Example 31 with Annotation
use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.
the class SBOLReader method parseGenericTopLevel.
/**
* @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 GenericTopLevel#GenericTopLevel(URI, QName)}, </li>
* <li>{@link GenericTopLevel#setDisplayId(String)}, </li>
* <li>{@link GenericTopLevel#setVersion(String)}, </li>
* <li>{@link GenericTopLevel#setWasDerivedFrom(URI)}, </li>
* <li>{@link Identified#setAnnotations(List)}, or</li>
* <li>{@link SBOLDocument#addGenericTopLevel(GenericTopLevel)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings("unchecked")
private static GenericTopLevel parseGenericTopLevel(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) 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<>();
QName type = topLevel.getType();
List<Annotation> annotations = new ArrayList<>();
for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
if (namedProperty.getName().equals(Sbol2Terms.Description.type)) {
String typeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
String nameSpace = URIcompliance.extractNamespace(URI.create(typeStr));
String localPart = URIcompliance.extractDisplayId(URI.create(typeStr));
String prefix = null;
if (nameSpace == null) {
if (typeStr.lastIndexOf('/') > typeStr.lastIndexOf('#')) {
if (typeStr.lastIndexOf('/') > typeStr.lastIndexOf(':')) {
nameSpace = typeStr.substring(0, typeStr.lastIndexOf('/') + 1);
localPart = typeStr.substring(typeStr.lastIndexOf('/') + 1);
} else {
nameSpace = typeStr.substring(0, typeStr.lastIndexOf(':') + 1);
localPart = typeStr.substring(typeStr.lastIndexOf(':') + 1);
}
} else if (typeStr.lastIndexOf('#') > typeStr.lastIndexOf(':')) {
nameSpace = typeStr.substring(0, typeStr.lastIndexOf('#') + 1);
localPart = typeStr.substring(typeStr.lastIndexOf('#') + 1);
} else {
nameSpace = typeStr.substring(0, typeStr.lastIndexOf(':') + 1);
localPart = typeStr.substring(typeStr.lastIndexOf(':') + 1);
}
prefix = SBOLDoc.getNamespacePrefix(URI.create(nameSpace));
if (prefix == null) {
prefix = "ns0";
int prefixCnt = 0;
while (SBOLDoc.getNamespace(prefix) != null) {
prefixCnt++;
prefix = "ns" + prefixCnt;
}
SBOLDoc.addNamespace(new QName(nameSpace, localPart, prefix));
}
} else {
prefix = SBOLDoc.getNamespacePrefix(URI.create(nameSpace));
}
if (!nameSpace.equals(Sbol2Terms.sbol2.getNamespaceURI()))
type = new QName(nameSpace, localPart, prefix);
} 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.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));
}
}
// GenericTopLevel t = SBOLDoc.createGenericTopLevel(topLevel.getIdentity(), topLevel.getType());
GenericTopLevel t = new GenericTopLevel(topLevel.getIdentity(), type);
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);
GenericTopLevel oldG = SBOLDoc.getGenericTopLevel(topLevel.getIdentity());
if (oldG == null) {
SBOLDoc.addGenericTopLevel(t);
} else {
if (!t.equals(oldG)) {
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 32 with Annotation
use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.
the class SBOLReader method parseSequence.
/**
* @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, 10402, 10403, ; or</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link Sequence#Sequence(URI, String, URI)}, </li>
* <li>{@link Sequence#setDisplayId(String)}, </li>
* <li>{@link Sequence#setVersion(String)}, </li>
* <li>{@link Sequence#setWasDerivedFrom(URI)}, </li>
* <li>{@link Identified#setAnnotations(List)}, or</li>
* <li>{@link SBOLDocument#addSequence(Sequence)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings("unchecked")
private static Sequence parseSequence(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) 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;
String elements = null;
URI encoding = 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.Sequence.elements)) {
if (!(namedProperty.getValue() instanceof Literal) || elements != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10402", topLevel.getIdentity());
}
elements = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Sequence.encoding)) {
if (!(namedProperty.getValue() instanceof Literal) || encoding != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10403", topLevel.getIdentity());
}
encoding = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
if (encoding.toString().equals("http://dx.doi.org/10.1021/bi00822a023")) {
encoding = Sequence.IUPAC_DNA;
}
} 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));
}
}
// Sequence sequence = SBOLDoc.createSequence(topLevel.getIdentity(), elements, encoding);
Sequence sequence = new Sequence(topLevel.getIdentity(), elements, encoding);
if (persistentIdentity != null)
sequence.setPersistentIdentity(persistentIdentity);
if (version != null)
sequence.setVersion(version);
if (displayId != null)
sequence.setDisplayId(displayId);
if (name != null)
sequence.setName(name);
if (description != null)
sequence.setDescription(description);
sequence.setWasDerivedFroms(wasDerivedFroms);
sequence.setWasGeneratedBys(wasGeneratedBys);
sequence.setAttachments(attachments);
if (!annotations.isEmpty())
sequence.setAnnotations(annotations);
Sequence oldS = SBOLDoc.getSequence(topLevel.getIdentity());
if (oldS == null) {
SBOLDoc.addSequence(sequence);
} else {
if (!sequence.equals(oldS)) {
throw new SBOLValidationException("sbol-10202", sequence);
}
}
return sequence;
}
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 33 with Annotation
use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.
the class SBOLReader method parseCut.
