Examples with RDFTerm org.apache.commons.rdf.api.RDFTerm used on opensource projects

Example 1 with RDFTerm

use of org.apache.commons.rdf.api.RDFTerm in project trellis by trellis-ldp.

the class JenaIOServiceTest method testUpdate.

@Test
void testUpdate() {
    final Graph graph = rdf.createGraph();
    getTriples().forEach(graph::add);
    assertEquals(3L, graph.size(), "Incorrect graph size!");
    service.update(graph, "DELETE WHERE { ?s <http://purl.org/dc/terms/title> ?o }", SPARQL_UPDATE, "test:info");
    assertEquals(2L, graph.size(), "Incorrect graph size, post update!");
    service.update(graph, "INSERT { " + "<> <http://purl.org/dc/terms/title> \"Other title\" } WHERE {}", SPARQL_UPDATE, "trellis:data/resource");
    assertEquals(3L, graph.size(), "Incorrect graph size, after adding triple!");
    service.update(graph, "DELETE WHERE { ?s ?p ?o };" + "INSERT { <> <http://purl.org/dc/terms/title> \"Other title\" } WHERE {}", SPARQL_UPDATE, "trellis:data/");
    assertEquals(1L, graph.size(), "Incorrect graph size after removing triples!");
    assertEquals("<trellis:data/>", graph.stream().findFirst().map(Triple::getSubject).map(RDFTerm::ntriplesString).get(), "Incorrect graph subject from updates!");
}

Example 2 with RDFTerm

use of org.apache.commons.rdf.api.RDFTerm in project trellis by trellis-ldp.

the class TriplestoreResourceService method initialize.

/**
 * This code is equivalent to the SPARQL queries below.
 *
 * <pre><code>
 * SELECT ?object WHERE {
 *   GRAPH trellis:PreferServerManaged { IDENTIFIER rdf:type ?object }
 * }
 * </code></pre>
 *
 * <pre><code>
 * INSERT DATA {
 *   GRAPH trellis:PreferServerManaged {
 *     IDENTIFIER rdf:type ldp:Container ;
 *                dc:modified "NOW"^^xsd:dateTime }
 *   GRAPH IDENTIFIER?ext=audit {
 *     IDENTIFIER prov:wasGeneratedBy [
 *       rdf:type prov:Activity , as:Create ;
 *       prov:wasAssociatedWith trellis:AdministorAgent ;
 *       prov:atTime "TIME"^^xsd:dateTime ] }
 *   GRAPH IDENTIFIER?ext=acl {
 *     IDENTIFIER acl:mode acl.Read , acl:Write , acl:Control ;
 *       acl:agentClass foaf:Agent ;
 *       acl:accessTo IDENTIFIER }
 * }
 *
 * </code></pre>
 */
@PostConstruct
public void initialize() {
    extensions = extensionGraphConfig.map(TriplestoreResourceService::buildExtensionMap).orElseGet(() -> Map.of(ACL_EXT, PreferAccessControl));
    supplier = idService.getSupplier();
    final IRI root = rdf.createIRI(TRELLIS_DATA_PREFIX);
    final Query q = new Query();
    q.setQuerySelectType();
    q.addResultVar(OBJECT);
    final ElementPathBlock epb = new ElementPathBlock();
    epb.addTriple(triple(toJena(root), toJena(type), OBJECT));
    final ElementNamedGraph ng = new ElementNamedGraph(toJena(PreferServerManaged), epb);
    final ElementGroup elg = new ElementGroup();
    elg.addElement(ng);
    q.setQueryPattern(elg);
    final Stream.Builder<RDFTerm> builder = builder();
    rdfConnection.querySelect(q, qs -> builder.accept(getObject(qs)));
    if (!builder.build().findFirst().isPresent()) {
        final Literal time = rdf.createLiteral(now().toString(), XSD.dateTime);
        final IRI auth = rdf.createIRI(TRELLIS_DATA_PREFIX + "#auth");
        final UpdateRequest update = new UpdateRequest();
        final QuadDataAcc sink = new QuadDataAcc();
        sink.addQuad(new Quad(toJena(PreferServerManaged), triple(toJena(root), toJena(type), toJena(LDP.BasicContainer))));
        sink.addQuad(new Quad(toJena(PreferServerManaged), triple(toJena(root), toJena(DC.modified), toJena(time))));
        sink.addQuad(new Quad(getExtIRI(root, ACL_EXT), triple(toJena(auth), toJena(ACL.mode), toJena(ACL.Read))));
        sink.addQuad(new Quad(getExtIRI(root, ACL_EXT), triple(toJena(auth), toJena(ACL.mode), toJena(ACL.Write))));
        sink.addQuad(new Quad(getExtIRI(root, ACL_EXT), triple(toJena(auth), toJena(ACL.mode), toJena(ACL.Control))));
        sink.addQuad(new Quad(getExtIRI(root, ACL_EXT), triple(toJena(auth), toJena(ACL.agentClass), toJena(FOAF.Agent))));
        sink.addQuad(new Quad(getExtIRI(root, ACL_EXT), triple(toJena(auth), toJena(ACL.accessTo), toJena(root))));
        update.add(new UpdateDataInsert(sink));
        rdfConnection.update(update);
    }
    LOGGER.info("Initialized Trellis Triplestore Resource Service");
}

