom = df.getOWLEquivalentDataPropertiesAxiom(dpe, annotations);
}
Set pairs = new HashSet<>();
for (OWLOntology ont : ontologies) {
pairs.add(new OntologyAxiomPair(ont, propertyAxiom));
}
return pairs;
}
private Set parseAnnotations() {
String next = peekToken();
Set annotations = Collections.emptySet();
if (ANNOTATIONS.matches(next)) {
consumeToken();
annotations = parseAnnotationList();
}
return annotations;
}
private Set parseAnnotations(OWLAnnotationSubject s) {
String header = consumeToken();
if (!ANNOTATIONS.matches(header)) {
throw new ExceptionBuilder().withKeyword(ANNOTATIONS).build();
}
Set onts = getOntologies();
Set pairs = new HashSet<>();
Set annos = parseAnnotationList();
for (OWLOntology ont : onts) {
for (OWLAnnotation anno : annos) {
if (getOntologyLoaderConfiguration().isLoadAnnotationAxioms()) {
pairs.add(new OntologyAxiomPair(ont, df.getOWLAnnotationAssertionAxiom(s, anno)));
}
}
}
return pairs;
}
private Set parseAnnotationList() {
String sep = COMMA.keyword();
Set annos = new HashSet<>();
while (COMMA.matches(sep)) {
potentialKeywords.clear();
Set annotations = parseAnnotations();
OWLAnnotation anno = parseAnnotation();
anno = anno.getAnnotatedAnnotation(annotations);
annos.add(anno);
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
return annos;
}
protected OWLAnnotation parseAnnotation() {
OWLAnnotationProperty annoProp = parseAnnotationProperty();
String obj = peekToken();
if (isIndividualName(obj) || isClassName(obj) || isObjectPropertyName(obj) || isDataPropertyName(obj)) {
consumeToken();
OWLAnnotationValue value;
if (obj.startsWith("_:")) {
value = anonProvider.getOWLAnonymousIndividual(obj);
} else {
value = getIRI(obj);
}
return df.getOWLAnnotation(annoProp, value);
}
if (obj.startsWith("<")) {
IRI value = parseIRI();
return df.getOWLAnnotation(annoProp, value);
}
OWLLiteral con = parseLiteral(null);
return df.getOWLAnnotation(annoProp, con);
}
@Override
public Set parseClassFrame() {
return parseClassFrame(false);
}
@Override
public Set parseClassFrameEOF() {
return parseClassFrame(true);
}
private Set parseClassFrame(boolean eof) {
String tok = consumeToken();
if (!CLASS.matches(tok)) {
throw new ExceptionBuilder().withKeyword(CLASS).build();
}
String subj = consumeToken();
OWLClass cls = getOWLClass(subj);
Set axioms = new HashSet<>();
axioms.add(new OntologyAxiomPair(defaultOntology, df.getOWLDeclarationAxiom(cls)));
parseFrameSections(eof, axioms, cls, classFrameSections);
return axioms;
}
private Set parseOntologyList() {
potentialKeywords.clear();
consumeToken(OPENBRACKET.keyword());
consumeToken("in");
String sep = COMMA.keyword();
Set onts = new HashSet<>();
while (COMMA.matches(sep)) {
String tok = consumeToken();
if (isOntologyName(tok)) {
OWLOntology ont = getOntology(tok);
if (ont != null) {
onts.add(ont);
}
} else {
throw new ExceptionBuilder().withOnto().build();
}
sep = consumeToken();
if (sep.equals(CLOSEBRACKET.keyword())) {
break;
} else if (!COMMA.matches(sep)) {
throw new ExceptionBuilder().withKeyword(COMMA, CLOSEBRACKET).build();
}
}
return onts;
}
private Set getOntologies() {
if (peekToken().equals(OPENBRACKET.keyword())) {
return parseOntologyList();
} else {
return CollectionFactory.createSet(defaultOntology);
}
}
@Override
public void setDefaultOntology(OWLOntology defaultOntology) {
this.defaultOntology = defaultOntology;
defaultOntology.axioms(AxiomType.DECLARATION, Imports.INCLUDED).forEach(this::processDeclaredEntities);
}
private boolean isEmptyFrameSection(Map parsers) {
if (!ALLOWEMPTYFRAMESECTIONS) {
return false;
}
String next = peekToken();
return !ANNOTATIONS.matches(next) && (parsers.containsKey(parse(next)) || eof(next));
}
private void parseFrameSections(boolean eof, Set axioms, F frameSubject,
Map> sectionParsers) {
while (true) {
String sect = peekToken();
AnnAxiom parser = sectionParsers.get(parse(sect));
if (parser != null) {
consumeToken();
Set onts = getOntologies();
if (!isEmptyFrameSection(sectionParsers)) {
axioms.addAll(parseAnnotatedListItems(frameSubject, parser, onts));
}
} else if (eof && !eof(sect)) {
List expected = new ArrayList<>();
expected.addAll(sectionParsers.keySet());
if (frameSubject instanceof OWLAnnotationSubject || frameSubject instanceof OWLEntity) {
expected.add(ANNOTATIONS);
}
throw new ExceptionBuilder().withKeyword(expected).build();
} else {
break;
}
}
}
@Override
public Set parseObjectPropertyFrame() {
return parseObjectPropertyFrame(false);
}
private Set parseObjectPropertyFrame(boolean eof) {
Set axioms = new HashSet<>();
consumeToken(OBJECT_PROPERTY);
String token = consumeToken();
OWLObjectProperty prop = getOWLObjectProperty(token);
if (!prop.isAnonymous()) {
axioms.add(new OntologyAxiomPair(defaultOntology, df.getOWLDeclarationAxiom(prop.asOWLObjectProperty())));
}
parseFrameSections(eof, axioms, prop, objectPropertyFrameSections);
return axioms;
}
@Override
public Set parseDataPropertyFrame() {
String tok = consumeToken();
if (!DATA_PROPERTY.matches(tok)) {
throw new ExceptionBuilder().withKeyword(DATA_PROPERTY).build();
}
String subj = consumeToken();
OWLDataProperty prop = getOWLDataProperty(subj);
Set axioms = new HashSet<>();
axioms.add(new OntologyAxiomPair(defaultOntology, df.getOWLDeclarationAxiom(prop)));
parseFrameSections(false, axioms, prop, dataPropertyFrameSections);
return axioms;
}
@Override
public Set parseAnnotationPropertyFrame() {
String tok = consumeToken();
if (!ANNOTATION_PROPERTY.matches(tok)) {
throw new ExceptionBuilder().withKeyword(ANNOTATION_PROPERTY).build();
}
String subj = consumeToken();
OWLAnnotationProperty prop = getOWLAnnotationProperty(subj);
Set axioms = new HashSet<>();
for (OWLOntology ont : getOntologies()) {
axioms.add(new OntologyAxiomPair(ont, df.getOWLDeclarationAxiom(prop)));
