Examples with ManchesterOWLSyntaxOntologyFormat org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat used on opensource projects

Example 1 with ManchesterOWLSyntaxOntologyFormat

use of org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat in project opentheso by miledrousset.

the class testApiSkosOfficial method testingOWL.

// TODO add test methods here.
// The methods must be annotated with annotation @Test. For example:
// 
// @Test
// public void hello() {}
/*
 * Copyright (C) 2007, University of Manchester
 *
 * Modifications to the initial code base are copyright of their
 * respective authors, or their employers as appropriate.  Authorship
 * of the modifications may be determined from the ChangeLog placed at
 * the end of this file.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.

 * This library 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
 * Lesser General Public License for more details.

 * You should have received a copy of the GNU Lesser General Public
 * License along with this library; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 */
/**
 * Author: Simon Jupp<br>
 * Date: Mar 17, 2008<br>
 * The University of Manchester<br>
 * Bio-Health Informatics Group<br>
 */
// @Test
public void testingOWL() throws OWLOntologyCreationException, OWLOntologyStorageException {
    // Get hold of an ontology manager
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    // Load an ontology from the Web.  We load the ontology from a document IRI
    IRI docIRI = IRI.create("http://www.w3.org/2009/08/skos-reference/skos.rdf");
    OWLOntology skos = manager.loadOntologyFromOntologyDocument(docIRI);
    System.out.println("Loaded ontology: " + skos);
    System.out.println();
    // Save a local copy of the ontology.  (Specify a path appropriate to your setup)
    File file = new File("/Users/Miled/Downloads/downloadAndSaveOWLFile.owl");
    manager.saveOntology(skos, IRI.create(file.toURI()));
    // Ontologies are saved in the format from which they were loaded.
    // We can get information about the format of an ontology from its manager
    OWLOntologyFormat format = (OWLOntologyFormat) manager.getOntologyFormat(skos);
    System.out.println("    format: " + format);
    System.out.println();
    // Save the ontology in owl/xml format
    OWLXMLOntologyFormat owlxmlFormat = new OWLXMLOntologyFormat();
    // so that we have nicely abbreviated IRIs in the new ontology document
    if (format.isPrefixOWLOntologyFormat()) {
        owlxmlFormat.copyPrefixesFrom(format.asPrefixOWLOntologyFormat());
    }
    // manager.saveOntology(skos, (OWLOntologyFormat) (OWLDocumentFormat) owlxmlFormat, IRI.create(file.toURI()));
    // Dump an ontology to System.out by specifying a different OWLOntologyOutputTarget
    // Note that we can write an ontology to a stream in a similar way
    // using the StreamOutputTarget class
    OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
    // Try another format - The Manchester OWL Syntax
    ManchesterOWLSyntaxOntologyFormat manSyntaxFormat = new ManchesterOWLSyntaxOntologyFormat();
    if (format.isPrefixOWLOntologyFormat()) {
        manSyntaxFormat.copyPrefixesFrom(format.asPrefixOWLOntologyFormat());
    }
// manager.saveOntology(skos, (OWLOntologyFormat) (OWLDocumentFormat) manSyntaxFormat, documentTarget);
}

Example 2 with ManchesterOWLSyntaxOntologyFormat

use of org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat in project stanbol by apache.

the class RecipeWriter method writeTo.

