use of org.sbolstandard.core2.URIcompliance.createCompliantURI 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);
}
use of org.sbolstandard.core2.URIcompliance.createCompliantURI in project libSBOLj by SynBioDex.
the class VariableComponent method addVariant.
/**
* Adds the given variant to the list of variants.
*
* @param uriPrefix
* URI prefix for variant
* @param displayId
* display id for variant
* @param version
* version for variant
* @throws SBOLValidationException if the following SBOL validation rule was violated:
*/
public void addVariant(String uriPrefix, String displayId, String version) throws SBOLValidationException {
URI uri = URIcompliance.createCompliantURI(uriPrefix, displayId, version);
ComponentDefinition componentDefinition = this.getSBOLDocument().getComponentDefinition(uri);
addVariant(componentDefinition.getIdentity());
}
use of org.sbolstandard.core2.URIcompliance.createCompliantURI in project libSBOLj by SynBioDex.
the class VariableComponent method addVariantCollection.
/**
* Adds the given variant collection to the list of variant collections.
*
* @param uriPrefix
* URI prefix for variant collection
* @param displayId
* display id for variant collection
* @param version
* version for variant collection
* @throws SBOLValidationException if the following SBOL validation rule was violated:
*/
public void addVariantCollection(String uriPrefix, String displayId, String version) throws SBOLValidationException {
URI uri = URIcompliance.createCompliantURI(uriPrefix, displayId, version);
Collection collection = this.getSBOLDocument().getCollection(uri);
addVariantCollection(collection.getIdentity());
}
use of org.sbolstandard.core2.URIcompliance.createCompliantURI in project libSBOLj by SynBioDex.
the class SBOLDocument method updateReferences.
// TODO: need to update persistentIdentities too
private void updateReferences(HashMap<URI, URI> uriMap) throws SBOLValidationException {
for (TopLevel topLevel : getTopLevels()) {
for (URI wasDerivedFrom : topLevel.getWasDerivedFroms()) {
if (uriMap.get(wasDerivedFrom) != null) {
topLevel.removeWasDerivedFrom(wasDerivedFrom);
topLevel.addWasDerivedFrom(uriMap.get(wasDerivedFrom));
}
}
for (URI wasGeneratedBy : topLevel.getWasGeneratedBys()) {
if (uriMap.get(wasGeneratedBy) != null) {
topLevel.removeWasGeneratedBy(wasGeneratedBy);
topLevel.addWasGeneratedBy(uriMap.get(wasGeneratedBy));
}
}
for (URI attachmentURI : topLevel.getAttachmentURIs()) {
if (uriMap.get(attachmentURI) != null) {
topLevel.removeAttachment(attachmentURI);
topLevel.addAttachment(uriMap.get(attachmentURI));
}
}
}
for (Collection collection : getCollections()) {
for (URI memberURI : collection.getMemberURIs()) {
if (uriMap.get(memberURI) != null) {
collection.removeMember(memberURI);
collection.addMember(uriMap.get(memberURI));
}
}
updateReferences(collection, uriMap);
}
for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
updateReferences(componentDefinition, uriMap);
for (Component component : componentDefinition.getComponents()) {
if (uriMap.get(component.getDefinitionURI()) != null) {
component.setDefinition(uriMap.get(component.getDefinitionURI()));
for (MapsTo mapsTo : component.getMapsTos()) {
ComponentDefinition cd = getComponentDefinition(component.getDefinitionURI());
if (cd != null) {
String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
mapsTo.setRemote(newURI);
}
}
}
updateReferences(component, uriMap);
for (MapsTo mapsTo : component.getMapsTos()) {
updateReferences(mapsTo, uriMap);
}
}
for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
for (Location loc : sa.getLocations()) {
updateReferences(loc, uriMap);
}
updateReferences(sa, uriMap);
}
for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
updateReferences(sc, uriMap);
}
for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
if (uriMap.get(sequenceURI) != null) {