}
parseFrameSections(false, axioms, prop, annotationPropertyFrameSections);
return axioms;
}
@Override
public Set parseIndividualFrame() {
String tok = consumeToken();
if (!INDIVIDUAL.matches(tok)) {
throw new ExceptionBuilder().withKeyword(INDIVIDUAL).build();
}
String subj = consumeToken();
OWLIndividual ind = getOWLIndividual(subj);
Set axioms = new HashSet<>();
if (!ind.isAnonymous()) {
axioms.add(new OntologyAxiomPair(getOntology(null), df.getOWLDeclarationAxiom(ind.asOWLNamedIndividual())));
}
parseFrameSections(false, axioms, ind, individualFrameSections);
return axioms;
}
protected OWLAxiom parseFact(OWLIndividual ind) {
boolean negative = false;
if (NOT.matches(peekToken())) {
consumeToken();
negative = true;
}
String prop = peekToken();
if (isDataPropertyName(prop)) {
OWLDataProperty p = parseDataProperty();
OWLLiteral con = parseLiteral(null);
if (!negative) {
return df.getOWLDataPropertyAssertionAxiom(p, ind, con);
} else {
return df.getOWLNegativeDataPropertyAssertionAxiom(p, ind, con);
}
} else if (isObjectPropertyName(prop) || INVERSE.matches(prop)) {
OWLObjectPropertyExpression p = parseObjectPropertyExpression(false);
if (!negative) {
return df.getOWLObjectPropertyAssertionAxiom(p, ind, parseIndividual());
} else {
return df.getOWLNegativeObjectPropertyAssertionAxiom(p, ind, parseIndividual());
}
} else {
consumeToken();
throw new ExceptionBuilder().withObject().withData().build();
}
}
@Override
public Set parseValuePartitionFrame() {
String section = consumeToken();
if (!VALUE_PARTITION.matches(section)) {
throw new ExceptionBuilder().withKeyword(VALUE_PARTITION).build();
}
OWLObjectPropertyExpression prop = parseObjectPropertyExpression(false);
String clsName = consumeToken();
if (eof(clsName)) {
throw new ExceptionBuilder().withObject().build();
}
OWLClass cls = getOWLClass(clsName);
Set axioms = new HashSet<>();
Set onts = getOntologies();
axioms.addAll(parseValuePartitionValues(onts, cls));
for (OWLOntology ont : onts) {
axioms.add(new OntologyAxiomPair(ont, df.getOWLFunctionalObjectPropertyAxiom(prop)));
axioms.add(new OntologyAxiomPair(ont, df.getOWLObjectPropertyRangeAxiom(prop, cls)));
}
return axioms;
}
private Set parseValuePartitionValues(Set onts, OWLClass superclass) {
Set axioms = new HashSet<>();
Set siblings = new HashSet<>();
consumeToken(OPENBRACKET.keyword());
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
String clsName = consumeToken();
OWLClass cls = getOWLClass(clsName);
siblings.add(cls);
OWLSubClassOfAxiom ax = df.getOWLSubClassOfAxiom(cls, superclass);
for (OWLOntology ont : onts) {
axioms.add(new OntologyAxiomPair(ont, ax));
}
if (peekToken().equals(OPENBRACKET.keyword())) {
axioms.addAll(parseValuePartitionValues(onts, cls));
}
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
consumeToken(CLOSEBRACKET.keyword());
OWLAxiom ax = df.getOWLDisjointClassesAxiom(siblings);
for (OWLOntology ont : onts) {
axioms.add(new OntologyAxiomPair(ont, ax));
}
return axioms;
}
@Override
public List parseRuleFrame() {
String section = consumeToken();
if (!RULE.matches(section)) {
throw new ExceptionBuilder().withKeyword(RULE).build();
}
Set ontologies = getOntologies();
List body = parseRuleAtoms();
String tok = consumeToken();
if (!DASH.matches(tok)) {
throw new ExceptionBuilder().withKeyword(DASH, COMMA).build();
}
consumeToken(">");
List head = parseRuleAtoms();
SWRLRule rule = df.getSWRLRule(new LinkedHashSet<>(body), new LinkedHashSet<>(head));
List pairs = new ArrayList<>();
for (OWLOntology ont : ontologies) {
pairs.add(new OntologyAxiomPair(ont, rule));
}
return pairs;
}
private List parseRuleAtoms() {
String sep = COMMA.keyword();
List atoms = new ArrayList<>();
while (COMMA.matches(sep)) {
potentialKeywords.remove(COMMA);
SWRLAtom atom = parseRuleAtom();
atoms.add(atom);
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
potentialKeywords.add(COMMA);
}
return atoms;
}
private SWRLAtom parseRuleAtom() {
String predicate = peekToken();
if (isClassName(predicate)) {
return parseClassAtom();
} else if (OPEN.matches(predicate)) {
return parseClassAtom();
} else if (isObjectPropertyName(predicate)) {
return parseObjectPropertyAtom();
} else if (isDataPropertyName(predicate)) {
return parseDataPropertyAtom();
} else if (isDatatypeName(predicate)) {
return parseDataRangeAtom();
} else if (DIFFERENT_FROM.matchesEitherForm(predicate)) {
return parseDifferentFromAtom();
} else if (SAME_AS.matchesEitherForm(predicate)) {
return parseSameAsAtom();
} else if (isSWRLBuiltin(predicate) || predicate.startsWith("<")) {
return parseBuiltInAtom();
} else {
consumeToken();
Set kw = new TreeSet<>();
kw.addAll(ruleBuiltIns.keySet());
kw.add(DIFFERENT_FROM.toString());
kw.add(SAME_AS.toString());
throw new ExceptionBuilder().withKeyword(kw).withClass().withObject().withData().build();
}
}
private SWRLAtom parseDataPropertyAtom() {
String predicate = consumeToken();
if (!isDataPropertyName(predicate)) {
throw new ExceptionBuilder().withData().build();
}
consumeToken(OPEN.keyword());
SWRLIArgument obj1 = parseIObject();
consumeToken(COMMA.keyword());
SWRLDArgument obj2 = parseDObject();
consumeToken(CLOSE.keyword());
return df.getSWRLDataPropertyAtom(getOWLDataProperty(predicate), obj1, obj2);
}
private SWRLAtom parseDataRangeAtom() {
OWLDataRange range = parseDataRange();
consumeToken(OPEN.keyword());
SWRLVariable obj1 = parseDVariable();
consumeToken(CLOSE.keyword());
return df.getSWRLDataRangeAtom(range, obj1);
}
private SWRLAtom parseObjectPropertyAtom() {
String predicate = consumeToken();
if (!isObjectPropertyName(predicate)) {
throw new ExceptionBuilder().withObject().build();
}
consumeToken(OPEN.keyword());
SWRLIArgument obj1 = parseIObject();
