use of org.sbolstandard.core2.Implementation in project libSBOLj by SynBioDex.
the class SBOLDocument method updateReferences.
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 (Experiment experiment : getExperiments()) {
for (URI experimentalDatumURI : experiment.getExperimentalDataURIs()) {
if (uriMap.get(experimentalDatumURI) != null) {
experiment.removeExperimentalData(experimentalDatumURI);
experiment.addExperimentalData(uriMap.get(experimentalDatumURI));
}
}
updateReferences(experiment, uriMap);
}
for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
updateReferences(componentDefinition, uriMap);
for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
if (uriMap.get(sequenceURI) != null) {
componentDefinition.removeSequence(sequenceURI);
componentDefinition.addSequence(uriMap.get(sequenceURI));
}
}
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 (Location sourceLocation : component.getSourceLocations()) {
if (sourceLocation.isSetSequence() && uriMap.get(sourceLocation.getSequenceURI()) != null) {
sourceLocation.setSequence(uriMap.get(sourceLocation.getSequenceURI()));
}
}
}
for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
for (Location loc : sa.getLocations()) {
if (loc.isSetSequence() && uriMap.get(loc.getSequenceURI()) != null) {
loc.setSequence(uriMap.get(loc.getSequenceURI()));
}
updateReferences(loc, uriMap);
}
updateReferences(sa, uriMap);
}
for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
updateReferences(sc, uriMap);
}
}
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()) {
if (uriMap.get(model.getSource()) != null) {
model.setSource(uriMap.get(model.getSource()));
}
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()) {
for (URI variantURI : variableComponent.getVariantURIs()) {
if (uriMap.get(variantURI) != null) {
variableComponent.removeVariant(variantURI);
variableComponent.addVariant(uriMap.get(variantURI));
}
}
for (URI variantCollectionURI : variableComponent.getVariantCollectionURIs()) {
if (uriMap.get(variantCollectionURI) != null) {
variableComponent.removeVariantCollection(variantCollectionURI);
variableComponent.addVariantCollection(uriMap.get(variantCollectionURI));
}
}
for (URI variantDerivationURI : variableComponent.getVariantDerivationURIs()) {
if (uriMap.get(variantDerivationURI) != null) {
variableComponent.removeVariantDerivation(variantDerivationURI);
variableComponent.addVariantDerivation(uriMap.get(variantDerivationURI));
}
}
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.Implementation in project libSBOLj by SynBioDex.
the class SBOLReader method parseImplementation.
/**
* @param SBOLDoc
* @param topLevel
* @param nested
* @return
*/
@SuppressWarnings("unchecked")
private static Implementation parseImplementation(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;
URI built = null;
String version = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
Set<URI> attachments = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
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.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.Implementation.built)) {
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-13102", topLevel.getIdentity());
}
built = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getValue() instanceof IdentifiableDocument) {
if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ModuleDefinition.ModuleDefinition)) {
ModuleDefinition md = parseModuleDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
built = md.getIdentity();
} else if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
ComponentDefinition md = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
built = md.getIdentity();
} else {
throw new SBOLValidationException("sbol-13102", topLevel.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-13102", topLevel.getIdentity());
}
} 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.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.TopLevel.hasAttachment)) {
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-10306", 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-10306", topLevel.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-10306", topLevel.getIdentity());
}
} 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.Description.type) && ((Literal<QName>) namedProperty.getValue()).getValue().toString().equals(Sbol2Terms.Implementation.Implementation.getNamespaceURI() + Sbol2Terms.Implementation.Implementation.getLocalPart())) {
} else {
annotations.add(new Annotation(namedProperty));
}
}
Implementation i = new Implementation(topLevel.getIdentity());
if (displayId != null)
i.setDisplayId(displayId);
if (persistentIdentity != null)
i.setPersistentIdentity(persistentIdentity);
if (name != null)
i.setName(name);
if (description != null)
i.setDescription(description);
if (!annotations.isEmpty())
i.setAnnotations(annotations);
if (version != null)
i.setVersion(version);
if (built != null)
i.setBuilt(built);
i.setWasDerivedFroms(wasDerivedFroms);
i.setWasGeneratedBys(wasGeneratedBys);
i.setAttachments(attachments);
Implementation oldI = SBOLDoc.getImplementation(topLevel.getIdentity());
if (oldI == null) {
SBOLDoc.addImplementation(i);
} else {
if (!i.equals(oldI)) {
throw new SBOLValidationException("sbol-10202", i);
}
}
return i;
}
use of org.sbolstandard.core2.Implementation in project libSBOLj by SynBioDex.
