use of org.hl7.fhir.r4.model.Reference in project kindling by HL7.
the class FhirTurtleGenerator method processTypes.
private void processTypes(String baseResourceName, FHIRResource baseResource, ElementDefn td, String predicateBase, boolean innerIsBackbone) throws Exception {
for (ElementDefn ed : td.getElements()) {
String predicateName = predicateBase + "." + (ed.getName().endsWith("[x]") ? ed.getName().substring(0, ed.getName().length() - 3) : ed.getName());
FHIRResource predicateResource;
if (ed.getName().endsWith("[x]")) {
predicateResource = fact.fhir_objectProperty(predicateName);
// Choice entry
if (ed.typeCode().equals("*")) {
// Wild card -- any element works (probably should be more restrictive but...)
Resource targetResource = RDFNamespace.FHIR.resourceRef("Element");
baseResource.restriction(fact.fhir_cardinality_restriction(predicateResource.resource, targetResource, ed.getMinCardinality(), ed.getMaxCardinality()));
predicateResource.domain(baseResource);
predicateResource.range(targetResource);
} else {
// Create a restriction on the union of possible types
List<Resource> typeOpts = new ArrayList<Resource>();
for (TypeRef tr : ed.getTypes()) {
// TODO: Figure out how to get the type reference code
String trName = tr.getName();
if (trName.equals("SimpleQuantity"))
trName = "Quantity";
String qualifiedPredicateName = predicateName + Utilities.capitalize(trName);
Resource targetRes = fact.fhir_class(tr.getName()).resource;
FHIRResource qualifiedPredicate = fact.fhir_objectProperty(qualifiedPredicateName, predicateResource.resource).domain(baseResource).range(targetRes);
typeOpts.add(fact.fhir_cardinality_restriction(qualifiedPredicate.resource, targetRes, ed.getMinCardinality(), ed.getMaxCardinality()));
}
baseResource.restriction(fact.fhir_union(typeOpts));
}
} else {
FHIRResource baseDef;
if (ed.getTypes().isEmpty()) {
predicateResource = fact.fhir_objectProperty(predicateName);
String targetClassName = mapComponentName(baseResourceName, ed.getDeclaredTypeName());
baseDef = fact.fhir_class(targetClassName, innerIsBackbone ? "BackboneElement" : "Element").addDefinition(ed.getDefinition());
processTypes(targetClassName, baseDef, ed, predicateName, innerIsBackbone);
} else {
TypeRef targetType = ed.getTypes().get(0);
String targetName = targetType.getName();
if (targetName.startsWith("@")) {
// Link to earlier definition
ElementDefn targetRef = getElementForPath(targetName.substring(1));
String targetRefName = targetRef.getName();
String targetClassName = baseResourceName + Character.toUpperCase(targetRefName.charAt(0)) + targetRefName.substring(1);
baseDef = fact.fhir_class(targetClassName, innerIsBackbone ? "BackboneElement" : "Element").addDefinition(ed.getDefinition()).addTitle(ed.getShortDefn());
if (!processing.contains(targetRefName)) {
processing.add(targetRefName);
processTypes(targetClassName, baseDef, targetRef, predicateName, innerIsBackbone);
processing.remove(targetRefName);
}
} else {
// A placeholder entry. The rest of the information will be supplied elsewhere
baseDef = fact.fhir_class(targetName);
}
// XHTML the exception, in that the html doesn't derive from Primitive
if (targetName.equals("xhtml"))
predicateResource = fact.fhir_dataProperty(predicateName);
else
predicateResource = fact.fhir_objectProperty(predicateName);
}
predicateResource.addTitle(ed.getShortDefn()).addDefinition(ed.getDefinition()).domain(baseResource);
baseResource.restriction(fact.fhir_cardinality_restriction(predicateResource.resource, baseDef.resource, ed.getMinCardinality(), ed.getMaxCardinality()));
predicateResource.range(baseDef.resource);
if (!Utilities.noString(ed.getW5()))
predicateResource.addObjectProperty(RDFS.subPropertyOf, RDFNamespace.W5.resourceRef(ed.getW5()));
}
}
}
use of org.hl7.fhir.r4.model.Reference in project kindling by HL7.
the class FhirTurtleGenerator method genBaseMetadata.
