use of org.hl7.fhir.r4b.model.ConceptMap.SourceElementComponent in project org.hl7.fhir.core by hapifhir.
the class StructureMapUtilities method translate.
public Base translate(TransformContext context, StructureMap map, Base source, String conceptMapUrl, String fieldToReturn) throws FHIRException {
Coding src = new Coding();
if (source.isPrimitive()) {
src.setCode(source.primitiveValue());
} else if ("Coding".equals(source.fhirType())) {
Base[] b = source.getProperty("system".hashCode(), "system", true);
if (b.length == 1)
src.setSystem(b[0].primitiveValue());
b = source.getProperty("code".hashCode(), "code", true);
if (b.length == 1)
src.setCode(b[0].primitiveValue());
} else if ("CE".equals(source.fhirType())) {
Base[] b = source.getProperty("codeSystem".hashCode(), "codeSystem", true);
if (b.length == 1)
src.setSystem(b[0].primitiveValue());
b = source.getProperty("code".hashCode(), "code", true);
if (b.length == 1)
src.setCode(b[0].primitiveValue());
} else
throw new FHIRException("Unable to translate source " + source.fhirType());
String su = conceptMapUrl;
if (conceptMapUrl.equals("http://hl7.org/fhir/ConceptMap/special-oid2uri")) {
String uri = worker.oid2Uri(src.getCode());
if (uri == null)
uri = "urn:oid:" + src.getCode();
if ("uri".equals(fieldToReturn))
return new UriType(uri);
else
throw new FHIRException("Error in return code");
} else {
ConceptMap cmap = null;
if (conceptMapUrl.startsWith("#")) {
for (Resource r : map.getContained()) {
if (r instanceof ConceptMap && r.getId().equals(conceptMapUrl.substring(1))) {
cmap = (ConceptMap) r;
su = map.getUrl() + "#" + conceptMapUrl;
}
}
if (cmap == null)
throw new FHIRException("Unable to translate - cannot find map " + conceptMapUrl);
} else {
if (conceptMapUrl.contains("#")) {
String[] p = conceptMapUrl.split("\\#");
StructureMap mapU = worker.fetchResource(StructureMap.class, p[0]);
for (Resource r : mapU.getContained()) {
if (r instanceof ConceptMap && r.getId().equals(p[1])) {
cmap = (ConceptMap) r;
su = conceptMapUrl;
}
}
}
if (cmap == null)
cmap = worker.fetchResource(ConceptMap.class, conceptMapUrl);
}
Coding outcome = null;
boolean done = false;
String message = null;
if (cmap == null) {
if (services == null)
message = "No map found for " + conceptMapUrl;
else {
outcome = services.translate(context.getAppInfo(), src, conceptMapUrl);
done = true;
}
} else {
List<SourceElementComponentWrapper> list = new ArrayList<SourceElementComponentWrapper>();
for (ConceptMapGroupComponent g : cmap.getGroup()) {
for (SourceElementComponent e : g.getElement()) {
if (!src.hasSystem() && src.getCode().equals(e.getCode()))
list.add(new SourceElementComponentWrapper(g, e));
else if (src.hasSystem() && src.getSystem().equals(g.getSource()) && src.getCode().equals(e.getCode()))
list.add(new SourceElementComponentWrapper(g, e));
}
}
if (list.size() == 0)
done = true;
else if (list.get(0).getComp().getTarget().size() == 0)
message = "Concept map " + su + " found no translation for " + src.getCode();
else {
for (TargetElementComponent tgt : list.get(0).getComp().getTarget()) {
if (tgt.getRelationship() == null || EnumSet.of(ConceptMapRelationship.RELATEDTO, ConceptMapRelationship.EQUIVALENT, ConceptMapRelationship.SOURCEISNARROWERTHANTARGET).contains(tgt.getRelationship())) {
if (done) {
message = "Concept map " + su + " found multiple matches for " + src.getCode();
done = false;
} else {
done = true;
outcome = new Coding().setCode(tgt.getCode()).setSystem(list.get(0).getGroup().getTarget());
}
}
}
if (!done)
message = "Concept map " + su + " found no usable translation for " + src.getCode();
}
}
if (!done)
throw new FHIRException(message);
if (outcome == null)
return null;
if ("code".equals(fieldToReturn))
return new CodeType(outcome.getCode());
else
return outcome;
}
}
use of org.hl7.fhir.r4b.model.ConceptMap.SourceElementComponent in project pathling by aehrc.
the class ConceptMapBuilder method build.