Example 3 with RDFTerm

use of org.apache.commons.rdf.api.RDFTerm in project minerva by geneontology.

the class ShexValidator method getAllMatchedShapes.

public Set<String> getAllMatchedShapes(RDFTerm value, Typing typing) {
    Set<Label> all_shapes_in_schema = getAllShapesInSchema();
    Set<String> obj_matched_shapes = new HashSet<String>();
    for (Label target_shape_label : all_shapes_in_schema) {
        Pair<RDFTerm, Label> p = new Pair<RDFTerm, Label>(value, target_shape_label);
        Status r = typing.getStatusMap().get(p);
        if (r.equals(Status.CONFORMANT)) {
            obj_matched_shapes.add(getCurie(target_shape_label.stringValue()));
        }
    }
    return obj_matched_shapes;
}

Example 4 with RDFTerm

use of org.apache.commons.rdf.api.RDFTerm in project minerva by geneontology.

the class ShexValidator method runShapeMapValidationWithRecursiveSingleNodeValidation.

public ShexValidationReport runShapeMapValidationWithRecursiveSingleNodeValidation(Model test_model, boolean stream_output) throws Exception {
    ShexValidationReport r = new ShexValidationReport();
    JenaRDF jr = new JenaRDF();
    // this shex implementation likes to use the commons JenaRDF interface, nothing exciting here
    JenaGraph shexy_graph = jr.asGraph(test_model);
    // recursive only checks the focus node against the chosen shape.
    RecursiveValidationWithMemorization shex_model_validator = new RecursiveValidationWithMemorization(schema, shexy_graph);
    // for each shape in the query map (e.g. MF, BP, CC, etc.)
    boolean all_good = true;
    Map<Resource, Set<String>> node_s_shapes = getShapesToTestForEachResource(test_model);
    for (Resource focus_node_resource : node_s_shapes.keySet()) {
        Set<String> shape_nodes = node_s_shapes.get(focus_node_resource);
        for (String shapelabel : shape_nodes) {
            Label shape_label = new Label(rdfFactory.createIRI(shapelabel));
            if (focus_node_resource == null) {
                System.out.println("null focus node for shape " + shape_label);
                continue;
            }
            // check for use of properties not defined for this shape (okay if OPEN, not if CLOSED)
            Typing typing = validateNodeWithTimeout(shex_model_validator, focus_node_resource, shape_label);
            if (typing != null) {
                Set<ShexViolation> extra_prop_violations = checkForExtraProperties(focus_node_resource, test_model, shape_label, typing);
                if (extra_prop_violations != null && !extra_prop_violations.isEmpty()) {
                    for (Violation v : extra_prop_violations) {
                        r.addViolation(v);
                    }
                    all_good = false;
                }
                // run the validation on the node if possible..
                RDFTerm focus_node = null;
                String focus_node_id = "";
                if (focus_node_resource.isURIResource()) {
                    focus_node = rdfFactory.createIRI(focus_node_resource.getURI());
                    focus_node_id = focus_node_resource.getURI();
                } else {
