use of org.sbolstandard.core2.Agent 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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