use of org.sbolstandard.core2.Participation in project libSBOLj by SynBioDex.
the class ModuleDefinition method flattenRecurse.
/**
* @return flattened ModuleDefinition
* @throws SBOLValidationException if either of the following condition is satisfied:
* <ul>
* <li>The following SBOL validation rule was violated: 10811; or</li>
*
* <li>if an SBOL validation rule violation occurred in any of the following methods:</li>
* <ul>
* <li>{@link #deepCopy()},</li>
* <li>{@link #flattenRecurse()},</li>
* <li>{@link FunctionalComponent#setDefinition(URI)},</li>
* <li>{@link FunctionalComponent#deepCopy()},</li>
* <li>{@link FunctionalComponent#updateCompliantURI(String, String, String)},</li>
* <li>{@link #addFunctionalComponent(FunctionalComponent)},</li>
* <li>{@link Participation#setParticipant(URI)},</li>
* <li>{@link #addInteraction(Interaction)}, or</li>
* <li>{@link Interaction#deepCopy()}.</li>
* </ul>
* </ul>
*/
private ModuleDefinition flattenRecurse() throws SBOLValidationException {
ModuleDefinition flatModuleDefinition = this.deepCopy();
for (Module module : this.getModules()) {
ModuleDefinition flatModule = module.getDefinition().flattenRecurse();
for (FunctionalComponent fc : flatModule.getFunctionalComponents()) {
boolean foundIt = false;
URI oldURI = fc.getIdentity();
URI newURI = null;
for (MapsTo mapsTo : module.getMapsTos()) {
if (mapsTo.getRemoteURI().equals(fc.getIdentity())) {
newURI = mapsTo.getLocalURI();
FunctionalComponent topFc = flatModuleDefinition.getFunctionalComponent(newURI);
if (mapsTo.getRefinement() == RefinementType.USEREMOTE) {
topFc.setDefinition(fc.getDefinitionURI());
} else if (mapsTo.getRefinement() == RefinementType.VERIFYIDENTICAL) {
if (!topFc.getDefinitionURI().equals(fc.getDefinitionURI())) {
// + "' are not identical.");
throw new SBOLValidationException("sbol-10811", mapsTo);
}
} else if (mapsTo.getRefinement() == RefinementType.MERGE) {
// TODO: merge?
}
foundIt = true;
break;
}
}
if (!foundIt) {
FunctionalComponent newFC = fc.deepCopy();
newFC.updateCompliantURI(this.getPersistentIdentity().toString(), module.getDisplayId() + "__" + fc.getDisplayId(), this.getVersion());
newURI = newFC.getIdentity();
flatModuleDefinition.addFunctionalComponent(newFC);
}
for (Interaction i : flatModule.getInteractions()) {
for (Participation p : i.getParticipations()) {
if (p.getParticipantURI().equals(oldURI)) {
p.setParticipant(newURI);
}
}
}
}
for (Interaction i : flatModule.getInteractions()) {
flatModuleDefinition.addInteraction(i.deepCopy());
}
}
flatModuleDefinition.clearModules();
return flatModuleDefinition;
}
use of org.sbolstandard.core2.Participation in project libSBOLj by SynBioDex.
the class SBOLReader method parseParticipation.
/**
* @param participation
* @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, 11906, 12002, 12004; or
*</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link Participation#Participation(URI, URI, Set)},</li>
* <li>{@link Participation#setDisplayId(String)},</li>
* <li>{@link Participation#setVersion(String)},</li>
* <li>{@link Participation#setWasDerivedFrom(URI)}, or</li>
* <li>{@link Identified#setAnnotations(List)}.</li>
* </ul>
* </li>
* </ul>
*/
private static Participation parseParticipation(NestedDocument<QName> participation) throws SBOLValidationException {
// URIcompliance.extractDisplayId(participation.getIdentity());
String displayId = null;
String name = null;
String description = null;
// URI.create(URIcompliance.extractPersistentId(participation.getIdentity()));
URI persistentIdentity = null;
String version = null;
Set<URI> roles = new HashSet<>();
URI participant = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
for (NamedProperty<QName> namedProperty : participation.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", participation.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", participation.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", participation.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", participation.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", participation.getIdentity());
}
description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Participation.role)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-12004", participation.getIdentity());
}
roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.Participation.hasParticipant)) {
if (!(namedProperty.getValue() instanceof Literal) || participant != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-12002", participation.getIdentity());
}
participant = URI.create(((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", participation.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", participation.getIdentity());
}
wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
annotations.add(new Annotation(namedProperty));
}
}
Participation p = new Participation(participation.getIdentity(), participant, roles);
if (displayId != null)
p.setDisplayId(displayId);
if (name != null)
p.setName(name);
if (description != null)
p.setDescription(description);
if (persistentIdentity != null)
p.setPersistentIdentity(persistentIdentity);
if (version != null)
p.setVersion(version);
p.setWasDerivedFroms(wasDerivedFroms);
p.setWasGeneratedBys(wasGeneratedBys);
if (!annotations.isEmpty())
p.setAnnotations(annotations);
return p;
}
use of org.sbolstandard.core2.Participation in project libSBOLj by SynBioDex.
the class SBOLDocument method updateReferences.