consumeToken(COMMA.keyword());
SWRLIArgument obj2 = parseIObject();
consumeToken(CLOSE.keyword());
return df.getSWRLObjectPropertyAtom(getOWLObjectProperty(predicate), obj1, obj2);
}
private SWRLAtom parseClassAtom() {
OWLClassExpression predicate = parseUnion();
consumeToken(OPEN.keyword());
SWRLIArgument obj = parseIObject();
consumeToken(CLOSE.keyword());
return df.getSWRLClassAtom(predicate, obj);
}
private SWRLDifferentIndividualsAtom parseDifferentFromAtom() {
consumeToken(ManchesterOWLSyntax.DIFFERENT_FROM.toString());
consumeToken(OPEN.keyword());
SWRLIArgument obj1 = parseIObject();
consumeToken(COMMA.keyword());
SWRLIArgument obj2 = parseIObject();
consumeToken(CLOSE.keyword());
return df.getSWRLDifferentIndividualsAtom(obj1, obj2);
}
private SWRLSameIndividualAtom parseSameAsAtom() {
consumeToken(ManchesterOWLSyntax.SAME_AS.toString());
consumeToken(OPEN.keyword());
SWRLIArgument obj1 = parseIObject();
consumeToken(COMMA.keyword());
SWRLIArgument obj2 = parseIObject();
consumeToken(CLOSE.keyword());
return df.getSWRLSameIndividualAtom(obj1, obj2);
}
private SWRLIArgument parseIObject() {
String s = peekToken();
if (isIndividualName(s)) {
return parseIIndividualObject();
} else if ("?".equals(s)) {
return parseIVariable();
} else {
consumeToken();
throw new ExceptionBuilder().withInd().withKeyword("?$var$").build();
}
}
private SWRLVariable parseIVariable() {
return df.getSWRLVariable(parseVariable());
}
private SWRLIndividualArgument parseIIndividualObject() {
return df.getSWRLIndividualArgument(parseIndividual());
}
@Override
public IRI parseVariable() {
consumeToken("?");
String fragment = peekToken();
if (fragment.startsWith("<")) {
// then the variable was saved with a full IRI
// preserve the namespace
return parseIRI();
} else {
consumeToken();
}
return IRI.create("urn:swrl#", fragment);
}
private SWRLDArgument parseDObject() {
String s = peekToken();
if ("?".equals(s)) {
return parseDVariable();
} else {
try {
return parseLiteralObject();
} catch (ParserException e) {
e.getExpectedKeywords().add("?");
throw e;
}
}
}
private SWRLVariable parseDVariable() {
IRI var = parseVariable();
return df.getSWRLVariable(var);
}
private SWRLLiteralArgument parseLiteralObject() {
OWLLiteral lit = parseLiteral(null);
return df.getSWRLLiteralArgument(lit);
}
private SWRLBuiltInAtom parseBuiltInAtom() {
String predicate = consumeToken();
consumeToken(OPEN.keyword());
SWRLBuiltInsVocabulary v = null;
IRI iri;
if (!ruleBuiltIns.containsKey(predicate)) {
iri = getIRI(predicate);
} else {
v = ruleBuiltIns.get(predicate);
iri = v.getIRI();
}
List args = new ArrayList<>();
if (v != null && v.getMaxArity() >= 0) {
// We know the arity!
for (int i = 0; i < v.getMaxArity(); i++) {
SWRLDArgument obj = parseDObject();
args.add(obj);
// parse at least the minumum arity
if (i < v.getMinArity() - 1) {
consumeToken(COMMA.keyword());
} else if (i < v.getMaxArity() - 1) {
if (peekToken().equals(COMMA.keyword())) {
consumeToken();
} else {
break;
}
}
}
} else {
// Unknown arity so just parse as many arguments as we can
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
SWRLDArgument arg = parseDObject();
args.add(arg);
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
}
consumeToken(CLOSE.keyword());
return df.getSWRLBuiltInAtom(iri, args);
}
private Set parseDisjointClasses() {
String section = consumeToken();
if (!DISJOINT_CLASSES.matches(section)) {
throw new ExceptionBuilder().withKeyword(DISJOINT_CLASSES).build();
}
Set ontologies = getOntologies();
Set annotations = parseAnnotations();
Set classExpressions = parseClassExpressionList();
Set pairs = new HashSet<>();
for (OWLOntology ont : ontologies) {
pairs.add(new OntologyAxiomPair(ont, df.getOWLDisjointClassesAxiom(classExpressions, annotations)));
}
return pairs;
}
private Set parseSameIndividual() {
String section = consumeToken();
if (!SAME_INDIVIDUAL.matches(section)) {
throw new ExceptionBuilder().withKeyword(SAME_INDIVIDUAL).build();
}
Set individuals = parseIndividualList();
Set ontologies = getOntologies();
Set annotations = parseAnnotations();
Set pairs = new HashSet<>();
for (OWLOntology ont : ontologies) {
pairs.add(new OntologyAxiomPair(ont, df.getOWLSameIndividualAxiom(individuals, annotations)));
}
return pairs;
}
private Set parseDisjointProperties() {
String section = consumeToken();
if (!DISJOINT_PROPERTIES.matches(section)) {
throw new ExceptionBuilder().withKeyword(DISJOINT_PROPERTIES).build();
}
Set ontologies = getOntologies();
Set annotations = parseAnnotations();
Set props = parsePropertyList();
Set pairs = new HashSet<>();
OWLAxiom propertiesAxiom;
if (props.iterator().next().isObjectPropertyExpression()) {
Set ope = new HashSet<>();
props.forEach(pe -> ope.add(pe.asObjectPropertyExpression()));
propertiesAxiom = df.getOWLDisjointObjectPropertiesAxiom(ope, annotations);
} else {
Set dpe = new HashSet<>();
props.forEach(pe -> dpe.add(pe.asDataPropertyExpression()));
propertiesAxiom = df.getOWLDisjointDataPropertiesAxiom(dpe, annotations);
}
for (OWLOntology ont : ontologies) {
pairs.add(new OntologyAxiomPair(ont, propertiesAxiom));
}
return pairs;
}
private Set parseDifferentIndividuals() {
String section = consumeToken();
if (!DIFFERENT_INDIVIDUALS.matches(section)) {
throw new ExceptionBuilder().withKeyword(DIFFERENT_INDIVIDUALS).build();
}
Set ontologies = getOntologies();
Set annotations = parseAnnotations();
Set individuals = parseIndividualList();
Set pairs = new HashSet<>();
for (OWLOntology ontology : ontologies) {
pairs.add(new OntologyAxiomPair(ontology, df.getOWLDifferentIndividualsAxiom(individuals, annotations)));
}
return pairs;
}
protected OWLObjectPropertyCharacteristicAxiom parseObjectPropertyCharacteristic(OWLObjectPropertyExpression prop) {
