Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.Clause

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                    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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            @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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            @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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        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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            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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                } 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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        if (tag == null) {
            if (annVal instanceof IRI && FrameType.TERM.equals(frame.getType())
                    && isMetadataTag(prop)) {
                String propId = this.getIdentifier(prop);
                if (propId != null) {
                    Clause clause = new Clause(OboFormatTag.TAG_RELATIONSHIP);
                    clause.addValue(propId);
                    clause.addValue(getIdentifier((IRI) annVal));
                    addQualifiers(clause, qualifiers);
                    frame.addClause(clause);
                    return true;
                }
            }
            // annotation property does not correspond to a mapping to a tag in
            // the OBO syntax -
            // use the property_value tag
            return trGenericPropertyValue(prop, annVal, qualifiers, frame);
        }
        String value = getValue(annVal, tagString);
        if (!value.trim().isEmpty()) {
            if (tag == OboFormatTag.TAG_ID) {
                if (!frame.getId().equals(value)) {
                    warn("Conflicting id definitions: 1) " + frame.getId()
                            + "  2)" + value);
                    return false;
                }
                return true;
            }
            Clause clause = new Clause(tag);
            if (tag == OboFormatTag.TAG_DATE) {
                try {
                    clause.addValue(OBOFormatConstants.headerDateFormat()
                            .parseObject(value));
                } catch (ParseException e) {
                    error("Could not parse date string: " + value, true);
                    return false;
                }
            } else {
                clause.addValue(value);
            }
            Set<OWLAnnotation> unprocessedQualifiers = new HashSet<>(qualifiers);
            if (tag == OboFormatTag.TAG_DEF) {
                for (OWLAnnotation aan : qualifiers) {
                    String propId = owlObjectToTag(aan.getProperty());
                    if ("xref".equals(propId)) {
                        OWLAnnotationValue v = aan.getValue();
                        String xrefValue;
                        if (v instanceof IRI) {
                            xrefValue = v.toString();
                        } else {
                            xrefValue = ((OWLLiteral) v).getLiteral();
                        }
                        Xref xref = new Xref(xrefValue);
                        clause.addXref(xref);
                        unprocessedQualifiers.remove(aan);
                    }
                }
            } else if (tag == OboFormatTag.TAG_XREF) {
                Xref xref = new Xref(value);
                for (OWLAnnotation annotation : qualifiers) {
                    if (fac.getRDFSLabel().equals(annotation.getProperty())) {
                        OWLAnnotationValue owlAnnotationValue = annotation
                                .getValue();
                        if (owlAnnotationValue instanceof OWLLiteral) {
                            unprocessedQualifiers.remove(annotation);
                            String xrefAnnotation = ((OWLLiteral) owlAnnotationValue)
                                    .getLiteral();
                            xrefAnnotation = xrefAnnotation.trim();
                            if (!xrefAnnotation.isEmpty()) {
                                xref.setAnnotation(xrefAnnotation);
                            }
                        }
                    }
                }
                clause.setValue(xref);
            } else if (tag == OboFormatTag.TAG_EXACT
                    || tag == OboFormatTag.TAG_NARROW
                    || tag == OboFormatTag.TAG_BROAD
                    || tag == OboFormatTag.TAG_RELATED) {
                handleSynonym(qualifiers, tag.getTag(), clause,
                        unprocessedQualifiers);
            } else if (tag == OboFormatTag.TAG_SYNONYM) {
                // This should never happen.
                // All synonyms need to be qualified with a type.
