Examples with LiteratureEntry ambit2.base.data.LiteratureEntry used on opensource projects

Example 1 with LiteratureEntry

use of ambit2.base.data.LiteratureEntry in project ambit-mirror by ideaconsult.

the class BundleChemicalsResource method setGroupProperties.

protected void setGroupProperties(Context context, Request request, Response response) throws ResourceException {
    groupProperties = new Profile();
    Form form = getParams();
    String[] gp = OpenTox.params.sameas.getValuesArray(form);
    if (gp == null || gp.length == 0)
        gp = new String[] { "http://www.opentox.org/api/1.1#ChemicalName", "http://www.opentox.org/api/1.1#CASRN", "http://www.opentox.org/api/1.1#EINECS" };
    for (String g : gp) {
        Property p = new Property(g);
        p.setEnabled(true);
        p.setLabel(g);
        groupProperties.add(p);
    }
    if (enableFeatures) {
        LiteratureEntry ref = LiteratureEntry.getBundleReference(bundle);
        Property p = new Property("tag", ref);
        p.setEnabled(true);
        groupProperties.add(p);
        p = new Property("remarks", ref);
        p.setEnabled(true);
        groupProperties.add(p);
    }
}

Example 2 with LiteratureEntry

use of ambit2.base.data.LiteratureEntry 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 3 with LiteratureEntry

use of ambit2.base.data.LiteratureEntry 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 4 with LiteratureEntry

use of ambit2.base.data.LiteratureEntry 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 5 with LiteratureEntry

use of ambit2.base.data.LiteratureEntry in project ambit-mirror by ideaconsult.

the class MetaDatasetResourceTest method testUpdateExistingEntry.

@Test
public void testUpdateExistingEntry() throws Exception {
    // name and license uri can be updated only (for now)
    String name = "New dataset name";
    String title = "AAAA";
    String url = "BBBB";
    SourceDataset p = new SourceDataset(name, new LiteratureEntry(title, url));
    p.setLicenseURI(ISourceDataset.license.CC0_1_0.getURI());
    OntModel model = OT.createModel();
    DatasetURIReporter uriReporter = new DatasetURIReporter(new Reference(String.format("http://localhost:%d", port)));
    MetadataRDFReporter.addToModel(model, p, uriReporter.getURI(p));
    StringWriter writer = new StringWriter();
    model.write(writer, "RDF/XML");
    System.out.println(writer.toString());
    Response response = testPut(getTestURI(), 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 * FROM src_dataset join catalog_references using(idreference) where name='%s' and licenseURI='%s' ", name, ISourceDataset.license.CC0_1_0.getURI()));
    Assert.assertEquals(1, table.getRowCount());
    c.close();
    Assert.assertEquals("http://localhost:8181/dataset/1/metadata", response.getLocationRef().toString());
}