the class SBOLWorkshop2018 method main.
public static void main(String[] args) throws SBOLValidationException, IOException, SBOLConversionException, SynBioHubException {
/* Getting a Device from an SBOL Compliant XML */
// Start a new SBOL Document to hold the device
SBOLDocument doc = new SBOLDocument();
doc.setCreateDefaults(true);
// Set your Homespace. All new SBOL objects will be created in this namespace
String my_namespace = "http://my_namespace.org/";
doc.setDefaultURIprefix(my_namespace);
// Create a new device
ComponentDefinition my_device = doc.createComponentDefinition("my_device", version, ComponentDefinition.DNA_REGION);
System.out.println(my_device.getIdentity());
System.out.println("");
// Load some genetic parts taken from the Cello paper
// TODO: need to fill in path
SBOLDocument cello_parts = SBOLReader.read("/Users/myers/Downloads/parts.xml");
System.out.println(len(cello_parts));
printCounts(cello_parts);
System.out.println("");
// componentDefinitions and sequences
for (TopLevel topLevel : cello_parts.getTopLevels()) {
System.out.println(topLevel.getIdentity());
}
System.out.println("");
// Import these objects into your Document
doc.createCopy(cello_parts);
for (TopLevel topLevel : doc.getTopLevels()) {
System.out.println(topLevel.getIdentity());
}
System.out.println("");
// Retrieve an object from the Document using its uniform resource identifier (URI)
Collection promoter_collection = doc.getCollection(URI.create("http://examples.org/Collection/promoters/1"));
// A Collection contains a list of URI references to objects, not the object themselves
for (TopLevel topLevel : promoter_collection.getMembers()) {
System.out.println(topLevel.getIdentity());
}
System.out.println("");
// Retrieve a component, using its full URI
ComponentDefinition promoter = doc.getComponentDefinition(URI.create("http://examples.org/ComponentDefinition/pPhlF/1"));
// Review the BioPAX and Sequence Ontology terms that describe this component
System.out.println(promoter.getTypes());
System.out.println(promoter.getRoles());
System.out.println("");
/* Getting a Device from Synbiohub */
// Start an interface to the part shop
SynBioHubFrontend part_shop = new SynBioHubFrontend("https://synbiohub.org");
// Search for records from the interlab study
ArrayList<IdentifiedMetadata> records = part_shop.getMatchingComponentDefinitionMetadata("interlab", null, null, null, 0, 50);
for (IdentifiedMetadata record : records) {
System.out.println(record.getDisplayId() + ": " + record.getUri());
}
System.out.println("");
// Import the medium device into the user's Document
doc.createCopy(part_shop.getSBOL(URI.create("https://synbiohub.org/public/iGEM_2016_interlab/Medium_2016Interlab/1")));
// Explore the new parts
for (TopLevel topLevel : doc.getTopLevels()) {
System.out.println(topLevel.getClass().getSimpleName() + ": " + topLevel.getIdentity());
}
System.out.println("");
/* Extracting a ComponentDefinition from a Pre-existing Device */
// Extract the medium strength promoter
ComponentDefinition medium_strength_promoter = doc.getComponentDefinition(URI.create("https://synbiohub.org/public/igem/BBa_J23106/1"));
// Get parts for a new circuit
ComponentDefinition rbs = doc.getComponentDefinition(URI.create("http://examples.org/ComponentDefinition/Q2/1"));
ComponentDefinition cds = doc.getComponentDefinition(URI.create("http://examples.org/ComponentDefinition/LuxR/1"));
ComponentDefinition terminator = doc.getComponentDefinition(URI.create("http://examples.org/ComponentDefinition/ECK120010818/1"));
// Assemble a new gene
my_device.createSequenceConstraint("constraint1", RestrictionType.PRECEDES, medium_strength_promoter.getIdentity(), rbs.getIdentity());
my_device.createSequenceConstraint("constraint2", RestrictionType.PRECEDES, rbs.getIdentity(), cds.getIdentity());
my_device.createSequenceConstraint("constraint3", RestrictionType.PRECEDES, cds.getIdentity(), terminator.getIdentity());
// Annotate the target construct with a Sequence Ontology term
my_device.addRole(SequenceOntology.ENGINEERED_REGION);
// Explore the newly assembled gene
for (Component component : my_device.getComponents()) {
System.out.println(component.getDisplayId());
}
