* 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

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    @Test

    public void shouldRoundtripAnnotationAssertionsWithAnnotations()

            throws OWLOntologyCreationException, OWLOntologyStorageException {

        String input = "Prefix: o: <urn:test#>\nOntology: <urn:test>\n AnnotationProperty: o:bob\n Annotations:\n rdfs:label \"bob-label\"@en";

        OWLOntology o = loadOntologyFromString(input);

        assertEquals("Prefix: o: <urn:test#>"

                + "Prefix: dc: <http://purl.org/dc/elements/1.1/>"

                + "Prefix: owl: <http://www.w3.org/2002/07/owl#>"

                + "Prefix: rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>"

                + "Prefix: xml: <http://www.w3.org/XML/1998/namespace>"

                + "Prefix: xsd: <http://www.w3.org/2001/XMLSchema#>"

                + "Prefix: rdfs: <http://www.w3.org/2000/01/rdf-schema#>"

                + "Ontology: <urn:test>" + "AnnotationProperty: rdfs:label"

                + "AnnotationProperty: o:bob" + "Annotations: "

                + "rdfs:label \"bob-label\"@en" + "Datatype: rdf:PlainLiteral",

                saveOntology(o).toString().replace("\n", "")

                        .replace("    ", ""));

        OWLOntology o2 = roundTrip(o);

        equal(o, o2);

    }

    @Test

    public void shouldRoundTrip() throws Exception {

        // given

        IRI iri = IRI("http://protege.org/ontologies" + "#p");

        OWLOntology ontology = m

                .createOntology(IRI("http://protege.org/ontologies"));

        m.addAxiom(ontology, Declaration(DataProperty(iri)));

        // when

        ontology = roundTrip(ontology);

        // then

        assertTrue(ontology.containsDataPropertyInSignature(iri, EXCLUDED));

    }

    @Test

    public void shouldRenderCorrectly() throws Exception {

        // given

        OWLObjectProperty prop = ObjectProperty(IRI("urn:test#p"));

        OWLClass led = Class(IRI("urn:test#led"));

        OWLClass crt = Class(IRI("urn:test#crt"));

        OWLClass display = Class(IRI("urn:test#display"));

        OWLOntology ontology = m

                .createOntology(IRI("http://protege.org/ontologies"));

        OWLObjectSomeValuesFrom r = df.getOWLObjectSomeValuesFrom(prop,

                df.getOWLObjectUnionOf(led, crt));

        OWLSubClassOfAxiom axiom = df.getOWLSubClassOfAxiom(display, r);

        m.addAxiom(ontology, axiom);

        StringDocumentTarget target = saveOntology(ontology,

                new ManchesterSyntaxDocumentFormat());

        assertFalse(target.toString().contains(

                "((<urn:test#crt> or <urn:test#led>))"));

    }

    @Test

    public void shouldRoundtripDisjointUnion() throws Exception {

        OWLOntology o = m.createOntology();

        OWLClass a = Class(IRI("http://iri/#a"));

        OWLClass b = Class(IRI("http://iri/#b"));

        OWLClass c = Class(IRI("http://iri/#c"));

        OWLClass d = Class(IRI("http://iri/#d"));

        OWLDisjointUnionAxiom axiom = DisjointUnion(a, b, c, d);

        o.getOWLOntologyManager().addAxiom(o, axiom);

        o.getOWLOntologyManager().addAxiom(o, Declaration(a));

        o.getOWLOntologyManager().addAxiom(o, Declaration(b));

        o.getOWLOntologyManager().addAxiom(o, Declaration(c));

        o.getOWLOntologyManager().addAxiom(o, Declaration(d));

        OWLOntology roundtripped = roundTrip(o,

                new ManchesterSyntaxDocumentFormat());

        assertEquals(o.getAxioms(), roundtripped.getAxioms());

    }

    @Test(expected = ParserException.class)

    public void testManSyntaxEditorParser() throws Exception {

        String onto = "<?xml version=\"1.0\"?>"

                + "<!DOCTYPE rdf:RDF ["

                + "<!ENTITY vin  \"http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#\" >"

                + "<!ENTITY food \"http://www.w3.org/TR/2003/PR-owl-guide-20031209/food#\" >"

                + "<!ENTITY owl  \"http://www.w3.org/2002/07/owl#\" >"

                + "<!ENTITY xsd  \"http://www.w3.org/2001/XMLSchema#\" >"

                + "]>"

                + "<rdf:RDF "

                + "xmlns     = \"http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#\" "

                + "xmlns:vin = \"http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#\" "

