Examples with DateTimeType org.hl7.fhir.dstu2.model.DateTimeType used on opensource projects

Example 81 with DateTimeType

use of org.hl7.fhir.dstu2.model.DateTimeType in project cqf-ruler by DBCG.

the class ExtractProvider method createObservationFromItemAnswer.

private Bundle.BundleEntryComponent createObservationFromItemAnswer(QuestionnaireResponse.QuestionnaireResponseItemAnswerComponent answer, String linkId, Date authored, QuestionnaireResponse questionnaireResponse, Map<String, Coding> questionnaireCodeMap) {
    Observation obs = new Observation();
    obs.setEffective(new DateTimeType(authored));
    obs.setStatus(Observation.ObservationStatus.FINAL);
    obs.setSubject(questionnaireResponse.getSubject());
    Coding qrCategoryCoding = new Coding();
    qrCategoryCoding.setCode("survey");
    qrCategoryCoding.setSystem("http://hl7.org/fhir/observation-category");
    obs.setCategory(Collections.singletonList(new CodeableConcept().addCoding(qrCategoryCoding)));
    obs.setCode(new CodeableConcept().addCoding(questionnaireCodeMap.get(linkId)));
    obs.setId("qr" + questionnaireResponse.getIdElement().getIdPart() + "." + linkId);
    switch(answer.getValue().fhirType()) {
        case "string":
            obs.setValue(new StringType(answer.getValueStringType().getValue()));
            break;
        case "Coding":
            obs.setValue(new CodeableConcept().addCoding(answer.getValueCoding()));
            break;
        case "boolean":
            obs.setValue(new BooleanType(answer.getValueBooleanType().booleanValue()));
            break;
    }
    Reference questionnaireResponseReference = new Reference();
    questionnaireResponseReference.setReference("QuestionnaireResponse" + "/" + questionnaireResponse.getIdElement().getIdPart());
    Observation.ObservationRelatedComponent related = new Observation.ObservationRelatedComponent().setType(Observation.ObservationRelationshipType.DERIVEDFROM).setTarget(questionnaireResponseReference);
    obs.setRelated(Collections.singletonList(related));
    Extension linkIdExtension = new Extension();
    linkIdExtension.setUrl("http://hl7.org/fhir/uv/sdc/StructureDefinition/derivedFromLinkId");
    Extension innerLinkIdExtension = new Extension();
    innerLinkIdExtension.setUrl("text");
    innerLinkIdExtension.setValue(new StringType(linkId));
    linkIdExtension.setExtension(Collections.singletonList(innerLinkIdExtension));
    obs.addExtension(linkIdExtension);
    Bundle.BundleEntryRequestComponent berc = new Bundle.BundleEntryRequestComponent();
    berc.setMethod(Bundle.HTTPVerb.PUT);
    berc.setUrl("Observation/" + obs.getId());
    Bundle.BundleEntryComponent bec = new Bundle.BundleEntryComponent();
    bec.setResource(obs);
    bec.setRequest(berc);
    return bec;
}

Example 82 with DateTimeType

use of org.hl7.fhir.dstu2.model.DateTimeType in project cqf-ruler by DBCG.

the class ExtractProvider method createObservationFromItemAnswer.