componentDefinition.removeSequence(sequenceURI);
componentDefinition.addSequence(uriMap.get(sequenceURI));
}
}
}
for (ModuleDefinition moduleDefinition : getModuleDefinitions()) {
updateReferences(moduleDefinition, uriMap);
for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
if (uriMap.get(functionalComponent.getDefinitionURI()) != null) {
functionalComponent.setDefinition(uriMap.get(functionalComponent.getDefinitionURI()));
for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
ComponentDefinition cd = getComponentDefinition(functionalComponent.getDefinitionURI());
if (cd != null) {
String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
mapsTo.setRemote(newURI);
}
}
}
updateReferences(functionalComponent, uriMap);
for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
updateReferences(mapsTo, uriMap);
}
}
for (Module module : moduleDefinition.getModules()) {
if (uriMap.get(module.getDefinitionURI()) != null) {
module.setDefinition(uriMap.get(module.getDefinitionURI()));
for (MapsTo mapsTo : module.getMapsTos()) {
ModuleDefinition md = getModuleDefinition(module.getDefinitionURI());
if (md != null) {
String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
URI newURI = URIcompliance.createCompliantURI(md.getPersistentIdentity().toString(), displayId, md.getVersion());
mapsTo.setRemote(newURI);
}
}
}
updateReferences(module, uriMap);
for (MapsTo mapsTo : module.getMapsTos()) {
updateReferences(mapsTo, uriMap);
}
}
for (Interaction interaction : moduleDefinition.getInteractions()) {
updateReferences(interaction, uriMap);
for (Participation participation : interaction.getParticipations()) {
updateReferences(participation, uriMap);
}
}
for (URI modelURI : moduleDefinition.getModelURIs()) {
if (uriMap.get(modelURI) != null) {
moduleDefinition.removeModel(modelURI);
moduleDefinition.addModel(uriMap.get(modelURI));
}
}
}
for (Model model : getModels()) {
updateReferences(model, uriMap);
}
for (Sequence sequence : getSequences()) {
updateReferences(sequence, uriMap);
}
for (Attachment attachment : getAttachments()) {
updateReferences(attachment, uriMap);
}
for (Implementation implementation : getImplementations()) {
if (implementation.isSetBuilt()) {
URI built = implementation.getBuiltURI();
if (uriMap.get(built) != null) {
implementation.setBuilt(uriMap.get(built));
}
}
updateReferences(implementation, uriMap);
}
for (GenericTopLevel genericTopLevel : getGenericTopLevels()) {
updateReferences(genericTopLevel, uriMap);
}
for (CombinatorialDerivation combinatorialDerivation : getCombinatorialDerivations()) {
updateReferences(combinatorialDerivation, uriMap);
if (uriMap.get(combinatorialDerivation.getTemplateURI()) != null) {
combinatorialDerivation.setTemplate(uriMap.get(combinatorialDerivation.getTemplateURI()));
ComponentDefinition cd = getComponentDefinition(combinatorialDerivation.getTemplateURI());
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, uriMap);
}
}
for (Activity activity : getActivities()) {
updateReferences(activity, uriMap);
for (Association association : activity.getAssociations()) {
if (uriMap.get(association.getAgentURI()) != null) {
association.setAgent(uriMap.get(association.getAgentURI()));
}
if (uriMap.get(association.getPlanURI()) != null) {
association.setPlan(uriMap.get(association.getPlanURI()));
}
updateReferences(association, uriMap);
}
for (Usage usage : activity.getUsages()) {
if (uriMap.get(usage.getEntityURI()) != null) {
usage.setEntity(uriMap.get(usage.getEntityURI()));
}
updateReferences(usage, uriMap);
}
}
for (Agent agent : getAgents()) {
updateReferences(agent, uriMap);
}
for (Plan plan : getPlans()) {
updateReferences(plan, uriMap);
}
}
use of org.sbolstandard.core2.URIcompliance.createCompliantURI 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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