Example 21 with Component
use of org.sbolstandard.core2.Component in project ice by JBEI.
the class SBOL2Visitor method visit.
public void visit(Sequence sequence) throws SBOLValidationException, URISyntaxException {
// ice data model conflates the sequence and component
Entry entry = sequence.getEntry();
// Set required properties
String partId = entry.getPartNumber();
String dcUri = sequence.getComponentUri();
if (dcUri == null) {
componentDefinition = doc.createComponentDefinition(uriString, partId, "1", ComponentDefinition.DNA);
} else {
String displayId = StringUtils.isBlank(sequence.getIdentifier()) ? displayIdFromUri(dcUri) : sequence.getIdentifier();
String prefix = prefixFromUri(dcUri);
componentDefinition = doc.createComponentDefinition(prefix, displayId, "1", ComponentDefinition.DNA);
}
componentDefinition.setName(entry.getName());
componentDefinition.setDescription(entry.getShortDescription());
org.sbolstandard.core2.Sequence dnaSequence;
String dsUri = sequence.getUri();
if (dsUri == null || dsUri.isEmpty()) {
dsUri = "sequence_" + sequence.getFwdHash().replaceAll("[\\s\\-()]", "");
dnaSequence = doc.createSequence(uriString, dsUri, "1", sequence.getSequence(), org.sbolstandard.core2.Sequence.IUPAC_DNA);
} else {
dnaSequence = doc.createSequence(prefixFromUri(dsUri), displayIdFromUri(dsUri), "1", sequence.getSequence(), org.sbolstandard.core2.Sequence.IUPAC_DNA);
}
dnaSequence.setElements(sequence.getSequence());
componentDefinition.addSequence(dnaSequence);
List<SequenceFeature> features = new ArrayList<>(sequence.getSequenceFeatures());
Collections.sort(features, new SequenceFeatureComparator());
for (SequenceFeature feature : features) {
visit(feature);
}
componentDefinition.createAnnotation(new QName(ICE_NS, "id", ICE_PREFIX), entry.getId());
if (entry.getRecordId() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "recordId", ICE_PREFIX), entry.getRecordId());
if (entry.getVersionId() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "versionId", ICE_PREFIX), entry.getVersionId());
if (entry.getRecordType() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "recordType", ICE_PREFIX), entry.getRecordType());
if (entry.getOwner() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "owner", ICE_PREFIX), entry.getOwner());
if (entry.getOwnerEmail() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "ownerEmail", ICE_PREFIX), entry.getOwnerEmail());
if (entry.getCreator() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "creator", ICE_PREFIX), entry.getCreator());
if (entry.getCreatorEmail() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "creatorEmail", ICE_PREFIX), entry.getCreatorEmail());
if (entry.getStatus() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "status", ICE_PREFIX), entry.getStatus());
if (entry.getAlias() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "alias", ICE_PREFIX), entry.getAlias());
for (SelectionMarker selectionMarker : entry.getSelectionMarkers()) {
componentDefinition.createAnnotation(new QName(ICE_NS, "selectionMarker", ICE_PREFIX), selectionMarker.getName());
}
if (entry.getLinks() != null) {
for (Link link : entry.getLinks()) {
componentDefinition.createAnnotation(new QName(ICE_NS, link.getLink(), ICE_PREFIX), link.getUrl());
}
}
if (entry.getKeywords() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "keywords", ICE_PREFIX), entry.getKeywords());
if (entry.getShortDescription() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "shortDescription", ICE_PREFIX), entry.getShortDescription());
if (entry.getLongDescription() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "longDescription", ICE_PREFIX), entry.getLongDescription());
if (entry.getLongDescriptionType() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "longDescriptionType", ICE_PREFIX), entry.getLongDescriptionType());
if (entry.getReferences() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "references", ICE_PREFIX), entry.getReferences());
if (entry.getCreationTime() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "creationTime", ICE_PREFIX), entry.getCreationTime().toString());
if (entry.getModificationTime() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "modificationTime", ICE_PREFIX), entry.getModificationTime().toString());
if (entry.getBioSafetyLevel() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "bioSafetyLevel", ICE_PREFIX), entry.getBioSafetyLevel());
if (entry.getIntellectualProperty() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "intellectualProperty", ICE_PREFIX), entry.getIntellectualProperty());
if (entry.getVisibility() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "visibility", ICE_PREFIX), entry.getVisibility());
if (entry.getParameters() != null) {
for (Parameter parameter : entry.getParameters()) {
componentDefinition.createAnnotation(new QName(ICE_NS, parameter.getKey(), ICE_PREFIX), parameter.getValue());
}
}
if (entry.getFundingSource() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "fundingSource", ICE_PREFIX), entry.getFundingSource());
if (entry.getPrincipalInvestigator() != null)
componentDefinition.createAnnotation(new QName(ICE_NS, "principalInvestigator", ICE_PREFIX), entry.getPrincipalInvestigator());
// TODO: samples
// TODO: attachments
}
Also used :
QName(javax.xml.namespace.QName)
org.sbolstandard.core2(org.sbolstandard.core2)
Example 22 with Component
use of org.sbolstandard.core2.Component in project libSBOLj by SynBioDex.