                    focus_node = rdfFactory.createBlankNode(focus_node_resource.getId().getLabelString());
                    focus_node_id = focus_node_resource.getId().getLabelString();
                }
                // deal with curies for output
                String node = focus_node_id;
                node = getCurie(focus_node_id);
                Status status = typing.getStatus(focus_node, shape_label);
                if (status.equals(Status.CONFORMANT)) {
                    Set<String> shape_ids = r.node_matched_shapes.get(node);
                    if (shape_ids == null) {
                        shape_ids = new HashSet<String>();
                    }
                    shape_ids.add(shapelabel);
                    r.node_matched_shapes.put(node, shape_ids);
                } else if (status.equals(Status.NONCONFORMANT)) {
                    all_good = false;
                    // implementing a start on a generic violation report structure here
                    ShexViolation violation = new ShexViolation(node);
                    ShexExplanation explanation = new ShexExplanation();
                    String shape_curie = getCurie(shapelabel);
                    explanation.setShape(shape_curie);
                    Set<ShexConstraint> unmet_constraints = getUnmetConstraints(focus_node_resource, shape_label, test_model, typing);
                    if (unmet_constraints != null) {
                        for (ShexConstraint constraint : unmet_constraints) {
                            explanation.addConstraint(constraint);
                            violation.addExplanation(explanation);
                        }
                    } else {
                        explanation.setErrorMessage("explanation computation timed out");
                        violation.addExplanation(explanation);
                    }
                    r.addViolation(violation);
                } else if (status.equals(Status.NOTCOMPUTED)) {
                    // if any of these are not computed, there is a problem
                    String error = focus_node_id + " was not tested against " + shapelabel;
                    LOGGER.error(error);
                }
            } else {
                LOGGER.info("shex validation failed for node " + focus_node_resource.getURI());
                all_good = false;
                ShexViolation violation = new ShexViolation(focus_node_resource.getURI());
                ShexExplanation explanation = new ShexExplanation();
                explanation.setErrorMessage("Validating this node was canceled because it took more then " + timeout_mill + " milliseconds");
                String shape_curie = getCurie(shapelabel);
                explanation.setShape(shape_curie);
                violation.addExplanation(explanation);
                r.addViolation(violation);
            }
        }
    }
    if (all_good) {
        r.conformant = true;
    } else {
        r.conformant = false;
    }
    return r;
}

Example 5 with RDFTerm

use of org.apache.commons.rdf.api.RDFTerm in project minerva by geneontology.

the class ShexValidator method getUnmetConstraints.