String characteristic = consumeToken();
if (FUNCTIONAL.matches(characteristic)) {
return df.getOWLFunctionalObjectPropertyAxiom(prop);
} else if (INVERSE_FUNCTIONAL.matches(characteristic)) {
return df.getOWLInverseFunctionalObjectPropertyAxiom(prop);
} else if (SYMMETRIC.matches(characteristic)) {
return df.getOWLSymmetricObjectPropertyAxiom(prop);
} else if (ANTI_SYMMETRIC.matches(characteristic) || ASYMMETRIC.matches(characteristic)) {
return df.getOWLAsymmetricObjectPropertyAxiom(prop);
} else if (TRANSITIVE.matches(characteristic)) {
return df.getOWLTransitiveObjectPropertyAxiom(prop);
} else if (REFLEXIVE.matches(characteristic)) {
return df.getOWLReflexiveObjectPropertyAxiom(prop);
} else if (IRREFLEXIVE.matches(characteristic)) {
return df.getOWLIrreflexiveObjectPropertyAxiom(prop);
} else {
throw new ExceptionBuilder().withKeyword(FUNCTIONAL, INVERSE_FUNCTIONAL, SYMMETRIC, ANTI_SYMMETRIC,
TRANSITIVE, REFLEXIVE, IRREFLEXIVE).build();
}
}
protected OWLDataPropertyCharacteristicAxiom parseDataPropertyCharacteristic(OWLDataPropertyExpression prop) {
String characteristic = consumeToken();
if (FUNCTIONAL.matches(characteristic)) {
return df.getOWLFunctionalDataPropertyAxiom(prop);
} else {
throw new ExceptionBuilder().withKeyword(FUNCTIONAL).build();
}
}
@Override
public Set parseClassExpressionList() {
Set descs = new HashSet<>();
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
potentialKeywords.remove(COMMA);
descs.add(parseUnion());
potentialKeywords.add(COMMA);
sep = peekToken();
if (COMMA.matches(sep)) {
sep = consumeToken();
}
}
return descs;
}
private Set parseClassExpressionList(ManchesterOWLSyntax expectedOpen,
ManchesterOWLSyntax expectedClose) {
String open = consumeToken();
if (!expectedOpen.matches(open)) {
throw new ExceptionBuilder().withKeyword(expectedOpen).build();
}
String sep = COMMA.keyword();
Set descs = new HashSet<>();
while (COMMA.matches(sep)) {
potentialKeywords.remove(COMMA);
OWLClassExpression desc = parseUnion();
potentialKeywords.add(COMMA);
descs.add(desc);
sep = peekToken();
if (COMMA.matches(sep)) {
sep = consumeToken();
}
}
String close = consumeToken();
if (!expectedClose.matches(close)) {
throw new ExceptionBuilder().withKeyword(expectedClose).build();
}
return descs;
}
@Override
public Set parsePropertyList() {
Set props = new HashSet<>();
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
props.add(parsePropertyExpression());
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
return props;
}
@Override
public Set parseObjectPropertyList() {
Set props = new HashSet<>();
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
props.add(parseObjectPropertyExpression(false));
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
return props;
}
@Override
public Set parseDataPropertyList() {
Set props = new HashSet<>();
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
props.add(parseDataProperty());
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
return props;
}
@Override
public Set parseAnnotationPropertyList() {
Set props = new HashSet<>();
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
props.add(parseAnnotationProperty());
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
return props;
}
@Override
public Set parseIndividualList() {
Set inds = new HashSet<>();
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
inds.add(parseIndividual());
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
return inds;
}
@Override
public List parseObjectPropertyChain() {
String delim = "o";
List properties = new ArrayList<>();
while ("o".equals(delim)) {
properties.add(parseObjectPropertyExpression(false));
delim = peekToken();
if ("o".equals(delim)) {
consumeToken();
}
}
return properties;
}
protected OWLIndividual parseIndividual() {
String name = consumeToken();
if (!isIndividualName(name) && !name.startsWith("_:")) {
throw new ExceptionBuilder().withInd().build();
}
return getOWLIndividual(name);
}
protected OWLDataProperty parseDataProperty() {
String name = consumeToken();
if (!isDataPropertyName(name)) {
throw new ExceptionBuilder().withData().build();
}
return getOWLDataProperty(name);
}
protected OWLAnnotationProperty parseAnnotationProperty() {
String name = consumeToken();
if (!isAnnotationPropertyName(name)) {
throw new ExceptionBuilder().withAnn().build();
}
return getOWLAnnotationProperty(name);
}
private Map parsePrefixDeclaration() {
consumeToken(PREFIX);
Map map = new HashMap<>(2);
String prefixName = consumeToken();
// Handle legacy = character if necessart
if ("=".equals(peekToken())) {
// Legacy
consumeToken();
}
IRI iri = parseIRI();
map.put(prefixName, iri);
return map;
}
private OWLImportsDeclaration parseImportsDeclaration() {
consumeToken(IMPORT);
return df.getOWLImportsDeclaration(parseIRI());
}
protected IRI parseIRI() {
String iriString = consumeToken();
if (!(iriString.startsWith("<") && iriString.endsWith(">"))) {
throw new ExceptionBuilder().withKeyword("<$IRI$>").build();
}
return IRI.create(iriString.substring(1, iriString.length() - 1));
}
private void processDeclaredEntities() {
for (int i = 0; i < tokens.size(); i++) {
String token = tokens.get(i).getToken();
String name = null;
if (i + 1 < tokens.size()) {
name = tokens.get(i + 1).getToken();
}
if (CLASS.matches(token)) {
if (name != null) {
classNames.add(name);
}
} else if (OBJECT_PROPERTY.matches(token)) {
if (name != null) {
objectPropertyNames.add(name);
}
} else if (DATA_PROPERTY.matches(token)) {
if (name != null) {
dataPropertyNames.add(name);
}
} else if (INDIVIDUAL.matches(token)) {
if (name != null) {
individualNames.add(name);
}
} else if (DATATYPE.matches(token)) {
if (name != null) {
dataTypeNames.add(name);
}
} else if (ANNOTATION_PROPERTY.matches(token)) {
