Examples of org.obolibrary.oboformat.model.Frame

org.obolibrary.oboformat.model.Frame
The Class Frame.

    @SuppressWarnings("null")
    @Nonnull
    protected OWLOntology tr(@Nonnull OWLOntology in)
            throws OWLOntologyCreationException {
        setOwlOntology(in);
        Frame hf = obodoc.getHeaderFrame();
        Clause ontClause = hf.getClause(OboFormatTag.TAG_ONTOLOGY);
        if (ontClause != null) {
            String ontOboId = (String) ontClause.getValue();
            defaultIDSpace = ontOboId;
            IRI ontIRI;
            if (ontOboId.contains(":")) {
                ontIRI = IRI.create(ontOboId);
            } else {
                ontIRI = IRI.create(DEFAULT_IRI_PREFIX + ontOboId + ".owl");
            }
            Clause dvclause = hf.getClause(OboFormatTag.TAG_DATA_VERSION);
            if (dvclause != null) {
                String dv = dvclause.getValue().toString();
                IRI vIRI = IRI.create(DEFAULT_IRI_PREFIX + ontOboId + '/' + dv
                        + '/' + ontOboId + ".owl");
                OWLOntologyID oid = new OWLOntologyID(Optional.of(ontIRI),
                        Optional.of(vIRI));
                // if the ontology being read has a differet id from the one
                // that was passed in, update it
                // when parsing, the original ontology is likely an anonymous,
                // empty one
                if (!oid.equals(in.getOntologyID())) {
                    manager.applyChange(new SetOntologyID(in, oid));
                }
            } else {
                // if the ontology being read has a differet id from the one
                // that was passed in, update it
                // when parsing, the original ontology is likely an anonymous,
                // empty one
                if (!ontIRI
                        .equals(in.getOntologyID().getOntologyIRI().orNull())) {
                    manager.applyChange(new SetOntologyID(in,
                            new OWLOntologyID(Optional.of(ontIRI), Optional
                                    .<IRI> absent())));
                }
            }
        } else {
            defaultIDSpace = "TEMP";
            manager.applyChange(new SetOntologyID(in,
                    new OWLOntologyID(Optional.of(IRI.create(DEFAULT_IRI_PREFIX
                            + defaultIDSpace)), Optional.<IRI> absent())));
            // TODO - warn
        }
        trHeaderFrame(hf);
        for (Frame f : obodoc.getTypedefFrames()) {
            trTypedefToAnnotationProperty(f);
        }
        for (Frame f : obodoc.getTypedefFrames()) {
            trTypedefFrame(f);
        }
        for (Frame f : obodoc.getTermFrames()) {
            trTermFrame(f);
        }
        // TODO - individuals
        for (Clause cl : hf.getClauses(OboFormatTag.TAG_IMPORT)) {
            String path = getURI(cl.getValue().toString());
            IRI importIRI = IRI.create(path);
            manager.loadOntology(importIRI);
            AddImport ai = new AddImport(in,
                    fac.getOWLImportsDeclaration(importIRI));

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     *        the quals
     * @return the oWL class expression
     */
    public OWLClassExpression trRel(@Nonnull String relId,
            @Nonnull String classId, @Nonnull Collection<QualifierValue> quals) {
        Frame relFrame = obodoc.getTypedefFrame(relId);
        OWLObjectPropertyExpression pe = trObjectProp(relId);
        OWLClassExpression ce = trClass(classId);
        assert pe != null;
        assert ce != null;
        Integer exact = getQVInt("cardinality", quals);
        Integer min = getQVInt("minCardinality", quals);
        Integer max = getQVInt("maxCardinality", quals);
        boolean allSome = getQVBoolean("all_some", quals);
        boolean allOnly = getQVBoolean("all_only", quals);
        // obo-format allows dangling references to classes in class
        // expressions;
        // create an explicit class declaration to be sure
        if (ce instanceof OWLClass) {
            add(fac.getOWLDeclarationAxiom((OWLClass) ce));
        }
        OWLClassExpression ex;
        if (exact != null && exact > 0) {
            ex = fac.getOWLObjectExactCardinality(exact, pe, ce);
        } else if (exact != null && exact == 0 || max != null && max == 0) {
            OWLObjectComplementOf ceCompl = fac.getOWLObjectComplementOf(ce);
            ex = fac.getOWLObjectAllValuesFrom(pe, ceCompl);
        } else if (max != null && min != null) {
            ex = fac.getOWLObjectIntersectionOf(
                    fac.getOWLObjectMinCardinality(min, pe, ce),
                    fac.getOWLObjectMaxCardinality(max, pe, ce));
        } else if (min != null) {
            ex = fac.getOWLObjectMinCardinality(min, pe, ce);
        } else if (max != null) {
            ex = fac.getOWLObjectMaxCardinality(max, pe, ce);
        } else if (allSome && allOnly) {
            ex = fac.getOWLObjectIntersectionOf(
                    fac.getOWLObjectSomeValuesFrom(pe, ce),
                    fac.getOWLObjectAllValuesFrom(pe, ce));
        } else if (allOnly) {
            ex = fac.getOWLObjectAllValuesFrom(pe, ce);
        } else if (relFrame != null
                && Boolean.TRUE.equals(relFrame
                        .getTagValue(OboFormatTag.TAG_IS_CLASS_LEVEL_TAG))) {
            // pun
            ex = fac.getOWLObjectHasValue(pe, trIndividual(classId));
        } else {
            // default

