Examples with Device org.hl7.fhir.dstu3.model.Device used on opensource projects

Example 51 with Device

use of org.hl7.fhir.dstu3.model.Device in project synthea by synthetichealth.

the class FhirStu3 method supplyDelivery.

/**
 * Map the JsonObject for a Supply into a FHIR SupplyDelivery and add it to the Bundle.
 *
 * @param rand           Source of randomness to use when generating ids etc
 * @param personEntry    The Person entry.
 * @param bundle         Bundle to add to.
 * @param supply         The supplied object to add.
 * @param encounter      The encounter during which the supplies were delivered
 * @return The added Entry.
 */
private static BundleEntryComponent supplyDelivery(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, HealthRecord.Supply supply, Encounter encounter) {
    SupplyDelivery supplyResource = new SupplyDelivery();
    supplyResource.setStatus(SupplyDeliveryStatus.COMPLETED);
    supplyResource.setPatient(new Reference(personEntry.getFullUrl()));
    CodeableConcept type = new CodeableConcept();
    type.addCoding().setCode("device").setDisplay("Device").setSystem("http://hl7.org/fhir/supply-item-type");
    supplyResource.setType(type);
    SupplyDeliverySuppliedItemComponent suppliedItem = new SupplyDeliverySuppliedItemComponent();
    suppliedItem.setItem(mapCodeToCodeableConcept(supply.codes.get(0), SNOMED_URI));
    SimpleQuantity quantity = new SimpleQuantity();
    quantity.setValue(supply.quantity);
    suppliedItem.setQuantity(quantity);
    supplyResource.setSuppliedItem(suppliedItem);
    supplyResource.setOccurrence(convertFhirDateTime(supply.start, true));
    return newEntry(rand, bundle, supplyResource);
}

Example 52 with Device

use of org.hl7.fhir.dstu3.model.Device in project synthea by synthetichealth.

the class FhirStu3 method convertToFHIR.

/**
 * Convert the given Person into a FHIR Bundle, containing the Patient and the
 * associated entries from their health record.
 *
 * @param person Person to generate the FHIR from
 * @param stopTime Time the simulation ended
 * @return FHIR Bundle containing the Person's health record.
 */
public static Bundle convertToFHIR(Person person, long stopTime) {
    Bundle bundle = new Bundle();
    if (TRANSACTION_BUNDLE) {
        bundle.setType(BundleType.TRANSACTION);
    } else {
        bundle.setType(BundleType.COLLECTION);
    }
    BundleEntryComponent personEntry = basicInfo(person, bundle, stopTime);
    for (Encounter encounter : person.record.encounters) {
        BundleEntryComponent encounterEntry = encounter(person, personEntry, bundle, encounter);
        for (HealthRecord.Entry condition : encounter.conditions) {
            condition(person, personEntry, bundle, encounterEntry, condition);
        }
        for (HealthRecord.Entry allergy : encounter.allergies) {
            allergy(person, personEntry, bundle, encounterEntry, allergy);
        }
        for (Observation observation : encounter.observations) {
            // Observation resources in stu3 don't support Attachments
            if (observation.value instanceof Attachment) {
                media(person, personEntry, bundle, encounterEntry, observation);
            } else {
                observation(person, personEntry, bundle, encounterEntry, observation);
            }
        }
        for (Procedure procedure : encounter.procedures) {
            procedure(person, personEntry, bundle, encounterEntry, procedure);
        }
        for (Medication medication : encounter.medications) {
            medication(person, personEntry, bundle, encounterEntry, medication);
        }
        for (HealthRecord.Entry immunization : encounter.immunizations) {
            immunization(person, personEntry, bundle, encounterEntry, immunization);
        }
        for (Report report : encounter.reports) {
            report(person, personEntry, bundle, encounterEntry, report);
        }
        for (CarePlan careplan : encounter.careplans) {
            careplan(person, personEntry, bundle, encounterEntry, careplan);
        }
        for (ImagingStudy imagingStudy : encounter.imagingStudies) {
            imagingStudy(person, personEntry, bundle, encounterEntry, imagingStudy);
        }
        for (HealthRecord.Device device : encounter.devices) {
            device(person, personEntry, bundle, device);
        }
        for (HealthRecord.Supply supply : encounter.supplies) {
            supplyDelivery(person, personEntry, bundle, supply, encounter);
        }
        // one claim per encounter
        BundleEntryComponent encounterClaim = encounterClaim(person, personEntry, bundle, encounterEntry, encounter.claim);
        explanationOfBenefit(personEntry, bundle, encounterEntry, person, encounterClaim, encounter);
    }
    return bundle;
}

