private static SupportedAssociation createSupportedAssociation(
String uri, String localId, String content) {
SupportedAssociation sa = new SupportedAssociation();
sa.setUri(uri);
sa.setLocalId(localId);
sa.setContent(content);
return sa;
}
private void add(
EntityReference entityReference,
ValueSetDefinitionEntry cts2Entry,
org.LexGrid.valueSets.ValueSetDefinition lexEvsVSD) {
URIAndEntityName uriAndName = new URIAndEntityName();
uriAndName.setName(entityReference.getEntityCode());
String namespace = entityReference.getEntityCodeNamespace();
if (StringUtils.isBlank(namespace)) {
namespace = lexEvsVSD.getDefaultCodingScheme();
}
uriAndName.setNamespace(namespace);
SupportedNamespace supportedNamespace = this.findNamespace(lexEvsVSD.getMappings(), namespace);
if (supportedNamespace == null) {
log.warn(
"EntityRefernece: "
+ entityReference.getEntityCodeNamespace()
+ ":"
+ entityReference.getEntityCode()
+ " does not have a valid namespace.");
try {
CodingScheme cs = this.lexBigService.resolveCodingScheme(namespace, null);
SupportedNamespace sns = new SupportedNamespace();
sns.setContent(cs.getCodingSchemeName());
sns.setEquivalentCodingScheme(cs.getCodingSchemeName());
sns.setLocalId(cs.getCodingSchemeName());
sns.setUri(cs.getCodingSchemeURI());
supportedNamespace = sns;
} catch (LBException e) {
log.info(e);
// we have to punt here
SupportedNamespace sns = new SupportedNamespace();
sns.setContent("unknown");
sns.setEquivalentCodingScheme("unknown");
sns.setLocalId("unknown");
sns.setUri("unknown");
}
}
uriAndName.setUri(
UriUtils.combine(supportedNamespace.getUri(), entityReference.getEntityCode()));
if (entityReference.getReferenceAssociation() != null) {
AssociatedEntitiesReference ref = new AssociatedEntitiesReference();
ref.setReferencedEntity(uriAndName);
ref.setDirection(
entityReference.getTargetToSource()
? AssociationDirection.TARGET_TO_SOURCE
: AssociationDirection.SOURCE_TO_TARGET);
String cs = supportedNamespace.getEquivalentCodingScheme();
SupportedCodingScheme supportedCodingScheme = this.findCodingScheme(lexEvsVSD, cs);
CodeSystemReference codingSchemeRef =
this.getTransformUtils()
.toCodeSystemReference(
supportedCodingScheme.getLocalId(), supportedCodingScheme.getUri());
ref.setCodeSystem(codingSchemeRef);
ref.setTransitivity(
entityReference.getTransitiveClosure()
? TransitiveClosure.TRANSITIVE_CLOSURE
: TransitiveClosure.DIRECTLY_ASSOCIATED);
ref.setLeafOnly(
entityReference.getLeafOnly() ? LeafOrAll.LEAF_ONLY : LeafOrAll.ALL_INTERMEDIATE_NODES);
String association = entityReference.getReferenceAssociation();
PredicateReference predicate = new PredicateReference();
predicate.setName(association);
// namespace for a predicate is not guaranteed in LexEVS... not sure
// how we want to handle this. For now, assume the same namespace
// as the starting entity.
SupportedAssociation supportedAssociation =
this.findAssociation(lexEvsVSD.getMappings(), association);
if (supportedAssociation == null) {
predicate.setNamespace(supportedCodingScheme.getLocalId());
predicate.setUri(UriUtils.combine(supportedCodingScheme.getUri(), association));
} else {
predicate.setNamespace(supportedAssociation.getEntityCodeNamespace());
if (StringUtils.isNotBlank(supportedAssociation.getUri())) {
predicate.setUri(supportedAssociation.getUri());
} else {
predicate.setUri(UriUtils.combine(supportedCodingScheme.getUri(), association));
}
}
ref.setPredicate(predicate);
cts2Entry.setAssociatedEntities(ref);
} else {
SpecificEntityList sel = new SpecificEntityList();
sel.addReferencedEntity(uriAndName);
cts2Entry.setEntityList(sel);
}
}