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     *        the id
     * @return mapped id
     */
    @Nonnull
    protected String mapPropId(@Nonnull String id) {
        Frame f = obodoc.getTypedefFrame(id);
        if (f != null) {
            Collection<Xref> xrefs = f.getTagValues(OboFormatTag.TAG_XREF,
                    Xref.class);
            for (Xref x : xrefs) {
                String xid = x.getIdref();
                if (OBODoc.isTreatXrefsAsEquivalent(getIdPrefix(xid))) {
                    return xid;

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    @Nonnull
    protected String translateShorthandIdToExpandedId(@Nonnull String id) {
        if (id.contains(":")) {
            return id;
        }
        Frame tdf = obodoc.getTypedefFrame(id);
        if (tdf == null) {
            return id;
        }
        Collection<Xref> xrefs = tdf.getTagValues(OboFormatTag.TAG_XREF,
                Xref.class);
        String matchingExpandedId = null;
        for (Xref xref : xrefs) {
            // System.err.println("ID:"+id+" xref:"+xref);
            if (xref != null) {

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        if (!untranslatableAxioms.isEmpty() && !discardUntranslatable) {
            try {
                String axiomString = OwlStringTools.translate(
                        untranslatableAxioms, manager);
                if (axiomString != null) {
                    Frame headerFrame = getObodoc().getHeaderFrame();
                    if (headerFrame == null) {
                        headerFrame = new Frame(FrameType.HEADER);
                        getObodoc().setHeaderFrame(headerFrame);
                    }
                    headerFrame.addClause(new Clause(
                            OboFormatTag.TAG_OWL_AXIOMS, axiomString));
                }
            } catch (OwlStringException e) {
                throw new OWLRuntimeException(e);
            }

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            @Nullable String tag, @Nullable String value,
            @Nonnull Set<OWLAnnotation> annotations) {
        if (prop == null || value == null) {
            return false;
        }
        Frame f = getTypedefFrame(prop);
        Clause clause;
        if (OboFormatTag.TAG_ID.getTag().equals(tag)) {
            clause = f.getClause(tag);
            if (tag != null) {
                clause.setValue(value);
            } else {
                clause = new Clause(tag, value);
                f.addClause(clause);
            }
        } else {
            clause = new Clause(tag, value);
            f.addClause(clause);
        }
        addQualifiers(clause, annotations);
        return true;
    }

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            String tag, @Nullable Boolean value,
            @Nonnull Set<OWLAnnotation> annotations) {
        if (prop == null || value == null) {
            return false;
        }
        Frame f = getTypedefFrame(prop);
        Clause clause = new Clause(tag);
        clause.addValue(value);
        f.addClause(clause);
        addQualifiers(clause, annotations);
        return true;
    }

