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

Example 51 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException in project ice by JBEI.

the class SBOL2Visitor method visit.

public void visit(Sequence sequence) throws SBOLValidationException, URISyntaxException {
    // ice data model conflates the sequence and component
    Entry entry = sequence.getEntry();
    // Set required properties
    String partId = entry.getPartNumber();
    String dcUri = sequence.getComponentUri();
    if (dcUri == null) {
        componentDefinition = doc.createComponentDefinition(uriString, partId, "1", ComponentDefinition.DNA);
    } else {
        String displayId = StringUtils.isBlank(sequence.getIdentifier()) ? displayIdFromUri(dcUri) : sequence.getIdentifier();
        String prefix = prefixFromUri(dcUri);
        componentDefinition = doc.createComponentDefinition(prefix, displayId, "1", ComponentDefinition.DNA);
    }
    componentDefinition.setName(entry.getName());
    componentDefinition.setDescription(entry.getShortDescription());
    org.sbolstandard.core2.Sequence dnaSequence;
    String dsUri = sequence.getUri();
    if (dsUri == null || dsUri.isEmpty()) {
        dsUri = "sequence_" + sequence.getFwdHash().replaceAll("[\\s\\-()]", "");
        dnaSequence = doc.createSequence(uriString, dsUri, "1", sequence.getSequence(), org.sbolstandard.core2.Sequence.IUPAC_DNA);
    } else {
        dnaSequence = doc.createSequence(prefixFromUri(dsUri), displayIdFromUri(dsUri), "1", sequence.getSequence(), org.sbolstandard.core2.Sequence.IUPAC_DNA);
    }
    dnaSequence.setElements(sequence.getSequence());
    componentDefinition.addSequence(dnaSequence);
    List<SequenceFeature> features = new ArrayList<>(sequence.getSequenceFeatures());
    Collections.sort(features, new SequenceFeatureComparator());
    for (SequenceFeature feature : features) {
        visit(feature);
    }
    componentDefinition.createAnnotation(new QName(ICE_NS, "id", ICE_PREFIX), entry.getId());
    if (entry.getRecordId() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "recordId", ICE_PREFIX), entry.getRecordId());
    if (entry.getVersionId() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "versionId", ICE_PREFIX), entry.getVersionId());
    if (entry.getRecordType() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "recordType", ICE_PREFIX), entry.getRecordType());
    if (entry.getOwner() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "owner", ICE_PREFIX), entry.getOwner());
    if (entry.getOwnerEmail() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "ownerEmail", ICE_PREFIX), entry.getOwnerEmail());
    if (entry.getCreator() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "creator", ICE_PREFIX), entry.getCreator());
    if (entry.getCreatorEmail() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "creatorEmail", ICE_PREFIX), entry.getCreatorEmail());
    if (entry.getStatus() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "status", ICE_PREFIX), entry.getStatus());
    if (entry.getAlias() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "alias", ICE_PREFIX), entry.getAlias());
    for (SelectionMarker selectionMarker : entry.getSelectionMarkers()) {
        componentDefinition.createAnnotation(new QName(ICE_NS, "selectionMarker", ICE_PREFIX), selectionMarker.getName());
    }
    if (entry.getLinks() != null) {
        for (Link link : entry.getLinks()) {
            componentDefinition.createAnnotation(new QName(ICE_NS, link.getLink(), ICE_PREFIX), link.getUrl());
        }
    }
    if (entry.getKeywords() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "keywords", ICE_PREFIX), entry.getKeywords());
    if (entry.getShortDescription() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "shortDescription", ICE_PREFIX), entry.getShortDescription());
    if (entry.getLongDescription() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "longDescription", ICE_PREFIX), entry.getLongDescription());
    if (entry.getLongDescriptionType() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "longDescriptionType", ICE_PREFIX), entry.getLongDescriptionType());
    if (entry.getReferences() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "references", ICE_PREFIX), entry.getReferences());
    if (entry.getCreationTime() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "creationTime", ICE_PREFIX), entry.getCreationTime().toString());
    if (entry.getModificationTime() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "modificationTime", ICE_PREFIX), entry.getModificationTime().toString());
    if (entry.getBioSafetyLevel() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "bioSafetyLevel", ICE_PREFIX), entry.getBioSafetyLevel());
    if (entry.getIntellectualProperty() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "intellectualProperty", ICE_PREFIX), entry.getIntellectualProperty());
    if (entry.getVisibility() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "visibility", ICE_PREFIX), entry.getVisibility());
    if (entry.getParameters() != null) {
        for (Parameter parameter : entry.getParameters()) {
            componentDefinition.createAnnotation(new QName(ICE_NS, parameter.getKey(), ICE_PREFIX), parameter.getValue());
        }
    }
    if (entry.getFundingSource() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "fundingSource", ICE_PREFIX), entry.getFundingSource());
    if (entry.getPrincipalInvestigator() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "principalInvestigator", ICE_PREFIX), entry.getPrincipalInvestigator());
// TODO: samples
// TODO: attachments
}

Example 52 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException in project ice by JBEI.

the class SBOL2Formatter method format.

@Override
public void format(Sequence sequence, OutputStream outputStream) throws FormatterException, IOException {
    SBOLDocument doc = new SBOLDocument();
    try {
        SBOL2Visitor visitor = new SBOL2Visitor(doc);
        visitor.visit(sequence);
        doc.write(outputStream);
    } catch (SBOLValidationException | SBOLConversionException | URISyntaxException e) {
        throw new FormatterException(e);
    }
}

Example 53 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException 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 54 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException 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 55 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException 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;
}