Examples with Annotation org.sbolstandard.core2.Annotation used on opensource projects

Example 26 with Annotation

use of org.sbolstandard.core2.Annotation in project zipkin by openzipkin.

the class V2SpanConverter method convert.

public V1Span convert(Span value) {
    md.parse(value);
    result.clear().traceId(value.traceId()).parentId(value.parentId()).id(value.id()).name(value.name()).debug(value.debug());
    // Don't report timestamp and duration on shared spans (should be server, but not necessarily)
    if (!Boolean.TRUE.equals(value.shared())) {
        result.timestamp(value.timestampAsLong());
        result.duration(value.durationAsLong());
    }
    boolean beginAnnotation = md.startTs != 0L && md.begin != null;
    boolean endAnnotation = md.endTs != 0L && md.end != null;
    Endpoint ep = value.localEndpoint();
    int annotationCount = value.annotations().size();
    if (beginAnnotation) {
        annotationCount++;
        result.addAnnotation(md.startTs, md.begin, ep);
    }
    for (int i = 0, length = value.annotations().size(); i < length; i++) {
        Annotation a = value.annotations().get(i);
        if (beginAnnotation && a.value().equals(md.begin))
            continue;
        if (endAnnotation && a.value().equals(md.end))
            continue;
        result.addAnnotation(a.timestamp(), a.value(), ep);
    }
    if (endAnnotation) {
        annotationCount++;
        result.addAnnotation(md.endTs, md.end, ep);
    }
    for (Map.Entry<String, String> b : value.tags().entrySet()) {
        result.addBinaryAnnotation(b.getKey(), b.getValue(), ep);
    }
    boolean writeLocalComponent = annotationCount == 0 && ep != null && value.tags().isEmpty();
    boolean hasRemoteEndpoint = md.addr != null && value.remoteEndpoint() != null;
    // write an empty "lc" annotation to avoid missing the localEndpoint in an in-process span
    if (writeLocalComponent)
        result.addBinaryAnnotation("lc", "", ep);
    if (hasRemoteEndpoint)
        result.addBinaryAnnotation(md.addr, value.remoteEndpoint());
    return result.build();
}

Example 27 with Annotation

use of org.sbolstandard.core2.Annotation in project zipkin-gcp by openzipkin.

the class LabelExtractor method extract.

/**
 * Extracts the Stackdriver span labels that are equivalent to the Zipkin Span annotations.
 *
 * @param zipkinSpan The Zipkin Span
 * @return A map of the Stackdriver span labels equivalent to the Zipkin annotations.
 */
Map<String, String> extract(Span zipkinSpan) {
    Map<String, String> result = new LinkedHashMap<>();
    for (Map.Entry<String, String> tag : zipkinSpan.tags().entrySet()) {
        result.put(getLabelName(tag.getKey()), tag.getValue());
    }
    // trace might not show the final destination.
    if (zipkinSpan.localEndpoint() != null && zipkinSpan.kind() == Span.Kind.SERVER) {
        if (zipkinSpan.localEndpoint().ipv4() != null) {
            result.put(getLabelName("endpoint.ipv4"), zipkinSpan.localEndpoint().ipv4());
        }
        if (zipkinSpan.localEndpoint().ipv6() != null) {
            result.put(getLabelName("endpoint.ipv6"), zipkinSpan.localEndpoint().ipv6());
        }
    }
    for (Annotation annotation : zipkinSpan.annotations()) {
        result.put(getLabelName(annotation.value()), formatTimestamp(annotation.timestamp()));
    }
    if (zipkinSpan.localEndpoint() != null && !zipkinSpan.localEndpoint().serviceName().isEmpty()) {
        result.put(kComponentLabelKey, zipkinSpan.localEndpoint().serviceName());
    }
    if (zipkinSpan.parentId() == null) {
        String agentName = System.getProperty("stackdriver.trace.zipkin.agent", "zipkin-java");
        result.put(kAgentLabelKey, agentName);
    }
    return result;
}

Example 28 with Annotation

use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.

the class SBOLReader method parseSequenceAnnotation.

