Example 11 with NestedDocument
use of org.sbolstandard.core.datatree.NestedDocument in project libSBOLj by SynBioDex.
the class SBOLReader method parseSequenceAnnotation.
/**
* @param sequenceAnnotation
* @param nested
* @return
* @throws SBOLValidationException if either of the following conditions is satisfied:
* <ul>
* <li>any of the following SBOL validation rules was violated:
* 10203, 10204, 10206, 10208, 10212, 10213,
* 10512,
* 10904; or
*</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link #parseLocation(NestedDocument)},</li>
* <li>{@link SequenceAnnotation#SequenceAnnotation(URI, Set)},</li>
* <li>{@link SequenceAnnotation#setDisplayId(String)},</li>
* <li>{@link SequenceAnnotation#setVersion(String)},</li>
* <li>{@link SequenceAnnotation#setComponent(URI)},</li>
* <li>{@link SequenceAnnotation#setWasDerivedFrom(URI)}, or</li>
* <li>{@link Identified#setAnnotations(List)}.</li>
* </ul>
* </li>
* </ul>
*/
private static SequenceAnnotation parseSequenceAnnotation(NestedDocument<QName> sequenceAnnotation, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
// URIcompliance.extractDisplayId(sequenceAnnotation.getIdentity());
String displayId = null;
String name = null;
String description = null;
// URI.create(URIcompliance.extractPersistentId(sequenceAnnotation.getIdentity()));
URI persistentIdentity = null;
Location location = null;
URI componentURI = null;
String version = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
Set<URI> roles = new HashSet<>();
Set<Location> locations = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
for (NamedProperty<QName> namedProperty : sequenceAnnotation.getProperties()) {
if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10203", sequenceAnnotation.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", sequenceAnnotation.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10206", sequenceAnnotation.getIdentity());
}
version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.SequenceAnnotation.roles)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10906", sequenceAnnotation.getIdentity());
}
roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.Location.Location)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !(nestedDocument.getType().equals(Sbol2Terms.Range.Range) || nestedDocument.getType().equals(Sbol2Terms.Cut.Cut) || nestedDocument.getType().equals(Sbol2Terms.GenericLocation.GenericLocation))) {
throw new SBOLValidationException("sbol-10902", sequenceAnnotation.getIdentity());
}
location = parseLocation((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.Range.Range) || nestedDocument.getType().equals(Sbol2Terms.Cut.Cut) || nestedDocument.getType().equals(Sbol2Terms.GenericLocation.GenericLocation))) {
throw new SBOLValidationException("sbol-10902", sequenceAnnotation.getIdentity());
}
location = parseLocation(nested.get(uri));
}
locations.add(location);
} else if (namedProperty.getName().equals(Sbol2Terms.SequenceAnnotation.hasComponent)) {
if (!(namedProperty.getValue() instanceof Literal) || componentURI != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10904", sequenceAnnotation.getIdentity());
}
componentURI = URI.create(((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", sequenceAnnotation.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", sequenceAnnotation.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", sequenceAnnotation.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", sequenceAnnotation.getIdentity());
}
wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
annotations.add(new Annotation(namedProperty));
}
}
SequenceAnnotation s = new SequenceAnnotation(sequenceAnnotation.getIdentity(), locations);
if (persistentIdentity != null)
s.setPersistentIdentity(persistentIdentity);
if (version != null)
s.setVersion(version);
if (displayId != null)
s.setDisplayId(displayId);
if (componentURI != null)
s.setComponent(componentURI);
if (name != null)
s.setName(name);
if (description != null)
s.setDescription(description);
s.setWasDerivedFroms(wasDerivedFroms);
s.setWasGeneratedBys(wasGeneratedBys);
if (!annotations.isEmpty())
s.setAnnotations(annotations);
if (!roles.isEmpty())
s.setRoles(roles);
// }
return s;
}
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)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
Example 12 with NestedDocument
use of org.sbolstandard.core.datatree.NestedDocument 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 13 with NestedDocument
use of org.sbolstandard.core.datatree.NestedDocument 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 14 with NestedDocument
use of org.sbolstandard.core.datatree.NestedDocument in project libSBOLj by SynBioDex.
the class SBOLReader method parseCollectionV1.