                + "xml:base  = \"http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#\" "

                + "xmlns:food= \"http://www.w3.org/TR/2003/PR-owl-guide-20031209/food#\" "

                + "xmlns:owl = \"http://www.w3.org/2002/07/owl#\" "

                + "xmlns:rdf = \"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" "

                + "xmlns:rdfs= \"http://www.w3.org/2000/01/rdf-schema#\" "

                + "xmlns:xsd = \"http://www.w3.org/2001/XMLSchema#\">"

                + "<owl:Ontology rdf:about=\"\"><rdfs:comment>An example OWL ontology</rdfs:comment>"

                + "<rdfs:label>Wine Ontology</rdfs:label></owl:Ontology>"

                + "<owl:Class rdf:ID=\"VintageYear\" />"

                + "<owl:DatatypeProperty rdf:ID=\"yearValue\"><rdfs:domain rdf:resource=\"#VintageYear\" />    <rdfs:range  rdf:resource=\"&xsd;positiveInteger\" />"

                + "</owl:DatatypeProperty></rdf:RDF>";

        String expression = "yearValue some ";

        OWLOntology wine = loadOntologyFromString(onto);

        Set<OWLOntology> ontologies = m.getOntologies();

        ShortFormProvider sfp = new ManchesterOWLSyntaxPrefixNameShortFormProvider(

                wine.getOWLOntologyManager().getOntologyFormat(wine));

        BidirectionalShortFormProvider shortFormProvider = new BidirectionalShortFormProviderAdapter(

                ontologies, sfp);

        ManchesterOWLSyntaxParser parser = OWLManager.createManchesterParser();

        parser.setStringToParse(expression);

        parser.setDefaultOntology(wine);

        parser.setOWLEntityChecker(new ShortFormEntityChecker(shortFormProvider));

        parser.parseClassExpression();

    }

    @Test

    public void shouldParseRuleInManSyntax() throws Exception {

        String inputManSyntax = "Prefix: owl: <http://www.w3.org/2002/07/owl#>\n"

                + "Prefix: rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"

                + "Prefix: xml: <http://www.w3.org/XML/1998/namespace>\n"

                + "Prefix: xsd: <http://www.w3.org/2001/XMLSchema#>\n"

                + "Prefix: rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n"

                + "Ontology: <http://www.owl-ontologies.com/Ontology1307394066.owl>\n"

                + "Datatype: xsd:decimal\n Datatype: xsd:int\n Datatype: xsd:dateTime\n"

                + "DataProperty: <http://www.owl-ontologies.com/Ontology1307394066.owl#hasAge>\n Characteristics: \n Functional\n Range: \n xsd:int\n"

                + "DataProperty: <http://www.owl-ontologies.com/Ontology1307394066.owl#hasDate>\n Range: \n xsd:dateTime\n"

                + "Class: <http://www.owl-ontologies.com/Ontology1307394066.owl#Person>\n"

                + "Individual: <http://www.owl-ontologies.com/Ontology1307394066.owl#p1>\n Types: \n <http://www.owl-ontologies.com/Ontology1307394066.owl#Person>\n"

                + "Rule: \n xsd:decimal(?<urn:swrl#x>), <http://www.owl-ontologies.com/Ontology1307394066.owl#hasAge>(?<urn:swrl#p>, ?<urn:swrl#x>) -> <http://www.owl-ontologies.com/Ontology1307394066.owl#Person>(?<urn:swrl#p>)";

        OWLOntology o = loadOntologyFromString(inputManSyntax);

        OWLOntology o1 = roundTrip(o, new ManchesterSyntaxDocumentFormat());

        assertEquals(o.getLogicalAxioms(), o1.getLogicalAxioms());

    }

    @Test

    public void shouldParseRuleInManSimpleSyntax() throws Exception {

        String inputManSyntax = "Prefix: owl: <http://www.w3.org/2002/07/owl#>\n"

                + "Prefix: rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"

                + "Prefix: xml: <http://www.w3.org/XML/1998/namespace>\n"

                + "Prefix: xsd: <http://www.w3.org/2001/XMLSchema#>\n"

                + "Prefix: rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n"

                + "Ontology: <http://www.owl-ontologies.com/Ontology1307394066.owl>\n"

                + "Datatype: xsd:decimal\n"

                + "Datatype: xsd:int\n"

                + "Datatype: xsd:dateTime\n"

                + "DataProperty: <http://www.owl-ontologies.com/Ontology1307394066.owl#hasAge>\n"

                + "    Characteristics: \n"