Example 53 with Device

use of org.hl7.fhir.dstu3.model.Device in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ObservationFHIRConversionTest method extendedObservationTestMostMessages.

// Tests most fields of OBX
@ParameterizedTest
@ValueSource(strings = { "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A01|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A03|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A04|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A08|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A28|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A31|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|OMP^O09|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ORM^O01|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ORU^R01|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|PPR^PC1|||2.6||||||||2.6\r", // "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|PPR^PC3|||2.6||||||||2.6\r",
"MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|VXU^V04|||2.6||||||||2.6\r" })
// 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 extendedObservationTestMostMessages(String msh) throws IOException {
    String hl7message = msh + "OBX|1|CWE|DQW^Some text 1^SNM3|100|DQW^Other text 2^SNM3|mm^Text 3^SNM3|56-98|IND|25|ST|F|20210322153839|LKJ|20210320153850|N56|1111^ClinicianLastName^ClinicianFirstName^^^^Title|Manual^Text the 4th^SNM3|Device_1234567^mySystem|20210322153925|Observation Site^Text 5^SNM3|INST^Instance Identifier System||Radiology^Radiological Services|467 Albany Hospital^^Albany^NY|Cardiology^ContactLastName^Jane^Q^^Dr.^MD\r";
    // use special created engine
    String json = message.convert(hl7message, customEngine);
    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);
    Observation obs = (Observation) obsResource.get(0);
    assertThat(obs.hasValueCodeableConcept()).isTrue();
    // Check the coding  (OBX.3)
    assertThat(obs.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getCode(), "DQW", "Some text 1", "http://terminology.hl7.org/CodeSystem/SNM3", "Some text 1");
    // Check the value  (OBX.5)
    assertThat(obs.hasValueCodeableConcept()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getValueCodeableConcept(), "DQW", "Other text 2", "http://terminology.hl7.org/CodeSystem/SNM3", "Other text 2");
    // OBX.6 is ignored because the record can only have one valueX and this one is valueCodeableConcept. See test test_observation_NM_result.
    assertThat(obs.hasReferenceRange()).isTrue();
    assertThat(obs.getReferenceRange()).hasSize(1);
    ObservationReferenceRangeComponent range = obs.getReferenceRangeFirstRep();
    assertThat(range).isNotNull();
    assertThat(range.hasHigh()).isTrue();
    assertThat(range.hasLow()).isTrue();
    Quantity high = range.getHigh();
    assertThat(high.getUnit()).isEqualTo("mm");
    assertThat(high.getValue().floatValue()).isEqualTo(98.0f);
    Quantity low = range.getLow();
    assertThat(low.getValue().floatValue()).isEqualTo(56.0f);
    assertThat(low.getUnit()).isEqualTo("mm");
    // Check interpretation (OBX.8)
    assertThat(obs.hasInterpretation()).isTrue();
    assertThat(obs.getInterpretation()).hasSize(1);
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getInterpretationFirstRep(), "IND", "Indeterminate", "http://terminology.hl7.org/CodeSystem/v2-0078", null);
    // Check the effective Date Time  (OBX.14)
    assertThat(obs.hasEffective()).isTrue();
    assertThat(obs.hasEffectiveDateTimeType()).isTrue();
    assertThat(obs.getEffectiveDateTimeType().asStringValue()).isEqualTo("2021-03-20T15:38:50+08:00");
    // Check performer  (OBX.16 Practictioner + OBX.23/OBX.24/OBX.25 Organization)
    assertThat(obs.hasPerformer()).isTrue();
    // Practioner and Organization
