Example 6 with IdentifiableDocument
use of org.sbolstandard.core.datatree.IdentifiableDocument 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-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 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 {
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;
}
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)
IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
Example 7 with IdentifiableDocument
use of org.sbolstandard.core.datatree.IdentifiableDocument in project libSBOLj by SynBioDex.
the class SBOLReader method parseAgent.
@SuppressWarnings("unchecked")
private static Agent parseAgent(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException {
String displayId = null;
String name = null;
String description = null;
URI persistentIdentity = 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.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.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.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.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));
}
}
Agent t = new Agent(topLevel.getIdentity());
if (persistentIdentity != null)
t.setPersistentIdentity(persistentIdentity);
if (version != null)
t.setVersion(version);
if (displayId != null)
t.setDisplayId(displayId);
if (name != null)
t.setName(name);
if (description != null)
t.setDescription(description);
t.setWasDerivedFroms(wasDerivedFroms);
t.setWasGeneratedBys(wasGeneratedBys);
t.setAttachments(attachments);
if (!annotations.isEmpty())
t.setAnnotations(annotations);
Agent oldA = SBOLDoc.getAgent(topLevel.getIdentity());
if (oldA == null) {
SBOLDoc.addAgent(t);
} else {
if (!t.equals(oldA)) {
throw new SBOLValidationException("sbol-10202", t);
}
}
return t;
}
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)
IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
Example 8 with IdentifiableDocument
use of org.sbolstandard.core.datatree.IdentifiableDocument in project libSBOLj by SynBioDex.
the class SBOLReader method parseModule.
/**
* @param module
* @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, 11604, 11702; or
*</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
* <li>{@link Module#Module(URI, URI)},</li>
* <li>{@link Module#setDisplayId(String)},</li>
* <li>{@link Module#setVersion(String)},</li>
* <li>{@link Module#setWasDerivedFrom(URI)},</li>
* <li>{@link Identified#setAnnotations(List)}, or</li>
* <li>{@link Module#setMapsTos(Set)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings("unchecked")
private static Module parseModule(SBOLDocument SBOLDoc, NestedDocument<QName> module, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
// URIcompliance.extractDisplayId(module.getIdentity());
String displayId = null;
String name = null;
String description = null;
// URI.create(URIcompliance.extractPersistentId(module.getIdentity()));
URI persistentIdentity = null;
String version = null;
URI definitionURI = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
Set<MapsTo> mappings = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
for (NamedProperty<QName> namedProperty : module.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", module.getIdentity());
}
persistentIdentity = URI.create(((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", module.getIdentity());
}
version = ((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", module.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapsTo)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-11706", module.getIdentity());
}
mappings.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), false));
} 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.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-11706", module.getIdentity());
}
mappings.add(parseMapsTo(nested.get(uri), false));
}
} else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapping)) {
System.err.println("Warning: tag should be sbol:mapTo, not sbol:mapping.");
if (namedProperty.getValue() instanceof NestedDocument) {
mappings.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), true));
} else {
URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
mappings.add(parseMapsTo(nested.get(uri), true));
}
} else if (namedProperty.getName().equals(Sbol2Terms.Module.hasDefinition)) {
if (definitionURI != null) {
throw new SBOLValidationException("sbol-11702", module.getIdentity());
}
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-11702", module.getIdentity());
}
definitionURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getValue() instanceof IdentifiableDocument) {
if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ModuleDefinition.ModuleDefinition)) {
ModuleDefinition moduleDefinition = parseModuleDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
definitionURI = moduleDefinition.getIdentity();
} else {
throw new SBOLValidationException("sbol-11702", module.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-11702", module.getIdentity());
}
} 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", module.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", module.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", module.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", module.getIdentity());
}
wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
annotations.add(new Annotation(namedProperty));
}
}
Module submodule = new Module(module.getIdentity(), definitionURI);
if (persistentIdentity != null)
submodule.setPersistentIdentity(persistentIdentity);
if (version != null)
submodule.setVersion(version);
if (displayId != null)
submodule.setDisplayId(displayId);
if (!mappings.isEmpty())
submodule.setMapsTos(mappings);
if (name != null)
submodule.setName(name);
if (description != null)
submodule.setDescription(description);
submodule.setWasDerivedFroms(wasDerivedFroms);
submodule.setWasGeneratedBys(wasGeneratedBys);
if (!annotations.isEmpty())
submodule.setAnnotations(annotations);
return submodule;
}
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 9 with IdentifiableDocument
use of org.sbolstandard.core.datatree.IdentifiableDocument in project libSBOLj by SynBioDex.
the class SBOLReader method parseComponent.
