Examples with ReferenceURIReporter ambit2.rest.reference.ReferenceURIReporter used on opensource projects

Example 1 with ReferenceURIReporter

use of ambit2.rest.reference.ReferenceURIReporter in project ambit-mirror by ideaconsult.

the class PropertyResourceTest method testCreateEntry.

/**
 * <pre>
 * <rdf:RDF
 *     xmlns:j.0="http://purl.org/net/nknouf/ns/bibtex#"
 *     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
 *     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
 *     xmlns:ot="http://www.opentox.org/api/1.1#"
 *     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
 *     xmlns:owl="http://www.w3.org/2002/07/owl#"
 *     xmlns:dc="http://purl.org/dc/elements/1.1/" >
 *   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#units">
 *     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
 *   </rdf:Description>
 *   <rdf:Description rdf:about="http://purl.org/net/nknouf/ns/bibtex#Entry">
 *     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
 *   </rdf:Description>
 *   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#hasSource">
 *     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
 *   </rdf:Description>
 *   <rdf:Description rdf:nodeID="A0">
 *     <rdfs:seeAlso>bbb</rdfs:seeAlso>
 *     <dc:title>aaa</dc:title>
 *     <rdf:type rdf:resource="http://purl.org/net/nknouf/ns/bibtex#Entry"/>
 *   </rdf:Description>
 *   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#Feature">
 *     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
 *   </rdf:Description>
 *   <rdf:Description rdf:nodeID="A1">
 *     <dc:type>http://www.w3.org/2001/XMLSchema#string</dc:type>
 *     <ot:hasSource rdf:nodeID="A0"/>
 *     <owl:sameAs>CasRN</owl:sameAs>
 *     <ot:units></ot:units>
 *     <dc:title>cas</dc:title>
 *     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
 *   </rdf:Description>
 * </rdf:RDF>
 * </pre>
 *
 * @throws Exception
 */
@Test
public void testCreateEntry() throws Exception {
    OntModel model = OT.createModel();
    Property p = new Property("cas", new LiteratureEntry("aaa", "bbb"));
    p.setNominal(true);
    PropertyRDFReporter.addToModel(model, p, new PropertyURIReporter(new Reference(String.format("http://localhost:%d%s", port, PropertyResource.featuredef))), new ReferenceURIReporter());
    StringWriter writer = new StringWriter();
    model.write(writer, "RDF/XML");
    System.out.println(writer.toString());
    Response response = testPost(String.format("http://localhost:%d%s", port, PropertyResource.featuredef), MediaType.APPLICATION_RDF_XML, writer.toString());
    Assert.assertEquals(Status.SUCCESS_OK, response.getStatus());
    // Assert.assertEquals("http://localhost:8181/feature/4",
    // response.getLocationRef().toString());
    IDatabaseConnection c = getConnection();
    ITable table = c.createQueryTable("EXPECTED", String.format("SELECT * FROM properties join catalog_references using(idreference) where name='cas' and comments='%s' and title='aaa' and url='bbb' and isLocal=1", Property.opentox_CAS));
    Assert.assertEquals(1, table.getRowCount());
    c.close();
}

Example 2 with ReferenceURIReporter

use of ambit2.rest.reference.ReferenceURIReporter in project ambit-mirror by ideaconsult.

the class PropertyResourceTest method testUpdateExistingEntry.

@Test
public void testUpdateExistingEntry() throws Exception {
    // now we can only update by PUT, not POST
    Property p = new Property("Property 1", new LiteratureEntry("Dummy", "NA"));
    p.setLabel("Test");
    p.setNominal(true);
    OntModel model = OT.createModel();
    PropertyRDFReporter.addToModel(model, p, new PropertyURIReporter(new Reference(String.format("http://localhost:%d%s", port, PropertyResource.featuredef))), new ReferenceURIReporter());
    StringWriter writer = new StringWriter();
    model.write(writer, "RDF/XML");
    Response response = testPut(String.format("http://localhost:%d%s/1", port, PropertyResource.featuredef), MediaType.TEXT_URI_LIST, new StringRepresentation(writer.toString(), MediaType.APPLICATION_RDF_XML));
    Assert.assertEquals(Status.SUCCESS_OK, response.getStatus());
    IDatabaseConnection c = getConnection();
    ITable table = c.createQueryTable("EXPECTED", String.format("SELECT isLocal FROM properties join catalog_references using(idreference) where name='Property 1' and comments='%s' and title='Dummy' and url='NA'", "http://www.opentox.org/api/1.1#Test"));
    Assert.assertEquals(1, table.getRowCount());
    Assert.assertEquals(true, table.getValue(0, "isLocal"));
    c.close();
    Assert.assertEquals("http://localhost:8181/feature/1", response.getLocationRef().toString());
}