the class SBOLReader method parseDnaComponentV1.
/**
* @param SBOLDoc
* @param componentDef
* @return
* @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 #parseSequenceAnnotationV1(SBOLDocument, NestedDocument, List, String, int, Set)},</li>
* <li>{@link URIcompliance#createCompliantURI(String, String, String)},</li>
* <li>{@link Component#Component(URI, AccessType, URI)},</li>
* <li>{@link Component#setDisplayId(String)}, </li>
* <li>{@link Component#setVersion(String)}</li>
* <li>{@link SequenceAnnotation#setComponent(URI)}, </li>
* <li>{@link #parseDnaSequenceV1(SBOLDocument, IdentifiableDocument)}</li>
* <li>{@link RestrictionType#convertToURI(RestrictionType)},</li>
* <li>{@link SequenceConstraint#SequenceConstraint(URI, URI, URI, URI)},</li>
* <li>{@link SequenceConstraint#setDisplayId(String)},</li>
* <li>{@link SequenceConstraint#setVersion(String)},</li>
* <li>{@link ComponentDefinition#ComponentDefinition(URI, Set)},</li>
* <li>{@link ComponentDefinition#setVersion(String)},</li>
* <li>{@link ComponentDefinition#setWasDerivedFrom(URI)}, </li>
* <li>{@link Identified#setAnnotations(List)},</li>
* <li>{@link ComponentDefinition#setComponents(Set)}</li>
* <li>{@link ComponentDefinition#setSequenceConstraints(Set)}</li>
* <li>{@link ComponentDefinition#addSequence(URI)}</li>
* <li>{@link ComponentDefinition#addSequenceAnnotation(SequenceAnnotation)},</li>
* <li>{@link SBOLDocument#addComponentDefinition(ComponentDefinition)}, or</li>
* <li>{@link ComponentDefinition#copy(String, String, String)}; or</li>
* </ul>
* </li>
* <li>the following SBOL validation rule was violated: 10202.</li>
* </ul>
* @throws SBOLConversionException
*/
private static ComponentDefinition parseDnaComponentV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> componentDef) throws SBOLValidationException, SBOLConversionException {
String displayId = null;
String name = null;
String description = null;
URI seq_identity = null;
Set<URI> roles = new HashSet<>();
URI identity = componentDef.getIdentity();
String persIdentity = componentDef.getIdentity().toString();
List<Annotation> annotations = new ArrayList<>();
List<SequenceAnnotation> sequenceAnnotations = new ArrayList<>();
Set<String> instantiatedComponents = new HashSet<>();
Set<Component> components = new HashSet<>();
Set<SequenceConstraint> sequenceConstraints = new HashSet<>();
List<SBOLPair> precedePairs = new ArrayList<>();
Map<URI, URI> componentDefMap = new HashMap<>();
Set<URI> type = new HashSet<>();
type.add(ComponentDefinition.DNA);
type.add(SequenceOntology.LINEAR);
int component_num = 0;
int sa_num = 0;
if (URIPrefix != null) {
displayId = URIcompliance.findDisplayId(componentDef.getIdentity().toString());
identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
}
for (NamedProperty<QName> namedProperty : componentDef.getProperties()) {
if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.displayId)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10204", componentDef.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
displayId = URIcompliance.fixDisplayId(displayId);
if (URIPrefix != null) {
persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
}
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.name)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10212", componentDef.getIdentity());
}
name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.description)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10213", componentDef.getIdentity());
}
description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.type)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10507", componentDef.getIdentity());
}
URI convertedSO = SequenceOntology.convertSeqOntologyV1(((Literal<QName>) namedProperty.getValue()).getValue().toString());
roles.add(convertedSO);
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.annotations)) {
if (namedProperty.getValue() instanceof IdentifiableDocument) {
SequenceAnnotation sa = parseSequenceAnnotationV1(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), precedePairs, persIdentity, ++sa_num, instantiatedComponents);
sequenceAnnotations.add(sa);
URI component_identity = createCompliantURI(persIdentity, "component" + component_num, version);
URI component_persIdentity = createCompliantURI(persIdentity, "component" + component_num, "");
String component_displayId = "component" + component_num;
AccessType access = AccessType.PUBLIC;
URI instantiatedComponent = sa.getComponentURI();
ComponentDefinition instantiatedDef = SBOLDoc.getComponentDefinition(instantiatedComponent);