if (name != null) {
annotationPropertyNames.add(name);
}
} else if (VALUE_PARTITION.matches(token)) {
if (name != null) {
objectPropertyNames.add(name);
}
if (i + 2 < tokens.size()) {
classNames.add(tokens.get(i + 2).getToken());
}
}
}
}
private void processDeclaredEntities(OWLDeclarationAxiom ax) {
ax.getEntity().accept(new AddNames());
}
@Override
public ManchesterSyntaxDocumentFormat parseOntology(OWLOntology ont) {
Set axioms = new HashSet<>();
OWLOntologyID ontologyID = new OWLOntologyID();
Set imports = new HashSet<>();
Set ontologyAnnotations = new HashSet<>();
defaultOntology = ont;
processDeclaredEntities();
while (true) {
String section = peekToken();
if (ONTOLOGY.matches(section)) {
ontologyID = handleOntology(ont, imports, ontologyAnnotations);
} else if (DISJOINT_CLASSES.matches(section)) {
axioms.addAll(parseDisjointClasses());
} else if (EQUIVALENT_CLASSES.matches(section)) {
axioms.addAll(parseNaryEquivalentClasses());
} else if (EQUIVALENT_PROPERTIES.matches(section)) {
axioms.addAll(parseNaryEquivalentProperties());
} else if (DISJOINT_PROPERTIES.matches(section)) {
axioms.addAll(parseDisjointProperties());
} else if (DIFFERENT_INDIVIDUALS.matches(section)) {
axioms.addAll(parseDifferentIndividuals());
} else if (SAME_INDIVIDUAL.matches(section)) {
axioms.addAll(parseSameIndividual());
} else if (CLASS.matches(section)) {
axioms.addAll(parseClassFrame());
} else if (OBJECT_PROPERTY.matches(section)) {
axioms.addAll(parseObjectPropertyFrame());
} else if (DATA_PROPERTY.matches(section)) {
axioms.addAll(parseDataPropertyFrame());
} else if (INDIVIDUAL.matches(section)) {
axioms.addAll(parseIndividualFrame());
} else if (DATATYPE.matches(section)) {
axioms.addAll(parseDatatypeFrame());
} else if (ANNOTATION_PROPERTY.matches(section)) {
axioms.addAll(parseAnnotationPropertyFrame());
} else if (VALUE_PARTITION.matches(section)) {
axioms.addAll(parseValuePartitionFrame());
} else if (IMPORT.matches(section)) {
OWLImportsDeclaration decl = parseImportsDeclaration();
ont.getOWLOntologyManager().makeLoadImportRequest(decl, getOntologyLoaderConfiguration());
imports.add(new AddImport(ont, decl));
OWLOntology imported = ont.getOWLOntologyManager().getImportedOntology(decl);
if (imported != null) {
imported.axioms(AxiomType.DECLARATION).forEach(this::processDeclaredEntities);
}
} else if (PREFIX.matches(section)) {
parsePrefixDeclaration().forEach((k, v) -> pm.setPrefix(k, v.toString()));
} else if (RULE.matches(section)) {
axioms.addAll(parseRuleFrame());
} else if (eof(section)) {
break;
} else {
consumeToken();
throw new ExceptionBuilder().withKeyword(CLASS, OBJECT_PROPERTY, DATA_PROPERTY, INDIVIDUAL, DATATYPE,
ANNOTATION_PROPERTY, IMPORT, VALUE_PARTITION, PREFIX, EQUIVALENT_CLASSES, DISJOINT_CLASSES,
DISJOINT_PROPERTIES, DIFFERENT_INDIVIDUALS, SAME_INDIVIDUAL).build();
}
}
List changes = new ArrayList<>(axioms.size());
changes.addAll(imports);
changes.addAll(ontologyAnnotations);
for (OntologyAxiomPair pair : axioms) {
changes.add(new AddAxiom(ont, pair.getAxiom()));
}
changes.add(new SetOntologyID(ont, ontologyID));
ont.getOWLOntologyManager().applyChanges(changes);
ManchesterSyntaxDocumentFormat format = new ManchesterSyntaxDocumentFormat();
format.copyPrefixesFrom(pm);
return format;
}
protected OWLOntologyID handleOntology(OWLOntology ont, Set imports,
Set ontologyAnnotations) {
OWLOntologyID ontologyID;
ManchesterOWLSyntaxOntologyHeader header = parseOntologyHeader(false);
for (OWLImportsDeclaration decl : header.getImportsDeclarations()) {
assert decl != null;
imports.add(new AddImport(ont, decl));
ont.getOWLOntologyManager().makeLoadImportRequest(decl, getOntologyLoaderConfiguration());
OWLOntology imported = ont.getOWLOntologyManager().getImportedOntology(decl);
if (imported != null) {
imported.axioms(AxiomType.DECLARATION).forEach(this::processDeclaredEntities);
}
}
for (OWLAnnotation anno : header.getAnnotations()) {
ontologyAnnotations.add(new AddOntologyAnnotation(ont, anno));
}
ontologyID = header.getOntologyID();
return ontologyID;
}
private ManchesterOWLSyntaxOntologyHeader parseOntologyHeader(boolean toEOF) {
String tok = consumeToken();
if (!ONTOLOGY.matches(tok)) {
throw new ExceptionBuilder().withKeyword(ONTOLOGY).build();
}
IRI ontologyIRI = null;
IRI versionIRI = null;
if (peekToken().startsWith("<")) {
ontologyIRI = parseIRI();
if (peekToken().startsWith("<")) {
versionIRI = parseIRI();
}
}
Set annotations = new HashSet<>();
Set imports = new HashSet<>();
while (true) {
String section = peekToken();
if (IMPORT.matches(section)) {
handleImport(imports);
} else if (ANNOTATIONS.matches(section)) {
consumeToken();
annotations.addAll(parseAnnotationList());
} else if (eof(section)) {
break;
} else if (toEOF) {
throw new ExceptionBuilder().withKeyword(IMPORT, ANNOTATIONS).build();
} else {
break;
}
}
return new ManchesterOWLSyntaxOntologyHeader(ontologyIRI, versionIRI, annotations, imports);
}
protected void handleImport(Set imports) {
String tok;
consumeToken();
tok = peekToken();
Optional importedIRI = emptyOptional();
if (tok.startsWith("<")) {
importedIRI = optional(parseIRI());
} else if (isOntologyName(tok)) {
consumeToken();
OWLOntology ont = getOntology(tok);
if (ont != null) {
importedIRI = ont.getOntologyID().getOntologyIRI();
}
} else {
consumeToken();
throw new ExceptionBuilder().withOnto().withKeyword("<$ONTOLOGYYURI$>").build();
}
if (!importedIRI.isPresent()) {
throw new ExceptionBuilder().withOnto().withKeyword("Imported IRI is null").build();
}
IRI importedOntologyIRI = importedIRI.get();
imports.add(df.getOWLImportsDeclaration(importedOntologyIRI));
}
class AddNames implements OWLEntityVisitor {
@Override
public void visit(OWLAnnotationProperty property) {