/**
* @param typeCut
* @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,
* 11002, 11202; or
*</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link Cut#Cut(URI, int)},</li>
* <li>{@link Cut#setDisplayId(String)},</li>
* <li>{@link Cut#setVersion(String)},</li>
* <li>{@link Cut#setWasDerivedFrom(URI)}, or</li>
* <li>{@link Identified#setAnnotations(List)}.</li>
* </ul>
* </li>
* </ul>
*/
private static Cut parseCut(NestedDocument<QName> typeCut) throws SBOLValidationException {
// URIcompliance.extractDisplayId(typeCut.getIdentity());
String displayId = null;
String name = null;
String description = null;
// URI.create(URIcompliance.extractPersistentId(typeCut.getIdentity()));
URI persistentIdentity = null;
Integer at = null;
URI orientation = null;
String version = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
for (NamedProperty<QName> namedProperty : typeCut.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", typeCut.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", typeCut.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", typeCut.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", typeCut.getIdentity());
}
description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Cut.at)) {
if (!(namedProperty.getValue() instanceof Literal) || at != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-11202", typeCut.getIdentity());
}
String temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
// at = Integer.parseInt(temp);
try {
at = Integer.parseInt(temp);
} catch (NumberFormatException e) {
throw new SBOLValidationException("sbol-11202", typeCut.getIdentity());
}
} else if (namedProperty.getName().equals(Sbol2Terms.Cut.orientation)) {
if (!(namedProperty.getValue() instanceof Literal) || orientation != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-11002", typeCut.getIdentity());
}
orientation = 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", typeCut.getIdentity());
}
version = ((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", typeCut.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", typeCut.getIdentity());
}
wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
annotations.add(new Annotation(namedProperty));
}
}
if (at == null) {
throw new SBOLValidationException("Cut requires at property.");
}
Cut c = new Cut(typeCut.getIdentity(), at);
if (persistentIdentity != null)
c.setPersistentIdentity(persistentIdentity);
if (displayId != null)
c.setDisplayId(displayId);
if (name != null)
c.setName(name);
if (description != null)
c.setDescription(description);
if (orientation != null)
try {
c.setOrientation(OrientationType.convertToOrientationType(orientation));
} catch (SBOLValidationException e) {
throw new SBOLValidationException("sbol-11002", c);
}
if (version != null)
c.setVersion(version);
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)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
Example 34 with Annotation
use of org.sbolstandard.core2.Annotation 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 35 with Annotation
use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.
the class SBOLReader method parseAttachment.
@SuppressWarnings("unchecked")
private static Attachment parseAttachment(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) 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;
URI source = null;
URI format = null;
Long size = null;
String hash = 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.Attachment.source)) {
if (!(namedProperty.getValue() instanceof Literal) || source != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-13202", topLevel.getIdentity());
}
source = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getName().equals(Sbol2Terms.Attachment.format)) {
if (!(namedProperty.getValue() instanceof Literal) || format != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-13204", topLevel.getIdentity());
}
format = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getName().equals(Sbol2Terms.Attachment.size)) {
if (!(namedProperty.getValue() instanceof Literal) || size != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-13207", topLevel.getIdentity());
}
size = Long.valueOf(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getName().equals(Sbol2Terms.Attachment.hash)) {
if (!(namedProperty.getValue() instanceof Literal) || hash != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-13208", topLevel.getIdentity());
}
hash = ((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));
}
}
Attachment a = new Attachment(topLevel.getIdentity(), source);
if (persistentIdentity != null)
a.setPersistentIdentity(persistentIdentity);
if (version != null)
a.setVersion(version);
if (displayId != null)
a.setDisplayId(displayId);
if (name != null)
a.setName(name);
if (description != null)
a.setDescription(description);
a.setWasDerivedFroms(wasDerivedFroms);
a.setWasGeneratedBys(wasGeneratedBys);
a.setAttachments(attachments);
if (!annotations.isEmpty())
a.setAnnotations(annotations);
if (format != null)
a.setFormat(format);
if (size != null)
a.setSize(size);
if (hash != null)
a.setHash(hash);
Attachment oldA = SBOLDoc.getAttachment(topLevel.getIdentity());
if (oldA == null) {
SBOLDoc.addAttachment(a);
} else {
if (!a.equals(oldA)) {
throw new SBOLValidationException("sbol-10202", a);
}
}
return a;
}
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)
Aggregations
URI (java.net.URI)33
QName (javax.xml.namespace.QName)33
ArrayList (java.util.ArrayList)31
HashSet (java.util.HashSet)31
URIcompliance.createCompliantURI (org.sbolstandard.core2.URIcompliance.createCompliantURI)31
Literal (org.sbolstandard.core.datatree.Literal)30
StringifyQName (org.sbolstandard.core.io.json.StringifyQName)30
IdentifiableDocument (org.sbolstandard.core.datatree.IdentifiableDocument)17
NestedDocument (org.sbolstandard.core.datatree.NestedDocument)13
Annotation (zipkin2.Annotation)11
Map (java.util.Map)8
ComponentDefinition (org.sbolstandard.core2.ComponentDefinition)7
SBOLDocument (org.sbolstandard.core2.SBOLDocument)5
Endpoint (zipkin2.Endpoint)5
Activity (org.sbolstandard.core2.Activity)4
LinkedHashMap (java.util.LinkedHashMap)3
Test (org.junit.Test)3
Annotation (org.sbolstandard.core2.Annotation)3
Span (zipkin2.Span)3
JsonToken (com.fasterxml.jackson.core.JsonToken)2