                + "        Functional\n"

                + "    Range: \n"

                + "        xsd:int\n"

                + "DataProperty: <http://www.owl-ontologies.com/Ontology1307394066.owl#hasDate>\n"

                + "    Range: \n"

                + "        xsd:dateTime\n"

                + "Class: <http://www.owl-ontologies.com/Ontology1307394066.owl#Person>\n"

                + "Individual: <http://www.owl-ontologies.com/Ontology1307394066.owl#p1>\n"

                + "    Types: \n"

                + "        <http://www.owl-ontologies.com/Ontology1307394066.owl#Person>\n"

                + "Rule: \n"

                + "    xsd:decimal(?x), <http://www.owl-ontologies.com/Ontology1307394066.owl#hasAge>(?p, ?x) -> <http://www.owl-ontologies.com/Ontology1307394066.owl#Person>(?p)";

        OWLOntology o = loadOntologyFromString(inputManSyntax);

        OWLOntology o1 = roundTrip(o, new ManchesterSyntaxDocumentFormat());

        assertEquals(o.getLogicalAxioms(), o1.getLogicalAxioms());

    }

    @Test

    public void shouldAnnotateAndRoundTrip()

            throws OWLOntologyCreationException {

        String input = "Prefix: : <http://example.com/owl/families/>\n"

                + "Ontology: <http://example.com/owl/families>\n"

                + "Class: Person\n Annotations:  rdfs:comment \"Represents the set of all people.\"\n"

                + "Class: Man\n Annotations: rdfs:comment \"States that every man is a person.\"\n SubClassOf:  Person";

        OWLOntology o = loadOntologyFromString(input);

        Set<OWLAxiom> axioms = o.getAxioms();

        OWLClass person = Class(IRI("http://example.com/owl/families/Person"));

        OWLClass man = Class(IRI("http://example.com/owl/families/Man"));

        assertTrue(axioms.contains(Declaration(person)));

        assertTrue(axioms.contains(Declaration(man)));

        assertTrue(axioms.contains(SubClassOf(man, person)));

    }

    @Nonnull

    public static final String NS = "http://protege.org/ontologies/Test.owl";

    @Nonnull

    OWLDataProperty p;

    @Nonnull

    OWLDatatype dateTime;

    @Before

    public void setUpPAndDateTime() {

        p = DataProperty(IRI(NS + "#p"));

        dateTime = df.getOWLDatatype(XSDVocabulary.DATE_TIME.getIRI());

    }

    @Test

    public void shouldParseCorrectly() throws OWLOntologyCreationException {

        // given

        OWLClass a = Class(IRI(NS + "#A"));

        String text1 = "'GWAS study' and  has_publication_date some dateTime[< \"2009-01-01T00:00:00+00:00\"^^dateTime]";

        OWLClassExpression expected = df

                .getOWLObjectIntersectionOf(a, df

                        .getOWLDataSomeValuesFrom(p, df

                                .getOWLDatatypeRestriction(dateTime,

                                        OWLFacet.MAX_EXCLUSIVE,

                                        df.getOWLLiteral(

                                                "2009-01-01T00:00:00+00:00",

                                                dateTime))));

        // ontology creation including labels - this is the input ontology

        OWLOntology o = m.createOntology();

        m.addAxiom(o, df.getOWLDeclarationAxiom(a));

        m.addAxiom(o, df.getOWLDeclarationAxiom(p));

        m.addAxiom(o, df.getOWLDeclarationAxiom(dateTime));

        m.addAxiom(o, annotation(a, "'GWAS study'"));

        m.addAxiom(o, annotation(p, "has_publication_date"));

        m.addAxiom(o, annotation(dateTime, "dateTime"));

        // select a short form provider that uses annotations

        ShortFormProvider sfp = new AnnotationValueShortFormProvider(

                Arrays.asList(df.getRDFSLabel()),

                Collections.<OWLAnnotationProperty, List<String>> emptyMap(), m);

        BidirectionalShortFormProvider shortFormProvider = new BidirectionalShortFormProviderAdapter(

                m.getOntologies(), sfp);

        ManchesterOWLSyntaxParser parser = OWLManager.createManchesterParser();

        parser.setStringToParse(text1);

        ShortFormEntityChecker owlEntityChecker = new ShortFormEntityChecker(

                shortFormProvider);

        parser.setOWLEntityChecker(owlEntityChecker);

        parser.setDefaultOntology(o);

        // when

        // finally parse

        OWLClassExpression dsvf = parser.parseClassExpression();

