Examples of OBODoc

Examples of org.obolibrary.oboformat.model.OBODoc

8
9
10
11
12
13
14
15
16
public class XrefIRITest extends OboFormatTestBasics {

    @Test
    public void testConversion() throws Exception {
        OWLOntology ontology = parseOWLFile("xrefIRItest.owl");
        OBODoc doc = convert(ontology);
        doc.getTermFrame("FOO:1");
        writeOBO(doc);
    }
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

12
13
14
15
16
17
18
19
20
21
22
@SuppressWarnings("javadoc")
public class RoundTripLabeledXrefsTest extends RoundTripTest {

    @Test
    public void testRoundTrip() throws Exception {
        OBODoc source = parseOBOFile("labeled_xrefs.obo");
        String written = renderOboToString(source);
        OBODoc parsed = parseOboToString(written);
        List<Diff> diffs = OBODocDiffer.getDiffs(source, parsed);
        assertEquals(0, diffs.size());
    }
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

14
15
16
17
18
19
20
21
22
23
24
25
public class DanglingRestrictionOwl2OboTest extends OboFormatTestBasics {

    @Test
    public void testConversion() throws Exception {
        // this is a test ontology that has had its imports axioms removed
        OBODoc doc = convert(parseOWLFile("dangling_restriction_test.owl"));
        Frame f = doc.getTermFrame("FUNCARO:0000014");
        Clause rc = f.getClause(OboFormatTag.TAG_NAME);
        assertEquals("digestive system", rc.getValue());
        Collection<Clause> isas = f.getClauses(OboFormatTag.TAG_IS_A);
        assertEquals(1, isas.size());
        Collection<Clause> rs = f.getClauses(OboFormatTag.TAG_RELATIONSHIP);
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

23
24
25
26
27
28
29
30
31
32
33
34
35
    @Test
    public void testUntranslatableAxioms() throws Exception {
        OWLOntology original = parseOWLFile("untranslatable_axioms.owl");
        OWLAPIOwl2Obo owl2Obo = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc obo = owl2Obo.convert(original);
        renderOboToString(obo);
        Frame headerFrame = obo.getHeaderFrame();
        String owlAxiomString = headerFrame.getTagValue(
                OboFormatTag.TAG_OWL_AXIOMS, String.class);
        assertNotNull(owlAxiomString);
        OWLAPIObo2Owl obo2Owl = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

46
47
48
49
50
51
52
53
54
55
56
57
58
    @Test
    public void testUntranslatableAxioms2() throws Exception {
        OWLOntology original = parseOWLFile("untranslatable_axioms2.owl");
        OWLAPIOwl2Obo owl2Obo = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc obo = owl2Obo.convert(original);
        renderOboToString(obo);
        Frame headerFrame = obo.getHeaderFrame();
        String owlAxiomString = headerFrame.getTagValue(
                OboFormatTag.TAG_OWL_AXIOMS, String.class);
        assertNotNull(owlAxiomString);
        OWLAPIObo2Owl obo2Owl = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

20
21
22
23
24
25
26
27
28
29
30
31
32
33
@SuppressWarnings("javadoc")
public class RoundTripOboAnnotations extends RoundTripTest {

    @Test
    public void testIsInferredAnnotation() throws Exception {
        OBODoc input = parseOBOFile("is_inferred_annotation.obo");
        OWLOntology owl = convert(input);
        // check round trip
        OBODoc output = convert(owl);
        String outObo = renderOboToString(output);
        assertEquals(readResource("is_inferred_annotation.obo"), outObo);
        // check owl
        IRI t1 = IRI.create("http://purl.obolibrary.org/obo/TEST_0001");
        IRI t3 = IRI.create("http://purl.obolibrary.org/obo/TEST_0003");
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

15
16
17
18
19
20
21
22
23
24
@SuppressWarnings("javadoc")
public class RoundTripNamespaceIdRule extends RoundTripTest {