// TODO: need to update persistentIdentities too
private void updateReferences(URI originalIdentity, URI newIdentity) throws SBOLValidationException {
for (TopLevel topLevel : getTopLevels()) {
for (URI wasDerivedFrom : topLevel.getWasDerivedFroms()) {
if (wasDerivedFrom.equals(originalIdentity)) {
topLevel.removeWasDerivedFrom(originalIdentity);
topLevel.addWasDerivedFrom(newIdentity);
}
}
for (URI wasGeneratedBy : topLevel.getWasGeneratedBys()) {
if (wasGeneratedBy.equals(originalIdentity)) {
topLevel.removeWasGeneratedBy(originalIdentity);
topLevel.addWasGeneratedBy(newIdentity);
}
}
for (URI attachmentURI : topLevel.getAttachmentURIs()) {
if (attachmentURI.equals(originalIdentity)) {
topLevel.removeAttachment(originalIdentity);
topLevel.addAttachment(newIdentity);
}
}
}
for (Collection collection : getCollections()) {
for (URI memberURI : collection.getMemberURIs()) {
if (memberURI.equals(originalIdentity)) {
collection.removeMember(originalIdentity);
collection.addMember(newIdentity);
}
}
updateReferences(collection, originalIdentity, newIdentity);
}
for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
updateReferences(componentDefinition, originalIdentity, newIdentity);
for (Component component : componentDefinition.getComponents()) {
if (component.getDefinitionURI().equals(originalIdentity)) {
component.setDefinition(newIdentity);
for (MapsTo mapsTo : component.getMapsTos()) {
ComponentDefinition cd = getComponentDefinition(newIdentity);
if (cd != null) {
String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
mapsTo.setRemote(newURI);
}
}
}
updateReferences(component, originalIdentity, newIdentity);
for (MapsTo mapsTo : component.getMapsTos()) {
updateReferences(mapsTo, originalIdentity, newIdentity);
}
}
for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
for (Location loc : sa.getLocations()) {
updateReferences(loc, originalIdentity, newIdentity);
}
updateReferences(sa, originalIdentity, newIdentity);
}
for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
updateReferences(sc, originalIdentity, newIdentity);
}
for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
if (sequenceURI.equals(originalIdentity)) {
componentDefinition.removeSequence(originalIdentity);
componentDefinition.addSequence(newIdentity);
}
}
}
for (ModuleDefinition moduleDefinition : getModuleDefinitions()) {
updateReferences(moduleDefinition, originalIdentity, newIdentity);
for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
if (functionalComponent.getDefinitionURI().equals(originalIdentity)) {
functionalComponent.setDefinition(newIdentity);
for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
ComponentDefinition cd = getComponentDefinition(newIdentity);
if (cd != null) {
String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
mapsTo.setRemote(newURI);
}
}
}
updateReferences(functionalComponent, originalIdentity, newIdentity);
for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
updateReferences(mapsTo, originalIdentity, newIdentity);
}
}
for (Module module : moduleDefinition.getModules()) {
if (module.getDefinitionURI().equals(originalIdentity)) {
module.setDefinition(newIdentity);
for (MapsTo mapsTo : module.getMapsTos()) {
ModuleDefinition md = getModuleDefinition(newIdentity);
if (md != null) {
String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
URI newURI = URIcompliance.createCompliantURI(md.getPersistentIdentity().toString(), displayId, md.getVersion());
mapsTo.setRemote(newURI);
}
}
}
updateReferences(module, originalIdentity, newIdentity);
for (MapsTo mapsTo : module.getMapsTos()) {
updateReferences(mapsTo, originalIdentity, newIdentity);
}
}
for (Interaction interaction : moduleDefinition.getInteractions()) {
updateReferences(interaction, originalIdentity, newIdentity);
for (Participation participation : interaction.getParticipations()) {
updateReferences(participation, originalIdentity, newIdentity);
}
}
for (URI modelURI : moduleDefinition.getModelURIs()) {
if (modelURI.equals(originalIdentity)) {
moduleDefinition.removeModel(originalIdentity);
moduleDefinition.addModel(newIdentity);
}
}
}
for (Model model : getModels()) {
updateReferences(model, originalIdentity, newIdentity);
}
for (Attachment attachment : getAttachments()) {
updateReferences(attachment, originalIdentity, newIdentity);
}
for (Implementation implementation : getImplementations()) {
if (implementation.isSetBuilt() && implementation.getBuiltURI().equals(originalIdentity)) {
implementation.setBuilt(newIdentity);
}
updateReferences(implementation, originalIdentity, newIdentity);
}
for (Sequence sequence : getSequences()) {
updateReferences(sequence, originalIdentity, newIdentity);
}
for (GenericTopLevel genericTopLevel : getGenericTopLevels()) {
updateReferences(genericTopLevel, originalIdentity, newIdentity);
}
for (CombinatorialDerivation combinatorialDerivation : getCombinatorialDerivations()) {
updateReferences(combinatorialDerivation, originalIdentity, newIdentity);
if (combinatorialDerivation.getTemplateURI().equals(originalIdentity)) {
combinatorialDerivation.setTemplate(newIdentity);
ComponentDefinition cd = getComponentDefinition(newIdentity);
if (cd != null) {
for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
String displayId = URIcompliance.extractDisplayId(variableComponent.getVariableURI());
URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
variableComponent.setVariable(newURI);
}
}
}
for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
updateReferences(variableComponent, originalIdentity, newIdentity);
}
}
for (Activity activity : getActivities()) {
updateReferences(activity, originalIdentity, newIdentity);
for (Association association : activity.getAssociations()) {
if (association.getAgentURI().equals(originalIdentity)) {
association.setAgent(newIdentity);
}
if (association.isSetPlan() && association.getPlanURI().equals(originalIdentity)) {
association.setPlan(newIdentity);
}
updateReferences(association, originalIdentity, newIdentity);
}
for (Usage usage : activity.getUsages()) {
if (usage.getEntityURI().equals(originalIdentity)) {
usage.setEntity(newIdentity);
}
updateReferences(usage, originalIdentity, newIdentity);
}
}
for (Agent agent : getAgents()) {
updateReferences(agent, originalIdentity, newIdentity);
}
for (Plan plan : getPlans()) {
updateReferences(plan, originalIdentity, newIdentity);
}
}
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