use of org.hl7.fhir.r4b.model.ConceptMap.SourceElementComponent in project org.hl7.fhir.core by hapifhir.
the class ConceptMap method setProperty.
@Override
public void setProperty(String name, Base value) throws FHIRException {
if (name.equals("url"))
// UriType
this.url = castToUri(value);
else if (name.equals("identifier"))
// Identifier
this.identifier = castToIdentifier(value);
else if (name.equals("version"))
// StringType
this.version = castToString(value);
else if (name.equals("name"))
// StringType
this.name = castToString(value);
else if (name.equals("status"))
// Enumeration<ConformanceResourceStatus>
this.status = new ConformanceResourceStatusEnumFactory().fromType(value);
else if (name.equals("experimental"))
// BooleanType
this.experimental = castToBoolean(value);
else if (name.equals("publisher"))
// StringType
this.publisher = castToString(value);
else if (name.equals("contact"))
this.getContact().add((ConceptMapContactComponent) value);
else if (name.equals("date"))
// DateTimeType
this.date = castToDateTime(value);
else if (name.equals("description"))
// StringType
this.description = castToString(value);
else if (name.equals("useContext"))
this.getUseContext().add(castToCodeableConcept(value));
else if (name.equals("requirements"))
// StringType
this.requirements = castToString(value);
else if (name.equals("copyright"))
// StringType
this.copyright = castToString(value);
else if (name.equals("source[x]"))
// Type
this.source = (Type) value;
else if (name.equals("target[x]"))
// Type
this.target = (Type) value;
else if (name.equals("element"))
this.getElement().add((SourceElementComponent) value);
else
super.setProperty(name, value);
}
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 && ((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
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.appInfo, 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).comp.getTarget().size() == 0)
message = "Concept map " + su + " found no translation for " + src.getCode();
else {
for (TargetElementComponent tgt : list.get(0).comp.getTarget()) {
if (tgt.getEquivalence() == null || EnumSet.of(ConceptMapEquivalence.EQUAL, ConceptMapEquivalence.RELATEDTO, ConceptMapEquivalence.EQUIVALENT, ConceptMapEquivalence.WIDER).contains(tgt.getEquivalence())) {
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).group.getTarget());
}
} else if (tgt.getEquivalence() == ConceptMapEquivalence.UNMATCHED) {
done = true;
}
}
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 org.hl7.fhir.core by hapifhir.
the class ConceptMapEngineTest method codingTranslateFailsForMultipleCandidateMatches.
@Test
@DisplayName("Coding fails to translate due to multiple candidate matches in ConceptMap")
void codingTranslateFailsForMultipleCandidateMatches() throws IOException {
final ConceptMap.SourceElementComponent sourceElementComponent = getSourceElementComponent();
final ConceptMapEngine conceptMapEngine = getConceptMapEngine(Arrays.asList(sourceElementComponent, sourceElementComponent));
Coding coding = new Coding(null, SOURCE_CODE_STRING, "Body Weight");
assertThrows(FHIRException.class, () -> {
conceptMapEngine.translate(coding, CONCEPT_MAP_URL);
});
}
use of org.hl7.fhir.r4b.model.ConceptMap.SourceElementComponent in project org.hl7.fhir.core by hapifhir.
the class ConceptMapEngine method translateByJustCode.
private Coding translateByJustCode(ConceptMap cm, String code) throws FHIRException {
SourceElementComponent ct = null;
ConceptMapGroupComponent cg = null;
for (ConceptMapGroupComponent g : cm.getGroup()) {
for (SourceElementComponent e : g.getElement()) {
if (code.equals(e.getCode())) {
if (e != null)
throw new FHIRException("Unable to process translate " + code + " because multiple candidate matches were found in concept map " + cm.getUrl());
ct = e;
cg = g;
}
}
}
if (ct == null)
return null;
TargetElementComponent tt = null;
for (TargetElementComponent t : ct.getTarget()) {
if (!t.hasDependsOn() && !t.hasProduct() && isOkEquivalence(t.getEquivalence())) {
if (tt != null)
throw new FHIRException("Unable to process translate " + code + " because multiple targets were found in concept map " + cm.getUrl());
tt = t;
}
}
if (tt == null)
return null;
CanonicalPair cp = new CanonicalPair(cg.getTarget());
return new Coding().setSystem(cp.getUrl()).setVersion(cp.getVersion()).setCode(tt.getCode()).setDisplay(tt.getDisplay());
}
use of org.hl7.fhir.r4b.model.ConceptMap.SourceElementComponent in project org.hl7.fhir.core by hapifhir.
the class StructureMapUtilities method parseConceptMap.
private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
lexer.token("conceptmap");
ConceptMap map = new ConceptMap();
String id = lexer.readConstant("map id");
if (id.startsWith("#"))
throw lexer.error("Concept Map identifier must start with #");
map.setId(id);
// todo: how to add this to the text format
map.setStatus(PublicationStatus.DRAFT);
result.getContained().add(map);
lexer.token("{");
lexer.skipComments();
// lexer.token("source");
// map.setSource(new UriType(lexer.readConstant("source")));
// lexer.token("target");
// map.setSource(new UriType(lexer.readConstant("target")));
Map<String, String> prefixes = new HashMap<String, String>();
while (lexer.hasToken("prefix")) {
lexer.token("prefix");
String n = lexer.take();
lexer.token("=");
String v = lexer.readConstant("prefix url");
prefixes.put(n, v);
}
while (lexer.hasToken("unmapped")) {
lexer.token("unmapped");
lexer.token("for");
String n = readPrefix(prefixes, lexer);
ConceptMapGroupComponent g = getGroup(map, n, null);
lexer.token("=");
String v = lexer.take();
if (v.equals("provided")) {
g.getUnmapped().setMode(ConceptMapGroupUnmappedMode.PROVIDED);
} else
throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
}
while (!lexer.hasToken("}")) {
String srcs = readPrefix(prefixes, lexer);
lexer.token(":");
String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
ConceptMapEquivalence eq = readEquivalence(lexer);
String tgts = (eq != ConceptMapEquivalence.UNMATCHED) ? readPrefix(prefixes, lexer) : "";
ConceptMapGroupComponent g = getGroup(map, srcs, tgts);
SourceElementComponent e = g.addElement();
e.setCode(sc);
if (e.getCode().startsWith("\""))
e.setCode(lexer.processConstant(e.getCode()));
TargetElementComponent tgt = e.addTarget();
tgt.setEquivalence(eq);
if (tgt.getEquivalence() != ConceptMapEquivalence.UNMATCHED) {
lexer.token(":");
tgt.setCode(lexer.take());
if (tgt.getCode().startsWith("\""))
tgt.setCode(lexer.processConstant(tgt.getCode()));
}
if (lexer.hasComment())
tgt.setComment(lexer.take().substring(2).trim());
}
lexer.token("}");
}
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