    assertThat(obs.getPerformer()).hasSize(2);
    // Get Practitioner and see that it is populated with OBX.16 information
    assertThat(obs.getPerformer().get(0).hasReference()).isTrue();
    List<Resource> practitionerResource = e.stream().filter(v -> ResourceType.Practitioner == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(practitionerResource).hasSize(1);
    Practitioner doctor = ResourceUtils.getResourcePractitioner(practitionerResource.get(0), ResourceUtils.context);
    assertThat(doctor.getName().get(0).getFamily()).isEqualTo("ClinicianLastName");
    // Get Organization and see that it is populated with OBX.23/OBX.24/OBX.25 information
    assertThat(obs.getPerformer().get(1).hasReference()).isTrue();
    List<Resource> organizationResource = e.stream().filter(v -> ResourceType.Organization == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(organizationResource).hasSize(1);
    Organization org = ResourceUtils.getResourceOrganization(organizationResource.get(0), ResourceUtils.context);
    // from OBX.23
    assertThat(org.getName()).isEqualTo("Radiology");
    assertThat(org.getAddress().get(0).getLine().get(0).getValueAsString()).isEqualTo(// from OBX.24
    "467 Albany Hospital");
    // from OBX.24
    assertThat(org.getAddress().get(0).getCity()).isEqualTo("Albany");
    // from OBX.24
    assertThat(org.getAddress().get(0).getState()).isEqualTo("NY");
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getFamily()).isEqualTo("ContactLastName");
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getGiven().get(0).getValueAsString()).isEqualTo("Jane");
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getText()).isEqualTo("Dr. Jane Q ContactLastName");
    // purpose added because of OBX.25
    assertThat(org.getContact().get(0).hasPurpose()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(org.getContact().get(0).getPurpose(), "ADMIN", "Administrative", "http://terminology.hl7.org/CodeSystem/contactentity-type", "Organization Medical Director");
    // Check method  (OBX.17)
    assertThat(obs.hasMethod()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getMethod(), "Manual", "Text the 4th", "http://terminology.hl7.org/CodeSystem/SNM3", "Text the 4th");
    // Check device  (OBX.18)
    assertThat(obs.hasDevice()).isTrue();
    assertThat(obs.getDevice().hasReference()).isTrue();
    List<Resource> deviceResource = e.stream().filter(v -> ResourceType.Device == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(deviceResource).hasSize(1);
    Device device = ResourceUtils.getResourceDevice(deviceResource.get(0), ResourceUtils.context);
    assertThat(device.getIdentifier().get(0).getValue()).isEqualTo("Device_1234567");
    assertThat(device.getIdentifier().get(0).getSystem()).isEqualTo("urn:id:mySystem");
    // Check bodySite  (OBX.20)
    assertThat(obs.hasBodySite()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getBodySite(), "Observation Site", "Text 5", "http://terminology.hl7.org/CodeSystem/SNM3", "Text 5");
    // Check identifier  (OBX.21)
    assertThat(obs.hasIdentifier()).isTrue();
    assertThat(obs.getIdentifier()).hasSize(2);
    assertThat(obs.getIdentifier().get(1).getValue()).isEqualTo("INST");
    assertThat(obs.getIdentifier().get(1).getSystem()).isEqualTo("urn:id:Instance_Identifier_System");
    // OBX.23/OBX.24/OBX.25 went into Performer: Organization.  Checked above.
    // Check for ABSENCE of category (because no SPM)  Presence of category tested in extendedObservationUnusualRangesAndOtherTest
    assertThat(obs.hasCategory()).isFalse();
}

Example 54 with Device

use of org.hl7.fhir.dstu3.model.Device in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ObservationFHIRConversionTest method extendedObservationTestForRDEMessages.

