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

Example 36 with Annotation

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

the class SBOLReader method parseModel.

/**
 * @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, 10502, 10504, 10508; or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Model#Model(URI, URI, URI, URI)}, </li>
 * 		<li>{@link Model#setDisplayId(String)}, </li>
 * 		<li>{@link Model#setVersion(String)}, </li>
 * 		<li>{@link Model#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addModel(Model)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static Model parseModel(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;
    URI source = null;
    URI language = null;
    URI framework = 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.Model.source)) {
            if (!(namedProperty.getValue() instanceof Literal) || source != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10502", topLevel.getIdentity());
            }
            source = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Model.language)) {
            if (!(namedProperty.getValue() instanceof Literal) || language != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10504", topLevel.getIdentity());
            }
            language = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Model.framework)) {
            if (!(namedProperty.getValue() instanceof Literal) || framework != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10508", topLevel.getIdentity());
            }
            framework = 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", 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));
        }
    }
    // Model m = SBOLDoc.createModel(topLevel.getIdentity(), source, language, framework);
    Model m = new Model(topLevel.getIdentity(), source, language, framework);
    if (persistentIdentity != null)
        m.setPersistentIdentity(persistentIdentity);
    if (version != null)
        m.setVersion(version);
    if (displayId != null)
        m.setDisplayId(displayId);
    if (name != null)
        m.setName(name);
    if (description != null)
        m.setDescription(description);
    m.setWasDerivedFroms(wasDerivedFroms);
    m.setWasGeneratedBys(wasGeneratedBys);
    m.setAttachments(attachments);
    if (!annotations.isEmpty())
        m.setAnnotations(annotations);
    Model oldM = SBOLDoc.getModel(topLevel.getIdentity());
    if (oldM == null) {
        SBOLDoc.addModel(m);
    } else {
        if (!m.equals(oldM)) {
            throw new SBOLValidationException("sbol-10202", m);
        }
    }
    return m;
}

Example 37 with Annotation

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

the class SBOLReader method parseUsage.

private static Usage parseUsage(SBOLDocument SBOLDoc, NestedDocument<QName> usage, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    String displayId = null;
    String name = null;
    String description = null;
    URI persistentIdentity = null;
    String version = null;
    URI entityURI = null;
    Set<URI> roles = new HashSet<>();
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : usage.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", usage.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", usage.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", usage.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", usage.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", usage.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", usage.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", usage.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Usage.role)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-12502", usage.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Usage.entity)) {
            if (!(namedProperty.getValue() instanceof Literal) || entityURI != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-12502", usage.getIdentity());
            }
            entityURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Usage u = new Usage(usage.getIdentity(), entityURI);
    if (persistentIdentity != null)
        u.setPersistentIdentity(persistentIdentity);
    if (version != null)
        u.setVersion(version);
    if (displayId != null)
        u.setDisplayId(displayId);
    if (name != null)
        u.setName(name);
    if (description != null)
        u.setDescription(description);
    u.setWasDerivedFroms(wasDerivedFroms);
    u.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        u.setAnnotations(annotations);
    if (!roles.isEmpty())
        u.setRoles(roles);
    return u;
}

Example 38 with Annotation

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

the class SBOLReader method parseRange.

/**
 * @param typeRange
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10201, 10203, 10204, 10206, 10208, 10212, 10213, 11002, 11102, 11103; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Range#Range(URI, int, int)},</li>
 * 		<li>{@link Range#setDisplayId(String)},</li>
 * 		<li>{@link Range#setVersion(String)},</li>
 * 		<li>{@link Range#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
private static Location parseRange(NestedDocument<QName> typeRange) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(typeRange.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(typeRange.getIdentity()));
    URI persistentIdentity = null;
    Integer start = null;
    Integer end = null;
    URI orientation = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : typeRange.getProperties()) {
        String temp;
        if (namedProperty.getName().equals(Sbol2Terms.Range.start)) {
            if (!(namedProperty.getValue() instanceof Literal) || start != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11102", typeRange.getIdentity());
            }
            temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            // start = Integer.parseInt(temp);
            try {
                start = Integer.parseInt(temp);
            } catch (NumberFormatException e) {
                throw new SBOLValidationException("sbol-11102", typeRange.getIdentity());
            }
        } 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", typeRange.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", typeRange.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", typeRange.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", typeRange.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Range.end)) {
            if (!(namedProperty.getValue() instanceof Literal) || end != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11103", typeRange.getIdentity());
            }
            temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            // end  = Integer.parseInt(temp);
            try {
                end = Integer.parseInt(temp);
            } catch (NumberFormatException e) {
                throw new SBOLValidationException("sbol-11103", typeRange.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Range.orientation)) {
            if (!(namedProperty.getValue() instanceof Literal) || orientation != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11002", typeRange.getIdentity());
            }
            orientation = 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", typeRange.getIdentity());
            }
            version = ((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", typeRange.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", typeRange.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Location r = new Range(typeRange.getIdentity(), start, end);
    if (displayId != null)
        r.setDisplayId(displayId);
    if (name != null)
        r.setName(name);
    if (description != null)
        r.setDescription(description);
    if (persistentIdentity != null)
        r.setPersistentIdentity(persistentIdentity);
    if (orientation != null)
        try {
            r.setOrientation(OrientationType.convertToOrientationType(orientation));
        } catch (SBOLValidationException e) {
            throw new SBOLValidationException("sbol-11002", r);
        }
    if (version != null)
        r.setVersion(version);
    r.setWasDerivedFroms(wasDerivedFroms);
    r.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        r.setAnnotations(annotations);
    return r;
}

