Examples with Specimen org.hl7.fhir.r4.model.Specimen used on opensource projects

Example 26 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ORUMessageTest method test_orur01_with_encounter_present.

// 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")
@Test
void test_orur01_with_encounter_present() throws IOException {
    String hl7message = "MSH|^~\\&|PROSLOV|MYHOSPITAL|WHIA|IBM|20180520230000||ORU^R01|MSGID006552|T|2.6\r" + "PID|1||000065432^^^MRN^MR||ROSTENKOWSKI^BERNADETTE^||19840823|Female||1002-5|382 OTHERSTREET AVE^^PASADENA^LA^223343||4582143248||^French|S||53811||||U|||||||\r" + "PV1|1|O|||||9905^Adams^John|9906^Yellow^William^F|9907^Blue^Oren^J||||||||9908^Green^Mircea^||2462201|||||||||||||||||||||||||20180520230000\r" + "OBR|1||bbf1993ab|1122^Final Echocardiogram Report|||20180520230000|||||||||||||002|||||F|||550469^Tsadok550469^Janetary~660469^Merrit660469^Darren^F~770469^Das770469^Surjya^P~880469^Winter880469^Oscar^||||770469&Das770469&Surjya&P^^^6N^1234^A|\r" + "OBX|1|NM|2552^HRTRTMON|1|115||||||F|||20180520230000|||\r";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    // Verify that the right resources are created
    List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
    assertThat(patientResource).hasSize(1);
    List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
    assertThat(encounterResource).hasSize(1);
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(1);
    List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    assertThat(diagnosticReport).hasSize(1);
    List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    assertThat(servReqResource).hasSize(1);
    List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
    assertThat(practitionerResource).hasSize(5);
    // Expecting only the above resources, no extras!
    assertThat(e).hasSize(10);
    // /////////////////////////////////////////
    // Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
    // /////////////////////////////////////////
    DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
    // Verify status from OBR.25
    assertThat(diag.getStatus().toCode()).isEqualTo("final");
    // Verify category from OBR.24
    assertThat(diag.getCategory()).isEmpty();
    // Verify code from OBR.4
    assertThat(diag.hasCode()).isTrue();
    List<Coding> codings = diag.getCode().getCoding();
    assertThat(codings).hasSize(1);
    Coding coding = codings.get(0);
    assertThat(coding.hasDisplay()).isTrue();
    assertThat(coding.getDisplay()).hasToString("Final Echocardiogram Report");
    assertThat(coding.hasCode()).isTrue();
    assertThat(coding.getCode()).hasToString("1122");
    assertThat(coding.hasSystem()).isFalse();
    // Verify encounter reference
    assertThat(diag.getEncounter().isEmpty()).isFalse();
    // Verify subject reference
    assertThat(diag.getSubject().isEmpty()).isFalse();
    // Verify effectiveDateTime from OBR.7 and OBR.8
    // This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
    assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2018-05-20T23:00:00+08:00");
    // Verify issued from OBR.22
    assertThat(diag.getIssued()).isNull();
    // Verify resultsInterpreter from OBR.32
    assertThat(diag.getResultsInterpreter()).hasSize(1);
    // Verify basedOn is ref to the ServiceRequest created for ORC or OBR
    assertThat(diag.getBasedOn()).hasSize(1);
    assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
    // Verify specimen reference
    assertThat(diag.getSpecimen()).isEmpty();
    // Verify result reference
    List<Reference> obsRef = diag.getResult();
    assertThat(obsRef).hasSize(1);
    assertThat(obsRef.get(0).isEmpty()).isFalse();
    // Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX is not of type TX.
    List<Attachment> attachments = diag.getPresentedForm();
    Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
    // //////////////////////////////////
    for (Resource res : obsResource) {
        // Verify encounter reference exists
        Observation obs = (Observation) res;
        assertThat(obs.getEncounter().isEmpty()).isFalse();
        assertThat(obs.getEncounter().getReference().substring(0, 10)).isEqualTo("Encounter/");
        // Verify subject reference to Patient exists
        assertThat(obs.getSubject().isEmpty()).isFalse();
        assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
    }
}

Example 27 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ORUMessageTest method test_oru_with_multiple_observations.

