/**
* 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;
}
/**
* Returns a Resource in the specified model that is an instance of the specified type with the
* specified ID. The Resource will be created with an appropriate URI (@link {@link
* #OUTPUT_URI_PATTERN}).
*
* @param model the model in which to create the new Resource
* @param type the type (class) of the new instance
* @param id the id of the new instance
* @return a Resource view of the new instance
*/
public static Resource createInstance(Model model, Resource type, String id) {
Matcher matcher = TYPE_PATTERN.matcher(type.getURI());
if (matcher.find()) {
String namespace = matcher.group(1);
String uri = getURI(namespace, id);
Resource lsrnNode = model.createResource(uri, type);
SIOUtils.createAttribute(lsrnNode, SIO.has_identifier, getIdentifierClass(namespace), id);
return lsrnNode;
} else {
throw new IllegalArgumentException(
"at present this method only works with LSRN database record classes");
}
}
/**
* 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);
}
}
}
}
}