Example 39 with Annotation

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

the class SBOLReader method parseCollectionV1.

/**
 * @param SBOLDoc
 * @param topLevel
 * @return
 * @throws SBOLConversionException
 * @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 Collection#Collection(URI)},</li>
 * 		<li>{@link Collection#setVersion(String)},</li>
 * 		<li>{@link Collection#setWasDerivedFrom(URI)},</li>
 * 		<li>{@link Collection#setDisplayId(String)},</li>
 * 		<li>{@link Collection#setMembers(Set)},</li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addCollection(Collection)}; or</li>
 * 	</ul>
 * </li>
 * <li>the following SBOL validation rule was violated: 10202.</li>
 * </ul>
 */
private static Collection parseCollectionV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException, SBOLConversionException {
    URI identity = topLevel.getIdentity();
    URI persistentIdentity = null;
    String displayId = null;
    String name = null;
    String description = null;
    Set<URI> members = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    if (URIPrefix != null) {
        displayId = URIcompliance.findDisplayId(topLevel.getIdentity().toString());
        identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
        persistentIdentity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, "", typesInURI);
    }
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol1Terms.Collection.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            displayId = URIcompliance.fixDisplayId(displayId);
            if (URIPrefix != null) {
                identity = createCompliantURI(URIPrefix, TopLevel.COLLECTION, displayId, version, typesInURI);
                persistentIdentity = createCompliantURI(URIPrefix, TopLevel.COLLECTION, displayId, "", typesInURI);
            }
        } else if (namedProperty.getName().equals(Sbol1Terms.Collection.name)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((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(Sbol1Terms.Collection.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((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(Sbol1Terms.Collection.component)) {
            if (namedProperty.getValue() instanceof Literal) {
                members.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else {
                members.add(parseDnaComponentV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity());
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // Collection c = SBOLDoc.createCollection(identity);
    Collection c = new Collection(identity);
    if (persistentIdentity != null) {
        c.setPersistentIdentity(persistentIdentity);
        c.setVersion(version);
    }
    if (identity != topLevel.getIdentity())
        c.addWasDerivedFrom(topLevel.getIdentity());
    if (displayId != null)
        c.setDisplayId(displayId);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    if (!members.isEmpty())
        c.setMembers(members);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    Collection oldC = SBOLDoc.getCollection(topLevel.getIdentity());
    if (oldC == null) {
        SBOLDoc.addCollection(c);
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}

Example 40 with Annotation

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

the class SBOLReader method parseAssociation.

private static Association parseAssociation(SBOLDocument SBOLDoc, NestedDocument<QName> association, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    String displayId = null;
    String name = null;
    String description = null;
    URI persistentIdentity = null;
    String version = null;
    Set<URI> roles = new HashSet<>();
    URI planURI = null;
    URI agentURI = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : association.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", association.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", association.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", association.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", association.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", association.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", association.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", association.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Association.role)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-12602", association.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Association.agent)) {
            if (!(namedProperty.getValue() instanceof Literal) || agentURI != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-12605", association.getIdentity());
            }
            agentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Association.plan)) {
            if (!(namedProperty.getValue() instanceof Literal) || planURI != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-12603", association.getIdentity());
            }
            planURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Association a = new Association(association.getIdentity(), agentURI);
    if (persistentIdentity != null)
        a.setPersistentIdentity(persistentIdentity);
    if (version != null)
        a.setVersion(version);
    if (displayId != null)
        a.setDisplayId(displayId);
    if (name != null)
        a.setName(name);
    if (description != null)
        a.setDescription(description);
    a.setWasDerivedFroms(wasDerivedFroms);
    a.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        a.setAnnotations(annotations);
    if (!roles.isEmpty())
        a.setRoles(roles);
    if (planURI != null)
        a.setPlan(planURI);
    return a;
}