// Tests resources created for Observations from RDE messages
@ParameterizedTest
@ValueSource(strings = { "MSH|^~\\&|WHI_LOAD_GENERATOR|IBM_TORONTO_LAB||IBM|20210407191342|25739|RDE^O11|MSGID_f209e83f-20db-474d-a7ae-82e5c3894273|T|2.6\r", "MSH|^~\\&|WHI_LOAD_GENERATOR|IBM_TORONTO_LAB||IBM|20210407191342|25739|RDE^O25|MSGID_f209e83f-20db-474d-a7ae-82e5c3894273|T|2.6\r" })
// 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 extendedObservationTestForRDEMessages(String msh) throws IOException {
    String hl7message = msh + "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + "ORC|RE|||3200|||||20210407191342||2799^BY^VERIFIED||||20210407191342||||||ORDERING FAC NAME||||||||I\r" + "RXE|^Q24H&0600^^20210407191342^^ROU|DEFAULTMED^cefTRIAXone (ROCEPHIN) 2 g in sodium chloride 0.9 % 50 mL IVPB|2||g||||||||\n" + "OBX|1|NM|Most Current Weight^Most current measured weight (actual)||90|kg||IND||||||20210320153850||1111^ClinicianLastName^ClinicianFirstName^^^^Title|Manual^Text the 4th^SNM3|Device_1234567^mySystem|20210322153925|Observation Site^Text 5^SNM3|INST^Instance Identifier System||Radiology^Radiological Services|467 Albany Hospital^^Albany^NY|Cardiology^ContactLastName^Jane^Q^^Dr.^MD\r";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(1);
    Observation obs = (Observation) obsResource.get(0);
    // Check the coding  (OBX.3)
    assertThat(obs.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getCode(), "Most Current Weight", "Most current measured weight (actual)", null, "Most current measured weight (actual)");
    // Check the value  (OBX.5)
    assertNotNull(obs.getValueQuantity());
    Quantity q = obs.getValueQuantity();
    // code for unit
    assertNull(q.getCode());
    // unit units to OBX.6.1
    assertEquals("kg", q.getUnit());
    // system for unit
    assertNull(q.getSystem());
    assertEquals(90f, q.getValue().floatValue());
    // = is not put in comparator
    assertNull(q.getComparator());
    // Check that there is no reference range, OBX.6 and OBX.7
    assertThat(obs.hasReferenceRange()).isFalse();
    // Check interpretation (OBX.8)
    assertThat(obs.hasInterpretation()).isTrue();
    assertThat(obs.getInterpretation()).hasSize(1);
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getInterpretationFirstRep(), "IND", "Indeterminate", "http://terminology.hl7.org/CodeSystem/v2-0078", null);
    // Check the effective Date Time  (OBX.14)
    assertThat(obs.hasEffective()).isTrue();
    assertThat(obs.hasEffectiveDateTimeType()).isTrue();
    assertThat(obs.getEffectiveDateTimeType().asStringValue()).isEqualTo("2021-03-20T15:38:50+08:00");
    // Check performer  (OBX.16 Practictioner + OBX.23/OBX.24/OBX.25 Organization)
    assertThat(obs.hasPerformer()).isTrue();
    // Practioner and Organization
    assertThat(obs.getPerformer()).hasSize(2);
    // Get Practitioner and see that it is populated with OBX.16 information
    assertThat(obs.getPerformer().get(0).hasReference()).isTrue();
    List<Resource> practitionerResource = e.stream().filter(v -> ResourceType.Practitioner == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(practitionerResource).hasSize(1);
    Practitioner doctor = ResourceUtils.getResourcePractitioner(practitionerResource.get(0), ResourceUtils.context);
    assertThat(doctor.getName().get(0).getFamily()).isEqualTo("ClinicianLastName");
    // Get Organization and see that it is populated with OBX.23/OBX.24/OBX.25 information
    assertThat(obs.getPerformer().get(1).hasReference()).isTrue();