/**
* @param component
* @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, 10519, 10602, 10607; or
*</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
* <li>{@link Component#Component(URI, AccessType, URI)},</li>
* <li>{@link Component#setVersion(String)},</li>
* <li>{@link Component#setDisplayId(String)},</li>
* <li>{@link Component#setAccess(AccessType)},</li>
* <li>{@link Component#setMapsTos(Set)},</li>
* <li>{@link Component#setDefinition(URI)},</li>
* <li>{@link Component#setWasDerivedFrom(URI)}, or</li>
* <li>{@link Identified#setAnnotations(List)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings("unchecked")
private static Component parseComponent(SBOLDocument SBOLDoc, NestedDocument<QName> component, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
// URIcompliance.extractDisplayId(component.getIdentity());
String displayId = null;
String name = null;
String description = null;
// URI.create(URIcompliance.extractPersistentId(component.getIdentity()));
URI persistentIdentity = null;
String version = null;
URI subComponentURI = null;
AccessType access = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
Set<URI> roles = new HashSet<>();
URI roleIntegration = null;
List<Annotation> annotations = new ArrayList<>();
Set<MapsTo> mapsTo = new HashSet<>();
for (NamedProperty<QName> namedProperty : component.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", component.getIdentity());
}
persistentIdentity = URI.create(((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", component.getIdentity());
}
version = ((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", component.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Component.roles)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10702", component.getIdentity());
}
roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.Component.roleIntegration)) {
if (!(namedProperty.getValue() instanceof Literal) || roleIntegration != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10708", component.getIdentity());
}
roleIntegration = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.access)) {
if (!(namedProperty.getValue() instanceof Literal) || access != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10607", component.getIdentity());
}
String accessTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
if (accessTypeStr.startsWith("http://www.sbolstandard.org/")) {
System.err.println("Warning: namespace for access types should be http://sbols.org/v2#");
accessTypeStr = accessTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
}
try {
access = AccessType.convertToAccessType(URI.create(accessTypeStr));
} catch (SBOLValidationException e) {
throw new SBOLValidationException("sbol-10607", component.getIdentity());
}
} else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapsTo)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-10606", component.getIdentity());
}
mapsTo.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), false));
} 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.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-10606", component.getIdentity());
}
mapsTo.add(parseMapsTo(nested.get(uri), false));
}
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.hasComponentDefinition)) {
if (subComponentURI != null) {
throw new SBOLValidationException("sbol-10602", component.getIdentity());
}
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-10602", component.getIdentity());
}
subComponentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getValue() instanceof IdentifiableDocument) {
if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
ComponentDefinition componentDefinition = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
subComponentURI = componentDefinition.getIdentity();
} else {
throw new SBOLValidationException("sbol-10602", component.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-10602", component.getIdentity());
}
} 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", component.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", component.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", component.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", component.getIdentity());
}
wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
annotations.add(new Annotation(namedProperty));
}
}
Component c = new Component(component.getIdentity(), access, subComponentURI);
if (persistentIdentity != null)
c.setPersistentIdentity(persistentIdentity);
if (version != null)
c.setVersion(version);
if (displayId != null)
c.setDisplayId(displayId);
if (access != null)
c.setAccess(access);
if (roleIntegration != null)
try {
c.setRoleIntegration(RoleIntegrationType.convertToRoleIntegrationType(roleIntegration));
} catch (SBOLValidationException e) {
throw new SBOLValidationException("sbol-10708", c);
}
if (!roles.isEmpty())
c.setRoles(roles);
if (!mapsTo.isEmpty())
c.setMapsTos(mapsTo);
if (subComponentURI != null)
c.setDefinition(subComponentURI);
if (name != null)
c.setName(name);
if (description != null)
c.setDescription(description);
c.setWasDerivedFroms(wasDerivedFroms);
c.setWasGeneratedBys(wasGeneratedBys);
if (!annotations.isEmpty())
c.setAnnotations(annotations);
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 10 with IdentifiableDocument
use of org.sbolstandard.core.datatree.IdentifiableDocument in project libSBOLj by SynBioDex.