if (compliant && instantiatedDef != null && instantiatedDef.isSetDisplayId() && !instantiatedComponents.contains(instantiatedDef.getDisplayId())) {
component_identity = createCompliantURI(persIdentity, instantiatedDef.getDisplayId(), version);
component_persIdentity = createCompliantURI(persIdentity, instantiatedDef.getDisplayId(), "");
component_displayId = instantiatedDef.getDisplayId();
instantiatedComponents.add(instantiatedDef.getDisplayId());
} else {
component_num++;
}
Component component = new Component(component_identity, access, instantiatedComponent);
if (!persIdentity.equals("")) {
component.setPersistentIdentity(component_persIdentity);
component.setDisplayId(component_displayId);
component.setVersion(version);
}
components.add(component);
URI originalURI = ((NestedDocument<QName>) namedProperty.getValue()).getIdentity();
componentDefMap.put(originalURI, component_identity);
sa.setComponent(component_identity);
} else {
throw new SBOLConversionException("SequenceAnnotation must be nested in SBOL1.");
}
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.dnaSequence)) {
if (seq_identity != null) {
throw new SBOLValidationException("sbol-10512", componentDef.getIdentity());
}
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-10512", componentDef.getIdentity());
}
seq_identity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else {
seq_identity = parseDnaSequenceV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity();
}
} else {
annotations.add(new Annotation(namedProperty));
}
}
if (roles.isEmpty())
roles.add(SequenceOntology.ENGINEERED_REGION);
int sc_number = 0;
for (SBOLPair pair : precedePairs) {
URI sc_identity = createCompliantURI(persIdentity, "sequenceConstraint" + ++sc_number, version);
URI restrictionURI = RestrictionType.convertToURI(RestrictionType.PRECEDES);
// RestrictionType restriction = RestrictionType.convertToRestrictionType(restrictionURI);
URI subject = null;
URI object = null;
for (URI key : componentDefMap.keySet()) {
if (pair.getLeft().equals(key)) {
subject = componentDefMap.get(key);
} else if (pair.getRight().equals(key)) {
object = componentDefMap.get(key);
}
}
SequenceConstraint sc = null;
if (compliant && !persIdentity.equals("")) {
String subjectId = URIcompliance.extractDisplayId(subject);
String objectId = URIcompliance.extractDisplayId(object);
sc_identity = createCompliantURI(persIdentity, subjectId + "_cons_" + objectId, version);
sc = new SequenceConstraint(sc_identity, restrictionURI, subject, object);
sc.setPersistentIdentity(createCompliantURI(persIdentity, subjectId + "_cons_" + objectId, ""));
sc.setDisplayId(subjectId + "_cons_" + objectId);
sc.setVersion(version);
} else {
sc = new SequenceConstraint(sc_identity, restrictionURI, subject, object);
}
sequenceConstraints.add(sc);
}
ComponentDefinition c = new ComponentDefinition(identity, type);
if (!persIdentity.equals("")) {
c.setPersistentIdentity(URI.create(persIdentity));
c.setVersion(version);
}
if (roles != null)
c.setRoles(roles);
if (identity != componentDef.getIdentity())
c.addWasDerivedFrom(componentDef.getIdentity());
if (displayId != null)
c.setDisplayId(displayId);
if (name != null && !name.isEmpty())
c.setName(name);
if (description != null && !description.isEmpty())
c.setDescription(description);
if (seq_identity != null)
c.addSequence(seq_identity);
if (!annotations.isEmpty())
c.setAnnotations(annotations);
if (!components.isEmpty())
c.setComponents(components);
if (!sequenceAnnotations.isEmpty()) {
for (SequenceAnnotation sa : sequenceAnnotations) {
if (!dropObjectsWithDuplicateURIs || c.getSequenceAnnotation(sa.getIdentity()) == null) {
c.addSequenceAnnotation(sa);
}
}
}
if (!sequenceConstraints.isEmpty())
c.setSequenceConstraints(sequenceConstraints);
ComponentDefinition oldC = SBOLDoc.getComponentDefinition(identity);
if (oldC == null) {
SBOLDoc.addComponentDefinition(c);
} else if (c.getWasDerivedFroms().size() > 0 && oldC.getWasDerivedFroms().size() > 0 && !c.getWasDerivedFroms().equals(oldC.getWasDerivedFroms())) {
URI wasDerivedFrom = (URI) c.getWasDerivedFroms().toArray()[0];
Set<TopLevel> topLevels = SBOLDoc.getByWasDerivedFrom(wasDerivedFrom);
for (TopLevel topLevel : topLevels) {
if (topLevel instanceof ComponentDefinition) {
return (ComponentDefinition) topLevel;
}
}
do {
displayId = displayId + "_";
identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
} while (SBOLDoc.getComponentDefinition(identity) != null);
c = c.copy(URIPrefix, displayId, version);
