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

Example 16 with Sequence

use of org.sbolstandard.core2.Sequence in project OpenAM by OpenRock.

the class SecureLogHelperJSSImpl method AddToSecretStore.

/**
     * Adds  secret information to the secret Storage.
     * @param cryptoMaterial : The data to be added
     */
private SEQUENCE AddToSecretStore(byte[] cryptoMaterial, String DataType) throws Exception {
    SEQUENCE encSafeContents = new SEQUENCE();
    ASN1Value data = new OCTET_STRING(cryptoMaterial);
    byte[] localKeyId = createLocalKeyId(cryptoMaterial);
    SET keyAttrs = createBagAttrs(DataType, localKeyId);
    // attributes: user friendly name, Local Key ID
    SafeBag keyBag = new SafeBag(SafeBag.SECRET_BAG, data, keyAttrs);
    encSafeContents.addElement(keyBag);
    return encSafeContents;
}

Example 17 with Sequence

use of org.sbolstandard.core2.Sequence in project OpenAM by OpenRock.

the class SecureLogHelperJSSImpl method readFromSecretStore.

/**
     * Returns matched secret data from from the secret Storage. 
     * At a time there are only 3 things in logger's secure store file 
     *    - initialkey, currentkey and current signature
     * In the verifier secure store file there is just the initial key of the
     * logger and the currentKey
     * @param filename file for secret storage
     * @param dataType The kind of data to be read, whether it is a
     *                 signature or a key
     * @param password password for the file
     * @return secure data that is matched with dataType
     * @throws Exception if it fails to read secret data from secret store
     */
byte[] readFromSecretStore(String filename, String dataType, AMPassword password) throws Exception {
    // open input file for reading
    FileInputStream infile = null;
    infile = new FileInputStream(filename);
    // Decode the P12 file
    PFX.Template pfxt = new PFX.Template();
    PFX pfx = (PFX) pfxt.decode(new BufferedInputStream(infile, 2048));
    // Verify the MAC on the PFX.  This is important to be sure
    // it hasn't been tampered with.
    StringBuffer reason = new StringBuffer();
    MessageDigest md = MessageDigest.getInstance("SHA");
    Password jssPasswd = new Password(new String(md.digest(password.getByteCopy()), "UTF-8").toCharArray());
    md.reset();
    if (!pfx.verifyAuthSafes(jssPasswd, reason)) {
        throw new Exception("AuthSafes failed to verify because: " + reason.toString());
    }
    AuthenticatedSafes authSafes = pfx.getAuthSafes();
    SEQUENCE safeContentsSequence = authSafes.getSequence();
    byte[] cryptoData = null;
    // Loop over contents of the authenticated safes
    for (int i = 0; i < safeContentsSequence.size(); i++) {
        // The safeContents may or may not be encrypted.  We always send
        // the password in.  It will get used if it is needed.  If the
        // decryption of the safeContents fails for some reason (like
        // a bad password), then this method will throw an exception
        SEQUENCE safeContents = authSafes.getSafeContentsAt(jssPasswd, i);
        SafeBag safeBag = null;
        ASN1Value val = null;
        // Go through all the bags in this SafeContents
        for (int j = 0; j < safeContents.size(); j++) {
            safeBag = (SafeBag) safeContents.elementAt(j);
            // look for bag attributes and then choose the key
            SET attribs = safeBag.getBagAttributes();
            if (attribs == null) {
                Debug.error("Bag has no attributes");
            } else {
                for (int b = 0; b < attribs.size(); b++) {
                    Attribute a = (Attribute) attribs.elementAt(b);
                    if (a.getType().equals(SafeBag.FRIENDLY_NAME)) {
                        // the friendly name attribute is a nickname
                        BMPString bs = (BMPString) ((ANY) a.getValues().elementAt(0)).decodeWith(BMPString.getTemplate());
                        if (dataType.equals(bs.toString())) {
                            // look at the contents of the bag
                            val = safeBag.getInterpretedBagContent();
                            break;
                        }
                    }
                }
            }
        }
        if (val instanceof ANY)
            cryptoData = ((ANY) val).getContents();
    }
    // Close the file
    infile.close();
    return cryptoData;
}

Example 18 with Sequence

use of org.sbolstandard.core2.Sequence in project OpenAM by OpenRock.

the class SecureLogHelperJSSImpl method writeToSecretStore.

