/**
* Returns the identifier of an LSRN-typed Resource
*
* @param lsrnNode
* @return the identifier
*/
public static String getID(Resource lsrnNode) {
Set<String> namespaces = new HashSet<String>();
for (Iterator<Resource> types = RdfUtils.getTypes(lsrnNode); types.hasNext(); ) {
Resource type = types.next();
if (type.isURIResource()) {
String ns = getNamespaceFromLSRNTypeURI(type.getURI());
if (ns != null) namespaces.add(ns);
}
}
Iterator<Resource> ids =
RdfUtils.getPropertyValues(lsrnNode, SIO.has_identifier, null)
.andThen(RdfUtils.getPropertyValues(lsrnNode, SIO.has_attribute, null));
while (ids.hasNext()) {
Resource identifier = ids.next();
for (Iterator<Resource> types = RdfUtils.getTypes(identifier); types.hasNext(); ) {
Resource type = types.next();
if (type.isURIResource()) {
String ns = getNamespaceFromLSRNIdentifierTypeURI(type.getURI());
if (ns != null && namespaces.contains(ns)) {
Statement s = identifier.getProperty(SIO.has_value);
if (s != null) {
return s.getString();
}
}
}
}
}
return null;
}
/** @todo Add Documentation. */
@Override
public boolean isFedoraGraphSubject(Resource subject) {
checkArgument(subject != null, "null cannot be a Fedora object!");
assert (subject != null);
return subject.isURIResource() && subject.getURI().startsWith("info:fedora/");
}
/**
* Adds the LSRN SIO identifier structure to an LSRN-typed Resource. Attempts to use the URL of
* the Resource to determine the ID.
*
* @param lsrnNode
*/
public static void addIdentifier(Resource lsrnNode) {
if (lsrnNode.isURIResource()) {
Matcher idMatcher = ID_PATTERN.matcher(lsrnNode.getURI());
if (idMatcher.find()) {
String id = idMatcher.group(1);
for (Resource type : RdfUtils.getTypes(lsrnNode).toList()) {
if (!type.isURIResource()) continue;
Matcher typeMatcher = TYPE_PATTERN.matcher(type.getURI());
if (typeMatcher.find()) {
String idTypeURI = OUTPUT_ID_TYPE_PATTERN.replace("$NS", typeMatcher.group(1));
SIOUtils.createAttribute(
lsrnNode, SIO.has_identifier, ResourceFactory.createResource(idTypeURI), id);
}
}
}
}
}
public static String algorithmResourceToString(Resource algorithmResource)
throws InvalidSPDXAnalysisException {
String uri = algorithmResource.getURI();
if (!algorithmResource.isURIResource()) {
throw (new InvalidSPDXAnalysisException("Algorithm resource must be a URI"));
}
String retval = URI_TO_ALGORITHM.get(uri);
if (retval == null) {
throw (new InvalidSPDXAnalysisException("Invalid algorithm resource."));
}
return retval;
}
/* (non-Javadoc)
* @see org.sadiframework.client.Registry#findServicesByConnectedClass(com.hp.hpl.jena.rdf.model.Resource)
*/
@Override
public Collection<? extends Service> findServicesByConnectedClass(Resource clazz)
throws SADIException {
Set<String> classURIs = new HashSet<String>();
if (clazz.isURIResource()) classURIs.add(clazz.getURI());
if (clazz.canAs(OntClass.class)) {
for (Iterator<? extends OntClass> i = clazz.as(OntClass.class).listSubClasses();
i.hasNext(); ) {
OntClass c = i.next();
if (c.isURIResource()) classURIs.add(c.getURI());
}
}
return findServicesByConnectedClass(classURIs);
// TODO
// return findServices(RegistrySearchCriteria.findService().addConnectedClass(clazz));
}
/**
* Returns the LSRN identifier for the given node. The method will first try to obtain an
* explicitly specified ID as encoded by the following SIO attribute structure:
*
* <pre>{@code
* root [
* 'has attribute'/'has identifier' (SIO_000008/SIO_000067)
* [
* rdf:type $identifierClass;
* 'has value' (SIO_000300) $ID
* ]
* ]
* }</pre>
*
* <p>If no such structure is attached to root, then the method will fall back to parsing the ID
* from the root's URI, using the regular expressions associated with the given LSRN identifier
* class.
*
* @param root the root resource
* @param lsrnIdentifierType the LSRN identifier type URI (e.g. lsrn:UniProt_Identifier).
* @return the database identifier of the given node
*/
public static String getID(Resource root, Resource lsrnIdentifierType) {
Collection<String> identifiers = SIOUtils.getAttributeValues(root, lsrnIdentifierType);
identifiers.addAll(SIOUtils.getAttributeValues(root, SIO.has_identifier, lsrnIdentifierType));
if (identifiers.size() > 0) {
if (identifiers.size() > 1) {
log.warn(
String.format(
"%s has multiple IDs of type %s, returning only the first ID",
root, lsrnIdentifierType));
}
return identifiers.iterator().next();
}
log.info(String.format("%s has no explicit ID, attempting to parse URI", root));
if (!root.isURIResource()) {
log.warn(
"could not determine the database ID, resource has no attached LSRN ID and is a blank node");
return null;
}
String uri = root.getURI();
for (Pattern pattern : Config.getConfig().getURIPatterns(lsrnIdentifierType)) {
Matcher matcher = pattern.matcher(uri);
if (matcher.groupCount() < 1) {
log.warn(String.format("URI pattern '%s' does not contain any capturing groups", pattern));
continue;
}
if (matcher.find()) {
String match = matcher.group(1);
if (!match.isEmpty()) return match;
}
}
log.warn(
String.format(
"could not determine lsrn ID for %s, it has no attached ID and does not match any known URI pattern",
root));
return null;
}
public static boolean isLSRNIdentifierType(Resource type) {
return type.isURIResource() && isLSRNIdentifierType(type.getURI());
}