/**
* @param SBOLDoc
* @param topLevel
* @return
* @throws SBOLConversionException
* @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 Collection#Collection(URI)},</li>
* <li>{@link Collection#setVersion(String)},</li>
* <li>{@link Collection#setWasDerivedFrom(URI)},</li>
* <li>{@link Collection#setDisplayId(String)},</li>
* <li>{@link Collection#setMembers(Set)},</li>
* <li>{@link Identified#setAnnotations(List)}, or</li>
* <li>{@link SBOLDocument#addCollection(Collection)}; or</li>
* </ul>
* </li>
* <li>the following SBOL validation rule was violated: 10202.</li>
* </ul>
*/
private static Collection parseCollectionV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException, SBOLConversionException {
URI identity = topLevel.getIdentity();
URI persistentIdentity = null;
String displayId = null;
String name = null;
String description = null;
Set<URI> members = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
if (URIPrefix != null) {
displayId = URIcompliance.findDisplayId(topLevel.getIdentity().toString());
identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
persistentIdentity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, "", typesInURI);
}
for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
if (namedProperty.getName().equals(Sbol1Terms.Collection.displayId)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
displayId = URIcompliance.fixDisplayId(displayId);
if (URIPrefix != null) {
identity = createCompliantURI(URIPrefix, TopLevel.COLLECTION, displayId, version, typesInURI);
persistentIdentity = createCompliantURI(URIPrefix, TopLevel.COLLECTION, displayId, "", typesInURI);
}
} else if (namedProperty.getName().equals(Sbol1Terms.Collection.name)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((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(Sbol1Terms.Collection.description)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((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(Sbol1Terms.Collection.component)) {
if (namedProperty.getValue() instanceof Literal) {
members.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
members.add(parseDnaComponentV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity());
}
} else {
annotations.add(new Annotation(namedProperty));
}
}
// Collection c = SBOLDoc.createCollection(identity);
Collection c = new Collection(identity);
if (persistentIdentity != null) {
c.setPersistentIdentity(persistentIdentity);
c.setVersion(version);
}
if (identity != topLevel.getIdentity())
c.addWasDerivedFrom(topLevel.getIdentity());
if (displayId != null)
c.setDisplayId(displayId);
if (name != null)
c.setName(name);
if (description != null)
c.setDescription(description);
if (!members.isEmpty())
c.setMembers(members);
if (!annotations.isEmpty())
c.setAnnotations(annotations);
Collection oldC = SBOLDoc.getCollection(topLevel.getIdentity());
if (oldC == null) {
SBOLDoc.addCollection(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)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
Example 15 with NestedDocument
use of org.sbolstandard.core.datatree.NestedDocument in project libSBOLj by SynBioDex.
the class SBOLWriter method formatParticipations.
private static List<NestedDocument<QName>> formatParticipations(Set<Participation> participations) {
List<NestedDocument<QName>> nestedDoc = new ArrayList<>();
for (Participation p : participations) {
List<NamedProperty<QName>> list = new ArrayList<>();
formatCommonIdentifiedData(list, p);
for (URI r : p.getRoles()) list.add(NamedProperty(Sbol2Terms.Participation.role, r));
list.add(NamedProperty(Sbol2Terms.Participation.hasParticipant, p.getParticipantURI()));
nestedDoc.add(NestedDocument(Sbol2Terms.Participation.Participation, p.getIdentity(), NamedProperties(list)));
}
return nestedDoc;
}
Also used :
NamedProperty(org.sbolstandard.core.datatree.NamedProperty)
NamedProperty(org.sbolstandard.core.datatree.Datatree.NamedProperty)
ArrayList(java.util.ArrayList)
NestedDocument(org.sbolstandard.core.datatree.NestedDocument)
NestedDocument(org.sbolstandard.core.datatree.Datatree.NestedDocument)
URI(java.net.URI)
Aggregations
URI (java.net.URI)16
ArrayList (java.util.ArrayList)16
NestedDocument (org.sbolstandard.core.datatree.NestedDocument)16
QName (javax.xml.namespace.QName)15
StringifyQName (org.sbolstandard.core.io.json.StringifyQName)15
HashSet (java.util.HashSet)13
Literal (org.sbolstandard.core.datatree.Literal)13
URIcompliance.createCompliantURI (org.sbolstandard.core2.URIcompliance.createCompliantURI)13
IdentifiableDocument (org.sbolstandard.core.datatree.IdentifiableDocument)9
NamedProperty (org.sbolstandard.core.datatree.Datatree.NamedProperty)3
NestedDocument (org.sbolstandard.core.datatree.Datatree.NestedDocument)3
NamedProperty (org.sbolstandard.core.datatree.NamedProperty)3
HashMap (java.util.HashMap)1
Set (java.util.Set)1
DateTime (org.joda.time.DateTime)1
DateTimeFormatter (org.joda.time.format.DateTimeFormatter)1