the class SBOLReader method parseCollection.
/**
* @param SBOLDoc
* @param topLevel
* @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, 12102; or</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link Collection#Collection(URI)}, </li>
* <li>{@link Collection#setDisplayId(String)}, </li>
* <li>{@link Collection#setVersion(String)}, </li>
* <li>{@link Collection#setMembers(Set)}, </li>
* <li>{@link Collection#setWasDerivedFrom(URI)}, </li>
* <li>{@link Identified#setAnnotations(List)}, or</li>
* <li>{@link SBOLDocument#addCollection(Collection)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings({ "rawtypes", "unchecked" })
private static Collection parseCollection(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> members = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
for (NamedProperty<QName> namedProperty : topLevel.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", topLevel.getIdentity());
}
persistentIdentity = URI.create(((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", topLevel.getIdentity());
}
version = ((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.Collection.hasMembers)) {
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
}
members.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getValue() instanceof NestedDocument) {
if (((IdentifiableDocument) namedProperty).getType().equals(Sbol2Terms.Collection.Collection))
parseCollection(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ModuleDefinition.ModuleDefinition))
parseModuleDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Model.Model))
parseModel(SBOLDoc, (IdentifiableDocument) namedProperty);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Sequence.Sequence))
parseSequence(SBOLDoc, (IdentifiableDocument) namedProperty);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ComponentDefinition.ComponentDefinition))
parseComponentDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.CombinatorialDerivation.CombinatorialDerivation))
parseCombinatorialDerivation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Implementation.Implementation))
parseImplementation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Attachment.Attachment))
parseAttachment(SBOLDoc, (IdentifiableDocument) namedProperty);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Activity.Activity))
parseActivity(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Agent.Agent))
parseAgent(SBOLDoc, (IdentifiableDocument) namedProperty);
else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Plan.Plan))
parsePlan(SBOLDoc, (IdentifiableDocument) namedProperty);
else
parseGenericTopLevel(SBOLDoc, (IdentifiableDocument) namedProperty);
} else {
throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
}
} 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));
}
}
Collection c = new Collection(topLevel.getIdentity());
if (displayId != null)
c.setDisplayId(displayId);
if (version != null)
c.setVersion(version);
if (persistentIdentity != null)
c.setPersistentIdentity(persistentIdentity);
if (!members.isEmpty())
c.setMembers(members);
if (name != null)
c.setName(name);
if (description != null)
c.setDescription(description);
c.setWasDerivedFroms(wasDerivedFroms);
c.setWasGeneratedBys(wasGeneratedBys);
c.setAttachments(attachments);
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)
IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
Aggregations
URI (java.net.URI)17
ArrayList (java.util.ArrayList)17
HashSet (java.util.HashSet)17
QName (javax.xml.namespace.QName)17
IdentifiableDocument (org.sbolstandard.core.datatree.IdentifiableDocument)17
Literal (org.sbolstandard.core.datatree.Literal)17
StringifyQName (org.sbolstandard.core.io.json.StringifyQName)17
URIcompliance.createCompliantURI (org.sbolstandard.core2.URIcompliance.createCompliantURI)17
NestedDocument (org.sbolstandard.core.datatree.NestedDocument)9
HashMap (java.util.HashMap)1
Set (java.util.Set)1
DateTime (org.joda.time.DateTime)1
DateTimeFormatter (org.joda.time.format.DateTimeFormatter)1