private Bundle.BundleEntryComponent createObservationFromItemAnswer(QuestionnaireResponse.QuestionnaireResponseItemAnswerComponent answer, String linkId, Date authored, QuestionnaireResponse questionnaireResponse, Map<String, Coding> questionnaireCodeMap) {
    Observation obs = new Observation();
    obs.setEffective(new DateTimeType(authored));
    obs.setStatus(Observation.ObservationStatus.FINAL);
    obs.setSubject(questionnaireResponse.getSubject());
    Coding qrCategoryCoding = new Coding();
    qrCategoryCoding.setCode("survey");
    qrCategoryCoding.setSystem("http://hl7.org/fhir/observation-category");
    obs.setCategory(Collections.singletonList(new CodeableConcept().addCoding(qrCategoryCoding)));
    obs.setCode(new CodeableConcept().addCoding(questionnaireCodeMap.get(linkId)));
    obs.setId("qr" + questionnaireResponse.getIdElement().getIdPart() + "." + linkId);
    switch(answer.getValue().fhirType()) {
        case "string":
            obs.setValue(new StringType(answer.getValueStringType().getValue()));
            break;
        case "Coding":
            obs.setValue(new CodeableConcept().addCoding(answer.getValueCoding()));
            break;
        case "boolean":
            obs.setValue(new BooleanType(answer.getValueBooleanType().booleanValue()));
            break;
    }
    Reference questionnaireResponseReference = new Reference();
    questionnaireResponseReference.setReference("QuestionnaireResponse" + "/" + questionnaireResponse.getIdElement().getIdPart());
    obs.setDerivedFrom(Collections.singletonList(questionnaireResponseReference));
    Extension linkIdExtension = new Extension();
    linkIdExtension.setUrl("http://hl7.org/fhir/uv/sdc/StructureDefinition/derivedFromLinkId");
    Extension innerLinkIdExtension = new Extension();
    innerLinkIdExtension.setUrl("text");
    innerLinkIdExtension.setValue(new StringType(linkId));
    linkIdExtension.setExtension(Collections.singletonList(innerLinkIdExtension));
    obs.addExtension(linkIdExtension);
    Bundle.BundleEntryRequestComponent berc = new Bundle.BundleEntryRequestComponent();
    berc.setMethod(Bundle.HTTPVerb.PUT);
    berc.setUrl("Observation/" + obs.getId());
    Bundle.BundleEntryComponent bec = new Bundle.BundleEntryComponent();
    bec.setResource(obs);
    bec.setRequest(berc);
    return bec;
}

Example 83 with DateTimeType

use of org.hl7.fhir.dstu2.model.DateTimeType in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7OrderRequestFHIRConversionTest method testBroadORCPlusOBRFields.

