Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.Frame

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         */
        public abstract void expand(@Nonnull Frame sf, String id, String xRef);

        @Nonnull
        protected Frame getTargetFrame(String id) {
            Frame f = getTargetDoc(idSpace).getTermFrame(id);
            if (f == null) {
                f = new Frame();
                f.setId(id);
                try {
                    getTargetDoc(idSpace).addTermFrame(f);
                } catch (FrameMergeException e) {
                    // this should be impossible
                    LOG.error("Frame merge exceptions should not be possible",
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    public OBODoc parse(BufferedReader reader) throws IOException {
        setReader(reader);
        OBODoc obodoc = new OBODoc();
        parseOBODoc(obodoc);
        // handle imports
        Frame hf = obodoc.getHeaderFrame();
        List<OBODoc> imports = new LinkedList<>();
        if (hf != null) {
            for (Clause cl : hf.getClauses(OboFormatTag.TAG_IMPORT)) {
                @SuppressWarnings("null")
                String path = resolvePath(cl.getValue(String.class));
                // TBD -- changing the relative path to absolute
                cl.setValue(path);
                if (followImport) {
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     *        obodoc
     * @throws OBOFormatParserException
     *         parser exception
     */
    public void parseOBODoc(@Nonnull OBODoc obodoc) {
        Frame h = new Frame(FrameType.HEADER);
        obodoc.setHeaderFrame(h);
        parseHeaderFrame(h);
        parseZeroOrMoreWsOptCmtNl();
        while (!stream.eof()) {
            parseEntityFrame(obodoc);
            parseZeroOrMoreWsOptCmtNl();
        }
        // set OBO namespace in frames
        String defaultOboNamespace = h.getTagValue(
                OboFormatTag.TAG_DEFAULT_NAMESPACE, String.class);
        if (defaultOboNamespace != null) {
            addOboNamespace(obodoc.getTermFrames(), defaultOboNamespace);
            addOboNamespace(obodoc.getTypedefFrames(), defaultOboNamespace);
            addOboNamespace(obodoc.getInstanceFrames(), defaultOboNamespace);
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     *        obodoc
     * @throws OBOFormatParserException
     *         parser exception
     */
    public void parseTermFrame(@Nonnull OBODoc obodoc) {
        Frame f = new Frame(FrameType.TERM);
        parseZeroOrMoreWsOptCmtNl();
        if (stream.consume("[Term]")) {
            forceParseNlOrEof();
            parseIdLine(f);
            parseZeroOrMoreWsOptCmtNl();
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     *        obodoc
     * @throws OBOFormatParserException
     *         parser exception
     */
    public void parseTypedefFrame(@Nonnull OBODoc obodoc) {
        Frame f = new Frame(FrameType.TYPEDEF);
        parseZeroOrMoreWsOptCmtNl();
        if (stream.consume("[Typedef]")) {
            forceParseNlOrEof();
            parseIdLine(f);
            parseZeroOrMoreWsOptCmtNl();
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        assertTrue(foundRel2);
        // convert back to OBO
        OWLAPIOwl2Obo owl2Obo = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc convertedOboDoc = owl2Obo.convert(owlOntology);
        Frame convertedFrame = convertedOboDoc.getTermFrame("PR:000027136");
        Collection<Clause> clauses = convertedFrame
                .getClauses(OboFormatTag.TAG_RELATIONSHIP);
        // check that round trip still contains relationships
        assertEquals(2, clauses.size());
        for (Clause clause : clauses) {
            Collection<QualifierValue> qualifierValues = clause
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    public void testConvertXPs() throws Exception {
        OWLOntology owlOnt = convertOBOFile("dangling_roundtrip_test.obo");
        OWLAPIOwl2Obo revbridge = new OWLAPIOwl2Obo(
                OWLManager.createOWLOntologyManager());
        OBODoc d2 = revbridge.convert(owlOnt);
        Frame f = d2.getTermFrame("UBERON:0000020");
        Clause rc = f.getClause(OboFormatTag.TAG_NAME);
        assertEquals("sense organ", rc.getValue());
        OBOFormatWriter w = new OBOFormatWriter();
        w.setCheckStructure(true);
        w.write(d2, "/tmp/z.obo");
    }
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public class DanglingOwl2OboTest extends OboFormatTestBasics {

    @Test
    public void testConversion() throws Exception {
        OBODoc doc = convert(parseOWLFile("dangling_owl2_obo_test.owl"));
        Frame f = doc.getTermFrame("UBERON:0000020");
        Clause rc = f.getClause(OboFormatTag.TAG_NAME);
        assertEquals("sense organ", rc.getValue());
        Collection<Clause> ics = f.getClauses(OboFormatTag.TAG_INTERSECTION_OF);
        assertEquals(2, ics.size());
        writeOBO(doc);
    }
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    @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);
        assertEquals(1, rs.size());
        writeOBO(doc);
    }
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        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());
        OWLOntology converted = obo2Owl.convert(obo);
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Related Classes of org.obolibrary.oboformat.model.Frame

  • org.obolibrary.obo2owl.BFOROXrefTest
  • org.obolibrary.obo2owl.CommentRemarkConversionTest
  • org.obolibrary.obo2owl.DanglingOwl2OboTest
  • org.obolibrary.obo2owl.DanglingRestrictionOwl2OboTest
  • org.obolibrary.obo2owl.DanglingRoundTripTest
  • org.obolibrary.obo2owl.EquivalentToTest
  • org.obolibrary.obo2owl.GCIQualifierTest
  • org.obolibrary.obo2owl.IDsTest
  • org.obolibrary.obo2owl.LogicalDefinitionPropertyViewTest
  • org.obolibrary.obo2owl.ObsoleteTermTest
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