/**
 * @param sequenceAnnotation
 * @param nested
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10203, 10204, 10206, 10208, 10212, 10213,
 * 10512,
 * 10904; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseLocation(NestedDocument)},</li>
 * 		<li>{@link SequenceAnnotation#SequenceAnnotation(URI, Set)},</li>
 * 		<li>{@link SequenceAnnotation#setDisplayId(String)},</li>
 * 		<li>{@link SequenceAnnotation#setVersion(String)},</li>
 * 		<li>{@link SequenceAnnotation#setComponent(URI)},</li>
 * 		<li>{@link SequenceAnnotation#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
private static SequenceAnnotation parseSequenceAnnotation(NestedDocument<QName> sequenceAnnotation, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(sequenceAnnotation.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(sequenceAnnotation.getIdentity()));
    URI persistentIdentity = null;
    Location location = null;
    URI componentURI = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> roles = new HashSet<>();
    Set<Location> locations = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : sequenceAnnotation.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
            if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10203", sequenceAnnotation.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", sequenceAnnotation.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
            if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10206", sequenceAnnotation.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.SequenceAnnotation.roles)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10906", sequenceAnnotation.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Location.Location)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !(nestedDocument.getType().equals(Sbol2Terms.Range.Range) || nestedDocument.getType().equals(Sbol2Terms.Cut.Cut) || nestedDocument.getType().equals(Sbol2Terms.GenericLocation.GenericLocation))) {
                    throw new SBOLValidationException("sbol-10902", sequenceAnnotation.getIdentity());
                }
                location = parseLocation((NestedDocument<QName>) namedProperty.getValue());
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !(nestedDocument.getType().equals(Sbol2Terms.Range.Range) || nestedDocument.getType().equals(Sbol2Terms.Cut.Cut) || nestedDocument.getType().equals(Sbol2Terms.GenericLocation.GenericLocation))) {
                    throw new SBOLValidationException("sbol-10902", sequenceAnnotation.getIdentity());
                }
                location = parseLocation(nested.get(uri));
            }
            locations.add(location);
        } else if (namedProperty.getName().equals(Sbol2Terms.SequenceAnnotation.hasComponent)) {
            if (!(namedProperty.getValue() instanceof Literal) || componentURI != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10904", sequenceAnnotation.getIdentity());
            }
            componentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", sequenceAnnotation.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", sequenceAnnotation.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10208", sequenceAnnotation.getIdentity());
            }
            wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10221", sequenceAnnotation.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    SequenceAnnotation s = new SequenceAnnotation(sequenceAnnotation.getIdentity(), locations);
    if (persistentIdentity != null)
        s.setPersistentIdentity(persistentIdentity);
    if (version != null)
        s.setVersion(version);
    if (displayId != null)
        s.setDisplayId(displayId);
    if (componentURI != null)
        s.setComponent(componentURI);
    if (name != null)
        s.setName(name);
    if (description != null)
        s.setDescription(description);
    s.setWasDerivedFroms(wasDerivedFroms);
    s.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        s.setAnnotations(annotations);
    if (!roles.isEmpty())
        s.setRoles(roles);
    // }
    return s;
}

Example 29 with Annotation

use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.

the class SBOLReader method parseVariableComponent.

