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

Example 31 with SBOLValidationException

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

the class SBOLReader method parseDnaSequenceV1.

/**
 * @param SBOLDoc
 * @param topLevel
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>if an SBOL validation rule violation occurred in any of the following constructors or methods:
 * 	<ul>
 * 		<li>{@link URIcompliance#createCompliantURI(String, String, String, String, boolean)},</li>
 * 		<li>{@link Sequence#Sequence(URI, String, URI)},</li>
 * 		<li>{@link Sequence#setVersion(String)},</li>
 * 		<li>{@link Sequence#setWasDerivedFrom(URI)},</li>
 * 		<li>{@link Sequence#setDisplayId(String)},</li>
 * 		<li>{@link Identified#setAnnotations(List)},</li>
 * 		<li>{@link Sequence#setIdentity(URI)}, or </li>
 * 		<li>{@link SBOLDocument#addSequence(Sequence)}; or</li>
 * 	</ul>
 * </li>
 * <li>any of the following SBOL validation rules was violated: 10202, 10204, 10212, 10213.</li>
 * </ul>
 */
private static Sequence parseDnaSequenceV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException {
    String elements = null;
    String displayId = null;
    String name = null;
    String description = null;
    URI identity = topLevel.getIdentity();
    URI persistentIdentity = topLevel.getIdentity();
    URI encoding = Sequence.IUPAC_DNA;
    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.DNASequence.nucleotides)) {
            elements = ((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();
            if (URIPrefix != null) {
                identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
            }
        } 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 {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Sequence sequence = new Sequence(identity, elements, encoding);
    if (persistentIdentity != null) {
        sequence.setPersistentIdentity(persistentIdentity);
        sequence.setVersion(version);
    }
    if (identity != topLevel.getIdentity())
        sequence.addWasDerivedFrom(topLevel.getIdentity());
    if (displayId != null)
        sequence.setDisplayId(displayId);
    if (name != null)
        sequence.setName(name);
    if (description != null)
        sequence.setDescription(description);
    if (!annotations.isEmpty())
        sequence.setAnnotations(annotations);
    Sequence oldS = SBOLDoc.getSequence(identity);
    if (oldS == null) {
        SBOLDoc.addSequence(sequence);
    } else if (sequence.getWasDerivedFroms().size() > 0 && oldS.getWasDerivedFroms().size() > 0 && !sequence.getWasDerivedFroms().equals(oldS.getWasDerivedFroms())) {
        URI wasDerivedFrom = (URI) sequence.getWasDerivedFroms().toArray()[0];
        Set<TopLevel> topLevels = SBOLDoc.getByWasDerivedFrom(wasDerivedFrom);
        for (TopLevel top : topLevels) {
            if (top instanceof Sequence) {
                return (Sequence) top;
            }
        }
        do {
            displayId = displayId + "_";
            identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
            persistentIdentity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, "", typesInURI);
        } while (SBOLDoc.getSequence(identity) != null);
        sequence.setIdentity(identity);
        sequence.setDisplayId(displayId);
        sequence.setPersistentIdentity(persistentIdentity);
        SBOLDoc.addSequence(sequence);
    } else if (dropObjectsWithDuplicateURIs) {
        return oldS;
    } else {
        if (!sequence.equals(oldS)) {
            throw new SBOLValidationException("sbol-10202", sequence);
        }
    }
    return sequence;
}

Example 32 with SBOLValidationException

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

the class SBOLReader method parseCollection.

/**
 * @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, 12102; or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Collection#Collection(URI)}, </li>
 * 		<li>{@link Collection#setDisplayId(String)}, </li>
 * 		<li>{@link Collection#setVersion(String)}, </li>
 * 		<li>{@link Collection#setMembers(Set)}, </li>
 * 		<li>{@link Collection#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addCollection(Collection)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings({ "rawtypes", "unchecked" })
private static Collection parseCollection(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> members = 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.Collection.hasMembers)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
                }
                members.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof NestedDocument) {
                if (((IdentifiableDocument) namedProperty).getType().equals(Sbol2Terms.Collection.Collection))
                    parseCollection(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ModuleDefinition.ModuleDefinition))
                    parseModuleDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Model.Model))
                    parseModel(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Sequence.Sequence))
                    parseSequence(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ComponentDefinition.ComponentDefinition))
                    parseComponentDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.CombinatorialDerivation.CombinatorialDerivation))
                    parseCombinatorialDerivation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Implementation.Implementation))
                    parseImplementation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Attachment.Attachment))
                    parseAttachment(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Activity.Activity))
                    parseActivity(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Agent.Agent))
                    parseAgent(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Plan.Plan))
                    parsePlan(SBOLDoc, (IdentifiableDocument) namedProperty);
                else
                    parseGenericTopLevel(SBOLDoc, (IdentifiableDocument) namedProperty);
            } else {
                throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
            }
        } 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));
        }
    }
    Collection c = new Collection(topLevel.getIdentity());
    if (displayId != null)
        c.setDisplayId(displayId);
    if (version != null)
        c.setVersion(version);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (!members.isEmpty())
        c.setMembers(members);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    c.setAttachments(attachments);
    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 33 with SBOLValidationException