/**
* Emit all the basic atoms that are implicit in the actual model
*/
private void genBaseMetadata() {
// Declare these for now - they will get filled in more completely later on
FHIRResource Resource = fact.fhir_class("Resource");
FHIRResource Element = fact.fhir_class("Element");
FHIRResource Reference = fact.fhir_class("Reference");
// Primitive isn't in the actual model - added here
fact.fhir_class("Primitive").addTitle("Types with only a value").addDefinition("Types with only a value and no additional elements as children").restriction(fact.fhir_restriction(value, RDFS.Literal));
// A resource can have an optional nodeRole
FHIRResource treeRoot = fact.fhir_class("treeRoot").addTitle("Class of FHIR base documents");
FHIRResource nodeRole = fact.fhir_objectProperty("nodeRole").addTitle("Identifies role of subject in context of a given document").domain(Resource).range(treeRoot.resource);
Resource.restriction(fact.fhir_cardinality_restriction(nodeRole.resource, treeRoot.resource, 0, 1));
// Any element can have an index to assign order in a list
FHIRResource index = fact.fhir_dataProperty("index").addTitle("Ordering value for list").domain(Element).range(XSD.nonNegativeInteger);
Element.restriction(fact.fhir_cardinality_restriction(index.resource, XSD.nonNegativeInteger, 0, 1));
// References have an optional link
FHIRResource link = fact.fhir_objectProperty("link").addTitle("URI of a reference");
Reference.restriction(fact.fhir_cardinality_restriction(link.resource, Resource.resource, 0, 1));
// XHTML is an XML Literal -- but it isn't recognized by OWL so we use string
FHIRResource NarrativeDiv = fact.fhir_dataProperty("Narrative.div");
fact.fhir_class("xhtml", "Primitive").restriction(fact.fhir_cardinality_restriction(value, fact.fhir_datatype(XSD.xstring).resource, 1, 1));
}
use of org.hl7.fhir.r4.model.Reference in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7EncounterFHIRConversionTest method test_encounter_PV2segment_missing.
// Test messages with PV1 segment and no PV2 segment, and no serviceProvider provided
// Extension list should be empty and serviceProvider should be null
@ParameterizedTest
@ValueSource(strings = { "ADT^A01", /* "ADT^A02", "ADT^A03", "ADT^A04", */
"ADT^A08", // MDM messages are not tested here because they do not have PV2 segments
"OMP^O09", "ORU^R01", "RDE^O11", "RDE^O25", "VXU^V04" })
void test_encounter_PV2segment_missing(String message) {
String hl7message = "MSH|^~\\&|WHI_LOAD_GENERATOR|IBM_TORONTO_LAB||IBM|20210330144208|8078780|" + message + "|MSGID_4e1c575f-6c6d-47b2-ab9f-829f20c96db2|T|2.3\n" + "EVN||20210330144208||ADT_EVENT|007|20210309140700\n" + "PID|1||0a8a1752-e336-43e1-bf7f-0c8f6f437ca3^^^MRN||Patient^Load^Generator||19690720|M|Patient^Alias^Generator|AA|9999^^CITY^STATE^ZIP^CAN|COUNTY|(866)845-0900||ENGLISH^ENGLISH|SIN|NONE|Account_0a8a1752-e336-43e1-bf7f-0c8f6f437ca3|123-456-7890|||N|BIRTH PLACE|N||||||N\n" + "PV1||I|^^^^^5642 Hilly Av||||2905^Doctor^Attending^M^IV^^M.D|5755^Doctor^Referring^^Sr|770542^Doctor^Consulting^Jr||||||||59367^Doctor^Admitting||Visit_0a3be81e-144b-4885-9b4e-c5cd33c8f038|||||||||||||||||||||||||20210407191342\n";
Encounter encounter = ResourceUtils.getEncounter(ftv, hl7message);
Narrative encText = encounter.getText();
assertNull(encText.getStatus());
assertThat(encText.getDiv().getChildNodes()).isEmpty();
List<Extension> extensionList = encounter.getExtension();
assertNotNull(extensionList);
assertThat(extensionList).isEmpty();
Reference serviceProvider = encounter.getServiceProvider();
assertThat(serviceProvider).isNotNull();
assertThat(serviceProvider.getReference()).isNull();
}
use of org.hl7.fhir.r4.model.Reference in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7EncounterFHIRConversionTest method test_encounter_PV1_serviceProvider.