@Nonnull
public ConceptMap build() {
final Map<Pair<VersionedSystem, VersionedSystem>, List<ConceptMapEntry>> mappingsBySystem = entries.stream().collect(Collectors.groupingBy(ConceptMapBuilder::getVersionedSystems));
final ConceptMap result = new ConceptMap();
result.setStatus(PublicationStatus.ACTIVE);
mappingsBySystem.forEach((srcAndTarget, systemMappings) -> {
final ConceptMapGroupComponent group = result.addGroup();
group.setSource(srcAndTarget.getLeft().getSystem());
group.setSourceVersion(srcAndTarget.getLeft().getVersion());
group.setTarget(srcAndTarget.getRight().getSystem());
group.setTargetVersion(srcAndTarget.getRight().getVersion());
systemMappings.forEach(m -> {
final SourceElementComponent sourceElement = group.addElement();
sourceElement.setCode(m.getSource().getCode());
final TargetElementComponent targetElement = sourceElement.addTarget();
targetElement.setCode(m.getTarget().getCode());
targetElement.setEquivalence(m.getEquivalence());
});
});
return result;
}
use of org.hl7.fhir.r4b.model.ConceptMap.SourceElementComponent in project bunsen by cerner.
the class ConceptMaps method expandMappingsIterator.
private static Iterator<Mapping> expandMappingsIterator(ConceptMap map) {
List<Mapping> mappings = new ArrayList<>();
for (ConceptMapGroupComponent group : map.getGroup()) {
for (SourceElementComponent element : group.getElement()) {
for (TargetElementComponent target : element.getTarget()) {
Mapping mapping = new Mapping();
mapping.setConceptMapUri(map.getUrl());
mapping.setConceptMapVersion(map.getVersion());
try {
String sourceValue = map.getSource() instanceof UriType ? map.getSourceUriType().getValue() : map.getSourceReference().getReference();
mapping.setSourceValueSet(sourceValue);
String targetValue = map.getTarget() instanceof UriType ? map.getTargetUriType().getValue() : map.getTargetReference().getReference();
mapping.setTargetValueSet(targetValue);
} catch (FHIRException fhirException) {
// an exception.
throw new RuntimeException(fhirException);
}
mapping.setSourceSystem(group.getSource());
mapping.setSourceValue(element.getCode());
mapping.setTargetSystem(group.getTarget());
mapping.setTargetValue(target.getCode());
if (target.getEquivalence() != null) {
mapping.setEquivalence(target.getEquivalence().toCode());
}
mappings.add(mapping);
}
}
}
return mappings.iterator();
}
use of org.hl7.fhir.r4b.model.ConceptMap.SourceElementComponent in project bunsen by cerner.
the class ConceptMaps method addToConceptMap.
@Override
protected void addToConceptMap(ConceptMap map, Dataset<Mapping> mappings) {
// Sort the items so they are grouped together optimally, and so
// we consistently produce the same ordering, therefore making
// inspection and comparison of the concept maps easier.
List<Mapping> sortedMappings = mappings.sort("sourceSystem", "targetSystem", "sourceValue", "targetValue").collectAsList();
ConceptMapGroupComponent currentGroup = null;
SourceElementComponent element = null;
// Workaround for the decoder producing an immutable array by
// replacing it with a mutable one.
map.setGroup(new ArrayList<>(map.getGroup()));
for (Mapping mapping : sortedMappings) {
// Add a new group if we don't match the previous one.
if (currentGroup == null || !mapping.getSourceSystem().equals(currentGroup.getSource()) || !mapping.getTargetSystem().equals(currentGroup.getTarget())) {
currentGroup = null;
// Find a matching group.
for (ConceptMapGroupComponent candidate : map.getGroup()) {
if (mapping.getSourceSystem().equals(candidate.getSource()) && mapping.getTargetSystem().equals(candidate.getTarget())) {
currentGroup = candidate;
// Workaround for the decoder producing an immutable array by
// replacing it with a mutable one.
currentGroup.setElement(new ArrayList<>(currentGroup.getElement()));
break;
}
}
// No matching group found, so add it.
if (currentGroup == null) {
currentGroup = map.addGroup();
currentGroup.setSource(mapping.getSourceSystem());
currentGroup.setTarget(mapping.getTargetSystem());
// Ensure a new element is created for the newly created group.
element = null;
}
}
// so add one if it does not match the previous.
if (element == null || !mapping.getSourceValue().equals(element.getCode())) {
element = currentGroup.addElement();
element.setCode(mapping.getSourceValue());
}
element.addTarget().setCode(mapping.getTargetValue());
}
}
use of org.hl7.fhir.r4b.model.ConceptMap.SourceElementComponent in project bunsen by cerner.
the class ConceptMaps method expandMappingsIterator.
private static Iterator<Mapping> expandMappingsIterator(ConceptMap map) {
List<Mapping> mappings = new ArrayList<>();
for (ConceptMapGroupComponent group : map.getGroup()) {
for (SourceElementComponent element : group.getElement()) {
for (TargetElementComponent target : element.getTarget()) {
Mapping mapping = new Mapping();
mapping.setConceptMapUri(map.getUrl());
mapping.setConceptMapVersion(map.getVersion());
try {
String sourceValue = map.getSource() instanceof UriType ? map.getSourceUriType().getValue() : map.getSourceUriType().getValue();
mapping.setSourceValueSet(sourceValue);
String targetValue = map.getTarget() instanceof UriType ? map.getTargetUriType().getValue() : map.getTargetUriType().getValue();
mapping.setTargetValueSet(targetValue);
} catch (FHIRException fhirException) {
// an exception.
throw new RuntimeException(fhirException);
}
mapping.setSourceSystem(group.getSource());
mapping.setSourceValue(element.getCode());
mapping.setTargetSystem(group.getTarget());
mapping.setTargetValue(target.getCode());
if (target.getEquivalence() != null) {
mapping.setEquivalence(target.getEquivalence().toCode());
}
mappings.add(mapping);
}
}
}
return mappings.iterator();
}
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