// 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")
@Test
// Observation resources are created instead of attachments in the diagReport because they are not type TX.
void test_oru_with_multiple_observations() throws IOException {
    String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + // OBR.24 creates a DiagnosticReport.category
    "OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|1051-2^New Born Screening^LN|||20151009173644|||||||||||||002||||CUS|F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3065^Mahoney^Paul^J|\r" + "OBX|1|ST|TS-F-01-002^Endocrine Disorders^L||obs report||||||F\r" + "OBX|2|ST|GA-F-01-024^Galactosemia^L||ECHOCARDIOGRAPHIC REPORT||||||F\r";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    // Verify correct resources created
    List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
    assertThat(patientResource).hasSize(1);
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(2);
    List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
    assertThat(practitionerResource).hasSize(1);
    List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    assertThat(diagnosticReport).hasSize(1);
    List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    assertThat(servReqResource).hasSize(1);
    // Expecting only the above resources, no extras!
    assertThat(e).hasSize(6);
    // /////////////////////////////////////////
    // Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
    // /////////////////////////////////////////
    DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
    // Verify status from OBR.25
    assertThat(diag.getStatus().toCode()).isEqualTo("final");
    // Verify category from OBR.24
    assertThat(diag.getCategory()).hasSize(1);
    DatatypeUtils.checkCommonCodeableConceptAssertions(diag.getCategoryFirstRep(), "CUS", "Cardiac Ultrasound", "http://terminology.hl7.org/CodeSystem/v2-0074", "CUS");
    // Verify code from OBR.4
    assertThat(diag.hasCode()).isTrue();
    List<Coding> codings = diag.getCode().getCoding();
    assertThat(codings).hasSize(1);
    Coding coding = codings.get(0);
    assertThat(coding.hasDisplay()).isTrue();
    assertThat(coding.getDisplay()).hasToString("New Born Screening");
    assertThat(coding.hasCode()).isTrue();
    assertThat(coding.getCode()).hasToString("1051-2");
    assertThat(coding.hasSystem()).isTrue();
    assertThat(coding.getSystem()).hasToString("http://loinc.org");
    // Verify encounter reference
    assertThat(diag.getEncounter().isEmpty()).isTrue();
    // Verify subject reference
    assertThat(diag.getSubject().isEmpty()).isFalse();
    // Verify effectiveDateTime from OBR.7 and OBR.8
    assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo(// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
    "2015-10-09T17:36:44+08:00");
    // Verify issued from OBR.22
    assertThat(diag.getIssued()).isNull();
    // Verify resultsInterpreter from OBR.32
    assertThat(diag.getResultsInterpreter()).hasSize(1);
    // Verify basedOn is ref to the ServiceRequest created for ORC or OBR
    assertThat(diag.getBasedOn()).hasSize(1);
    assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
    // Verify specimen reference
    assertThat(diag.getSpecimen()).isEmpty();
    // Verify result reference
    List<Reference> obsRef = diag.getResult();
    assertThat(obsRef).hasSize(2);
    assertThat(obsRef.get(0).isEmpty()).isFalse();
    assertThat(obsRef.get(1).isEmpty()).isFalse();
    // Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX of type TX have ids.
    List<Attachment> attachments = diag.getPresentedForm();
    Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
    // //////////////////////////////////
    for (Resource res : obsResource) {
        // Verify encounter reference is not set
        Observation obs = (Observation) res;
        assertThat(obs.getEncounter().isEmpty()).isTrue();
        // Verify subject reference to Patient exists
        assertThat(obs.getSubject().isEmpty()).isFalse();
        assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
    }
}

Example 28 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ORUMessageTest method test_oru_multipleOBXWithMixedType.