                String synonymType = null;
                handleSynonym(qualifiers, synonymType, clause,
                        unprocessedQualifiers);
            }
            addQualifiers(clause, unprocessedQualifiers);
            // before adding the clause check for redundant clauses
            boolean redundant = false;
            for (Clause frameClause : frame.getClauses()) {
                if (clause.equals(frameClause)) {
                    redundant = handleDuplicateClause(frame, frameClause);
                }
            }
            if (!redundant) {
                frame.addClause(clause);
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    @SuppressWarnings("null")
    protected boolean trGenericPropertyValue(OWLAnnotationProperty prop,
            OWLAnnotationValue annVal, @Nonnull Set<OWLAnnotation> qualifiers,
            @Nonnull Frame frame) {
        // no built-in obo tag for this: use the generic property_value tag
        Clause clause = new Clause(OboFormatTag.TAG_PROPERTY_VALUE.getTag());
        String propId = getIdentifier(prop);
        addQualifiers(clause, qualifiers);
        if (!propId.equals("shorthand")) {
            clause.addValue(propId);
            if (annVal instanceof OWLLiteral) {
                OWLLiteral owlLiteral = (OWLLiteral) annVal;
                clause.addValue(owlLiteral.getLiteral());
                OWLDatatype datatype = owlLiteral.getDatatype();
                IRI dataTypeIri = datatype.getIRI();
                if (!OWL2Datatype.isBuiltIn(dataTypeIri)) {
                    error("Untranslatable axiom due to unknown data type: "
                            + annVal, true);
                    return false;
                }
                if (Namespaces.XSD.inNamespace(dataTypeIri)) {
                    clause.addValue(dataTypeIri.prefixedBy("xsd:"));
                } else if (dataTypeIri.isPlainLiteral()) {
                    clause.addValue("xsd:string");
                } else {
                    clause.addValue(dataTypeIri.toString());
                }
            } else if (annVal instanceof IRI) {
                clause.addValue(getIdentifier((IRI) annVal));
            }
            frame.addClause(clause);
        }
        return true;
    }
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     */
    protected void tr(@Nonnull OWLOntology ontology) {
        Frame f = new Frame(FrameType.HEADER);
        getObodoc().setHeaderFrame(f);
        for (IRI iri : ontology.getDirectImportsDocuments()) {
            Clause c = new Clause(OboFormatTag.TAG_IMPORT.getTag());
            // c.setValue(getOntologyId(iri));
            c.setValue(iri.toString());
            f.addClause(c);
        }
        String id = getOntologyId(ontology);
        Clause c = new Clause(OboFormatTag.TAG_ONTOLOGY.getTag());
        c.setValue(id);
        f.addClause(c);
        String vid = getDataVersion(ontology);
        if (vid != null) {
            Clause c2 = new Clause(OboFormatTag.TAG_DATA_VERSION.getTag());
            c2.setValue(vid);
            f.addClause(c2);
        }
        for (OWLAnnotation ann : ontology.getAnnotations()) {
            OWLAnnotationProperty property = ann.getProperty();
            String tagString = owlObjectToTag(property);
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        }
        boolean isUntranslateable = false;
        List<Clause> equivalenceAxiomClauses = new ArrayList<>();
        String cls2 = getIdentifier(ce2);
        if (cls2 != null) {
            Clause c = new Clause(OboFormatTag.TAG_EQUIVALENT_TO.getTag());
            c.setValue(cls2);
            f.addClause(c);
            addQualifiers(c, ax.getAnnotations());
        } else if (ce2 instanceof OWLObjectUnionOf) {
            List<OWLClassExpression> list2 = ((OWLObjectUnionOf) ce2)
                    .getOperandsAsList();
            for (OWLClassExpression oce : list2) {
                String id = getIdentifier(oce);
                if (id == null) {
                    isUntranslateable = true;
                    error(ax, true);
                    return;
                }
                Clause c = new Clause(OboFormatTag.TAG_UNION_OF.getTag());
                c.setValue(id);
                equivalenceAxiomClauses.add(c);
                addQualifiers(c, ax.getAnnotations());
            }
        } else if (ce2 instanceof OWLObjectIntersectionOf) {
            List<OWLClassExpression> list2 = ((OWLObjectIntersectionOf) ce2)
                    .getOperandsAsList();
            for (OWLClassExpression ce : list2) {
                String r = null;
                cls2 = getIdentifier(ce);
                Integer exact = null; // cardinality
                Integer min = null; // minCardinality
                Integer max = null; // maxCardinality
                Boolean allSome = null; // all_some
                Boolean allOnly = null; // all_only
                if (ce instanceof OWLObjectSomeValuesFrom) {
                    OWLObjectSomeValuesFrom ristriction = (OWLObjectSomeValuesFrom) ce;
                    r = getIdentifier(ristriction.getProperty());
                    cls2 = getIdentifier(ristriction.getFiller());
                } else if (ce instanceof OWLObjectExactCardinality) {
                    OWLObjectExactCardinality card = (OWLObjectExactCardinality) ce;
                    r = getIdentifier(card.getProperty());
                    cls2 = getIdentifier(card.getFiller());
                    exact = card.getCardinality();
                } else if (ce instanceof OWLObjectMinCardinality) {
                    OWLObjectMinCardinality card = (OWLObjectMinCardinality) ce;
                    r = getIdentifier(card.getProperty());