/**
     * Writes to the secret Storage. If the data to be written is a key, then
     * writes the older signature also. If it is a signature then writes the
     * older key also
     * @param cryptoMaterial The data to be written to the secret storage
     * @param filename The file for secret storage
     * @param password The password for the file
     * @param dataType The kind of cryptoMaterial, whether it is a signature
     * or a key
     * @throws Exception if it fails to write secret data from secret store
     */
void writeToSecretStore(byte[] cryptoMaterial, String filename, AMPassword password, String dataType) throws Exception {
    byte[] oldDataFromSecretStorage = null;
    String oldDataType = null;
    MessageDigest md = MessageDigest.getInstance("SHA");
    Password jssPasswd = new Password(new String(md.digest(password.getByteCopy()), "UTF-8").toCharArray());
    md.reset();
    // Do this only when the logger's file is being used
    if (filename.equals(logFileName) && loggerInitialized) {
        // current signature in the PKCS12 file
        if (dataType.equals(currentSignature)) {
            oldDataFromSecretStorage = readFromSecretStore(logFileName, currentKey, password);
            oldDataType = currentKey;
        } else if (dataType.equals(currentKey)) {
            // need to read the currentSignature 
            // for the same reason as above
            oldDataFromSecretStorage = readFromSecretStore(logFileName, currentSignature, password);
            oldDataType = currentSignature;
        }
    }
    // Start building the new contents by adding the older content first
    AuthenticatedSafes newAuthSafes = new AuthenticatedSafes();
    if (oldDataFromSecretStorage != null) {
        SEQUENCE oldSafeContents = AddToSecretStore(oldDataFromSecretStorage, oldDataType);
        // Add the old contents to the existing safe
        newAuthSafes.addEncryptedSafeContents(PBEAlgorithm.PBE_SHA1_DES3_CBC, jssPasswd, null, AuthenticatedSafes.DEFAULT_ITERATIONS, oldSafeContents);
    }
    // not being added for the first time
    if ((filename.equals(logFileName)) && !dataType.equals(initialKey) && loggerInitialized) {
        byte[] key = readFromSecretStore(filename, initialKey, password);
        if (key != null) {
            SEQUENCE initialKeySafeContents = AddToSecretStore(key, initialKey);
            newAuthSafes.addEncryptedSafeContents(PBEAlgorithm.PBE_SHA1_DES3_CBC, jssPasswd, null, AuthenticatedSafes.DEFAULT_ITERATIONS, initialKeySafeContents);
        }
    }
    if ((filename.equals(verifierFileName)) && !dataType.equals(initialKey) && verifierInitialized) {
        byte[] key = readFromSecretStore(filename, initialKey, password);
        if (key != null) {
            SEQUENCE initialKeySafeContents = AddToSecretStore(key, initialKey);
            newAuthSafes.addEncryptedSafeContents(PBEAlgorithm.PBE_SHA1_DES3_CBC, jssPasswd, null, AuthenticatedSafes.DEFAULT_ITERATIONS, initialKeySafeContents);
        }
    }
    // Add the new contents
    SEQUENCE encSafeContents = AddToSecretStore(cryptoMaterial, dataType);
    // Add the new contents to the existing safe
    newAuthSafes.addEncryptedSafeContents(PBEAlgorithm.PBE_SHA1_DES3_CBC, jssPasswd, null, AuthenticatedSafes.DEFAULT_ITERATIONS, encSafeContents);
    PFX newpfx = new PFX(newAuthSafes);
    newpfx.computeMacData(jssPasswd, null, 5);
    // write the new PFX out to the logger
    FileOutputStream fos = new FileOutputStream(filename);
    newpfx.encode(fos);
    fos.close();
}

Example 19 with Sequence

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

the class SBOLReader method parseSequence.

/**
 * @param SBOLDoc
 * @param topLevel
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10202, 10203, 10204, 10206, 10208, 10212, 10213, 10402, 10403, ; or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Sequence#Sequence(URI, String, URI)}, </li>
 * 		<li>{@link Sequence#setDisplayId(String)}, </li>
 * 		<li>{@link Sequence#setVersion(String)}, </li>
 * 		<li>{@link Sequence#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addSequence(Sequence)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static Sequence parseSequence(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(topLevel.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(topLevel.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    String elements = null;
    URI encoding = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : topLevel.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", topLevel.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", topLevel.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", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Sequence.elements)) {
            if (!(namedProperty.getValue() instanceof Literal) || elements != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10402", topLevel.getIdentity());
            }
            elements = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Sequence.encoding)) {
            if (!(namedProperty.getValue() instanceof Literal) || encoding != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10403", topLevel.getIdentity());
            }
            encoding = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            if (encoding.toString().equals("http://dx.doi.org/10.1021/bi00822a023")) {
                encoding = Sequence.IUPAC_DNA;
            }
        } 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", topLevel.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", topLevel.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", topLevel.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", topLevel.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.TopLevel.hasAttachment)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
                attachments.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Attachment.Attachment)) {
                    Attachment attachment = parseAttachment(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    attachments.add(attachment.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // Sequence sequence = SBOLDoc.createSequence(topLevel.getIdentity(), elements, encoding);
    Sequence sequence = new Sequence(topLevel.getIdentity(), elements, encoding);
    if (persistentIdentity != null)
        sequence.setPersistentIdentity(persistentIdentity);
    if (version != null)
        sequence.setVersion(version);
    if (displayId != null)
        sequence.setDisplayId(displayId);
    if (name != null)
        sequence.setName(name);
    if (description != null)
        sequence.setDescription(description);
    sequence.setWasDerivedFroms(wasDerivedFroms);
    sequence.setWasGeneratedBys(wasGeneratedBys);
    sequence.setAttachments(attachments);
    if (!annotations.isEmpty())
        sequence.setAnnotations(annotations);
    Sequence oldS = SBOLDoc.getSequence(topLevel.getIdentity());
    if (oldS == null) {
        SBOLDoc.addSequence(sequence);
    } else {
        if (!sequence.equals(oldS)) {
            throw new SBOLValidationException("sbol-10202", sequence);
        }
    }
    return sequence;
}

Example 20 with Sequence

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

the class SBOLReader method parseComponentDefinition.

