use of org.hl7.fhir.r4b.model.Extension in project hl7v2-fhir-converter by LinuxForHealth.
the class CodeableConceptTest method testSimilarCWEToCodeableConcepts.
@ParameterizedTest
@MethodSource("parmsTestSimilarCWEInputs")
void testSimilarCWEToCodeableConcepts(String cwe, String code, String display, String system, String text) {
// See inputs and test explanation above
String patientWithCodeableConcept = "MSH|^~\\&|MIICEHRApplication|MIIC|MIIC|MIIC|201705130822||VXU^V04^VXU_V04|test1100|P|2.5.1|||AL|AL|||||Z22^CDCPHINVS|^^^^^MIIC^SR^^^MIIC|MIIC\n" + // Test text only race
"PID|1||12345678^^^^MR||TestPatientLastName^Jane^|||||" + cwe + "\n";
Patient patient = PatientUtils.createPatientFromHl7Segment(ftv, patientWithCodeableConcept);
assertThat(patient.hasExtension()).isTrue();
List<Extension> extensions = patient.getExtensionsByUrl(UrlLookup.getExtensionUrl("race"));
assertThat(extensions).isNotNull();
assertThat(extensions.size()).isEqualTo(1);
assertThat(extensions.get(0).hasValue()).isTrue();
CodeableConcept ccW = (CodeableConcept) extensions.get(0).getValue();
DatatypeUtils.checkCommonCodeableConceptAssertions(ccW, code, display, system, text);
}
use of org.hl7.fhir.r4b.model.Extension in project hl7v2-fhir-converter by LinuxForHealth.
the class CodeableConceptTest method testCodeableConceptDoubleRaceWithVersionAndAlternate.
@Test
void testCodeableConceptDoubleRaceWithVersionAndAlternate() {
// This has both a known and an unknown system.
// "valueCodeableConcept": {
// "coding": [ {
// "system": <known-to-FHIR>, << FIRST CODING
// "display": <original-display-value>
// "code": <code-from-input>
// "version": <version>
// },
// {
// "system": <unknown, so made up "urn:id:L">, << SECOND (ALTERNATE CODING)
// "display": <original-alternate display-value>
// "code": <altenate-code>
// "version": <alternate-version>
// } ],
// "text": <original-display-value>
// },
String patientWithDoubleRaceWithVersionAndAlternate = "MSH|^~\\&|MIICEHRApplication|MIIC|MIIC|MIIC|201705130822||VXU^V04^VXU_V04|test1100|P|2.5.1|||AL|AL|||||Z22^CDCPHINVS|^^^^^MIIC^SR^^^MIIC|MIIC\n" + // Test double race in the SAME CWE (not a second CWE) and versions. Use made up Cauc to ensure test doesn't mix up whites.
"PID|1||12345678^^^^MR||TestPatientLastName^Jane|||||2106-3^White^CDCREC^CA^Caucasian^L^1.1^4|\n";
Patient patient = PatientUtils.createPatientFromHl7Segment(ftv, patientWithDoubleRaceWithVersionAndAlternate);
assertThat(patient.hasExtension()).isTrue();
List<Extension> extensions = patient.getExtensionsByUrl(UrlLookup.getExtensionUrl("race"));
assertThat(extensions).isNotNull();
assertThat(extensions.size()).isEqualTo(1);
assertThat(extensions.get(0).hasValue()).isTrue();
CodeableConcept ccW = (CodeableConcept) extensions.get(0).getValue();
assertThat(ccW.hasCoding()).isTrue();
assertThat(ccW.hasText()).isTrue();
assertThat(ccW.getText()).hasToString("White");
List<Coding> codings = ccW.getCoding();
assertThat(codings.size()).isEqualTo(2);
DatatypeUtils.checkCommonCodingAssertions(codings.get(0), "2106-3", "White", V3_RACE_SYSTEM, "1.1");
DatatypeUtils.checkCommonCodingAssertions(codings.get(1), "CA", "Caucasian", "urn:id:L", "4");
}
use of org.hl7.fhir.r4b.model.Extension in project hl7v2-fhir-converter by LinuxForHealth.
the class FHIRExtensionsTest method testTextOnlyReligion.
