Examples with Literal org.sbolstandard.core.datatree.Literal used on opensource projects

Example 21 with Literal

use of org.sbolstandard.core.datatree.Literal in project libSBOLj by SynBioDex.

the class SBOLReader method parseCut.

/**
 * @param typeCut
 * @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,
 * 11002, 11202; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Cut#Cut(URI, int)},</li>
 * 		<li>{@link Cut#setDisplayId(String)},</li>
 * 		<li>{@link Cut#setVersion(String)},</li>
 * 		<li>{@link Cut#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
private static Cut parseCut(NestedDocument<QName> typeCut) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(typeCut.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(typeCut.getIdentity()));
    URI persistentIdentity = null;
    Integer at = 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 : typeCut.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", typeCut.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", typeCut.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", typeCut.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", typeCut.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Cut.at)) {
            if (!(namedProperty.getValue() instanceof Literal) || at != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11202", typeCut.getIdentity());
            }
            String temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            // at 			= Integer.parseInt(temp);
            try {
                at = Integer.parseInt(temp);
            } catch (NumberFormatException e) {
                throw new SBOLValidationException("sbol-11202", typeCut.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Cut.orientation)) {
            if (!(namedProperty.getValue() instanceof Literal) || orientation != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11002", typeCut.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", typeCut.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", typeCut.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", typeCut.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    if (at == null) {
        throw new SBOLValidationException("Cut requires at property.");
    }
    Cut c = new Cut(typeCut.getIdentity(), at);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    if (orientation != null)
        try {
            c.setOrientation(OrientationType.convertToOrientationType(orientation));
        } catch (SBOLValidationException e) {
            throw new SBOLValidationException("sbol-11002", c);
        }
    if (version != null)
        c.setVersion(version);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    return c;
}

Example 22 with Literal

use of org.sbolstandard.core.datatree.Literal 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;
}

Example 23 with Literal

use of org.sbolstandard.core.datatree.Literal in project libSBOLj by SynBioDex.

the class SBOLReader method parseAttachment.

@SuppressWarnings("unchecked")
private static Attachment parseAttachment(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 format = null;
    Long size = null;
    String hash = 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.Attachment.source)) {
            if (!(namedProperty.getValue() instanceof Literal) || source != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-13202", topLevel.getIdentity());
            }
            source = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Attachment.format)) {
            if (!(namedProperty.getValue() instanceof Literal) || format != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-13204", topLevel.getIdentity());
            }
            format = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Attachment.size)) {
            if (!(namedProperty.getValue() instanceof Literal) || size != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-13207", topLevel.getIdentity());
            }
            size = Long.valueOf(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Attachment.hash)) {
            if (!(namedProperty.getValue() instanceof Literal) || hash != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-13208", topLevel.getIdentity());
            }
            hash = ((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));
        }
    }
    Attachment a = new Attachment(topLevel.getIdentity(), source);
    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);
    a.setAttachments(attachments);
    if (!annotations.isEmpty())
        a.setAnnotations(annotations);
    if (format != null)
        a.setFormat(format);
    if (size != null)
        a.setSize(size);
    if (hash != null)
        a.setHash(hash);
    Attachment oldA = SBOLDoc.getAttachment(topLevel.getIdentity());
    if (oldA == null) {
        SBOLDoc.addAttachment(a);
    } else {
        if (!a.equals(oldA)) {
            throw new SBOLValidationException("sbol-10202", a);
        }
    }
    return a;
}

Example 24 with Literal

use of org.sbolstandard.core.datatree.Literal 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 25 with Literal

use of org.sbolstandard.core.datatree.Literal 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;
}