// This test is a companion to testBroadORCFields.   ORC and OBR records often have repeated data; one taking priority over the other.
// Read comments carefully.  This sometimes tests the secondary value and may be the opposite to the tests in testBroadORCFields.
@Test
// Suppress warnings about too many assertions in a test.  Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
void testBroadORCPlusOBRFields() {
    String hl7message = "MSH|^~\\&|||||20180924152907|34001|ORU^R01^ORU_R01|213|T|2.6|||||||||||\n" + // PID.18 is used as backup identifier visit number because PV1.19 is empty
    "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||665544||||||||||||\n" + // PV1.19 is empty and not used as visit number identifier
    "PV1|1|E|||||||||||||||||||||||||||||||||||||||||||\n" + // 7. ORC.16 is set to a reason code (but it is ignored because it is secondary to OBR.31, which is present in this case and therefore overrides ORC.16)
    "ORC|RE|248648498^|248648498^|||||||||||||042^Human immunodeficiency virus [HIV] disease [42]^I9CDX^^^^29|||||||||||||||\n" + // 14. OBR.6 creates ServiceRequest.authoredOn
    "OBR|1|248648498^|248648498^|83036E^HEMOGLOBIN A1C^PACSEAP^^^^^^HEMOGLOBIN A1C||20120606120606|20170707150707||||L|||||54321678^SCHMIDT^FRIEDA^^MD^^^^NPI^D^^^NPI||||||20180924152900|||F||||||HIV^HIV/Aids^L^^^^V1|323232&Mahoney&Paul&J||||||||||||||||||\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> serviceRequestList = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    // Important that we have exactly one service request (no duplication).  OBR creates it as a reference.
    assertThat(serviceRequestList).hasSize(1);
    ServiceRequest serviceRequest = ResourceUtils.getResourceServiceRequest(serviceRequestList.get(0), context);
    assertThat(serviceRequest.hasStatus()).isTrue();
    assertThat(serviceRequest.hasIdentifier()).isTrue();
    assertThat(serviceRequest.getIdentifier()).hasSize(3);
    // Identifier 1: visit number should be set by in this test by secondary PID.18
    // ORU_RO1 records do not create the ServiceRequest directly.  They create a DiagnosticReport and it creates the ServiceRequest.
    // This makes sure the specification for ORU_RO1.DiagnosticReport is specifying PID correctly in AdditionalSegments.
    // Extensive testing of identifiers is done in Hl7IdentifierFHIRConversionTest.java
    Identifier identifier = serviceRequest.getIdentifier().get(0);
    String value = identifier.getValue();
    String system = identifier.getSystem();
    // PID.18
    assertThat(value).isEqualTo("665544");
    assertThat(system).isNull();
    CodeableConcept type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "VN", "Visit number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
    // No requisition in the serviceRequest.
    assertThat(serviceRequest.hasRequisition()).isFalse();
    // OBR.6 should create authoredOn because ORC.9 is not filled in
    assertThat(serviceRequest.hasAuthoredOn()).isTrue();
    assertThat(serviceRequest.getAuthoredOnElement().toString()).containsPattern("2012-06-06T12:06:06");
    // OBR.7 is used to create an ServiceRequest.occurrenceDateTime date because ORC.15 is empty
    assertThat(serviceRequest.hasOccurrenceDateTimeType()).isTrue();
    assertThat(serviceRequest.getOccurrenceDateTimeType().toString()).containsPattern("2017-07-07T15:07:07");
    // OBR.31 should create the ServiceRequest.reasonCode CWE
    assertThat(serviceRequest.hasReasonCode()).isTrue();
    assertThat(serviceRequest.getReasonCode()).hasSize(1);
    DatatypeUtils.checkCommonCodeableConceptVersionedAssertions(serviceRequest.getReasonCodeFirstRep(), "HIV", "HIV/Aids", "urn:id:L", "HIV/Aids", "V1");
    // OBR.16 should create an ServiceRequest.requester reference & display
    assertThat(serviceRequest.hasRequester()).isTrue();
    assertThat(serviceRequest.getRequester().hasDisplay()).isTrue();
    assertThat(serviceRequest.getRequester().getDisplay()).isEqualTo("FRIEDA SCHMIDT MD");
    assertThat(serviceRequest.getRequester().hasReference()).isTrue();
    String requesterRef = serviceRequest.getRequester().getReference();
    Practitioner pract = ResourceUtils.getSpecificPractitionerFromBundleEntriesList(e, requesterRef);
    // Confirm that the matching practitioner by ID has the correct content (simple validation)
    // Should be OBR.16 because ORC.12 is empty.
    // Check the practitioner content in detail, validating subfields.
    assertThat(pract.getIdentifier()).hasSize(1);
    // OBR.16.1
    assertThat(pract.getIdentifierFirstRep().getValue()).isEqualTo("54321678");
    // OBR.16.9, tests known system logic
    assertThat(pract.getIdentifierFirstRep().getSystem()).isEqualTo("http://hl7.org/fhir/sid/us-npi");
    DatatypeUtils.checkCommonCodeableConceptAssertions(pract.getIdentifierFirstRep().getType(), "NPI", "National provider identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", // OBR.16.13
    null);
    assertThat(pract.getName()).hasSize(1);
    // Combined OBR.16.2 - OBR.16.7
    assertThat(pract.getNameFirstRep().getTextElement().toString()).hasToString("FRIEDA SCHMIDT MD");
    // OBR.16.10
    assertThat(pract.getNameFirstRep().getUseElement().getCode()).isEqualTo("usual");
    // OBR.4 maps to ServiceRequest.code.  Verify resulting CodeableConcept.
    assertThat(serviceRequest.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(serviceRequest.getCode(), "83036E", "HEMOGLOBIN A1C", "urn:id:PACSEAP", "HEMOGLOBIN A1C");
    List<Resource> diagnosticReportList = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    assertThat(diagnosticReportList).hasSize(1);
    DiagnosticReport diagnosticReport = ResourceUtils.getResourceDiagnosticReport(diagnosticReportList.get(0), context);
    // OBR.4 ALSO maps to DiagnosticReport.code.  Verify resulting CodeableConcept.
    assertThat(diagnosticReport.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(diagnosticReport.getCode(), "83036E", "HEMOGLOBIN A1C", "urn:id:PACSEAP", "HEMOGLOBIN A1C");
    assertThat(diagnosticReport.hasBasedOn()).isTrue();
    assertThat(diagnosticReport.getBasedOn()).hasSize(1);
    // OBR.7 maps to create an DiagnosticReport.effectiveDateTime
    assertThat(diagnosticReport.hasEffectiveDateTimeType()).isTrue();
    assertThat(diagnosticReport.getEffectiveDateTimeType().toString()).containsPattern("2017-07-07T15:07:07");
    // Check for DiagnosticReport.issued instant of OBR.22
    assertThat(diagnosticReport.hasIssued()).isTrue();
    // NOTE: The data is kept as an InstantType, and is extracted with .toInstant
    // thus results in a different format than other time stamps that are based on DateTimeType
    assertThat(diagnosticReport.getIssued().toInstant().toString()).contains("2018-09-24T07:29:00Z");
    // Get the diagnosticReport.resultsInterpreter, which should match the Practitioner data from OBR.32
    assertThat(diagnosticReport.hasResultsInterpreter()).isTrue();
    assertThat(diagnosticReport.getResultsInterpreter()).hasSize(1);
    String resultsInterpreterRef = diagnosticReport.getResultsInterpreter().get(0).getReference();
    pract = ResourceUtils.getSpecificPractitionerFromBundleEntriesList(e, resultsInterpreterRef);
    // Confirm that the matching practitioner by ID has the correct content (simple validation)
    // Should be the value OBR.32
    assertThat(pract.getIdentifierFirstRep().getValue()).isEqualTo("323232");
    assertThat(pract.getName()).hasSize(1);
    assertThat(pract.getName().get(0).getTextElement()).hasToString("Paul J Mahoney");
    // Check for OBR.25 mapped to DiagnosticReport.status
    assertThat(diagnosticReport.hasStatus()).isTrue();
    assertThat(diagnosticReport.getStatusElement().getCode()).isEqualTo("final");
}

