Examples with OntModel org.apache.jena.ontology.OntModel used on opensource projects

Example 16 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class VClassDaoJena method isSubClassOf.

public boolean isSubClassOf(String vclassURI1, String vclassURI2) {
    if (vclassURI1 == null || vclassURI2 == null) {
        return false;
    }
    OntModel ontModel = getOntModel();
    try {
        ontModel.enterCriticalSection(Lock.READ);
        Resource oc1 = ontModel.getResource(vclassURI1);
        Resource oc2 = ontModel.getResource(vclassURI2);
        return ontModel.contains(oc1, RDFS.subClassOf, oc2);
    } finally {
        ontModel.leaveCriticalSection();
    }
}

Example 17 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class VClassDaoJena method getOntologyRootClasses.

public List<VClass> getOntologyRootClasses(String ontologyURI) {
    if (ontologyURI == null) {
        throw new RuntimeException("can't find root classes for null ontology URI");
    }
    // return getRootClasses(ontologyURI);
    List<VClass> ontologyRootClasses = new ArrayList<VClass>();
    OntModel ontModel = getOntModel();
    ontModel.enterCriticalSection(Lock.READ);
    try {
        Iterator<Resource> ontClassIt = ontModel.listResourcesWithProperty(RDF.type, OWL.Class);
        while (ontClassIt.hasNext()) {
            Resource ontClass = ontClassIt.next();
            if (ontologyURI.equals(ontClass.getNameSpace())) {
                boolean root = true;
                StmtIterator superStmtIt = ontModel.listStatements(ontClass, RDFS.subClassOf, (RDFNode) null);
                try {
                    while (superStmtIt.hasNext()) {
                        Statement superStmt = superStmtIt.nextStatement();
                        if (superStmt.getObject().isResource() && ontologyURI.equals(((Resource) superStmt.getObject()).getNameSpace())) {
                            root = false;
                            break;
                        }
                    }
                } finally {
                    superStmtIt.close();
                }
                if (root && ontClass.canAs(OntClass.class)) {
                    ontologyRootClasses.add(new VClassJena((OntClass) ontClass.as(OntClass.class), getWebappDaoFactory()));
                }
            }
        }
    } finally {
        ontModel.leaveCriticalSection();
    }
    return ontologyRootClasses;
}

Example 18 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class WebappDaoFactoryJena method getCommentsForResource.

@Override
public List<String> getCommentsForResource(String resourceURI) {
    List<String> commentList = new LinkedList<String>();
    OntModel ontModel = ontModelSelector.getFullModel();
    ontModel.enterCriticalSection(Lock.READ);
    try {
        OntResource res = ontModel.getOntResource(resourceURI);
        if (res != null) {
            ClosableIterator<RDFNode> closeIt = res.listComments(null);
            try {
                for (Iterator<RDFNode> commIt = closeIt; commIt.hasNext(); ) {
                    Literal lit = (Literal) commIt.next();
                    commentList.add(lit.getLexicalForm());
                }
            } finally {
                closeIt.close();
            }
        }
    } finally {
        ontModel.leaveCriticalSection();
    }
    return commentList;
}

Example 19 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class WebappDaoFactoryJena method makeInMemoryDataset.

public static Dataset makeInMemoryDataset(Model assertions, Model inferences) {
    Dataset dataset = DatasetFactory.createMem();
    OntModel union = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
    if (assertions != null) {
        dataset.addNamedModel(ModelNames.ABOX_ASSERTIONS, assertions);
        union.addSubModel(assertions);
    }
    if (inferences != null) {
        dataset.addNamedModel(ModelNames.ABOX_INFERENCES, inferences);
        union.addSubModel(inferences);
    }
    dataset.setDefaultModel(union);
    return dataset;
}

Example 20 with OntModel

use of org.apache.jena.ontology.OntModel in project Vitro by vivo-project.

the class WebappDaoFactoryJena method setSpecialDataModel.

/**
 * Method for using a special model, such as the display model, with the
 * WebappDaoFactory.  The goal here is to modify this WebappDaoFactory so
 * that it is using specialModel, specialTboxModel and specialDisplayModel
 * for individual editing.
 *
 * DAOs related to the application configuration and user accounts
 * should remain unchanged.
 */
public void setSpecialDataModel(OntModel specialModel, OntModel specialTboxModel, OntModel specialDisplayModel) {
    if (specialModel == null)
        throw new IllegalStateException("specialModel must not be null");
    // Can we get the "original" models here from somewhere?
    OntModelSelector originalSelector = this.getOntModelSelector();
    // Set up model selector for this special WDF
    // The selector is used by the object property DAO, therefore should be
    // set up even though we use the new webapp dao factory object to
    // generate portions to overwrite the regular webapp dao factory.
    // The WDF expects the full model in the OntModelSelect that has
    // both the ABox and TBox.  This is used to run SPARQL queries against.
    OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
    unionModel.addSubModel(specialModel);
    OntModelSelectorImpl specialSelector = new OntModelSelectorImpl();
    specialSelector.setFullModel(unionModel);
    // Keeping original application metadata model and adding special model.
    // Adding both  allows us to prevent errors in  ApplicationDao which may
    // depend on a specific individual from the regular application metadata
    // model to  pick the theme.   Adding the new  model would  take care of
    // special  situations  where  the switch  model  may  contain important
    // information.
    OntModel newApplicationModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
    newApplicationModel.add(specialModel);
    newApplicationModel.add(originalSelector.getApplicationMetadataModel());
    specialSelector.setApplicationMetadataModel(newApplicationModel);
    if (specialDisplayModel != null) {
        specialSelector.setDisplayModel(specialDisplayModel);
        unionModel.addSubModel(specialDisplayModel);
    } else {
        OntModel selectorDisplayModel = originalSelector.getDisplayModel();
        if (selectorDisplayModel != null) {
            specialSelector.setDisplayModel(originalSelector.getDisplayModel());
        }
    }
    if (specialTboxModel != null) {
        unionModel.addSubModel(specialTboxModel);
        specialSelector.setTBoxModel(specialTboxModel);
    } else {
        OntModel selectorTboxModel = originalSelector.getTBoxModel();
        if (selectorTboxModel != null) {
            specialSelector.setTBoxModel(originalSelector.getTBoxModel());
        }
    }
    specialSelector.setABoxModel(specialModel);
    specialSelector.setUserAccountsModel(specialModel);
    // Although we're only using part of the new wadf and copy over below,
    // the object property dao utilizes methods that will employ the display
    // model returned from the simple ontmodel selector, so if the object
    // property dao is to be copied over we need to ensure we have the
    // correct display model and tbox model.
    WebappDaoFactoryJena specialWadfj = new WebappDaoFactoryJena(specialSelector);
    entityWebappDao = specialWadfj.getIndividualDao();
    vClassGroupDao = specialWadfj.getVClassGroupDao();
    // To allow for testing, add a property group, this will allow
    // the unassigned group method section to be executed and main Image to
    // be assigned to that group.  Otherwise, the dummy group does not allow
    // for the unassigned group to be executed.
    propertyGroupDao = specialWadfj.getPropertyGroupDao();
    objectPropertyDao = specialWadfj.getObjectPropertyDao();
    objectPropertyStatementDao = specialWadfj.getObjectPropertyStatementDao();
    dataPropertyDao = specialWadfj.getDataPropertyDao();
    dataPropertyStatementDao = specialWadfj.getDataPropertyStatementDao();
    // Why can't we set the selector to be the same?
    ontModelSelector = specialSelector;
}