/**
 * We no there is a problem with the focus node and the shape here.  This tries to figure out the constraints that caused the problem and provide some explanation.
 * @param focus_node
 * @param shape_label
 * @param model
 * @param typing
 * @return
 * @throws IOException
 */
private Set<ShexConstraint> getUnmetConstraints(Resource focus_node, Label shape_label, Model model, Typing typing) throws IOException {
    Set<ShexConstraint> unmet_constraints = new HashSet<ShexConstraint>();
    Set<String> node_types = getNodeTypes(model, focus_node.getURI());
    Map<String, Set<String>> expected_property_ranges = shape_expected_property_ranges.get(shape_label);
    // check for assertions with properties in the target shape
    for (String prop_uri : expected_property_ranges.keySet()) {
        Property prop = model.getProperty(prop_uri);
        Interval cardinality = shape_expected_property_cardinality.get(shape_label).get(prop_uri);
        // checking on objects of this property for the problem node.
        int n_objects = 0;
        for (StmtIterator i = focus_node.listProperties(prop); i.hasNext(); ) {
            while (i.hasNext()) {
                n_objects++;
                RDFNode obj = i.nextStatement().getObject();
                // check the computed shapes for this individual
                if (!obj.isResource()) {
                    continue;
                // no checks on literal values at this time
                } else if (prop_uri.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#type") && obj.asResource().getURI().equals("http://www.w3.org/2002/07/owl#NamedIndividual")) {
                    // ignore type owl individual
                    continue;
                }
                RDFTerm range_obj = rdfFactory.createIRI(obj.asResource().getURI());
                // does it hit any allowable shapes?
                boolean good = false;
                // TODO many property ranges are MISSING from previous step
                // e.g. any OR will not show up here.
                Set<String> expected_ranges = expected_property_ranges.get(prop_uri);
                for (String target_shape_uri : expected_ranges) {
                    if (target_shape_uri.equals(".")) {
                        // anything is fine
                        good = true;
                    // break;
                    } else if (target_shape_uri.trim().equals("<http://www.w3.org/2001/XMLSchema#string>")) {
                        // ignore syntax type checking for now
                        good = true;
                    // break;
                    }
                    Label target_shape_label = new Label(rdfFactory.createIRI(target_shape_uri));
                    // Typing typing = validateNodeWithTimeout(shex_model_validator, obj.asResource(), shape_label);
                    if (typing != null) {
                        // capture the result
                        // Typing shape_test = shex_model_validator.getTyping();
                        // Pair<RDFTerm, Label> p = new Pair<RDFTerm, Label>(range_obj, target_shape_label);
                        // Status r = shape_test.getStatusMap().get(p);
                        Status r = typing.getStatus(range_obj, target_shape_label);
                        if (r != null && r.equals(Status.CONFORMANT)) {
                            good = true;
                        // break;
                        }
                    } else {
                        good = false;
                    }
                }
                if (!good) {
                    // add violated range constraint to explanation
                    if (obj.isURIResource()) {
                        String object = obj.toString();
                        Set<String> object_types = getNodeTypes(model, obj.toString());
                        String property = prop.toString();
                        object = getCurie(object);
                        property = getCurie(property);
                        Set<String> expected = new HashSet<String>();
                        for (String e : expected_property_ranges.get(prop_uri)) {
                            String curie_e = getCurie(e);
                            expected.add(curie_e);
                        }
                        ShexConstraint constraint = new ShexConstraint(object, property, expected, node_types, object_types);
                        // return all shapes that are matched by this node for explanation
                        Set<String> obj_matched_shapes = getAllMatchedShapes(range_obj, typing);
                        constraint.setMatched_range_shapes(obj_matched_shapes);
                        unmet_constraints.add(constraint);
                    } else {
                        ShexConstraint constraint = new ShexConstraint(obj.toString(), getCurie(prop.toString()), null, node_types, null);
                        // return all shapes that are matched by this node for explanation
                        Set<String> obj_matched_shapes = getAllMatchedShapes(range_obj, typing);
                        constraint.setMatched_range_shapes(obj_matched_shapes);
                        unmet_constraints.add(constraint);
                    }
                }
            }
        }
        // check for cardinality violations
        if (!prop_uri.contentEquals("http://www.w3.org/1999/02/22-rdf-syntax-ns#type")) {
            // skip types - should always allow multiple..
            if (!cardinality.contains(n_objects)) {
                System.out.println("cardinality violation!");
                System.out.println("problem node " + focus_node);
                System.out.println("prop " + prop);
                System.out.println("Intended Interval " + cardinality.toString());
                System.out.println("Actual " + n_objects);
                ShexConstraint constraint = new ShexConstraint(getCurie(prop.toString()), cardinality.toString(), n_objects);
                unmet_constraints.add(constraint);
            }
        }
    }
    return unmet_constraints;
}