Example 3 with ReferenceURIReporter

use of ambit2.rest.reference.ReferenceURIReporter in project ambit-mirror by ideaconsult.

the class PropertyResourceTest method testUpdateExistingEntry1.

// this fails because of mysql foreign key constraints
public void testUpdateExistingEntry1() throws Exception {
    Property p = new Property("Property 1", new LiteratureEntry("Dummy 1", "NA"));
    p.setLabel("Test");
    p.setId(1);
    OntModel model = OT.createModel();
    PropertyRDFReporter.addToModel(model, p, new PropertyURIReporter(new Reference(String.format("http://localhost:%d%s", port))), new ReferenceURIReporter());
    StringWriter writer = new StringWriter();
    model.write(writer, "RDF/XML");
    Response response = testPost(String.format("http://localhost:%d%s/2", port, PropertyResource.featuredef), MediaType.APPLICATION_RDF_XML, writer.toString());
    Assert.assertEquals(Status.SUCCESS_OK, response.getStatus());
    IDatabaseConnection c = getConnection();
    ITable table = c.createQueryTable("EXPECTED", String.format("SELECT * FROM properties join catalog_references using(idreference) where name='Property 1' and comments='%s' and title='Dummy' and url='NA'", "http://www.opentox.org/api/1.1#Test"));
    Assert.assertEquals(1, table.getRowCount());
    c.close();
    Assert.assertEquals("http://localhost:8181/feature/2", response.getLocationRef().toString());
}

Example 4 with ReferenceURIReporter

use of ambit2.rest.reference.ReferenceURIReporter in project ambit-mirror by ideaconsult.

the class PropertyRDFReporter method addToModel.

