private EntityListEntry createEntityListEntry() {
/* EntityDescription */
EntityDescription entityDescription = new EntityDescription();
NamedEntityDescription namedEntityDescription = new NamedEntityDescription();
ScopedEntityName name = new ScopedEntityName();
name.setName("test");
name.setNamespace("test");
CodeSystemVersionReference ref = new CodeSystemVersionReference();
ref.setCodeSystem(new CodeSystemReference("test.ref"));
ref.setVersion(new NameAndMeaningReference("test.ref.version"));
namedEntityDescription.setEntityID(name);
namedEntityDescription.setDescribingCodeSystemVersion(ref);
namedEntityDescription.setAbout("test.about");
URIAndEntityName uriAndEntityName = new URIAndEntityName();
uriAndEntityName.setName("test.entityType");
uriAndEntityName.setNamespace("test.namespace");
uriAndEntityName.setUri("http://my/uri");
List<URIAndEntityName> uriAndEntityNameList = new ArrayList<URIAndEntityName>(1);
uriAndEntityNameList.add(uriAndEntityName);
namedEntityDescription.setEntityType(uriAndEntityNameList);
entityDescription.setNamedEntity(namedEntityDescription);
/* EntityListEntry */
EntityListEntry entry = new EntityListEntry();
entry.setEntry(entityDescription);
return entry;
}
private EntityDescriptionBase createEntityDescription() {
EntityDescriptionBase entityDescription = new NamedEntityDescription();
entityDescription.setAbout("test.about");
CodeSystemVersionReference versionRef = new CodeSystemVersionReference();
versionRef.setCodeSystem(new CodeSystemReference("test.codesystem"));
NameAndMeaningReference nameRef = new NameAndMeaningReference("test.nameref");
versionRef.setVersion(nameRef);
entityDescription.setDescribingCodeSystemVersion(versionRef);
URIAndEntityName uriAndEntityName = new URIAndEntityName();
uriAndEntityName.setName("test.urientityname");
uriAndEntityName.setNamespace("test");
uriAndEntityName.setUri("http://my/uri");
URIAndEntityName uriAndEntityNames[] = new URIAndEntityName[1];
uriAndEntityNames[0] = uriAndEntityName;
entityDescription.setEntityType(uriAndEntityNames);
return entityDescription;
}
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);
}
}