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        if (pEx.isAnonymous()) {
            error(ax, false);
            return;
        }
        OWLObjectProperty p = pEx.asOWLObjectProperty();
        Frame f = getTypedefFrame(p);
        if (p.isBottomEntity() || p.isTopEntity()) {
            error("Property chains using Top or Bottom entities are not supported in OBO.",
                    ax, false);
            return;
        }
        List<OWLObjectPropertyExpression> list = ax.getPropertyChain();
        if (list.size() != 2) {
            error(ax, false);
            return;
        }
        OWLObjectPropertyExpression exp1 = list.get(0);
        OWLObjectPropertyExpression exp2 = list.get(1);
        if (exp1.isBottomEntity() || exp1.isTopEntity()
                || exp2.isBottomEntity() || exp2.isTopEntity()) {
            error("Property chains using Top or Bottom entities are not supported in OBO.",
                    ax, false);
            return;
        }
        String rel1 = getIdentifier(exp1);
        String rel2 = getIdentifier(exp2);
        if (rel1 == null || rel2 == null) {
            error(ax, false);
            return;
        }
        Clause clause;
        // set of unprocessed annotations
        Set<OWLAnnotation> unprocessedAnnotations = new HashSet<>(
                ax.getAnnotations());
        if (rel1.equals(f.getId())) {
            clause = new Clause(OboFormatTag.TAG_TRANSITIVE_OVER, rel2);
        } else {
            OboFormatTag tag = OboFormatTag.TAG_HOLDS_OVER_CHAIN;
            for (OWLAnnotation ann : ax.getAnnotations()) {
                if (OWLAPIObo2Owl.IRI_PROP_ISREVERSIBLEPROPERTYCHAIN.equals(ann
                        .getProperty().getIRI().toString())) {
                    tag = OboFormatTag.TAG_EQUIVALENT_TO_CHAIN;
                    // remove annotation from unprocessed set.
                    unprocessedAnnotations.remove(ann);
                    break;
                }
            }
            clause = new Clause(tag);
            clause.addValue(rel1);
            clause.addValue(rel2);
        }
        f.addClause(clause);
        addQualifiers(clause, unprocessedAnnotations);
    }

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                && sup instanceof OWLObjectProperty) {
            String supId = getIdentifier(sup);
            if (supId.startsWith("owl:")) {
                return;
            }
            Frame f = getTypedefFrame((OWLObjectProperty) sub);
            Clause clause = new Clause(OboFormatTag.TAG_IS_A, supId);
            f.addClause(clause);
            addQualifiers(clause, ax.getAnnotations());
        } else {
            error(ax, true);
        }
    }

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                    name = ((OWLLiteral) axiom.getValue()).getLiteral();
                } else if (OboFormatTag.TAG_SCOPE.getTag().equals(tg)) {
                    scope = owlObjectToTag(axiom.getValue());
                }
            }
            Frame hf = getObodoc().getHeaderFrame();
            Clause clause = new Clause(OboFormatTag.TAG_SYNONYMTYPEDEF);
            clause.addValue(getIdentifier(sub));
            clause.addValue(name);
            if (scope != null) {
                clause.addValue(scope);
            }
            addQualifiers(clause, ax.getAnnotations());
            if (!hf.getClauses().contains(clause)) {
                hf.addClause(clause);
            } else {
                LOG.error("duplicate clause: {} in header", clause);
            }
            return;
        } else if (OboFormatTag.TAG_SUBSETDEF.getTag().equals(tagObject)) {
            String comment = "";
            for (OWLAnnotationAssertionAxiom axiom : getOWLOntology()
                    .getAnnotationAssertionAxioms(sub.getIRI())) {
                String tg = owlObjectToTag(axiom.getProperty());
                if (OboFormatTag.TAG_COMMENT.getTag().equals(tg)) {
                    comment = ((OWLLiteral) axiom.getValue()).getLiteral();
                    break;
                }
            }
            Frame hf = getObodoc().getHeaderFrame();
            Clause clause = new Clause(OboFormatTag.TAG_SUBSETDEF);
            clause.addValue(getIdentifier(sub));
            clause.addValue(comment);
            if (!hf.getClauses().contains(clause)) {
                hf.addClause(clause);
            } else {
                LOG.error("duplicate clause: {} in header", clause);
            }
            addQualifiers(clause, ax.getAnnotations());
            return;
        }
        if (sub instanceof OWLObjectProperty
                && sup instanceof OWLObjectProperty) {
            String supId = getIdentifier(sup); // getIdentifier(sup);
            if (supId.startsWith("owl:")) {
                return;
            }
            Frame f = getTypedefFrame(sub);
            Clause clause = new Clause(OboFormatTag.TAG_IS_A, supId);
            f.addClause(clause);
            addQualifiers(clause, ax.getAnnotations());
        } else {
            error(ax, true);
        }
    }

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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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