annotationPropertyNames.add(pm.getShortForm(property.getIRI()));
}
@Override
public void visit(OWLDatatype datatype) {
dataTypeNames.add(pm.getShortForm(datatype.getIRI()));
}
@Override
public void visit(OWLNamedIndividual individual) {
individualNames.add(pm.getShortForm(individual.getIRI()));
}
@Override
public void visit(OWLDataProperty property) {
dataPropertyNames.add(pm.getShortForm(property.getIRI()));
}
@Override
public void visit(OWLObjectProperty property) {
objectPropertyNames.add(pm.getShortForm(property.getIRI()));
}
@Override
public void visit(OWLClass cls) {
classNames.add(pm.getShortForm(cls.getIRI()));
}
}
protected class ExceptionBuilder {
boolean ontologyNameExpected = false;
boolean classNameExpected = false;
boolean objectPropertyNameExpected = false;
boolean dataPropertyNameExpected = false;
boolean individualNameExpected = false;
boolean datatypeNameExpected = false;
boolean annotationPropertyNameExpected = false;
boolean integerExpected = false;
Set keywords = new HashSet<>();
List tokenSequence;
int start = -1;
int line = -1;
int column = -1;
ExceptionBuilder() {
withKeyword(potentialKeywords);
}
ExceptionBuilder(ParserException e) {
ontologyNameExpected = e.isOntologyNameExpected();
classNameExpected = e.isClassNameExpected();
objectPropertyNameExpected = e.isObjectPropertyNameExpected();
dataPropertyNameExpected = e.isDataPropertyNameExpected();
individualNameExpected = e.isIndividualNameExpected();
dataPropertyNameExpected = e.isDatatypeNameExpected();
annotationPropertyNameExpected = e.isAnnotationPropertyNameExpected();
integerExpected = e.isIntegerExpected();
withKeyword(e.getExpectedKeywords());
tokenSequence = e.getTokenSequence();
start = e.getStartPos();
line = e.getLineNumber();
column = e.getColumnNumber();
}
public ExceptionBuilder withOnto() {
ontologyNameExpected = true;
return this;
}
public ExceptionBuilder withInt() {
integerExpected = true;
return this;
}
public ExceptionBuilder withClass() {
classNameExpected = true;
return this;
}
public ExceptionBuilder withObject() {
objectPropertyNameExpected = true;
withKeyword(INVERSE);
return this;
}
public ExceptionBuilder withData() {
dataPropertyNameExpected = true;
return this;
}
public ExceptionBuilder withInd() {
individualNameExpected = true;
return this;
}
public ExceptionBuilder withDt() {
datatypeNameExpected = true;
return this;
}
public ExceptionBuilder withAnn() {
annotationPropertyNameExpected = true;
return this;
}
public ExceptionBuilder withKeyword(String s) {
keywords.add(s);
return this;
}
public ExceptionBuilder withKeyword(ManchesterOWLSyntax s) {
keywords.add(s.keyword());
return this;
}
public ExceptionBuilder withKeyword(String... strings) {
for (String s : strings) {
keywords.add(s);
}
return this;
}
public ExceptionBuilder withKeyword(ManchesterOWLSyntax... keys) {
for (ManchesterOWLSyntax s : keys) {
keywords.add(s.keyword());
}
return this;
}
public ExceptionBuilder withKeyword(Collection keys) {
for (T s : keys) {
if (s instanceof String) {
withKeyword((String) s);
}
if (s instanceof ManchesterOWLSyntax) {
withKeyword((ManchesterOWLSyntax) s);
}
}
return this;
}
public ParserException build() {
if (tokenSequence == null) {
Token lastToken = getLastToken();
tokenSequence = getTokenSequence();
start = lastToken.getPos();
line = lastToken.getRow();
column = lastToken.getCol();
}
return new ParserException(tokenSequence, start, line, column, ontologyNameExpected, classNameExpected,
objectPropertyNameExpected, dataPropertyNameExpected, individualNameExpected, datatypeNameExpected,
annotationPropertyNameExpected, integerExpected, keywords);
}
}
protected List getTokenSequence() {
List seq = new ArrayList<>();
int index = tokenIndex - 1;
if (index < 0) {
index = 0;
}
while (index < tokens.size() && seq.size() < 4 && !seq.contains(EOFTOKEN)) {
seq.add(tokens.get(index).getToken());
index++;
}
if (seq.isEmpty()) {
seq.add(EOFTOKEN);
}
return seq;
}
class DefaultEntityChecker implements OWLEntityChecker {
@Override
@Nullable
public OWLClass getOWLClass(String name) {
if ("Thing".equals(name) || "owl:Thing".equals(name)) {
return df.getOWLThing();
} else if ("Nothing".equals(name) || "owl:Nothing".equals(name)) {
return df.getOWLNothing();
} else if (classNames.contains(name)) {
return df.getOWLClass(getIRI(name));
}
return null;
}
@Override
@Nullable
public OWLObjectProperty getOWLObjectProperty(String name) {
if (objectPropertyNames.contains(name)) {
return df.getOWLObjectProperty(getIRI(name));
}
return null;
}
@Override
@Nullable
public OWLDataProperty getOWLDataProperty(String name) {
if (dataPropertyNames.contains(name)) {
return df.getOWLDataProperty(getIRI(name));
}
return null;
}
@Override
@Nullable
public OWLNamedIndividual getOWLIndividual(String name) {
if (individualNames.contains(name)) {
return df.getOWLNamedIndividual(getIRI(name));
}
return null;
}
@Override
@Nullable
public OWLDatatype getOWLDatatype(String name) {
if (dataTypeNames.contains(name)) {
return df.getOWLDatatype(getIRI(name));
}
return null;
}
@Override
@Nullable
public OWLAnnotationProperty getOWLAnnotationProperty(String name) {
if (annotationPropertyNames.contains(name)) {
return df.getOWLAnnotationProperty(getIRI(name));
}
return null;
}
}
protected IRI getIRI(String inputName) {
String name = inputName;
boolean fullIRI = "<".equals(name);
if (fullIRI) {
name = consumeToken();
consumeToken();
}
IRI uri = nameIRIMap.get(name);
if (uri != null) {
return uri;
}
if (fullIRI) {
uri = IRI.create(name);
} else {
int colonIndex = name.indexOf(':');
if (colonIndex == -1) {
name = ":" + name;
}
uri = pm.getIRI(name);
}
nameIRIMap.put(name, uri);
return uri;
}
@Override
public OWLAxiom parseAxiom() {
String token = peekToken();