// TODO: FIX COMMENTED SECTION
@SuppressWarnings("unchecked")
private static VariableComponent parseVariableComponent(SBOLDocument SBOLDoc, NestedDocument<QName> variableComponent, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    String displayId = null;
    String name = null;
    String description = null;
    URI persistentIdentity = null;
    String version = null;
    List<Annotation> annotations = new ArrayList<>();
    URI variable = null;
    OperatorType operator = null;
    HashSet<URI> variants = new HashSet<>();
    HashSet<URI> variantCollections = new HashSet<>();
    HashSet<URI> variantDerivations = new HashSet<>();
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    for (NamedProperty<QName> namedProperty : variableComponent.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
            if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10203", variableComponent.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
            if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10206", variableComponent.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", variableComponent.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", variableComponent.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", variableComponent.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasVariable)) {
            if (!(namedProperty.getValue() instanceof Literal) || variable != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-13004", variableComponent.getIdentity());
            }
            variable = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasVariants)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-13007", variableComponent.getIdentity());
                }
                variants.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
                    ComponentDefinition cd = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    variants.add(cd.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-13007", variableComponent.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-13007", variableComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasVariantCollections)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-13009", variableComponent.getIdentity());
                }
                variantCollections.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Collection.Collection)) {
                    Collection cd = parseCollection(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    variantCollections.add(cd.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-13009", variableComponent.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-13009", variableComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasVariantDerivations)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-13013", variableComponent.getIdentity());
                }
                variantDerivations.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Collection.Collection)) {
                    CombinatorialDerivation cd = parseCombinatorialDerivation(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    variantDerivations.add(cd.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-13013", variableComponent.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-13013", variableComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasOperator)) {
            if (!(namedProperty.getValue() instanceof Literal) || operator != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-13002", variableComponent.getIdentity());
            }
            String operatorTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            try {
                operator = OperatorType.convertToOperatorType(URI.create(operatorTypeStr));
            } catch (SBOLValidationException e) {
                throw new SBOLValidationException("sbol-13003", variableComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10208", variableComponent.getIdentity());
            }
            wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10221", variableComponent.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    VariableComponent c = new VariableComponent(variableComponent.getIdentity(), operator, variable);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (version != null)
        c.setVersion(version);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (!variants.isEmpty())
        c.setVariants(variants);
    if (!variantCollections.isEmpty())
        c.setVariantCollections(variantCollections);
    if (!variantDerivations.isEmpty())
        c.setVariantDerivations(variantDerivations);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    return c;
}

Example 30 with Annotation

use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.

the class SBOLReader method parseDnaComponentV1.