/**
 * Verifies ORU messages with mixed OBX types
 *
 * @throws IOException
 */
@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 test_oru_multipleOBXWithMixedType() throws IOException {
    String json = ftv.convert(new File("src/test/resources/ORU-multiline-short-mixed.hl7"), OPTIONS_PRETTYPRINT);
    assertThat(json).isNotBlank();
    LOGGER.debug("FHIR json result:\n" + json);
    // Verify conversion
    FHIRContext context = new FHIRContext();
    IBaseResource bundleResource = context.getParser().parseResource(json);
    Bundle b = (Bundle) bundleResource;
    assertThat(bundleResource).isNotNull();
    Assertions.assertSame(BundleType.COLLECTION, b.getType(), "Bundle type not expected");
    List<BundleEntryComponent> e = b.getEntry();
    // Verify that the right resources have been created
    List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
    assertThat(patientResource).hasSize(1);
    List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
    assertThat(encounterResource).hasSize(1);
    List<Resource> organizationResource = ResourceUtils.getResourceList(e, ResourceType.Organization);
    // We expect an organization created from an Encounter.serviceProvider reference
    assertThat(organizationResource).hasSize(1);
    List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
    assertThat(practitionerResource).hasSize(4);
    List<Resource> messageHeader = ResourceUtils.getResourceList(e, ResourceType.MessageHeader);
    assertThat(messageHeader).hasSize(1);
    // Verify one Observation is created (from the ST, not the TX)
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    // TODO: When NTE is implemented, then update this.
    assertThat(obsResource).hasSize(1);
    // Verify Diagnostic Report is created as expected
    List<Resource> reportResource = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    assertThat(reportResource).hasSize(1);
    List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    assertThat(servReqResource).hasSize(1);
    // Verify there are no extra resources created
    assertThat(e).hasSize(11);
    // /////////////////////////////////////////
    // Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
    // /////////////////////////////////////////
    DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(reportResource.get(0), context);
    // Verify status from OBR.25
    assertThat(diag.getStatus().toCode()).isEqualTo("final");
    // Verify category from OBR.24
    assertThat(diag.getCategory()).hasSize(1);
    assertThat(diag.getCategory().get(0).getCoding()).hasSize(1);
    assertThat(diag.getCategory().get(0).getCoding().get(0).getSystem()).isEqualTo("http://terminology.hl7.org/CodeSystem/v2-0074");
    assertThat(diag.getCategory().get(0).getCoding().get(0).getCode()).isEqualTo("CT");
    assertThat(diag.getCategory().get(0).getCoding().get(0).getDisplay()).isEqualTo("CAT Scan");
    assertThat(diag.getCategory().get(0).getText()).isEqualTo("CT");
    // Verify code from OBR.4; This tests scenario of the code not being in the default loinc system.
    assertThat(diag.hasCode()).isTrue();
    List<Coding> codings = diag.getCode().getCoding();
    assertThat(codings).hasSize(1);
    Coding coding = codings.get(0);
    assertThat(coding.hasDisplay()).isTrue();
    assertThat(coding.getDisplay()).hasToString("ECHO CARDIOGRAM COMPLETE");
    assertThat(coding.hasCode()).isTrue();
    assertThat(coding.getCode()).hasToString("1487");
    assertThat(coding.hasSystem()).isFalse();
    // Verify encounter reference
    assertThat(diag.getEncounter().isEmpty()).isFalse();
    // Verify subject reference
    assertThat(diag.getSubject().isEmpty()).isFalse();
    // Verify effectiveDateTime from OBR.7 and OBR.8
    // This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
    assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2020-08-02T12:44:55+08:00");
    // Verify issued from OBR.22
    assertThat(diag.getIssued()).isNull();
    // Verify resultsInterpreter from OBR.32
    assertThat(diag.getResultsInterpreter()).isEmpty();
    // Verify basedOn is ref to the ServiceRequest created for ORC or OBR
    assertThat(diag.getBasedOn()).hasSize(1);
    assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
    // Verify specimen reference
    List<Reference> spmRef = diag.getSpecimen();
    assertThat(spmRef).isEmpty();
    // Verify result reference
    List<Reference> obsRef = diag.getResult();
    assertThat(obsRef).isNotEmpty().hasSize(1);
    assertThat(obsRef.get(0).isEmpty()).isFalse();
    // No attachment created since OBX with TX and no id is not first
    List<Attachment> attachments = diag.getPresentedForm();
    Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
    // //////////////////////////////////
    for (Resource res : obsResource) {
        // Verify encounter reference exists
        Observation obs = (Observation) res;
        assertThat(obs.getEncounter().isEmpty()).isFalse();
        assertThat(obs.getEncounter().getReference().substring(0, 10)).isEqualTo("Encounter/");
        // Verify subject reference to Patient exists
        assertThat(obs.getSubject().isEmpty()).isFalse();
        assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
    }
}