        // then

        assertEquals(expected, dsvf);

    }

    @Nonnull

    public OWLAxiom annotation(@Nonnull OWLEntity e, @Nonnull String s) {

        return df.getOWLAnnotationAssertionAxiom(e.getIRI(),

                df.getOWLAnnotation(df.getRDFSLabel(), df.getOWLLiteral(s)));

    }

    @Test

    public void shouldDoPrecedenceWithParentheses()

            throws OWLOntologyCreationException {

        // given

        OWLClass a = Class(IRI("urn:test#a"));

        OWLClass b = Class(IRI("urn:test#b"));

        OWLClass c = Class(IRI("urn:test#c"));

        OWLClass d = Class(IRI("urn:test#all"));

        String text1 = "(a and b) or c";

        OWLClassExpression expected = df.getOWLObjectUnionOf(

                df.getOWLObjectIntersectionOf(a, b), c);

        OWLOntology o = m.createOntology();

        m.addAxiom(o, df.getOWLDeclarationAxiom(a));

        m.addAxiom(o, df.getOWLDeclarationAxiom(b));

        m.addAxiom(o, df.getOWLDeclarationAxiom(c));

        m.addAxiom(o, df.getOWLDeclarationAxiom(d));

        m.addAxiom(o, df.getOWLSubClassOfAxiom(expected, d));

        // select a short form provider that uses annotations

        ShortFormProvider sfp = new AnnotationValueShortFormProvider(

                Arrays.asList(df.getRDFSLabel()),

                Collections.<OWLAnnotationProperty, List<String>> emptyMap(), m);

        BidirectionalShortFormProvider shortFormProvider = new BidirectionalShortFormProviderAdapter(

                m.getOntologies(), sfp);

        ManchesterOWLSyntaxParser parser = OWLManager.createManchesterParser();

        parser.setStringToParse(text1);

        ShortFormEntityChecker owlEntityChecker = new ShortFormEntityChecker(

                shortFormProvider);

        parser.setOWLEntityChecker(owlEntityChecker);

        parser.setDefaultOntology(o);

        // when

        // finally parse

        OWLClassExpression dsvf = parser.parseClassExpression();

        // then

        assertEquals("Expected " + expected + " actual " + dsvf, expected, dsvf);

    }

    @Test

    public void shouldParseCorrectlydecimal()

            throws OWLOntologyCreationException {

        // given

        String text1 = "p some decimal[<=2.0, >= 1.0]";

        OWLDatatype decimal = df.getOWLDatatype(OWL2Datatype.XSD_DECIMAL

                .getIRI());

        OWLFacetRestriction max = df.getOWLFacetRestriction(

                OWLFacet.MAX_INCLUSIVE, df.getOWLLiteral("2.0", decimal));

        OWLFacetRestriction min = df.getOWLFacetRestriction(

                OWLFacet.MIN_INCLUSIVE, df.getOWLLiteral("1.0", decimal));

        OWLClassExpression expected = df.getOWLDataSomeValuesFrom(p,

                df.getOWLDatatypeRestriction(decimal, max, min));

        // ontology creation including labels - this is the input ontology

        OWLOntology o = m.createOntology();

        m.addAxiom(o, df.getOWLDeclarationAxiom(p));

        m.addAxiom(o, df.getOWLDeclarationAxiom(decimal));

        m.addAxiom(o, annotation(p, "p"));

        // select a short form provider that uses annotations

        ShortFormProvider sfp = new AnnotationValueShortFormProvider(

                Arrays.asList(df.getRDFSLabel()),

                Collections.<OWLAnnotationProperty, List<String>> emptyMap(), m);

        BidirectionalShortFormProvider shortFormProvider = new BidirectionalShortFormProviderAdapter(

                m.getOntologies(), sfp);

        ManchesterOWLSyntaxParser parser = OWLManager.createManchesterParser();

        parser.setStringToParse(text1);

        ShortFormEntityChecker owlEntityChecker = new ShortFormEntityChecker(

                shortFormProvider);

        parser.setOWLEntityChecker(owlEntityChecker);

        parser.setDefaultOntology(o);

        // when

        // finally parse

        OWLClassExpression dsvf = parser.parseClassExpression();

        // then

        assertEquals(expected, dsvf);

    }

    @Test

    public void shouldParseCorrectlydecimalNotSpecified()

            throws OWLOntologyCreationException {

        // given

        OWLAxiom expected = df.getOWLDataPropertyRangeAxiom(df

                .getOWLDataProperty(IRI.create("urn:a")), df.getOWLDataOneOf(df

                .getOWLLiteral("1.2", OWL2Datatype.XSD_DECIMAL)));