@Override
public void writeTo(Recipe recipe, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    if (mediaType.toString().equals(MediaType.TEXT_PLAIN)) {
        String recipeString = recipe.toString();
        out.write(recipeString.getBytes());
    } else if (mediaType.toString().equals(MediaType.TEXT_HTML)) {
        String recipeString = recipe.toString();
        out.write(recipeString.getBytes());
    } else {
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLDataFactory factory = OWLManager.getOWLDataFactory();
        OWLOntology ontology;
        try {
            ontology = manager.createOntology();
            RuleList rules = recipe.getRuleList();
            IRI recipeID = recipe.getRecipeID();
            String recipeURI = recipeID.toString().replace("<", "").replace(">", "");
            org.semanticweb.owlapi.model.IRI recipeIRI = org.semanticweb.owlapi.model.IRI.create(recipeURI);
            OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI);
            String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
            org.semanticweb.owlapi.model.IRI descriptionIRI = org.semanticweb.owlapi.model.IRI.create(descriptionURI);
            OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
            OWLAxiom axiom;
            String recipeDescription = recipe.getRecipeDescription();
            if (recipeDescription != null) {
                axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, recipeIndividual, recipeDescription);
                manager.addAxiom(ontology, axiom);
            }
            if (rules != null) {
                for (Rule rule : rules) {
                    IRI ruleID = rule.getRuleID();
                    String ruleName = rule.getRuleName();
                    String ruleDescription = rule.getDescription();
                    String ruleURI = ruleID.toString().replace("<", "").replace(">", "");
                    String ruleNameURI = Symbols.ruleName.toString().replace("<", "").replace(">", "");
                    String ruleBodyURI = Symbols.ruleBody.toString().replace("<", "").replace(">", "");
                    String ruleHeadURI = Symbols.ruleHead.toString().replace("<", "").replace(">", "");
                    String hasRuleURI = Symbols.hasRule.toString().replace("<", "").replace(">", "");
                    String ruleContent = rule.toString();
                    String[] ruleParts = ruleContent.split("\\->");
                    org.semanticweb.owlapi.model.IRI ruleIRI = org.semanticweb.owlapi.model.IRI.create(ruleURI);
                    org.semanticweb.owlapi.model.IRI ruleNameIRI = org.semanticweb.owlapi.model.IRI.create(ruleNameURI);
                    org.semanticweb.owlapi.model.IRI ruleBodyIRI = org.semanticweb.owlapi.model.IRI.create(ruleBodyURI);
                    org.semanticweb.owlapi.model.IRI ruleHeadIRI = org.semanticweb.owlapi.model.IRI.create(ruleHeadURI);
                    org.semanticweb.owlapi.model.IRI hasRuleIRI = org.semanticweb.owlapi.model.IRI.create(hasRuleURI);
                    OWLIndividual ruleIndividual = factory.getOWLNamedIndividual(ruleIRI);
                    OWLObjectProperty hasRule = factory.getOWLObjectProperty(hasRuleIRI);
                    OWLDataProperty nameProperty = factory.getOWLDataProperty(ruleNameIRI);
                    OWLDataProperty ruleBodyProperty = factory.getOWLDataProperty(ruleBodyIRI);
                    OWLDataProperty ruleHeadProperty = factory.getOWLDataProperty(ruleHeadIRI);
                    // add the name to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(nameProperty, ruleIndividual, ruleName);
                    manager.addAxiom(ontology, axiom);
                    // add the description to the rule individual
                    if (ruleDescription != null) {
                        axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, ruleIndividual, ruleDescription);
                        manager.addAxiom(ontology, axiom);
                    }
                    // add the rule body to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(ruleBodyProperty, ruleIndividual, ruleParts[0]);
                    manager.addAxiom(ontology, axiom);
                    // add the rule head to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(ruleHeadProperty, ruleIndividual, ruleParts[1]);
                    manager.addAxiom(ontology, axiom);
                    // bind the rule to the recipe
                    axiom = factory.getOWLObjectPropertyAssertionAxiom(hasRule, recipeIndividual, ruleIndividual);
                    manager.addAxiom(ontology, axiom);
                }
            }
            if (mediaType.toString().equals(KRFormat.RDF_XML)) {
                try {
                    manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
                try {
                    manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
                try {
                    manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
                try {
                    manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
                try {
                    manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
                Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
                RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
                provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
            }
        } catch (OWLOntologyCreationException e1) {
            log.error("An error occurred.", e1);
        }
    }
    out.flush();
}

Example 3 with ManchesterOWLSyntaxOntologyFormat

use of org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat in project stanbol by apache.

the class RecipeListWriter method writeTo.