@Test
void testTextOnlyReligion() {
String patientWithDataForExtensions = "MSH|^~\\&|MIICEHRApplication|MIIC|MIIC|MIIC|201705130822||VXU^V04^VXU_V04|test1100|P|2.5.1|||AL|AL|||||Z22^CDCPHINVS|^^^^^MIIC^SR^^^MIIC|MIIC\n" + // Test text only religion
"PID|1||12345678^^^^MR||Jane^TestPatientLastName||||||||||||Methodist|\n";
Patient patient = PatientUtils.createPatientFromHl7Segment(ftv, patientWithDataForExtensions);
assertThat(patient.hasExtension()).isTrue();
Extension ext = patient.getExtensionByUrl(UrlLookup.getExtensionUrl("religion"));
assertThat(ext).isNotNull();
CodeableConcept cc = (CodeableConcept) ext.getValue();
assertThat(cc.hasCoding()).isTrue();
assertThat(cc.hasText()).isFalse();
Coding coding = cc.getCodingFirstRep();
assertThat(coding).isNotNull();
assertThat(coding.hasCode()).isFalse();
String theSystem = V3ReligiousAffiliation._1029.getSystem();
assertThat(coding.hasSystem()).isTrue();
assertThat(coding.getSystem()).isEqualTo(theSystem);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).containsPattern("Invalid.*Methodist.*" + theSystem);
}
use of org.hl7.fhir.r4b.model.Extension in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7PatientFHIRConversionTest method validate_data_lineage.
private void validate_data_lineage(String hl7message, String messageType, boolean millis) {
String json = ftv.convert(hl7message, PatientUtils.OPTIONS);
assertThat(json).isNotBlank();
LOGGER.debug(json);
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
List<BundleEntryComponent> e = b.getEntry();
// Get bundle meta extensions *not using these currently*
// Meta bundleMeta = b.getMeta();
// List<Extension> bundleMetaExtensions = bundleMeta.getExtension();
LOGGER.debug("Found {} resources.", e.stream().count());
e.stream().forEach(bec -> {
LOGGER.debug("Validating " + bec.getResource().getResourceType());
Meta meta = bec.getResource().getMeta();
List<Extension> extensions = meta.getExtension();
LOGGER.debug("Found " + extensions.size() + " meta extensions");
validate_lineage_json(extensions, messageType, millis);
});
}
use of org.hl7.fhir.r4b.model.Extension in project hl7v2-fhir-converter by LinuxForHealth.
the class InputTimeZoneIdTest method validateTimeZoneIdSettingViaOption.
@Test
void validateTimeZoneIdSettingViaOption() {
// NOTE: This simple Condition (PRB) segment is used for testing time because it has both
// standard DateTime conversions (abatementDateTime, recordedDate) and value conversions (extension).
String hl7message = "MSH|^~\\&|||||20040629164652|1|PPR^PC1|331|P|2.3.1||\r" + "PID||||||||||||||||||||||||||||||\r" + "PV1||I||||||||||||||||||||||||||||||||||||||||||\r" + // PRB.16 to onsetDateTime (check time ZoneId)
"PRB|AD|20020202020000|K80.00^Cholelithiasis^I10|53956|||20070707070000||20090909090000|||||||20160616160000\r";
// FIRST test with city based ZoneId passed through options
ConverterOptions customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().withZoneIdText("America/Chicago").build();
// "America/Chicago" will become -06:00 in winter (CST) -05:00 in spring/summer/fall (CDT). This is expected.
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
// Find the condition from the FHIR bundle.
List<Resource> conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
assertThat(conditionResource).hasSize(1);
Condition condition = (Condition) conditionResource.get(0);
// PRB.2 Chicago Central STANDARD Time
assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00-06:00");
// PRB.9 Chicago Central DAYLIGHT Time
assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00-05:00");
// PRB.16 Chicago CDT
assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00-05:00");
assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7 Chicago CDT
"2007-07-07T07:00:00-05:00");
// SECOND test with fixed ZoneId passed through options
customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().withZoneIdText("+03:00").build();
e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
// Find the condition from the FHIR bundle.
conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
assertThat(conditionResource).hasSize(1);
condition = (Condition) conditionResource.get(0);
// PRB.2 fixed ZoneId
assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00+03:00");
// PRB.9
assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00+03:00");
// PRB.16
assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00+03:00");
assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7
"2007-07-07T07:00:00+03:00");
// THIRD test with no ZoneId passed through options, so it uses the config.properties ZoneId
customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().build();
e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
// Find the condition from the FHIR bundle.
conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
assertThat(conditionResource).hasSize(1);
condition = (Condition) conditionResource.get(0);
// PRB.2 config.properties ZoneId
assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00+08:00");
// PRB.9
assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00+08:00");
// PRB.16
assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00+08:00");
assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7
"2007-07-07T07:00:00+08:00");
}
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