Example 84 with DateTimeType

use of org.hl7.fhir.dstu2.model.DateTimeType in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7PatientFHIRConversionTest method validate_lineage_json.

private void validate_lineage_json(List<Extension> extensions, String messageType, boolean millis) {
    assertThat(extensions.size()).isEqualTo(6);
    for (Extension extension : extensions) {
        // Get the URL
        String url = extension.getUrl();
        LOGGER.debug("URL:" + url);
        // Get the value
        String value = extension.getValue().toString();
        // If the value is a codeable concept and not a simple value - parse the value out of the codeable concept.
        if (value.indexOf("CodeableConcept") >= 0) {
            String codeableConceptValue = extension.getValue().getChildByName("coding").getValues().get(0).getNamedProperty("code").getValues().get(0).toString();
            LOGGER.debug("CodeableConceptValue:" + codeableConceptValue.toString());
            value = codeableConceptValue.toString();
        }
        // Get the Name from the URL
        String name = url.substring(url.lastIndexOf("/") + 1, url.length());
        LOGGER.debug("Name:" + name);
        LOGGER.debug("Value:" + value);
        LOGGER.debug("Message Type:" + messageType);
        String[] messageParts = messageType.split("\\^");
        // test value based off the name.
        switch(name) {
            case "source-event-timestamp":
                if (millis)
                    assertThat(value).isEqualTo("DateTimeType[2006-09-15T21:00:00.567+08:00]");
                else
                    assertThat(value).isEqualTo("DateTimeType[2006-09-15T21:00:00+08:00]");
                break;
            case "source-record-id":
                assertThat(value).isEqualTo("1473973200100600");
                break;
            case "source-data-model-version":
                assertThat(value).isEqualTo("2.3");
                break;
            case "process-client-id":
                assertThat(value).isEqualTo("SendingApplication");
                break;
            case "source-event-trigger":
                assertThat(value).isEqualTo(messageParts[1]);
                break;
            case "source-record-type":
                assertThat(value).isEqualTo(messageParts[0]);
                break;
            default:
                // this shouldn't happen
                LOGGER.debug("Not found");
                Assertions.fail();
                break;
        }
    }
}

Example 85 with DateTimeType

use of org.hl7.fhir.dstu2.model.DateTimeType in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7AllergyFHIRConversionTest method test_allergy_onset.

@Test
/**
 * Verifies AL1-6 is put into AllergyIntolerance.onsetDateTime; AllergyIntolerance.reaction.onset is not set.
 */
void test_allergy_onset() {
    String hl7message = "MSH|^~\\&|SE050|050|PACS|050|20120912011230||ADT^A01|102|T|2.6|||AL|NE\r" + "PID|0010||PID1234||DOE^JANE|||F\r" + "AL1|1|DA|00000741^OXYCODONE||HYPOTENSION|20210101\r";
    AllergyIntolerance allergy = ResourceUtils.getAllergyResource(ftv, hl7message);
    assertThat(allergy.getCategory().get(0).getCode()).isEqualTo("medication");
    assertThat(allergy.getReaction().get(0).getManifestation()).extracting(m -> m.getText()).containsExactly("HYPOTENSION");
    Date onsetReaction = allergy.getReaction().get(0).getOnset();
    Assertions.assertNull(onsetReaction);
    DateTimeType onsetAllergy = allergy.getOnsetDateTimeType();
    assertThat(onsetAllergy.getValueAsString()).isEqualTo("2021-01-01");
}