if (identity != componentDef.getIdentity()) {
c.clearWasDerivedFroms();
c.addWasDerivedFrom(componentDef.getIdentity());
}
SBOLDoc.addComponentDefinition(c);
} else if (dropObjectsWithDuplicateURIs) {
return oldC;
} else {
if (!c.equals(oldC)) {
throw new SBOLValidationException("sbol-10202", c);
}
}
return c;
}
Also used :
HashSet(java.util.HashSet)
Set(java.util.Set)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI)
URI(java.net.URI)
NestedDocument(org.sbolstandard.core.datatree.NestedDocument)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
StringifyQName(org.sbolstandard.core.io.json.StringifyQName)
QName(javax.xml.namespace.QName)
IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument)
Example 23 with Component
use of org.sbolstandard.core2.Component in project libSBOLj by SynBioDex.
the class SBOLReader method parseComponentDefinition.
/**
* @param SBOLDoc
* @param topLevel
* @param nested
* @return
* @throws SBOLValidationException if either of the following conditions is satisfied:
* <ul>
* <li>any of the following SBOL validation rules was violated:
* 10202, 10203, 10204, 10206, 10208, 10212, 10213, 10502, 10507, 10512, or</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link #parseComponent(NestedDocument, Map)},</li>
* <li>{@link #parseSequenceAnnotation(NestedDocument, Map)},</li>
* <li>{@link ComponentDefinition#ComponentDefinition(URI, Set)}, </li>
* <li>{@link ComponentDefinition#setDisplayId(String)}, </li>
* <li>{@link ComponentDefinition#setVersion(String)}, </li>
* <li>{@link ComponentDefinition#setWasDerivedFrom(URI)}, </li>
* <li>{@link Identified#setAnnotations(List)},</li>
* <li>{@link ComponentDefinition#setComponents(Set)},</li>
* <li>{@link ComponentDefinition#setSequenceAnnotations(Set)},</li>
* <li>{@link ComponentDefinition#setSequenceConstraints(Set)}, or</li>
* <li>{@link SBOLDocument#addComponentDefinition(ComponentDefinition)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings("unchecked")
private static ComponentDefinition parseComponentDefinition(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;
String version = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
Set<URI> attachments = new HashSet<>();
Set<URI> type = new HashSet<>();
Set<URI> roles = new HashSet<>();
Set<URI> sequences = new HashSet<>();
Set<Component> components = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
Set<SequenceAnnotation> sequenceAnnotations = new HashSet<>();
Set<SequenceConstraint> sequenceConstraints = new HashSet<>();
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.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.ComponentDefinition.type)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10502", topLevel.getIdentity());
}
type.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.roles)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10507", topLevel.getIdentity());
}
roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasComponent) || namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSubComponent)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Component.Component)) {
throw new SBOLValidationException("sbol-10519", topLevel.getIdentity());
}
components.add(parseComponent(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), nested));
} else {
URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
NestedDocument<QName> nestedDocument = nested.get(uri);
if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Component.Component)) {
throw new SBOLValidationException("sbol-10519", topLevel.getIdentity());
}
components.add(parseComponent(SBOLDoc, nested.get(uri), nested));
}
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequence)) {
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
}
sequences.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getValue() instanceof IdentifiableDocument) {
if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Sequence.Sequence)) {
Sequence sequence = parseSequence(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
sequences.add(sequence.getIdentity());
} else {
throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
}
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceAnnotations)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceAnnotation.SequenceAnnotation)) {
throw new SBOLValidationException("sbol-10521", topLevel.getIdentity());
}
sequenceAnnotations.add(parseSequenceAnnotation(((NestedDocument<QName>) namedProperty.getValue()), nested));
} else {
URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