/**
 * @param SBOLDoc
 * @param componentDef
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>if an SBOL validation rule violation occurred in any of the following constructors or methods:
 * 	<ul>
 * 		<li>{@link URIcompliance#createCompliantURI(String, String, String, String, boolean)},</li>
 * 		<li>{@link #parseSequenceAnnotationV1(SBOLDocument, NestedDocument, List, String, int, Set)},</li>
 * 		<li>{@link URIcompliance#createCompliantURI(String, String, String)},</li>
 * 		<li>{@link Component#Component(URI, AccessType, URI)},</li>
 * 		<li>{@link Component#setDisplayId(String)}, </li>
 * 		<li>{@link Component#setVersion(String)}</li>
 * 		<li>{@link SequenceAnnotation#setComponent(URI)}, </li>
 * 		<li>{@link #parseDnaSequenceV1(SBOLDocument, IdentifiableDocument)}</li>
 * 		<li>{@link RestrictionType#convertToURI(RestrictionType)},</li>
 * 		<li>{@link SequenceConstraint#SequenceConstraint(URI, URI, URI, URI)},</li>
 * 		<li>{@link SequenceConstraint#setDisplayId(String)},</li>
 * 		<li>{@link SequenceConstraint#setVersion(String)},</li>
 * 		<li>{@link ComponentDefinition#ComponentDefinition(URI, Set)},</li>
 * 		<li>{@link ComponentDefinition#setVersion(String)},</li>
 * 		<li>{@link ComponentDefinition#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)},</li>
 * 		<li>{@link ComponentDefinition#setComponents(Set)}</li>
 * 		<li>{@link ComponentDefinition#setSequenceConstraints(Set)}</li>
 * 		<li>{@link ComponentDefinition#addSequence(URI)}</li>
 * 		<li>{@link ComponentDefinition#addSequenceAnnotation(SequenceAnnotation)},</li>
 * 		<li>{@link SBOLDocument#addComponentDefinition(ComponentDefinition)}, or</li>
 * 		<li>{@link ComponentDefinition#copy(String, String, String)}; or</li>
 * 	</ul>
 * </li>
 * <li>the following SBOL validation rule was violated: 10202.</li>
 * </ul>
 * @throws SBOLConversionException
 */
private static ComponentDefinition parseDnaComponentV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> componentDef) throws SBOLValidationException, SBOLConversionException {
    String displayId = null;
    String name = null;
    String description = null;
    URI seq_identity = null;
    Set<URI> roles = new HashSet<>();
    URI identity = componentDef.getIdentity();
    String persIdentity = componentDef.getIdentity().toString();
    List<Annotation> annotations = new ArrayList<>();
    List<SequenceAnnotation> sequenceAnnotations = new ArrayList<>();
    Set<String> instantiatedComponents = new HashSet<>();
    Set<Component> components = new HashSet<>();
    Set<SequenceConstraint> sequenceConstraints = new HashSet<>();
    List<SBOLPair> precedePairs = new ArrayList<>();
    Map<URI, URI> componentDefMap = new HashMap<>();
    Set<URI> type = new HashSet<>();
    type.add(ComponentDefinition.DNA);
    type.add(SequenceOntology.LINEAR);
    int component_num = 0;
    int sa_num = 0;
    if (URIPrefix != null) {
        displayId = URIcompliance.findDisplayId(componentDef.getIdentity().toString());
        identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
        persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
    }
    for (NamedProperty<QName> namedProperty : componentDef.getProperties()) {
        if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", componentDef.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            displayId = URIcompliance.fixDisplayId(displayId);
            if (URIPrefix != null) {
                persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
                identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
            }
        } else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.name)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", componentDef.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", componentDef.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.type)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10507", componentDef.getIdentity());
            }
            URI convertedSO = SequenceOntology.convertSeqOntologyV1(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            roles.add(convertedSO);
        } else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.annotations)) {
            if (namedProperty.getValue() instanceof IdentifiableDocument) {
                SequenceAnnotation sa = parseSequenceAnnotationV1(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), precedePairs, persIdentity, ++sa_num, instantiatedComponents);
                sequenceAnnotations.add(sa);
                URI component_identity = createCompliantURI(persIdentity, "component" + component_num, version);
                URI component_persIdentity = createCompliantURI(persIdentity, "component" + component_num, "");
                String component_displayId = "component" + component_num;
                AccessType access = AccessType.PUBLIC;
                URI instantiatedComponent = sa.getComponentURI();
                ComponentDefinition instantiatedDef = SBOLDoc.getComponentDefinition(instantiatedComponent);
                if (compliant && instantiatedDef != null && instantiatedDef.isSetDisplayId() && !instantiatedComponents.contains(instantiatedDef.getDisplayId())) {
                    component_identity = createCompliantURI(persIdentity, instantiatedDef.getDisplayId(), version);
                    component_persIdentity = createCompliantURI(persIdentity, instantiatedDef.getDisplayId(), "");
                    component_displayId = instantiatedDef.getDisplayId();
