use of org.hl7.fhir.r4.model.IntegerType in project pathling by aehrc.
the class TestData method newConditionWithExtensions.
public static Condition newConditionWithExtensions() {
// Condition
// - extension:
// - url: uuid:ext1
// - value: ext1
// - extension:
// - url: uuid:ext2
// - value: 2
// - extension:
// - url: uuid:ext4
// - extension
// - url: uuid:nested
// - value: nested
// - identifier
// - id: uuid:identifier1
// - extension:
// - url: uuid:ext10
// - value: ext10
// - extension:
// - url: uuid:ext11
// - value: 11
// - stage
// - type
// - extension
// - url: uuid:ext12
// - value: ext12
final Condition conditionWithExtension = new Condition();
conditionWithExtension.setId("someId");
final Extension nestedExtension = new Extension("uuid:ext4");
nestedExtension.addExtension(new Extension("uuid:nested", new StringType("nested")));
conditionWithExtension.setExtension(Arrays.asList(new Extension("uuid:ext1", new StringType("ext1")), new Extension("uuid:ext2", new IntegerType(2)), nestedExtension));
conditionWithExtension.setMeta(new Meta().setVersionId("MetVersion"));
conditionWithExtension.setOnset(new Range());
conditionWithExtension.setSeverity(new CodeableConcept().addCoding(new Coding("sys", "code", "name")));
final Identifier identifier = conditionWithExtension.getIdentifierFirstRep();
identifier.setId("uuid:identifier1");
identifier.setExtension(Arrays.asList(new Extension("uuid:ext10", new StringType("ext10")), new Extension("uuid:ext11", new IntegerType(11))));
final ConditionStageComponent stage = conditionWithExtension.getStageFirstRep();
stage.getType().setExtension(Collections.singletonList(new Extension("uuid:ext12", new StringType("ext12"))));
return conditionWithExtension;
}
use of org.hl7.fhir.r4.model.IntegerType in project pathling by aehrc.
the class DefaultTerminologyServiceTest method testIntersectFiltersIllegalAndUnknownCodings.
@SuppressWarnings("ConstantConditions")
@Test
void testIntersectFiltersIllegalAndUnknownCodings() {
final ValueSet responseExpansion = new ValueSet();
responseExpansion.getExpansion().getContains().addAll(Arrays.asList(fromSimpleCoding(CODING1_VERSION1), fromSimpleCoding(CODING2_VERSION1)));
when(terminologyClient.expand(any(), any())).thenReturn(responseExpansion);
// setup SYSTEM1 as known system
when(terminologyClient.searchCodeSystems(refEq(new UriParam(SYSTEM1)), any())).thenReturn(Collections.singletonList(new CodeSystem()));
final Set<SimpleCoding> actualExpansion = terminologyService.intersect("uuid:value-set", Arrays.asList(CODING1_VERSION1, CODING2_VERSION1, CODING3_VERSION1, new SimpleCoding(SYSTEM1, null), new SimpleCoding(null, "code1"), new SimpleCoding(null, null), null));
final Set<SimpleCoding> expectedExpansion = ImmutableSet.of(CODING1_VERSION1, CODING2_VERSION1);
assertEquals(expectedExpansion, actualExpansion);
// verify behaviour
verify(terminologyClient).searchCodeSystems(refEq(new UriParam(SYSTEM1)), any());
verify(terminologyClient).searchCodeSystems(refEq(new UriParam(SYSTEM2)), any());
final ValueSet requestValueSet = new ValueSet();
final List<ConceptSetComponent> includes = requestValueSet.getCompose().getInclude();
includes.add(new ConceptSetComponent().addValueSet("uuid:value-set").setSystem(SYSTEM1).setVersion("version1").addConcept(new ConceptReferenceComponent().setCode("code1")).addConcept(new ConceptReferenceComponent().setCode("code2")));
verify(terminologyClient).expand(deepEq(requestValueSet), deepEq(new IntegerType(2)));
verifyNoMoreInteractions(terminologyClient);
}
use of org.hl7.fhir.r4.model.IntegerType in project redmatch by aehrc.
the class FhirExporter method getValue.
/**
* Resolves a value.
*
* @param value The value specified in the transformation rules.
* @param fhirType The type of the FHIR attribute where this value will be set.
* @param vertex A vertex with patient data.
* @param recordId The id of this record. Used to create the references to FHIR ids.
* @param enumFactory If the type is an enumeration, this is the factory to create an instance.
* @param fhirPackage The target FHIR package.
* @return The value or null if the value cannot be determined. This can also be a list.