// Test for serviceProvider reference in messages with both PV1 and PV2 segments
// Part 2: Field PV2.23 is provided but no PV2.23.8; serviceProvider id should use backup field PV1.3.4.1
@ParameterizedTest
@ValueSource(strings = { "ADT^A01", /* "ADT^A02", "ADT^A03", "ADT^A04", */
"ADT^A08", // MDM messages are not tested here because they do not have PV2 segments
"OMP^O09", "ORU^R01", "RDE^O11", "RDE^O25", "VXU^V04" })
void test_encounter_PV1_serviceProvider(String message) {
String hl7message = "MSH|^~\\&|TestSystem||TestTransformationAgent||20150502090000||" + message + "|controlID|P|2.6\r" + "EVN||20210330144208||ADT_EVENT|007|20210309140700\r" + "PID|1||0a8a1752-e336-43e1-bf7f-0c8f6f437ca3^^^MRN||Patient^Load^Generator||19690720|M|Patient^Alias^Generator|AA|9999^^CITY^STATE^ZIP^CAN|COUNTY|(866)845-0900||ENGLISH^ENGLISH|SIN|NONE|Account_0a8a1752-e336-43e1-bf7f-0c8f6f437ca3|123-456-7890|||N|BIRTH PLACE|N||||||N\r" + "PV1||I|^^^Toronto^^5642 Hilly Av||||2905^Doctor^Attending^M^IV^^M.D|5755^Doctor^Referring^^Sr|770542^Doctor^Consulting^Jr||||||||59367^Doctor^Admitting||Visit_0a3be81e-144b-4885-9b4e-c5cd33c8f038|||||||||||||||||||||||||20210407191342\r" + "PV2||TEL||||X-5546||20210330144208|20210309||||||||||||n|N|South Shore Hosptial Weymouth|||||||||N||||||\r";
String json = ftv.convert(hl7message, OPTIONS);
assertThat(json).isNotBlank();
LOGGER.debug("FHIR json result:\n" + json);
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
List<BundleEntryComponent> e = b.getEntry();
List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
assertThat(encounterResource).hasSize(1);
Encounter encounter = ResourceUtils.getResourceEncounter(encounterResource.get(0), context);
Reference serviceProvider = encounter.getServiceProvider();
assertThat(serviceProvider).isNotNull();
String providerString = serviceProvider.getReference();
assertThat(providerString).isEqualTo("Organization/toronto");
List<Resource> organizations = ResourceUtils.getResourceList(e, ResourceType.Organization);
assertThat(organizations).hasSize(1);
Organization orgResource = ResourceUtils.getResourceOrganization(organizations.get(0), context);
assertThat(orgResource.getId()).isEqualTo(providerString);
assertThat(orgResource.getName()).isEqualTo("South Shore Hosptial Weymouth");
assertThat(orgResource.getIdentifier()).hasSize(1);
// PV1.3.4.1
assertThat(orgResource.getIdentifierFirstRep().getValue()).hasToString("Toronto");
// Because ID is name based
assertThat(orgResource.getIdentifierFirstRep().getSystem()).hasToString("urn:id:extID");
}
use of org.hl7.fhir.r4.model.Reference in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7EncounterFHIRConversionTest method testEncounterReferencesObservationAndDiagnosis.
/**
* Testing Encounter correctly references Observation AND Diagnosis when both are present.
*/
@Test
void testEncounterReferencesObservationAndDiagnosis() throws IOException {
String hl7message = "MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A01|||2.6|\n" + "PID|||1234^^^^MR||DOE^JANE^|||F|||||||||||||||||||||\n" + "PV1|1|O|Location||||||||||||||||261938_6_201306171546|||||||||||||||||||||||||20130617134644|||||||||\n" + "OBX|1|SN|24467-3^CD3+CD4+ (T4 helper) cells [#/volume] in Blood^LN||=^440|{Cells}/uL^cells per microliter^UCUM|649-1346 cells/mcL|L|||F\r" + "DG1|1|ICD10|^Ovarian Cancer|||||||||||||||||||||\r";
String json = ftv.convert(hl7message, OPTIONS);
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
List<BundleEntryComponent> e = b.getEntry();
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(1);
List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
assertThat(encounterResource).hasSize(1);
Encounter enc = (Encounter) encounterResource.get(0);
List<Reference> reasonRefs = enc.getReasonReference();
assertEquals(2, reasonRefs.size());
// Guess at the order of the references
Reference refObservation = reasonRefs.get(0);
Reference refCondition = reasonRefs.get(1);
// If guessed wrong, reverse them
if (!refObservation.getReference().contains("Observation")) {
refObservation = reasonRefs.get(1);
refCondition = reasonRefs.get(0);
}
assertTrue(refObservation.getReference().contains("Observation"));
assertTrue(refCondition.getReference().contains("Condition"));
}
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