                    cls2 = getIdentifier(card.getFiller());
                    min = card.getCardinality();
                } else if (ce instanceof OWLObjectMaxCardinality) {
                    OWLObjectMaxCardinality card = (OWLObjectMaxCardinality) ce;
                    r = getIdentifier(card.getProperty());
                    cls2 = getIdentifier(card.getFiller());
                    max = card.getCardinality();
                } else if (ce instanceof OWLObjectAllValuesFrom) {
                    OWLObjectAllValuesFrom all = (OWLObjectAllValuesFrom) ce;
                    OWLClassExpression filler = all.getFiller();
                    if (filler instanceof OWLClass) {
                        r = getIdentifier(all.getProperty());
                        cls2 = getIdentifier(filler);
                        allOnly = Boolean.TRUE;
                    } else if (filler instanceof OWLObjectComplementOf) {
                        OWLObjectComplementOf restriction = (OWLObjectComplementOf) filler;
                        r = getIdentifier(all.getProperty());
                        cls2 = getIdentifier(restriction.getOperand());
                        exact = 0;
                    }
                } else if (ce instanceof OWLObjectIntersectionOf) {
                    // either a min-max or a some-all combination
                    Set<OWLClassExpression> operands = ((OWLObjectIntersectionOf) ce)
                            .getOperands();
                    if (operands.size() == 2) {
                        for (OWLClassExpression operand : operands) {
                            if (operand instanceof OWLObjectMinCardinality) {
                                OWLObjectMinCardinality card = (OWLObjectMinCardinality) operand;
                                r = getIdentifier(card.getProperty());
                                cls2 = getIdentifier(card.getFiller());
                                min = card.getCardinality();
                            } else if (operand instanceof OWLObjectMaxCardinality) {
                                OWLObjectMaxCardinality card = (OWLObjectMaxCardinality) operand;
                                r = getIdentifier(card.getProperty());
                                cls2 = getIdentifier(card.getFiller());
                                max = card.getCardinality();
                            } else if (operand instanceof OWLObjectAllValuesFrom) {
                                OWLObjectAllValuesFrom all = (OWLObjectAllValuesFrom) operand;
                                r = getIdentifier(all.getProperty());
                                cls2 = getIdentifier(all.getFiller());
                                allOnly = Boolean.TRUE;
                            } else if (operand instanceof OWLObjectSomeValuesFrom) {
                                OWLObjectSomeValuesFrom all = (OWLObjectSomeValuesFrom) operand;
                                r = getIdentifier(all.getProperty());
                                cls2 = getIdentifier(all.getFiller());
                                allSome = Boolean.TRUE;
                            }
                        }
                    }
                }
                if (cls2 != null) {
                    Clause c = new Clause(
                            OboFormatTag.TAG_INTERSECTION_OF.getTag());
                    if (r != null) {
                        c.addValue(r);
                    }
                    c.addValue(cls2);
                    equivalenceAxiomClauses.add(c);
                    if (exact != null) {
                        String string = exact.toString();
                        assert string != null;
                        c.addQualifierValue(new QualifierValue("cardinality",
                                string));
                    }
                    if (min != null) {
                        String string = min.toString();
                        assert string != null;
                        c.addQualifierValue(new QualifierValue(
                                "minCardinality", string));
                    }
                    if (max != null) {
                        String string = max.toString();
                        assert string != null;
                        c.addQualifierValue(new QualifierValue(
                                "maxCardinality", string));
                    }
                    if (allSome != null) {
                        String string = allSome.toString();
                        assert string != null;
                        c.addQualifierValue(new QualifierValue("all_some",
                                string));
                    }
                    if (allOnly != null) {
                        String string = allOnly.toString();
                        assert string != null;
                        c.addQualifierValue(new QualifierValue("all_only",
                                string));
                    }
                    addQualifiers(c, ax.getAnnotations());
                } else if (!f.getClauses(OboFormatTag.TAG_INTERSECTION_OF)
                        .isEmpty()) {
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Related Classes of org.obolibrary.oboformat.model.Clause

  • org.obolibrary.obo2owl.BFOROXrefTest
  • org.obolibrary.obo2owl.DanglingOwl2OboTest
  • org.obolibrary.obo2owl.DanglingRestrictionOwl2OboTest
  • org.obolibrary.obo2owl.DanglingRoundTripTest
  • org.obolibrary.obo2owl.IDsTest
  • org.obolibrary.obo2owl.ObsoleteTermTest
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  • org.obolibrary.obo2owl.OWLAPIOwl2Obo
  • org.obolibrary.obo2owl.RelationShorthandTest
  • org.obolibrary.obo2owl.RoundTripMultiLineDefTest
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