Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.Clause.addValue()

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                }
            }
            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);
            }
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            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;
                }
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                    && 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;
                }
            }
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                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;
                }
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                } 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());
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        // 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();
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        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);
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                    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());
                }
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                    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));
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                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);
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