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

the class Component method copy.

void copy(Component component) throws SBOLValidationException {
    ((ComponentInstance) this).copy((ComponentInstance) component);
    if (!component.getMapsTos().isEmpty()) {
        for (MapsTo mapsTo : component.getMapsTos()) {
            String displayId = URIcompliance.findDisplayId(mapsTo);
            String localDisplayId = URIcompliance.findDisplayId(mapsTo.getLocal());
            MapsTo newMapsTo = this.createMapsTo(displayId, mapsTo.getRefinement(), localDisplayId, mapsTo.getRemoteURI());
            newMapsTo.copy(mapsTo);
        }
    }
    for (URI role : component.getRoles()) {
        this.addRole(URI.create(role.toString()));
    }
}

Example 34 with SBOLValidationException

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

the class Component method createMapsTo.

/**
 * Creates a child mapsTo for this component with the given arguments, and then adds it to its list of mapsTos.
 * <p>
 * This method creates compliant local and remote URIs first.
 * The compliant local URI is created with this component's persistent identity URI, followed by
 * the given local component's display ID, followed by this component's version.
 * The compliant remote URI is created following the same pattern.
 * It then calls {@link #createMapsTo(String, RefinementType, URI, URI)} with the given mapsTo's display ID, its refinement type,
 * and the created compliant local and remote components' URIs.
 * <p>
 * This method calls {@link ComponentDefinition#createComponent(String, AccessType, String, String)} to automatically
 * create a local component with the given display ID of referenced local component definition,
 * {@link AccessType#PUBLIC}, and an empty version string, if all of the following conditions are satisfied:
 * <ul>
 * <li>the associated SBOLDocument instance for this component is not {@code null};</li>
 * <li>if default components should be automatically created when not present in the associated SBOLDocument instance,
 * i.e., {@link SBOLDocument#isCreateDefaults} returns {@code true};</li>
 * <li>if this component's parent ComponentDefinition instance exists; and</li>
 * <li>if this component's parent ComponentDefinition instance does not already have a component
 * with the created compliant local URI.</li>
 * </ul>
 * This automatically created created component has the same display ID as its referenced component definition.
 *
 * @param displayId the display ID of the mapsTo to be created
 * @param refinement the relationship between the local and remote components
 * @param localId the display ID of the local component
 * @param remoteId the display ID of the remote component
 * @return the created mapsTo
 * @throws SBOLValidationException if any of the following condition is satisfied:
 * <ul>
 * <li>if either of the following SBOL validation rules was violated: 10204, 10206;</li>
 * <li>an SBOL validation exception occurred in {@link ComponentDefinition#createComponent(String, AccessType, String, String)}; or</li>
 * <li>an SBOL validation exception occurred in {@link #createMapsTo(String, RefinementType, URI, URI)}.</li>
 * </ul>
 */
public MapsTo createMapsTo(String displayId, RefinementType refinement, String localId, String remoteId) throws SBOLValidationException {
    URI localURI = URIcompliance.createCompliantURI(componentDefinition.getPersistentIdentity().toString(), localId, componentDefinition.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && componentDefinition != null && componentDefinition.getComponent(localURI) == null) {
        componentDefinition.createComponent(localId, AccessType.PUBLIC, localId, "");
    }
    URI remoteURI = URIcompliance.createCompliantURI(getDefinition().getPersistentIdentity().toString(), remoteId, getDefinition().getVersion());
    return createMapsTo(displayId, refinement, localURI, remoteURI);
}

Example 35 with SBOLValidationException

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

the class ComponentDefinition method copy.

void copy(ComponentDefinition componentDefinition) throws SBOLValidationException {
    ((TopLevel) this).copy((TopLevel) componentDefinition);
    for (URI role : componentDefinition.getRoles()) {
        this.addRole(URI.create(role.toString()));
    }
    for (Component component : componentDefinition.getComponents()) {
        String displayId = URIcompliance.findDisplayId(component);
        Component newComponent = this.createComponent(displayId, component.getAccess(), component.getDefinitionURI());
        newComponent.copy(component);
    }
    for (SequenceConstraint sequenceConstraint : componentDefinition.getSequenceConstraints()) {
        String displayId = URIcompliance.findDisplayId(sequenceConstraint);
        String subjectDisplayId = URIcompliance.findDisplayId(sequenceConstraint.getSubject());
        String objectDisplayId = URIcompliance.findDisplayId(sequenceConstraint.getObject());
        SequenceConstraint newSequenceConstraint = this.createSequenceConstraint(displayId, sequenceConstraint.getRestriction(), subjectDisplayId, objectDisplayId);
        newSequenceConstraint.copy(sequenceConstraint);
    }
    for (SequenceAnnotation sequenceAnnotation : componentDefinition.getSequenceAnnotations()) {
        String displayId = URIcompliance.findDisplayId(sequenceAnnotation);
        SequenceAnnotation newSequenceAnnotation = this.createSequenceAnnotation(displayId, "DUMMY__LOCATION");
        newSequenceAnnotation.copy(sequenceAnnotation);
    }
    this.setSequences(componentDefinition.getSequenceURIs());
}