System.out.println("");
compile(doc, my_device);
Sequence seq = my_device.getSequenceByEncoding(Sequence.IUPAC_DNA);
System.out.println(seq.getElements());
System.out.println("");
/* Managing a Design-Build-Test-Learn workflow */
Activity workflow_step_1 = doc.createActivity("build_1", version);
Activity workflow_step_2 = doc.createActivity("build_2", version);
Activity workflow_step_3 = doc.createActivity("test_1", version);
Activity workflow_step_4 = doc.createActivity("analysis_1", version);
Plan workflow_step_1_plan = doc.createPlan("gibson_assembly", version);
Plan workflow_step_2_plan = doc.createPlan("transformation", version);
Plan workflow_step_3_plan = doc.createPlan("promoter_characterization", version);
Plan workflow_step_4_plan = doc.createPlan("parameter_optimization", version);
workflow_step_1.createAssociation("association", URI.create("mailto:jdoe@my_namespace.org")).setPlan(workflow_step_1_plan.getIdentity());
workflow_step_2.createAssociation("association", URI.create("mailto:jdoe@my_namespace.org")).setPlan(workflow_step_2_plan.getIdentity());
workflow_step_3.createAssociation("association", URI.create("http://sys-bio.org/plate_reader_1")).setPlan(workflow_step_3_plan.getIdentity());
workflow_step_4.createAssociation("association", URI.create("http://tellurium.analogmachine.org")).setPlan(workflow_step_4_plan.getIdentity());
Implementation gibson_mix = doc.createImplementation("gibson_mix", version);
gibson_mix.setBuilt(my_device);
gibson_mix.addWasGeneratedBy(workflow_step_1.getIdentity());
workflow_step_1.createUsage("usage", my_device.getIdentity());
Collection clones = doc.createCollection("clones", version);
Implementation clone1 = doc.createImplementation("clone1", version);
clone1.setBuilt(my_device);
clones.addMember(clone1.getIdentity());
Implementation clone2 = doc.createImplementation("clone2", version);
clone2.setBuilt(my_device);
clones.addMember(clone2.getIdentity());
Implementation clone3 = doc.createImplementation("clone3", version);
clone3.setBuilt(my_device);
clones.addMember(clone3.getIdentity());
clones.addWasGeneratedBy(workflow_step_2.getIdentity());
workflow_step_2.createUsage("usage", gibson_mix.getIdentity());
Collection experiment1 = doc.createCollection("experiment1", version);
experiment1.addWasGeneratedBy(workflow_step_3.getIdentity());
workflow_step_3.createUsage("usage", clones.getIdentity());
Collection analysis1 = doc.createCollection("analysis1", version);
analysis1.addWasGeneratedBy(workflow_step_4.getIdentity());
workflow_step_4.createUsage("usage", experiment1.getIdentity());
// Validate the Document
SBOLValidate.validateSBOL(doc, false, false, false);
for (String error : SBOLValidate.getErrors()) {
System.out.println(error);
}
System.out.println(analysis1.getIdentity());
System.out.println("");
/* Uploading the Device back to SynBioHub */
// TODO: Need to provide your credentials
String user_name = "myers";
String password = "MaWen69!";
part_shop.login(user_name, password);
// Upon submission, the Document will be converted to a Collection with the following properties
// The new Collection will have a URI that conforms to the following pattern:
// https://synbiohub.org/user/<USERNAME>/<DOC.DISPLAYID>/<DOC.DISPLAYID>_collection
String displayId = "my_device";
String name = "my device";
String description = "a description of the cassette";
part_shop.createCollection(displayId, version, name, description, "", true, doc);
// TODO: need to fill in your path
String attachment_path = "/Users/myers/Downloads/results.txt";
// Attach raw experimental data to the Test object here. Note the pattern
URI test_uri = URI.create("https://synbiohub.org/user/" + user_name + "/" + displayId + "/experiment1/1");
part_shop.attachFile(test_uri, attachment_path);
// Attach processed experimental data here
// TODO: need to fill in your path
String other_attachement_path = "/Users/myers/Downloads/results.txt";
URI analysis_uri = URI.create("https://synbiohub.org/user/" + user_name + "/" + displayId + "/analysis1/1");
part_shop.attachFile(analysis_uri, other_attachement_path);
System.out.println("Successfully uploaded");
}
use of org.sbolstandard.core2.Implementation in project libSBOLj by SynBioDex.