public static Individual addToModel(OntModel jenaModel, Property item, QueryURIReporter<Property, IQueryRetrieval<Property>> uriReporter, ReferenceURIReporter referenceReporter) {
    Individual feature = null;
    OTClass featureType = OTClass.Feature;
    String id = uriReporter.getURI(item);
    if ((uriReporter == null) || (uriReporter.getBaseReference() == null) || (item.getId() < 0)) {
        if (item.getClazz() == Dictionary.class) {
            feature = jenaModel.createIndividual(id, featureType.getOntClass(jenaModel));
        } else
            feature = jenaModel.createIndividual(featureType.getOntClass(jenaModel));
    } else {
        feature = jenaModel.createIndividual(id, featureType.getOntClass(jenaModel));
    }
    if (item.isNominal())
        feature.addOntClass(OTClass.NominalFeature.getOntClass(jenaModel));
    if (item.getClazz() == Number.class)
        feature.addOntClass(OTClass.NumericFeature.getOntClass(jenaModel));
    else if (item.getClazz() == Double.class)
        feature.addOntClass(OTClass.NumericFeature.getOntClass(jenaModel));
    else if (item.getClazz() == Float.class)
        feature.addOntClass(OTClass.NumericFeature.getOntClass(jenaModel));
    else if (item.getClazz() == Integer.class)
        feature.addOntClass(OTClass.NumericFeature.getOntClass(jenaModel));
    else if (item.getClazz() == Long.class)
        feature.addOntClass(OTClass.NumericFeature.getOntClass(jenaModel));
    else if (item.getClazz() == Dictionary.class)
        feature.addOntClass(OTClass.TupleFeature.getOntClass(jenaModel));
    if (item.getName() != null)
        feature.addProperty(DC.title, item.getName());
    if (item.getUnits() != null)
        feature.addProperty(OT.DataProperty.units.createProperty(jenaModel), item.getUnits());
    String uri = item.getLabel();
    if (uri == null)
        uri = Property.guessLabel(item.getName());
    if ((uri != null) && (uri.indexOf("http://") < 0) && (uri.indexOf("https://") < 0)) {
        uri = String.format("%s%s", OT.NS, Reference.encode(uri));
    }
    feature.addProperty(OWL.sameAs, jenaModel.createResource(uri));
    // ot:hasSource ; reference.title used as source URI, reference.url used
    // as object type -
    // somewhat awkward, but title is the unique field in the
    // catalog_references table
    uri = item.getTitle();
    // catch all
    if (uri.indexOf("/model/") > 0)
        feature.addOntClass(OT.OTClass.ModelPredictionFeature.getOntClass(jenaModel));
    // drop using /reference objects
    if ((uri.indexOf("http://") < 0) && (uri.indexOf("https://") < 0)) {
        Individual source = null;
        if (_type.Algorithm.equals(item.getReference().getType())) {
            uri = String.format("%s/algorithm/%s", uriReporter.getBaseReference(), Reference.encode(uri));
            source = jenaModel.createIndividual(uri, OT.OTClass.Algorithm.createOntClass(jenaModel));
            feature.addProperty(OT.OTProperty.hasSource.createProperty(jenaModel), source);
        } else if (_type.Model.equals(item.getReference().getType())) {
            uri = String.format("%s/model/%s", uriReporter.getBaseReference(), Reference.encode(uri));
            source = jenaModel.createIndividual(uri, OT.OTClass.Model.createOntClass(jenaModel));
            feature.addProperty(OT.OTProperty.hasSource.createProperty(jenaModel), source);
            feature.addOntClass(OT.OTClass.ModelPredictionFeature.getOntClass(jenaModel));
        } else if (_type.Feature.equals(item.getReference().getType())) {
            uri = String.format("%s/feature/%s", uriReporter.getBaseReference(), Reference.encode(uri));
            source = jenaModel.createIndividual(uri, OT.OTClass.Feature.createOntClass(jenaModel));
            feature.addProperty(OT.OTProperty.hasSource.createProperty(jenaModel), source);
        } else if (_type.Dataset.equals(item.getReference().getType())) {
            // this seems to confuse everybody's else parsers ...
            uri = String.format("%s/dataset/%s", uriReporter.getBaseReference(), Reference.encode(uri));
            Resource src = jenaModel.createResource(uri);
            feature.addProperty(OT.OTProperty.hasSource.createProperty(jenaModel), src);
        } else {
            feature.addProperty(OT.OTProperty.hasSource.createProperty(jenaModel), uri);
        }
        feature.addProperty(DC.creator, item.getReference().getURL());
    } else {
        feature.addProperty(OT.OTProperty.hasSource.createProperty(jenaModel), jenaModel.createResource(uri));
        feature.addProperty(DC.creator, item.getReference().getURL());
    }
    if (item.getAnnotations() != null)
        for (PropertyAnnotation a : item.getAnnotations()) try {
            PropertyAnnotationRDFReporter.annotation2RDF(a, jenaModel, feature, uriReporter.getBaseReference().toString());
        } catch (Exception x) {
            x.printStackTrace();
        }
    return feature;
}

Example 5 with ReferenceURIReporter

use of ambit2.rest.reference.ReferenceURIReporter in project ambit-mirror by ideaconsult.

the class PropertyAnnotationResourceTest method testCreateEntry.

@Test
public void testCreateEntry() throws Exception {
    OntModel model = OT.createModel();
    Property p = new Property("cas", new LiteratureEntry("aaa", "bbb"));
    p.setNominal(true);
    PropertyRDFReporter.addToModel(model, p, new PropertyURIReporter(new Reference(String.format("http://localhost:%d%s", port, PropertyResource.featuredef))), new ReferenceURIReporter());
    StringWriter writer = new StringWriter();
    model.write(writer, "RDF/XML");
    // System.out.println(writer.toString());
    Response response = testPost(String.format("http://localhost:%d%s", port, PropertyResource.featuredef), MediaType.APPLICATION_RDF_XML, writer.toString());
    Assert.assertEquals(Status.SUCCESS_OK, response.getStatus());
    // Assert.assertEquals("http://localhost:8181/feature/4",
    // response.getLocationRef().toString());
    IDatabaseConnection c = getConnection();
    ITable table = c.createQueryTable("EXPECTED", String.format("SELECT * FROM properties join catalog_references using(idreference) where name='cas' and comments='%s' and title='aaa' and url='bbb' and isLocal=1", Property.opentox_CAS));
    Assert.assertEquals(1, table.getRowCount());
    c.close();
}