Example 29 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ORUMessageTest method test_oru_patient_diagReport.

// DiagnosticReports are only created from ORU messages so the test of DiagnosticReport content is included in this test module.
// 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")
@Test
// Test the minimum scenario where the least possible segments and resource info are provided in the message
void test_oru_patient_diagReport() throws IOException {
    String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + "OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|1051-2^New Born Screening^LN|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^|||||\r";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    // Verify correct resources created
    List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
    assertThat(patientResource).hasSize(1);
    List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    assertThat(diagnosticReport).hasSize(1);
    List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    assertThat(servReqResource).hasSize(1);
    // Expecting only the above resources, no extras!
    assertThat(e).hasSize(3);
    // /////////////////////////////////////////
    // Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
    // /////////////////////////////////////////
    DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
    // Verify status from OBR.25
    assertThat(diag.getStatus().toCode()).isEqualTo("final");
    // Verify category from OBR.24
    assertThat(diag.getCategory()).isEmpty();
    // Verify code from OBR.4
    assertThat(diag.hasCode()).isTrue();
    List<Coding> codings = diag.getCode().getCoding();
    assertThat(codings).hasSize(1);
    Coding coding = codings.get(0);
    assertThat(coding.hasDisplay()).isTrue();
    assertThat(coding.getDisplay()).hasToString("New Born Screening");
    assertThat(coding.hasCode()).isTrue();
    assertThat(coding.getCode()).hasToString("1051-2");
    assertThat(coding.hasSystem()).isTrue();
    assertThat(coding.getSystem()).hasToString("http://loinc.org");
    // Verify encounter reference
    assertThat(diag.getEncounter().isEmpty()).isTrue();
    // Verify subject reference
    assertThat(diag.getSubject().isEmpty()).isFalse();
    // Verify effectiveDateTime from OBR.7 and OBR.8
    // This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
    assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
    // Verify issued from OBR.22
    assertThat(diag.getIssued()).isNull();
    // Verify resultsInterpreter from OBR.32
    assertThat(diag.getResultsInterpreter()).isEmpty();
    // Verify basedOn is ref to the ServiceRequest created for ORC or OBR
    assertThat(diag.getBasedOn()).hasSize(1);
    assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
    // Verify specimen reference
    assertThat(diag.getSpecimen()).isEmpty();
    // Verify result reference
    assertThat(diag.getResult()).isEmpty();
    // Verify presentedForm from OBX of type TX - In this case no attachments created since there are no OBX with type TX
    List<Attachment> attachments = diag.getPresentedForm();
    Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
}

Example 30 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project fhir-bridge by ehrbase.

the class SpecimenConverter method mapParentsOfProbe.

private void mapParentsOfProbe(ProbeCluster probe, Specimen specimenTarget) {
    if (specimenTarget.hasParent()) {
        for (Reference reference : specimenTarget.getParent()) {
            if (reference.hasIdentifier()) {
                ProbeIdentifikatorDerUebergeordnetenProbeElement identifikator = new ProbeIdentifikatorDerUebergeordnetenProbeElement();
                identifikator.setValue(DvIdentifierParser.parseIdentifierIntoDvIdentifier(reference.getIdentifier()));
                probe.getIdentifikatorDerUebergeordnetenProbe().add(identifikator);
            }
        }
    }
}