the class Implementation method copy.
/**
* @throws SBOLValidationException
* if an SBOL validation rule violation occurred in any of the
* following constructors or methods:
* <ul>
* <li>{@link #deepCopy()},</li>
* <li>{@link URIcompliance#createCompliantURI(String, String, String)},</li>
* <li>{@link #setDisplayId(String)},</li>
* <li>{@link #setVersion(String)},</li>
* <li>{@link #setWasDerivedFrom(URI)},</li>
* <li>{@link #setIdentity(URI)}</li>
* </ul>
*/
@Override
Implementation copy(String URIprefix, String displayId, String version) throws SBOLValidationException {
Implementation cloned = this.deepCopy();
cloned.setPersistentIdentity(createCompliantURI(URIprefix, displayId, ""));
cloned.setDisplayId(displayId);
cloned.setVersion(version);
URI newIdentity = createCompliantURI(URIprefix, displayId, version);
if (!this.getIdentity().equals(newIdentity)) {
cloned.addWasDerivedFrom(this.getIdentity());
} else {
cloned.setWasDerivedFroms(this.getWasDerivedFroms());
}
cloned.setIdentity(newIdentity);
return cloned;
}
use of org.sbolstandard.core2.Implementation in project libSBOLj by SynBioDex.
the class SBOLDocument method updateReferences.
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 (Experiment experiment : getExperiments()) {
for (URI experimentalDataURI : experiment.getExperimentalDataURIs()) {
if (experimentalDataURI.equals(originalIdentity)) {
experiment.removeExperimentalData(originalIdentity);
experiment.addExperimentalData(newIdentity);
}
}
updateReferences(experiment, originalIdentity, newIdentity);
}
for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
updateReferences(componentDefinition, originalIdentity, newIdentity);
for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
if (sequenceURI.equals(originalIdentity)) {
componentDefinition.removeSequence(originalIdentity);
componentDefinition.addSequence(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 (Location sourceLocation : component.getSourceLocations()) {
if (sourceLocation.isSetSequence() && sourceLocation.getSequenceURI().equals(originalIdentity)) {
sourceLocation.setSequence(newIdentity);
}
}
}
for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
for (Location loc : sa.getLocations()) {
if (loc.isSetSequence() && loc.getSequenceURI().equals(originalIdentity)) {
loc.setSequence(newIdentity);
}
updateReferences(loc, originalIdentity, newIdentity);
}
updateReferences(sa, originalIdentity, newIdentity);
}
for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
updateReferences(sc, originalIdentity, 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()) {
if (model.getSource().equals(originalIdentity)) {
model.setSource(newIdentity);
}
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()) {
for (URI variantURI : variableComponent.getVariantURIs()) {
if (variantURI.equals(originalIdentity)) {
variableComponent.removeVariant(variantURI);
variableComponent.addVariant(newIdentity);
}
}
for (URI variantCollectionURI : variableComponent.getVariantCollectionURIs()) {
if (variantCollectionURI.equals(originalIdentity)) {
variableComponent.removeVariantCollection(variantCollectionURI);
variableComponent.addVariantCollection(newIdentity);
}
}
for (URI variantDerivationURI : variableComponent.getVariantDerivationURIs()) {
if (variantDerivationURI.equals(originalIdentity)) {
variableComponent.removeVariantDerivation(variantDerivationURI);
variableComponent.addVariantDerivation(newIdentity);
}
}
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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