                    instantiatedComponents.add(instantiatedDef.getDisplayId());
                } else {
                    component_num++;
                }
                Component component = new Component(component_identity, access, instantiatedComponent);
                if (!persIdentity.equals("")) {
                    component.setPersistentIdentity(component_persIdentity);
                    component.setDisplayId(component_displayId);
                    component.setVersion(version);
                }
                components.add(component);
                URI originalURI = ((NestedDocument<QName>) namedProperty.getValue()).getIdentity();
                componentDefMap.put(originalURI, component_identity);
                sa.setComponent(component_identity);
            } else {
                throw new SBOLConversionException("SequenceAnnotation must be nested in SBOL1.");
            }
        } else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.dnaSequence)) {
            if (seq_identity != null) {
                throw new SBOLValidationException("sbol-10512", componentDef.getIdentity());
            }
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-10512", componentDef.getIdentity());
                }
                seq_identity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } else {
                seq_identity = parseDnaSequenceV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity();
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    if (roles.isEmpty())
        roles.add(SequenceOntology.ENGINEERED_REGION);
    int sc_number = 0;
    for (SBOLPair pair : precedePairs) {
        URI sc_identity = createCompliantURI(persIdentity, "sequenceConstraint" + ++sc_number, version);
        URI restrictionURI = RestrictionType.convertToURI(RestrictionType.PRECEDES);
        // RestrictionType restriction = RestrictionType.convertToRestrictionType(restrictionURI);
        URI subject = null;
        URI object = null;
        for (URI key : componentDefMap.keySet()) {
            if (pair.getLeft().equals(key)) {
                subject = componentDefMap.get(key);
            } else if (pair.getRight().equals(key)) {
                object = componentDefMap.get(key);
            }
        }
        SequenceConstraint sc = null;
        if (compliant && !persIdentity.equals("")) {
            String subjectId = URIcompliance.extractDisplayId(subject);
            String objectId = URIcompliance.extractDisplayId(object);
            sc_identity = createCompliantURI(persIdentity, subjectId + "_cons_" + objectId, version);
            sc = new SequenceConstraint(sc_identity, restrictionURI, subject, object);
            sc.setPersistentIdentity(createCompliantURI(persIdentity, subjectId + "_cons_" + objectId, ""));
            sc.setDisplayId(subjectId + "_cons_" + objectId);
            sc.setVersion(version);
        } else {
            sc = new SequenceConstraint(sc_identity, restrictionURI, subject, object);
        }
        sequenceConstraints.add(sc);
    }
    ComponentDefinition c = new ComponentDefinition(identity, type);
    if (!persIdentity.equals("")) {
        c.setPersistentIdentity(URI.create(persIdentity));
        c.setVersion(version);
    }
    if (roles != null)
        c.setRoles(roles);
    if (identity != componentDef.getIdentity())
        c.addWasDerivedFrom(componentDef.getIdentity());
    if (displayId != null)
        c.setDisplayId(displayId);
    if (name != null && !name.isEmpty())
        c.setName(name);
    if (description != null && !description.isEmpty())
        c.setDescription(description);
    if (seq_identity != null)
        c.addSequence(seq_identity);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    if (!components.isEmpty())
        c.setComponents(components);
    if (!sequenceAnnotations.isEmpty()) {
        for (SequenceAnnotation sa : sequenceAnnotations) {
            if (!dropObjectsWithDuplicateURIs || c.getSequenceAnnotation(sa.getIdentity()) == null) {
                c.addSequenceAnnotation(sa);
            }
        }
    }
    if (!sequenceConstraints.isEmpty())
        c.setSequenceConstraints(sequenceConstraints);
    ComponentDefinition oldC = SBOLDoc.getComponentDefinition(identity);
    if (oldC == null) {
        SBOLDoc.addComponentDefinition(c);
    } else if (c.getWasDerivedFroms().size() > 0 && oldC.getWasDerivedFroms().size() > 0 && !c.getWasDerivedFroms().equals(oldC.getWasDerivedFroms())) {
        URI wasDerivedFrom = (URI) c.getWasDerivedFroms().toArray()[0];
        Set<TopLevel> topLevels = SBOLDoc.getByWasDerivedFrom(wasDerivedFrom);
        for (TopLevel topLevel : topLevels) {
            if (topLevel instanceof ComponentDefinition) {
                return (ComponentDefinition) topLevel;
            }
        }
        do {
            displayId = displayId + "_";
            identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
            persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
        } while (SBOLDoc.getComponentDefinition(identity) != null);
        c = c.copy(URIPrefix, displayId, version);
        if (identity != componentDef.getIdentity()) {
            c.clearWasDerivedFroms();
            c.addWasDerivedFrom(componentDef.getIdentity());
        }
        SBOLDoc.addComponentDefinition(c);
    } else if (dropObjectsWithDuplicateURIs) {
        return oldC;
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}