    List<Resource> organizationResource = e.stream().filter(v -> ResourceType.Organization == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(organizationResource).hasSize(1);
    Organization org = ResourceUtils.getResourceOrganization(organizationResource.get(0), ResourceUtils.context);
    // from OBX.23
    assertThat(org.getName()).isEqualTo("Radiology");
    assertThat(org.getAddress().get(0).getLine().get(0).getValueAsString()).isEqualTo(// from OBX.24
    "467 Albany Hospital");
    // from OBX.24
    assertThat(org.getAddress().get(0).getCity()).isEqualTo("Albany");
    // from OBX.24
    assertThat(org.getAddress().get(0).getState()).isEqualTo("NY");
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getFamily()).isEqualTo("ContactLastName");
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getGiven().get(0).getValueAsString()).isEqualTo("Jane");
    // There should be no suffix, currently not putting degree 'Title' in suffix
    assertThat(org.getContact().get(0).getName().getSuffix()).isEmpty();
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getText()).isEqualTo("Dr. Jane Q ContactLastName");
    // purpose added because of OBX.25
    assertThat(org.getContact().get(0).hasPurpose()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(org.getContact().get(0).getPurpose(), "ADMIN", "Administrative", "http://terminology.hl7.org/CodeSystem/contactentity-type", "Organization Medical Director");
    // Check method  (OBX.17)
    assertThat(obs.hasMethod()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getMethod(), "Manual", "Text the 4th", "http://terminology.hl7.org/CodeSystem/SNM3", "Text the 4th");
    // Check device  (OBX.18)
    assertThat(obs.hasDevice()).isTrue();
    assertThat(obs.getDevice().hasReference()).isTrue();
    List<Resource> deviceResource = e.stream().filter(v -> ResourceType.Device == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(deviceResource).hasSize(1);
    Device device = ResourceUtils.getResourceDevice(deviceResource.get(0), ResourceUtils.context);
    assertThat(device.getIdentifier().get(0).getValue()).isEqualTo("Device_1234567");
    assertThat(device.getIdentifier().get(0).getSystem()).isEqualTo("urn:id:mySystem");
    // Check bodySite  (OBX.20)
    assertThat(obs.hasBodySite()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getBodySite(), "Observation Site", "Text 5", "http://terminology.hl7.org/CodeSystem/SNM3", "Text 5");
    // Check identifier  (OBX.21)
    assertThat(obs.hasIdentifier()).isTrue();
    assertThat(obs.getIdentifier()).hasSize(2);
    assertThat(obs.getIdentifier().get(1).getValue()).isEqualTo("INST");
    assertThat(obs.getIdentifier().get(1).getSystem()).isEqualTo("urn:id:Instance_Identifier_System");
    // OBX.23/OBX.24/OBX.25 went into Performer: Organization.  Checked above.
    // Check for ABSENCE of category (because no SPM)  Presence of category tested in extendedObservationUnusualRangesAndOtherTest
    assertThat(obs.hasCategory()).isFalse();
}

Example 55 with Device

use of org.hl7.fhir.dstu3.model.Device in project summary-care-record-api by NHSDigital.

the class ParticipantAgentMapper method setDeviceCoding.

private static void setDeviceCoding(org.hl7.fhir.r4.model.Device fhirDevice, Device agentDevice1) {
    CodeableConcept type = fhirDevice.getType();
    Coding coding = type.getCodingFirstRep();
    if (!type.isEmpty() && isNotEmpty(coding.getCode()) && isNotEmpty(coding.getDisplay())) {
        agentDevice1.setCodeCode(coding.getCode());
        agentDevice1.setCodeDisplayName(coding.getDisplay());
    } else {
        throw new FhirValidationException("Missing mandatory elements: Device.type");
    }
}