        String input = "Ontology:\n DataProperty: <urn:a>\n Range: {1.2}";

        OWLOntology o = loadOntologyFromString(input);

        Set<OWLLogicalAxiom> axioms = o.getLogicalAxioms();

        for (OWLLogicalAxiom ax : axioms) {

            assertEquals(expected, ax);

        }

    }

    @Test

    public void shouldDoPrecedenceWithoutParentheses()

            throws OWLOntologyCreationException {

        // given

        OWLClass a = Class(IRI("urn:test#a"));

        OWLClass b = Class(IRI("urn:test#b"));

        OWLClass c = Class(IRI("urn:test#c"));

        OWLClass d = Class(IRI("urn:test#all"));

        String text1 = "a and b or c";

        OWLClassExpression expected = df.getOWLObjectUnionOf(

                df.getOWLObjectIntersectionOf(a, b), c);

        OWLOntology o = m.createOntology();

        m.addAxiom(o, df.getOWLDeclarationAxiom(a));

        m.addAxiom(o, df.getOWLDeclarationAxiom(b));

        m.addAxiom(o, df.getOWLDeclarationAxiom(c));

        m.addAxiom(o, df.getOWLDeclarationAxiom(d));

        m.addAxiom(o, df.getOWLSubClassOfAxiom(expected, d));

        // select a short form provider that uses annotations

        ShortFormProvider sfp = new AnnotationValueShortFormProvider(

                Arrays.asList(df.getRDFSLabel()),

                Collections.<OWLAnnotationProperty, List<String>> emptyMap(), m);

        BidirectionalShortFormProvider shortFormProvider = new BidirectionalShortFormProviderAdapter(

                m.getOntologies(), sfp);

        ManchesterOWLSyntaxParser parser = OWLManager.createManchesterParser();

        parser.setStringToParse(text1);

        ShortFormEntityChecker owlEntityChecker = new ShortFormEntityChecker(

                shortFormProvider);

        parser.setOWLEntityChecker(owlEntityChecker);

        parser.setDefaultOntology(o);

        // when

        // finally parse

        OWLClassExpression dsvf = parser.parseClassExpression();

        // then

        assertEquals("Expected " + expected + " actual " + dsvf, expected, dsvf);

    }

    @Test

    public void shouldNotFailOnAnnotations() throws Exception {

        String in = "Ontology(<http://x.org/>\n"

                + "Declaration(Class(<http://x.org/c>))\n"

                + "AnnotationAssertion(<http://x.org/p> <http://x.org/c> \"v1\")\n"

                + "AnnotationAssertion(<http://x.org/p> <http://x.org/c> \"orifice\")\n"

                + "AnnotationAssertion(Annotation(<http://x.org/p2> \"foo\") <http://x.org/p> <http://x.org/c> \"v1\"))";

        OWLOntology o = loadOntologyFromString(in);

        OWLOntology result = roundTrip(o, new ManchesterSyntaxDocumentFormat());

        for (OWLAxiom ax : o.getAxioms()) {

            assert ax != null;

            assertTrue(result.containsAxiom(ax));

        }

    }

    @Test

    public void shouldNotFailSubclass() throws Exception {

        // given

        OWLClass a = Class(IRI("urn:test#A"));

        OWLClass b = Class(IRI("urn:test#B"));

        String in = "A SubClassOf B";

        OWLOntology o = m.createOntology();

        m.addAxiom(o, df.getOWLDeclarationAxiom(a));

        m.addAxiom(o, df.getOWLDeclarationAxiom(b));

        // select a short form provider that uses annotations

        ShortFormProvider sfp = new AnnotationValueShortFormProvider(

                Arrays.asList(df.getRDFSLabel()),

                Collections.<OWLAnnotationProperty, List<String>> emptyMap(), m);

        BidirectionalShortFormProvider shortFormProvider = new BidirectionalShortFormProviderAdapter(

                m.getOntologies(), sfp);

        ManchesterOWLSyntaxParser parser = OWLManager.createManchesterParser();

        parser.setStringToParse(in);

        ShortFormEntityChecker owlEntityChecker = new ShortFormEntityChecker(

                shortFormProvider);

        parser.setOWLEntityChecker(owlEntityChecker);

        parser.setDefaultOntology(o);

        // when

        // finally parse

        OWLAxiom axiom = parser.parseAxiom();

        // then

        assertEquals(df.getOWLSubClassOfAxiom(a, b), axiom);

    }

}