*/
private Base getValue(Value value, Class<?> fhirType, JsonObject vertex, String recordId, Class<?> enumFactory, VersionedFhirPackage fhirPackage) throws IOException {
// If this is a field-based value then make sure that there is a value and if not return null
if (value instanceof FieldBasedValue) {
FieldBasedValue fbv = (FieldBasedValue) value;
// Account for field ids of the form xx___y
String fieldId = fbv.getFieldId();
String shortFieldId = null;
String regex = "(?<fieldId>.*)___\\d+$";
Pattern pattern = Pattern.compile(regex);
Matcher matcher = pattern.matcher(fieldId);
if (matcher.find()) {
shortFieldId = matcher.group("fieldId");
log.debug("Transformed fieldId into '" + fieldId + "'");
}
boolean hasValue = false;
JsonElement jsonElement = vertex.get(fieldId);
if (jsonElement != null) {
String rawValue = jsonElement.getAsString();
if (!rawValue.isEmpty()) {
hasValue = true;
}
}
if (!hasValue && shortFieldId != null) {
jsonElement = vertex.get(shortFieldId);
if (jsonElement != null) {
String rawValue = jsonElement.getAsString();
if (!rawValue.isEmpty()) {
hasValue = true;
}
}
}
if (!hasValue) {
return null;
}
}
if (value instanceof BooleanValue) {
return new BooleanType(((BooleanValue) value).getValue());
} else if (value instanceof CodeLiteralValue) {
String code = ((CodeLiteralValue) value).getCode();
return getCode(code, enumFactory);
} else if (value instanceof ConceptLiteralValue) {
ConceptLiteralValue clv = (ConceptLiteralValue) value;
String system = clv.getSystem();
String code = clv.getCode();
String display = clv.getDisplay() != null ? clv.getDisplay() : "";
return getConcept(system, code, display, fhirType);
} else if (value instanceof DoubleValue) {
return new DecimalType(((DoubleValue) value).getValue());
} else if (value instanceof IntegerValue) {
return new IntegerType(((IntegerValue) value).getValue());
} else if (value instanceof ReferenceValue) {
ReferenceValue rv = (ReferenceValue) value;
Reference ref = new Reference();
String resourceType = rv.getResourceType();
String resourceId = rv.getResourceId();
boolean unique = uniqueIds.contains(resourceType + "<" + resourceId + ">");
CodeInfo codeInfo = terminologyService.lookup(fhirPackage, resourceType);
if (codeInfo.isProfile()) {
resourceType = StringUtils.getLastPath(codeInfo.getBaseResource());
}
if (unique) {
// This is a reference to a unique resource - no need to append row id
if (fhirResourceMap.containsKey(resourceId)) {
ref.setReference("/" + resourceType + "/" + resourceId);
} else {
log.debug("Did not find resource " + resourceType + "/" + resourceId);
}
} else {
if (fhirResourceMap.containsKey(resourceId + "-" + recordId)) {
ref.setReference("/" + resourceType + "/" + resourceId + "-" + recordId);
} else {
log.debug("Did not find resource " + resourceType + "/" + resourceId + "-" + recordId);
}
}
return ref;
} else if (value instanceof StringValue) {
if (fhirType.equals(StringType.class)) {
return new StringType(((StringValue) value).getStringValue());
} else if (fhirType.equals(MarkdownType.class)) {
return new MarkdownType(((StringValue) value).getStringValue());
} else if (fhirType.equals(IdType.class)) {
return new IdType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UriType.class)) {
return new UriType(((StringValue) value).getStringValue());
} else if (fhirType.equals(OidType.class)) {
return new OidType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UuidType.class)) {
return new UuidType(((StringValue) value).getStringValue());
} else if (fhirType.equals(CanonicalType.class)) {
return new CanonicalType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UrlType.class)) {
return new UrlType(((StringValue) value).getStringValue());
} else {
throw new TransformationException("Got StringValue for FHIR type " + fhirType.getName() + ". This should not happen!");
}
} else if (value instanceof CodeSelectedValue) {
CodeSelectedValue csv = (CodeSelectedValue) value;
String fieldId = csv.getFieldId();
Mapping m = getSelectedMapping(fieldId, vertex);
if (m == null) {
throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
}
return getTarget(m).getCodeElement();
} else if (value instanceof ConceptSelectedValue) {
ConceptSelectedValue csv = (ConceptSelectedValue) value;
String fieldId = csv.getFieldId();
Mapping m = getSelectedMapping(fieldId, vertex);
if (m == null) {
throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
}
if (fhirType.isAssignableFrom(Coding.class)) {
return getTarget(m);
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(getTarget(m));
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT_SELECTED.");
}
} else if (value instanceof ConceptValue) {
// Ontoserver REDCap plugin format: 74400008|Appendicitis|http://snomed.info/sct
ConceptValue cv = (ConceptValue) value;
String fieldId = cv.getFieldId();
Mapping m = getMapping(fieldId);
if (m != null) {
if (fhirType.isAssignableFrom(Coding.class)) {
return getTarget(m);
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(getTarget(m));
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
}
} else {
au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
Coding c = field.getCoding(vertex);
if (c != null) {
if (fhirType.isAssignableFrom(Coding.class)) {
return c;
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(c);
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
}
}
}
throw new TransformationException("Could not get concept for field " + fieldId + ".");
} else if (value instanceof FieldValue) {
FieldValue fv = (FieldValue) value;
String fieldId = fv.getFieldId();
FieldValue.DatePrecision pr = fv.getDatePrecision();
au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
return field.getValue(vertex, fhirType, pr);
} else {
throw new TransformationException("Unable to get VALUE for " + value);
}
}
use of org.hl7.fhir.r4.model.IntegerType in project bunsen by cerner.
the class TestData method newPatient.
/**
* Returns a FHIR Patient for testing purposes.
*/
public static Patient newPatient() {
Patient patient = new Patient();
patient.setId("test-patient");
patient.setMultipleBirth(new IntegerType(1));
return patient;
}
use of org.hl7.fhir.r4.model.IntegerType in project bunsen by cerner.
the class TestData method newPatient.
/**
* Returns a FHIR Patient for testing purposes.
*/
public static Patient newPatient() {
Patient patient = new Patient();
patient.setId("test-patient");
patient.setMultipleBirth(new IntegerType(1));
return patient;
}
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