    @Test
    public void testWrite() throws Exception {
        OBODoc oboDoc = parseOBOFile("namespace-id-rule.obo");
        String oboString = renderOboToString(oboDoc);
        assertTrue(oboString
                .contains("\nnamespace-id-rule: * test:$sequence(7,0,9999999)$\n"));
    }
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

28
29
30
31
32
33
34
35
36
37
38
        roundTripOBOFile("namespace-id-rule.obo", true);
    }

    @Test
    public void testWriteReadConvertedOWL() throws Exception {
        OBODoc oboDoc = parseOBOFile("namespace-id-rule.obo");
        OWLOntology owlOntology = convert(oboDoc);
        OWLOntologyManager manager = owlOntology.getOWLOntologyManager();
        StringDocumentTarget documentTarget = new StringDocumentTarget();
        manager.saveOntology(owlOntology, new OWLXMLDocumentFormat(),
                documentTarget);
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

44
45
46
47
48
49
50
51
52
53
54
55
56
                ok = true;
            }
        }
        assertTrue(ok);
        // CONVERT BACK TO OBO
        OBODoc obodoc = convert(ontology);
        // test that transitive over is converted back
        Frame tf = obodoc.getTypedefFrame("regulates");
        assert tf != null;
        assertEquals(3, tf.getClauses().size());
        assertEquals("regulates", tf.getTagValue(OboFormatTag.TAG_ID));
        assertEquals("regulates", tf.getTagValue(OboFormatTag.TAG_NAME));
        Clause clause = tf.getClause(OboFormatTag.TAG_TRANSITIVE_OVER);
View Full Code Here

Examples of org.obolibrary.oboformat.model.OBODoc

22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
public class RoundTripMultiLineDefTest extends OboFormatTestBasics {

    @Test
    public void testMultiLineDefinitions() throws Exception {
        // create minimal ontology
        OBODoc oboDocSource = new OBODoc();
        oboDocSource.setHeaderFrame(new Frame(FrameType.HEADER));
        oboDocSource.addDefaultOntologyHeader("caro");
        // add source frame that contains at least one new line
        Frame sourceFrame = new Frame(FrameType.TERM);
        sourceFrame.setId("CARO:0000049");
        sourceFrame
                .addClause(new Clause(
                        OboFormatTag.TAG_DEF,
                        "Sequential hermaphroditic organism that produces\ngametes first of the male sex, and then later of the\nfemale sex."));
        oboDocSource.addTermFrame(sourceFrame);
        // convert to OWL and retrieve def
        OWLAPIObo2Owl bridge = new OWLAPIObo2Owl(
                OWLManager.createOWLOntologyManager());
        OWLOntology owlOntology = bridge.convert(oboDocSource);
        OWLDataFactory factory = owlOntology.getOWLOntologyManager()
                .getOWLDataFactory();
        // IRI
        IRI iri = bridge.oboIdToIRI("CARO:0000049");
        OWLClass c = factory.getOWLClass(iri);
        // Def
        OWLAnnotationProperty defProperty = factory
                .getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_IAO_0000115
                        .getIRI());
        int counter = 0;
        for (OWLAnnotationAssertionAxiom ax : owlOntology
                .getAnnotationAssertionAxioms(c.getIRI())) {
            if (ax.getProperty().equals(defProperty)) {
                counter++;
                assertTrue(ax.getValue() instanceof OWLLiteral);
                String owlDef = ((OWLLiteral) ax.getValue()).getLiteral();
                // check that owl def also contains at least one new line
                assertTrue(owlDef.indexOf('\n') > 0);
            }
        }
        assertEquals(1, counter);
        // convert back to OBO
        OWLAPIOwl2Obo owl2Obo = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc convertedOboDoc = owl2Obo.convert(owlOntology);
        Frame convertedFrame = convertedOboDoc.getTermFrame("CARO:0000049");
        String convertedDef = convertedFrame.getTagValue(OboFormatTag.TAG_DEF,
                String.class);
        // check that round trip still contains newlines
        assertTrue(convertedDef.indexOf('\n') > 0);
    }
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.