@Override
public void writeTo(RecipeList recipeList, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLDataFactory factory = OWLManager.getOWLDataFactory();
    OWLOntology ontology;
    try {
        ontology = manager.createOntology();
        String recipeClassURI = Symbols.Recipe.toString().replace("<", "").replace(">", "");
        IRI recipeClassIRI = IRI.create(recipeClassURI);
        OWLClass owlRecipeClass = factory.getOWLClass(recipeClassIRI);
        String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
        IRI descriptionIRI = IRI.create(descriptionURI);
        OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
        if (recipeList != null) {
            log.info("Converting the recipe list to OWL.");
            for (Recipe recipe : recipeList) {
                String recipeURI = recipe.getRecipeID().toString().replace("<", "").replace(">", "");
                IRI recipeIRI = IRI.create(recipeURI);
                OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI);
                OWLAxiom axiom = factory.getOWLClassAssertionAxiom(owlRecipeClass, recipeIndividual);
                manager.addAxiom(ontology, axiom);
                String description = recipe.getRecipeDescription();
                if (description != null) {
                    axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, recipeIndividual, description);
                    manager.addAxiom(ontology, axiom);
                }
            }
        }
        if (mediaType.toString().equals(KRFormat.RDF_XML)) {
            try {
                manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
            try {
                manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
            try {
                manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
            try {
                manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
            try {
                manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
            Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
            RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
            provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
        }
    } catch (OWLOntologyCreationException e1) {
        log.error("An error occurred.", e1);
    }
    out.flush();
}

Example 4 with ManchesterOWLSyntaxOntologyFormat

use of org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat in project stanbol by apache.

the class RuleListWriter method writeTo.

@Override
public void writeTo(RuleList ruleList, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLDataFactory factory = OWLManager.getOWLDataFactory();
    OWLOntology ontology;
    try {
        ontology = manager.createOntology();
        String recipeClassURI = Symbols.Recipe.toString().replace("<", "").replace(">", "");
        IRI recipeClassIRI = IRI.create(recipeClassURI);
        OWLClass owlRecipeClass = factory.getOWLClass(recipeClassIRI);
        String ruleClassURI = Symbols.Rule.toString().replace("<", "").replace(">", "");
        IRI ruleClassIRI = IRI.create(ruleClassURI);
        OWLClass owlRuleClass = factory.getOWLClass(ruleClassIRI);
        String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
        IRI descriptionIRI = IRI.create(descriptionURI);
        OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
        String hasRuleURI = Symbols.hasRule.toString().replace("<", "").replace(">", "");
        IRI hasRuleIRI = IRI.create(hasRuleURI);
        OWLObjectProperty hasRule = factory.getOWLObjectProperty(hasRuleIRI);
        String ruleBodyURI = Symbols.ruleBody.toString().replace("<", "").replace(">", "");
        IRI ruleBodyIRI = IRI.create(ruleBodyURI);
        OWLDataProperty ruleBody = factory.getOWLDataProperty(ruleBodyIRI);
        String ruleHeadURI = Symbols.ruleHead.toString().replace("<", "").replace(">", "");
        IRI ruleHeadIRI = IRI.create(ruleHeadURI);
        OWLDataProperty ruleHead = factory.getOWLDataProperty(ruleHeadIRI);
        if (ruleList != null) {
            for (Rule rule : ruleList) {
                String recipeId = rule.getRecipe().getRecipeID().toString().replace("<", "").replace(">", "");
                IRI reicpeIRI = IRI.create(recipeId);
                OWLIndividual owlRecipe = factory.getOWLNamedIndividual(reicpeIRI);
                String ruleId = rule.getRuleID().toString().replace("<", "").replace(">", "");
                IRI ruleIRI = IRI.create(ruleId);
                OWLIndividual owlRule = factory.getOWLNamedIndividual(ruleIRI);
                OWLAxiom axiom = factory.getOWLClassAssertionAxiom(owlRecipeClass, owlRecipe);
                manager.addAxiom(ontology, axiom);
                axiom = factory.getOWLClassAssertionAxiom(owlRuleClass, owlRule);
                manager.addAxiom(ontology, axiom);
                axiom = factory.getOWLObjectPropertyAssertionAxiom(hasRule, owlRecipe, owlRule);
                manager.addAxiom(ontology, axiom);
                String recipeDescription = rule.getRecipe().getRecipeDescription();
                String ruleDescription = rule.getDescription();
                if (recipeDescription != null) {
                    axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, owlRecipe, recipeDescription);
                    manager.addAxiom(ontology, axiom);
                }
                if (ruleDescription != null) {
                    axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, owlRule, ruleDescription);
                    manager.addAxiom(ontology, axiom);
                }
                String ruleContent = rule.toString();
                String[] parts = ruleContent.split("\\->");
                axiom = factory.getOWLDataPropertyAssertionAxiom(ruleBody, owlRule, parts[0]);
                manager.addAxiom(ontology, axiom);
                axiom = factory.getOWLDataPropertyAssertionAxiom(ruleHead, owlRule, parts[1]);
                manager.addAxiom(ontology, axiom);
            }
        }
        if (mediaType.toString().equals(KRFormat.RDF_XML)) {
            try {
                manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
            try {
                manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
            try {
                manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
            try {
                manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
            try {
                manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
            Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
            RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
            provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
        }
    } catch (OWLOntologyCreationException e1) {
        log.error("An error occurred.", e1);
    }
    out.flush();
}