if (isClassName(token)) {
return parseAxiomWithClassExpressionStart();
} else if (isObjectPropertyName(token)) {
return parseAxiomWithObjectPropertyStart();
} else if (isDataPropertyName(token)) {
return parseAxiomWithDataPropertyStart();
} else if (isIndividualName(token)) {
return parseAxiomWithIndividualStart();
} else if (INV.matches(token)) {
return parseAxiomWithObjectPropertyStart();
} else if (OPEN.matches(token)) {
return parseAxiomWithClassExpressionStart();
} else if (OPENBRACE.matches(token)) {
return parseAxiomWithClassExpressionStart();
} else if (FUNCTIONAL.matches(token)) {
return parseFunctionPropertyAxiom();
} else if (INVERSE_FUNCTIONAL.matches(token)) {
return parseInverseFunctionalPropertyAxiom();
} else if (SYMMETRIC.matches(token)) {
return parseSymmetricPropertyAxiom();
} else if (ASYMMETRIC.matches(token)) {
return parseAsymmetricPropertyAxiom();
} else if (TRANSITIVE.matches(token)) {
return parseTransitivePropertyAxiom();
} else if (REFLEXIVE.matches(token)) {
return parseReflexivePropertyAxiom();
} else if (IRREFLEXIVE.matches(token)) {
return parseIrreflexivePropertyAxiom();
}
throw new ExceptionBuilder().withClass().withObject().withData().withKeyword(OPEN, OPENBRACE, INV, FUNCTIONAL,
INVERSE_FUNCTIONAL, SYMMETRIC, ASYMMETRIC, TRANSITIVE, REFLEXIVE, IRREFLEXIVE).build();
}
@Override
public OWLClassAxiom parseClassAxiom() {
return (OWLClassAxiom) parseAxiom();
}
private OWLAxiom parseAxiomWithIndividualStart() {
OWLIndividual ind = parseIndividual();
String kw = consumeToken();
if (TYPE.matches(kw)) {
OWLClassExpression type = parseClassExpression();
return df.getOWLClassAssertionAxiom(type, ind);
}
throw new ExceptionBuilder().withKeyword(TYPE).build();
}
private OWLAxiom parseAxiomWithDataPropertyStart() {
OWLDataPropertyExpression prop = parseDataProperty();
String kw = consumeToken();
if (SOME.matches(kw)) {
OWLDataRange dataRange = parseDataIntersectionOf();
return parseClassAxiomRemainder(df.getOWLDataSomeValuesFrom(prop, dataRange));
} else if (ONLY.matches(kw)) {
OWLDataRange dataRange = parseDataIntersectionOf();
return parseClassAxiomRemainder(df.getOWLDataAllValuesFrom(prop, dataRange));
} else if (MIN.matches(kw)) {
int cardi = parseInteger();
OWLDataRange dataRange = parseDataIntersectionOf();
return parseClassAxiomRemainder(df.getOWLDataMinCardinality(cardi, prop, dataRange));
} else if (MAX.matches(kw)) {
int cardi = parseInteger();
OWLDataRange dataRange = parseDataIntersectionOf();
return parseClassAxiomRemainder(df.getOWLDataMaxCardinality(cardi, prop, dataRange));
} else if (EXACTLY.matches(kw)) {
int cardi = parseInteger();
OWLDataRange dataRange = parseDataIntersectionOf();
return parseClassAxiomRemainder(df.getOWLDataExactCardinality(cardi, prop, dataRange));
} else if (SUB_PROPERTY_OF.matches(kw)) {
OWLDataPropertyExpression superProperty = parseDataPropertyExpression();
return df.getOWLSubDataPropertyOfAxiom(prop, superProperty);
} else if (EQUIVALENT_TO.matches(kw)) {
OWLDataPropertyExpression equivProp = parseDataPropertyExpression();
return df.getOWLEquivalentDataPropertiesAxiom(prop, equivProp);
} else if (DISJOINT_WITH.matches(kw)) {
OWLDataPropertyExpression disjProp = parseDataPropertyExpression();
return df.getOWLDisjointDataPropertiesAxiom(prop, disjProp);
} else if (DOMAIN.matches(kw)) {
OWLClassExpression domain = parseClassExpression();
return df.getOWLDataPropertyDomainAxiom(prop, domain);
} else if (RANGE.matches(kw)) {
OWLDataRange range = parseDataRange();
return df.getOWLDataPropertyRangeAxiom(prop, range);
} else {
throw new ExceptionBuilder().withKeyword(SOME, ONLY, MIN, MAX, EXACTLY, SUB_PROPERTY_OF, EQUIVALENT_TO,
DISJOINT_WITH, DOMAIN, RANGE).build();
}
}
private OWLDataPropertyExpression parseDataPropertyExpression() {
String tok = consumeToken();
if (!isDataPropertyName(tok)) {
throw new ExceptionBuilder().withData().build();
}
return getOWLDataProperty(tok);
}
private OWLAxiom parseAxiomWithClassExpressionStart() {
return parseClassAxiomRemainder(parseUnion());
}
private OWLAxiom parseClassAxiomRemainder(OWLClassExpression startExpression) {
String kw = consumeToken();
if (SUBCLASS_OF.matchesEitherForm(kw)) {
OWLClassExpression superClass = parseClassExpression();
return df.getOWLSubClassOfAxiom(startExpression, superClass);
} else if (DISJOINT_WITH.matchesEitherForm(kw)) {
OWLClassExpression disjointClass = parseClassExpression();
return df.getOWLDisjointClassesAxiom(startExpression, disjointClass);
} else if (EQUIVALENT_TO.matchesEitherForm(kw)) {
OWLClassExpression equivClass = parseClassExpression();
return df.getOWLEquivalentClassesAxiom(startExpression, equivClass);
} else if (AND.matchesEitherForm(kw)) {
OWLClassExpression conjunct = parseIntersection();
Set conjuncts = conjunct.asConjunctSet();
conjuncts.add(startExpression);
OWLClassExpression ce = df.getOWLObjectIntersectionOf(conjuncts);
return parseClassAxiomRemainder(ce);
} else if (OR.matchesEitherForm(kw)) {
OWLClassExpression disjunct = parseUnion();
Set disjuncts = disjunct.asDisjunctSet();
disjuncts.add(startExpression);
OWLClassExpression ce = df.getOWLObjectUnionOf(disjuncts);
return parseClassAxiomRemainder(ce);
} else {
throw new ExceptionBuilder().withKeyword(SUBCLASS_OF, DISJOINT_WITH, EQUIVALENT_TO, AND, OR).build();
}
}
private OWLAxiom parseAxiomWithObjectPropertyStart() {
OWLObjectPropertyExpression prop = parseObjectPropertyExpression(false);
String kw = consumeToken();
if (SOME.matches(kw)) {
OWLClassExpression filler = parseUnion();
return parseClassAxiomRemainder(df.getOWLObjectSomeValuesFrom(prop, filler));
} else if (ONLY.matches(kw)) {
OWLClassExpression filler = parseUnion();
return parseClassAxiomRemainder(df.getOWLObjectAllValuesFrom(prop, filler));