NestedDocument<QName> nestedDocument = nested.get(uri);
if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceAnnotation.SequenceAnnotation)) {
throw new SBOLValidationException("sbol-10521", topLevel.getIdentity());
}
sequenceAnnotations.add(parseSequenceAnnotation(nested.get(uri), nested));
}
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceConstraints)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceConstraint.SequenceConstraint)) {
throw new SBOLValidationException("sbol-10524", topLevel.getIdentity());
}
sequenceConstraints.add(parseSequenceConstraint(((NestedDocument<QName>) namedProperty.getValue())));
} else {
URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
NestedDocument<QName> nestedDocument = nested.get(uri);
if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceConstraint.SequenceConstraint)) {
throw new SBOLValidationException("sbol-10524", topLevel.getIdentity());
}
sequenceConstraints.add(parseSequenceConstraint(nested.get(uri)));
}
} 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.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.TopLevel.hasAttachment)) {
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-XXXXX", 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-XXXXX", topLevel.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
}
} else {
annotations.add(new Annotation(namedProperty));
}
}
// ComponentDefinition c = SBOLDoc.createComponentDefinition(topLevel.getIdentity(), type, roles);
// c.setPersistentIdentity(topLevel.getOptionalUriPropertyValue(Sbol2Terms.Identified.persistentIdentity));
// ComponentDefinition c = SBOLDoc.createComponentDefinition(topLevel.getIdentity(), type);
ComponentDefinition c = new ComponentDefinition(topLevel.getIdentity(), type);
if (roles != null)
c.setRoles(roles);
if (displayId != null)
c.setDisplayId(displayId);
if (persistentIdentity != null)
c.setPersistentIdentity(persistentIdentity);
if (!sequences.isEmpty())
c.setSequences(sequences);
if (!components.isEmpty())
c.setComponents(components);
if (!sequenceAnnotations.isEmpty())
c.setSequenceAnnotations(sequenceAnnotations);
if (!sequenceConstraints.isEmpty())
c.setSequenceConstraints(sequenceConstraints);
if (name != null)
c.setName(name);
if (description != null)
c.setDescription(description);
if (!annotations.isEmpty())
c.setAnnotations(annotations);
if (version != null)
c.setVersion(version);
c.setWasDerivedFroms(wasDerivedFroms);
c.setWasGeneratedBys(wasGeneratedBys);
c.setAttachments(attachments);
ComponentDefinition oldC = SBOLDoc.getComponentDefinition(topLevel.getIdentity());
if (oldC == null) {
SBOLDoc.addComponentDefinition(c);
} else {
if (!c.equals(oldC)) {
throw new SBOLValidationException("sbol-10202", c);
}
}
return c;
}
Also used :
StringifyQName(org.sbolstandard.core.io.json.StringifyQName)
QName(javax.xml.namespace.QName)
ArrayList(java.util.ArrayList)
URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI)
URI(java.net.URI)
NestedDocument(org.sbolstandard.core.datatree.NestedDocument)
IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
Example 24 with Component
use of org.sbolstandard.core2.Component 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);
}
}
Also used :
URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI)
URI(java.net.URI)
Example 25 with Component
use of org.sbolstandard.core2.Component 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);
}
Also used :
URI(java.net.URI)
URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI)
Aggregations
URI (java.net.URI)25
URIcompliance.createCompliantURI (org.sbolstandard.core2.URIcompliance.createCompliantURI)22
HashSet (java.util.HashSet)7
ComponentDefinition (org.sbolstandard.core2.ComponentDefinition)7
ArrayList (java.util.ArrayList)6
QName (javax.xml.namespace.QName)6
Point (java.awt.Point)5
Component (org.powerbot.script.rt6.Component)5
SBOLDocument (org.sbolstandard.core2.SBOLDocument)5
Condition (org.powerbot.script.Condition)4
Literal (org.sbolstandard.core.datatree.Literal)4
NestedDocument (org.sbolstandard.core.datatree.NestedDocument)4
StringifyQName (org.sbolstandard.core.io.json.StringifyQName)4
Component (org.sbolstandard.core2.Component)4
IdentifiableDocument (org.sbolstandard.core.datatree.IdentifiableDocument)3
FunctionalComponent (org.sbolstandard.core2.FunctionalComponent)3
Sequence (org.sbolstandard.core2.Sequence)3
SequenceAnnotation (org.sbolstandard.core2.SequenceAnnotation)3
Font (java.awt.Font)2
AtomicInteger (java.util.concurrent.atomic.AtomicInteger)2