Example 5 with ManchesterOWLSyntaxOntologyFormat

use of org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat in project stanbol by apache.

the class OWLOntologyWriter method writeTo.

@Override
public void writeTo(OWLOntology ontology, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    log.debug("Rendering ontology " + ontology.getOntologyID() + " to knowledge representation format " + mediaType);
    // Native formats first
    if (RDF_XML_TYPE.equals(mediaType) || OWL_XML_TYPE.equals(mediaType) || MANCHESTER_OWL_TYPE.equals(mediaType) || FUNCTIONAL_OWL_TYPE.equals(mediaType) || TURTLE_TYPE.equals(mediaType) || X_TURTLE_TYPE.equals(mediaType)) {
        OWLOntologyFormat format = null;
        if (RDF_XML_TYPE.equals(mediaType))
            format = new RDFXMLOntologyFormat();
        else if (OWL_XML_TYPE.equals(mediaType))
            format = new OWLXMLOntologyFormat();
        else if (MANCHESTER_OWL_TYPE.equals(mediaType))
            format = new ManchesterOWLSyntaxOntologyFormat();
        else if (FUNCTIONAL_OWL_TYPE.equals(mediaType))
            format = new OWLFunctionalSyntaxOntologyFormat();
        else if (TURTLE_TYPE.equals(mediaType) || X_TURTLE_TYPE.equals(mediaType))
            format = new TurtleOntologyFormat();
        if (format != null)
            try {
                manager.saveOntology(ontology, format, out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
                throw new WebApplicationException(e, Status.INTERNAL_SERVER_ERROR);
            }
        else
            throw new IOException();
    } else {
        // Non-native formats that require a conversion to Clerezza
        if (RDF_JSON_TYPE.equals(mediaType) || N3_TYPE.equals(mediaType) || TEXT_PLAIN.equals(mediaType.toString()) || N_TRIPLE_TYPE.equals(mediaType)) {
            Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
            SerializingProvider serializer = null;
            if (RDF_JSON_TYPE.equals(mediaType))
                serializer = new RdfJsonSerializingProvider();
            else if (N3_TYPE.equals(mediaType) || N_TRIPLE_TYPE.equals(mediaType) || TEXT_PLAIN.equals(mediaType.toString()))
                serializer = new JenaSerializerProvider();
            // text/plain is interpreted as N3.
            if (serializer != null)
                serializer.serialize(out, mGraph, TEXT_PLAIN.equals(mediaType.toString()) ? N3 : mediaType.toString());
        }
    }
    // JSON_LD not supported until both parser and serializer are stable.
    out.flush();
}