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

Example 46 with SBOLDocument

use of org.sbolstandard.core2.SBOLDocument 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 47 with SBOLDocument

use of org.sbolstandard.core2.SBOLDocument 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 48 with SBOLDocument

use of org.sbolstandard.core2.SBOLDocument 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;
}

Example 49 with SBOLDocument

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

the class ComponentDefinition method createSequenceConstraint.

/**
 * Creates a child sequence constraint for this component definition with the given arguments,
 * and then adds to this component definition's list of sequence constraints.
 * <p>
 * Creation of a sequence constraint requires URIs of a subject component and an object component.
 * This method creates compliant URIs for them respectively. The subject component compliant URI is created with this
 * component defintion's persistent identity URI, followed by the given subject component's display ID,
 * followed by this component's version. The object component compliant URI is created similarly.
 * This method then calls {@link #createSequenceConstraint(String, RestrictionType, URI, URI)} to create
 * the sequence constraint.
 * <p>
 * This method automatically creates a subject component if all of the following conditions are satisfied:
 * <ul>
 * <li>the associated SBOLDocument, i.e., the SBOLDocument instance hosting this component definition, is not {@code null};</li>
 * <li>if default components should be automatically created when not present for the associated SBOLDocument instance,
 * i.e., {@link SBOLDocument#isCreateDefaults} returns {@code true}; and</li>
 * <li>if this component definition does not already have a component with the created compliant subject component URI.</li>
 * </ul>
 * An object component is automatically created if the similar set of conditions hold.
 *
 * @param displayId the display ID of the sequence constraint to be created
 * @param restriction the structural restriction of the subject and object components
 * @param subjectId the display ID of the subject component
 * @param objectId the display ID of the object component
 * @return the created sequence constraint
 * @throws SBOLValidationException if any of the following condition is satisfied:
 * <ul>
 * <li>if any of the following SBOL validation rules was violated:
 * 10201, 10202, 10204, 10206, 10602, 10604, 10605, 10607, 10803; or</li>
 * <li>an SBOL validation rule violation occurred in {@link #createSequenceConstraint(String, RestrictionType, URI, URI)}.</li>
 * </ul>
 */
public SequenceConstraint createSequenceConstraint(String displayId, RestrictionType restriction, String subjectId, String objectId) throws SBOLValidationException {
    URI subjectURI = URIcompliance.createCompliantURI(this.getPersistentIdentity().toString(), subjectId, this.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && this.getComponent(subjectURI) == null) {
        this.createComponent(subjectId, AccessType.PUBLIC, subjectId, "");
    }
    URI objectURI = URIcompliance.createCompliantURI(this.getPersistentIdentity().toString(), objectId, this.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && this.getComponent(objectURI) == null) {
        this.createComponent(objectId, AccessType.PUBLIC, objectId, "");
    }
    return createSequenceConstraint(displayId, restriction, subjectURI, objectURI);
}

Example 50 with SBOLDocument

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

the class Module method createMapsTo.

/**
 * Creates a child mapsTo for this module 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 module's persistent identity URI, followed by
 * the given local module's display ID, followed by this module'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 functional components' URIs.
 * <p>
 * This method calls {@link ModuleDefinition#createFunctionalComponent(String, AccessType, String, String, DirectionType)}
 * to automatically create a local functional component with the given display ID of referenced local component definition,
 * {@link AccessType#PUBLIC}, an empty version string, and {@link DirectionType#INOUT}, if all of the following conditions are satisfied:
 * <ul>
 * <li>the associated SBOLDocument instance for this module is not {@code null};</li>
 * <li>if default functional 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 module's parent ModuleDefinition instance exists; and</li>
 * <li>if this module's parent ModuleDefinition instance does not already have a functional component
 * with the created compliant local URI.</li>
 * </ul>
 * This automatically created created functional 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 functional component
 * @param remoteId the display ID of the remote functional 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 ModuleDefinition#createFunctionalComponent(String, AccessType, String, String, DirectionType)}; 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(moduleDefinition.getPersistentIdentity().toString(), localId, moduleDefinition.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && moduleDefinition != null && moduleDefinition.getFunctionalComponent(localURI) == null) {
        moduleDefinition.createFunctionalComponent(localId, AccessType.PUBLIC, localId, "", DirectionType.INOUT);
    }
    URI remoteURI = URIcompliance.createCompliantURI(getDefinition().getPersistentIdentity().toString(), remoteId, getDefinition().getVersion());
    return createMapsTo(displayId, refinement, localURI, remoteURI);
}