public NameAndValueList getMappingAssociationNames(String scheme, String version) {
CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
if (version != null) {
csvt.setVersion(version);
}
NameAndValueList navList = new NameAndValueList();
try {
CodingScheme cs = lbSvc.resolveCodingScheme(scheme, csvt);
Relations[] relations = cs.getRelations();
for (int i = 0; i < relations.length; i++) {
Relations relation = relations[i];
Boolean isMapping = relation.isIsMapping();
if (isMapping != null && isMapping.equals(Boolean.TRUE)) {
AssociationPredicate[] associationPredicates = relation.getAssociationPredicate();
for (int j = 0; j < associationPredicates.length; j++) {
AssociationPredicate associationPredicate = associationPredicates[j];
String name = associationPredicate.getAssociationName();
NameAndValue vNameAndValue = new NameAndValue();
vNameAndValue.setName(name);
navList.addNameAndValue(vNameAndValue);
}
return navList;
} else {
return null;
}
}
} catch (Exception ex) {
ex.printStackTrace();
}
return null;
}
public ResolvedConceptReferencesIterator getMappingDataIterator(
String scheme, String version, List<MappingSortOption> sortOptionList) {
CodingSchemeVersionOrTag versionOrTag = new CodingSchemeVersionOrTag();
if (version != null) {
versionOrTag.setVersion(version);
}
String relationsContainerName = null;
try {
CodingScheme cs = lbSvc.resolveCodingScheme(scheme, versionOrTag);
if (cs == null) return null;
java.util.Enumeration<? extends Relations> relations = cs.enumerateRelations();
while (relations.hasMoreElements()) {
Relations relation = (Relations) relations.nextElement();
Boolean isMapping = relation.getIsMapping();
if (isMapping != null && isMapping.equals(Boolean.TRUE)) {
relationsContainerName = relation.getContainerName();
break;
}
}
if (relationsContainerName == null) {
return null;
}
MappingExtension mappingExtension =
(MappingExtension) lbSvc.getGenericExtension("MappingExtension");
ResolvedConceptReferencesIterator itr =
mappingExtension.resolveMapping(
scheme, versionOrTag, relationsContainerName, sortOptionList);
return itr;
} catch (Exception ex) {
ex.printStackTrace();
}
return null;
}
/**
* Return a list of Association names
*
* @param scheme
* @param version
* @return
*/
public Vector<String> getAssociationNames(String scheme, String version) {
Vector<String> association_vec = new Vector<String>();
try {
LexBIGService lbSvc = RemoteServerUtil.createLexBIGService();
CodingSchemeVersionOrTag versionOrTag = new CodingSchemeVersionOrTag();
if (version != null) {
versionOrTag.setVersion(version);
}
CodingScheme cs = lbSvc.resolveCodingScheme(scheme, versionOrTag);
SupportedHierarchy[] hierarchies = cs.getMappings().getSupportedHierarchy();
String[] ids = hierarchies[0].getAssociationNames();
for (int i = 0; i < ids.length; i++) {
if (!association_vec.contains(ids[i])) {
association_vec.add(ids[i]);
_logger.debug("AssociationName: " + ids[i]);
}
}
} catch (Exception ex) {
_logger.warn(ex.getMessage());
}
return association_vec;
}
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);
}
}