/**
 * @param SBOLDoc
 * @param topLevel
 * @param nested
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10202, 10203, 10204, 10206, 10208, 10212, 10213, 10502, 10507, 10512, or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseComponent(NestedDocument, Map)},</li>
 * 		<li>{@link #parseSequenceAnnotation(NestedDocument, Map)},</li>
 * 		<li>{@link ComponentDefinition#ComponentDefinition(URI, Set)}, </li>
 * 		<li>{@link ComponentDefinition#setDisplayId(String)}, </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#setSequenceAnnotations(Set)},</li>
 * 		<li>{@link ComponentDefinition#setSequenceConstraints(Set)}, or</li>
 * 		<li>{@link SBOLDocument#addComponentDefinition(ComponentDefinition)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static ComponentDefinition parseComponentDefinition(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(topLevel.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(topLevel.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    Set<URI> type = new HashSet<>();
    Set<URI> roles = new HashSet<>();
    Set<URI> sequences = new HashSet<>();
    Set<Component> components = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    Set<SequenceAnnotation> sequenceAnnotations = new HashSet<>();
    Set<SequenceConstraint> sequenceConstraints = new HashSet<>();
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        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", topLevel.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else 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", topLevel.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", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.type)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10502", topLevel.getIdentity());
            }
            type.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.roles)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10507", topLevel.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasComponent) || namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSubComponent)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Component.Component)) {
                    throw new SBOLValidationException("sbol-10519", topLevel.getIdentity());
                }
                components.add(parseComponent(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), nested));
            } 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.Component.Component)) {
                    throw new SBOLValidationException("sbol-10519", topLevel.getIdentity());
                }
                components.add(parseComponent(SBOLDoc, nested.get(uri), nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequence)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
                }
                sequences.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Sequence.Sequence)) {
                    Sequence sequence = parseSequence(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    sequences.add(sequence.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceAnnotations)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceAnnotation.SequenceAnnotation)) {
                    throw new SBOLValidationException("sbol-10521", topLevel.getIdentity());
                }
                sequenceAnnotations.add(parseSequenceAnnotation(((NestedDocument<QName>) namedProperty.getValue()), nested));
            } 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.SequenceAnnotation.SequenceAnnotation)) {
                    throw new SBOLValidationException("sbol-10521", topLevel.getIdentity());
                }
                sequenceAnnotations.add(parseSequenceAnnotation(nested.get(uri), nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceConstraints)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceConstraint.SequenceConstraint)) {
                    throw new SBOLValidationException("sbol-10524", topLevel.getIdentity());
                }
                sequenceConstraints.add(parseSequenceConstraint(((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.SequenceConstraint.SequenceConstraint)) {
                    throw new SBOLValidationException("sbol-10524", topLevel.getIdentity());
                }
                sequenceConstraints.add(parseSequenceConstraint(nested.get(uri)));
            }
        } 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", topLevel.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", topLevel.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", topLevel.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", topLevel.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.TopLevel.hasAttachment)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
                attachments.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Attachment.Attachment)) {
                    Attachment attachment = parseAttachment(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    attachments.add(attachment.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // ComponentDefinition c = SBOLDoc.createComponentDefinition(topLevel.getIdentity(), type, roles);
    // c.setPersistentIdentity(topLevel.getOptionalUriPropertyValue(Sbol2Terms.Identified.persistentIdentity));
    // ComponentDefinition c = SBOLDoc.createComponentDefinition(topLevel.getIdentity(), type);
    ComponentDefinition c = new ComponentDefinition(topLevel.getIdentity(), type);
    if (roles != null)
        c.setRoles(roles);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (!sequences.isEmpty())
        c.setSequences(sequences);
    if (!components.isEmpty())
        c.setComponents(components);
    if (!sequenceAnnotations.isEmpty())
        c.setSequenceAnnotations(sequenceAnnotations);
    if (!sequenceConstraints.isEmpty())
        c.setSequenceConstraints(sequenceConstraints);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    if (version != null)
        c.setVersion(version);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    c.setAttachments(attachments);
    ComponentDefinition oldC = SBOLDoc.getComponentDefinition(topLevel.getIdentity());
    if (oldC == null) {
        SBOLDoc.addComponentDefinition(c);
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}