} else if (MIN.matches(kw)) {
int cardi = parseInteger();
OWLClassExpression filler = parseUnion();
return parseClassAxiomRemainder(df.getOWLObjectMinCardinality(cardi, prop, filler));
} else if (MAX.matches(kw)) {
int cardi = parseInteger();
OWLClassExpression filler = parseUnion();
return parseClassAxiomRemainder(df.getOWLObjectMaxCardinality(cardi, prop, filler));
} else if (EXACTLY.matches(kw)) {
int cardi = parseInteger();
OWLClassExpression filler = parseUnion();
return parseClassAxiomRemainder(df.getOWLObjectExactCardinality(cardi, prop, filler));
} else if (SUB_PROPERTY_OF.matches(kw)) {
OWLObjectPropertyExpression superProperty = parseObjectPropertyExpression(false);
return df.getOWLSubObjectPropertyOfAxiom(prop, superProperty);
} else if (EQUIVALENT_TO.matches(kw)) {
OWLObjectPropertyExpression equivProp = parseObjectPropertyExpression(false);
return df.getOWLEquivalentObjectPropertiesAxiom(prop, equivProp);
} else if (INVERSE_OF.matches(kw)) {
OWLObjectPropertyExpression invProp = parseObjectPropertyExpression(false);
return df.getOWLInverseObjectPropertiesAxiom(prop, invProp);
} else if (DISJOINT_WITH.matches(kw)) {
OWLObjectPropertyExpression disjProp = parseObjectPropertyExpression(false);
return df.getOWLDisjointObjectPropertiesAxiom(prop, disjProp);
} else if (DOMAIN.matches(kw)) {
OWLClassExpression domain = parseClassExpression();
return df.getOWLObjectPropertyDomainAxiom(prop, domain);
} else if (RANGE.matches(kw)) {
OWLClassExpression range = parseClassExpression();
return df.getOWLObjectPropertyRangeAxiom(prop, range);
} else if (CHAIN_CONNECT.matches(kw)) {
String sep = kw;
List chain = new ArrayList<>();
chain.add(prop);
while ("o".equals(sep)) {
OWLObjectPropertyExpression chainProp = parseObjectPropertyExpression(false);
chain.add(chainProp);
sep = consumeToken();
}
if (!SUB_PROPERTY_OF.matches(sep)) {
throw new ExceptionBuilder().withKeyword(SUB_PROPERTY_OF).build();
}
OWLObjectPropertyExpression superProp = parseObjectPropertyExpression(false);
return df.getOWLSubPropertyChainOfAxiom(chain, superProp);
} else {
throw new ExceptionBuilder().withKeyword(SOME, ONLY, MIN, MAX, EXACTLY, SUB_PROPERTY_OF, EQUIVALENT_TO,
INVERSE_OF, DISJOINT_WITH, DOMAIN, RANGE, CHAIN_CONNECT).build();
}
}
private OWLAxiom parseInverseFunctionalPropertyAxiom() {
String kw = consumeToken();
if (!INVERSE_FUNCTIONAL.matches(kw)) {
throw new ExceptionBuilder().withKeyword(INVERSE_FUNCTIONAL).build();
}
return df.getOWLInverseFunctionalObjectPropertyAxiom(parseObjectPropertyExpression(false));
}
private OWLAxiom parseSymmetricPropertyAxiom() {
String kw = consumeToken();
if (!SYMMETRIC.matches(kw)) {
throw new ExceptionBuilder().withKeyword(SYMMETRIC).build();
}
return df.getOWLSymmetricObjectPropertyAxiom(parseObjectPropertyExpression(false));
}
private OWLAxiom parseAsymmetricPropertyAxiom() {
String kw = consumeToken();
if (!ASYMMETRIC.matches(kw)) {
throw new ExceptionBuilder().withKeyword(ASYMMETRIC).build();
}
return df.getOWLAsymmetricObjectPropertyAxiom(parseObjectPropertyExpression(false));
}
private OWLAxiom parseTransitivePropertyAxiom() {
String kw = consumeToken();
if (!TRANSITIVE.matches(kw)) {
throw new ExceptionBuilder().withKeyword(TRANSITIVE).build();
}
return df.getOWLTransitiveObjectPropertyAxiom(parseObjectPropertyExpression(false));
}
private OWLAxiom parseReflexivePropertyAxiom() {
String kw = consumeToken();
if (!REFLEXIVE.matches(kw)) {
throw new ExceptionBuilder().withKeyword(REFLEXIVE).build();
}
return df.getOWLReflexiveObjectPropertyAxiom(parseObjectPropertyExpression(false));
}
private OWLAxiom parseIrreflexivePropertyAxiom() {
String kw = consumeToken();
if (!IRREFLEXIVE.matches(kw)) {
throw new ExceptionBuilder().withKeyword(IRREFLEXIVE).build();
}
return df.getOWLIrreflexiveObjectPropertyAxiom(parseObjectPropertyExpression(false));
}
private OWLAxiom parseFunctionPropertyAxiom() {
String kw = consumeToken();
if (!FUNCTIONAL.matches(kw)) {
throw new ExceptionBuilder().withKeyword(FUNCTIONAL).build();
}
String name = peekToken();
if (isObjectPropertyName(name)) {
return df.getOWLFunctionalObjectPropertyAxiom(parseObjectPropertyExpression(false));
} else if (isDataPropertyName(name)) {
return df.getOWLFunctionalDataPropertyAxiom(parseDataProperty());
} else {
consumeToken();
throw new ExceptionBuilder().withObject().withData().build();
}
}
private Set parseAnnotatedListItems(F s, AnnAxiom itemParser,
Set ontologies) {
Set result = new HashSet<>();
String sep = COMMA.keyword();
while (COMMA.matches(sep)) {
Set annotations = parseAnnotations();
O item = itemParser.parse.apply(s);
OWLAxiom axiom = itemParser.createAxiom(s, item, annotations);
for (OWLOntology ontology : ontologies) {
result.add(new OntologyAxiomPair(ontology, axiom));
}
sep = peekToken();
if (COMMA.matches(sep)) {
consumeToken();
}
}
return result;
}
static OWLAxiom create(OWLDataFactory d, OWLIndividual s, Set o, Collection anns) {
Set individuals = new HashSet<>();
individuals.add(s);
individuals.addAll(o);
return d.getOWLDifferentIndividualsAxiom(individuals, anns);
}
static OWLAxiom create(OWLDataFactory d, OWLIndividual s, OWLAnnotation o, Collection anns) {
if (s.isAnonymous()) {
return d.getOWLAnnotationAssertionAxiom(s.asOWLAnonymousIndividual(), o, anns);
} else {
return d.getOWLAnnotationAssertionAxiom(s.asOWLNamedIndividual().getIRI(), o, anns);
}
}
static class AnnAxiom {
Function parse;
ManchesterOWLSyntax keyword;
Builder builder;
AnnAxiom(Function p, ManchesterOWLSyntax k, Builder b) {
parse = p;
keyword = k;
builder = b;
}
final OWLAxiom createAxiom(F s, O o, Collection anns) {
return builder.createAxiom(s, o, anns);
}
}
@FunctionalInterface
interface Builder {
OWLAxiom createAxiom(F s, O o, Collection anns);
}
}
