Examples with Resource org.openrdf.model.Resource used on opensource projects

Example 56 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class ModelComparer method recordIfBlankNode.

private void recordIfBlankNode(Value node, Statement statement, Set<Resource> bNodes, MultiMap<Resource, Statement> triples) {
    if (node instanceof BNode) {
        Resource resource = (Resource) node;
        bNodes.add(resource);
        triples.add(resource, statement);
    }
}

Example 57 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class RDFObjectCompositePool method getPrimaryResource.

public Resource getPrimaryResource(T object) {
    Class<T1> createdClass1 = pool1.getCreatedClass();
    if (createdClass1.isInstance(object)) {
        T1 object1 = createdClass1.cast(object);
        Resource primaryResource = pool1.getPrimaryResource(object1);
        if (primaryResource != null) {
            return primaryResource;
        }
    }
    Class<T2> createdClass2 = pool2.getCreatedClass();
    if (createdClass2.isInstance(object)) {
        T2 object2 = createdClass2.cast(object);
        Resource primaryResource = pool2.getPrimaryResource(object2);
        if (primaryResource != null) {
            return primaryResource;
        }
    }
    return null;
}

Example 58 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class RDFObjectSimplePool method remove.

public void remove(T object) {
    Set<Resource> resourcesToDelete = new HashSet<Resource>();
    Set<Resource> resources = object2resources.get(object);
    if (resources != null) {
        object2resources.remove(object);
        resourcesToDelete.addAll(resources);
    }
    Resource primaryResource = object2primaryResource.get(object);
    if (primaryResource != null) {
        object2primaryResource.remove(object);
        resourcesToDelete.add(primaryResource);
    }
    for (Resource resourceToDelete : resourcesToDelete) {
        resource2object.remove(resourceToDelete);
    }
}

Example 59 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class RDFResourceProjection method project.

public URI project(URI property) {
    Resource resourceMapped = map.get(property);
    URI propertyMapped = property;
    if (resourceMapped instanceof URI) {
        propertyMapped = (URI) resourceMapped;
    }
    return propertyMapped;
}

Example 60 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class UniProtExtractor method extractBox.

public UniProtBox extractBox() {
    UniProtBoxImp box = new UniProtBoxImp();
    Iterator<Statement> stmtIter1 = model.match(null, UniProtConstants.replaces, null);
    while (stmtIter1.hasNext()) {
        Statement statement = stmtIter1.next();
        Resource subject = statement.getSubject();
        Value object = statement.getObject();
        if (subject instanceof URI && object instanceof URI) {
            String idSubject = id((URI) subject);
            String idObject = id((URI) object);
            if (StringUtil.notEmpty(idSubject) && StringUtil.notEmpty(idObject)) {
                UniProtBox.Entry entrySubject = box.entry(idSubject);
                UniProtBox.Entry entryObject = box.entry(idObject);
                box.setReplaces(entrySubject, entryObject);
            }
        }
    }
    Iterator<Statement> stmtIter2 = model.match(null, UniProtConstants.replacedBy, null);
    while (stmtIter2.hasNext()) {
        Statement statement = stmtIter2.next();
        Resource subject = statement.getSubject();
        Value object = statement.getObject();
        if (subject instanceof URI && object instanceof URI) {
            String idSubject = id((URI) subject);
            String idObject = id((URI) object);
            if (StringUtil.notEmpty(idSubject) && StringUtil.notEmpty(idObject)) {
                UniProtBox.Entry entrySubject = box.entry(idSubject);
                UniProtBox.Entry entryObject = box.entry(idObject);
                box.setReplaces(entryObject, entrySubject);
            }
        }
    }
    Iterator<Statement> stmtIter3 = model.match(null, UniProtConstants.recommendedName, null);
    if (stmtIter3.hasNext()) {
        while (stmtIter3.hasNext()) {
            Statement statement = stmtIter3.next();
            Resource entryNode = statement.getSubject();
            Value nameNode = statement.getObject();
            if (nameNode instanceof Resource) {
                Resource nameResource = (Resource) nameNode;
                Iterator<Statement> stmtIter4 = model.match(nameResource, UniProtConstants.fullName, null);
                // System.out.println("hello world");
                while (stmtIter4.hasNext()) {
                    Statement statement2 = stmtIter4.next();
                    Value objectNode = statement2.getObject();
                    // System.out.println("hello moon");
                    if (entryNode instanceof URI && objectNode instanceof Literal) {
                        String name = ((Literal) objectNode).stringValue();
                        UniProtBox.Entry entry = box.entry(UniProtConstants.idFromResource((URI) entryNode));
                        System.out.println("UniProtExtractor: name: " + name + "\tid: " + entry.id());
                        entry.setRecommendedName(name);
                    }
                }
            }
        }
    } else {
        // sometimes, recommended name is not present for an uniprot id : check the full name
        stmtIter3 = model.match(null, UniProtConstants.fullName, null);
        while (stmtIter3.hasNext()) {
            Statement statement2 = stmtIter3.next();
            Resource entryNode = statement2.getSubject();
            Value objectNode = statement2.getObject();
            if (entryNode instanceof URI && objectNode instanceof Literal) {
                String name = ((Literal) objectNode).stringValue();
                UniProtBox.Entry entry = box.entry(UniProtConstants.idFromResource((URI) entryNode));
                entry.setRecommendedName(name);
                System.out.println("UniProtExtractor: name: " + name + "\tid: " + entry.id());
            }
        }
    }
    return box;
}