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

Example 41 with Device

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

the class FhirR4 method convertToFHIR.

/**
 * Convert the given Person into a FHIR Bundle of the Patient and the
 * associated entries from their health record.
 *
 * @param person   Person to generate the FHIR JSON for
 * @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.Allergy allergy : encounter.allergies) {
            allergy(person, personEntry, bundle, encounterEntry, allergy);
        }
        for (Observation observation : encounter.observations) {
            // Observation resources in v4 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 (HealthRecord.Device device : encounter.devices) {
            device(person, personEntry, bundle, device);
        }
        for (HealthRecord.Supply supply : encounter.supplies) {
            supplyDelivery(person, personEntry, bundle, supply, encounter);
        }
        for (Medication medication : encounter.medications) {
            medicationRequest(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) {
            BundleEntryComponent careTeamEntry = careTeam(person, personEntry, bundle, encounterEntry, careplan);
            carePlan(person, personEntry, bundle, encounterEntry, encounter.provider, careTeamEntry, careplan);
        }
        for (ImagingStudy imagingStudy : encounter.imagingStudies) {
            imagingStudy(person, personEntry, bundle, encounterEntry, imagingStudy);
        }
        if (USE_US_CORE_IG) {
            String clinicalNoteText = ClinicalNoteExporter.export(person, encounter);
            boolean lastNote = (encounter == person.record.encounters.get(person.record.encounters.size() - 1));
            clinicalNote(person, personEntry, bundle, encounterEntry, clinicalNoteText, lastNote);
        }
        // one claim per encounter
        BundleEntryComponent encounterClaim = encounterClaim(person, personEntry, bundle, encounterEntry, encounter.claim);
        explanationOfBenefit(personEntry, bundle, encounterEntry, person, encounterClaim, encounter);
    }
    if (USE_US_CORE_IG) {
        // Add Provenance to the Bundle
        provenance(bundle, person, stopTime);
    }
    return bundle;
}

Example 42 with Device

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

the class FhirR4 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://terminology.hl7.org/CodeSystem/supply-item-type");
    supplyResource.setType(type);
    SupplyDeliverySuppliedItemComponent suppliedItem = new SupplyDeliverySuppliedItemComponent();
    suppliedItem.setItem(mapCodeToCodeableConcept(supply.codes.get(0), SNOMED_URI));
    suppliedItem.setQuantity(new Quantity(supply.quantity));
    supplyResource.setSuppliedItem(suppliedItem);
    supplyResource.setOccurrence(convertFhirDateTime(supply.start, true));
    return newEntry(rand, bundle, supplyResource);
}

Example 43 with Device

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

the class FhirR4 method device.

/**
 * Map the HealthRecord.Device into a FHIR Device 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 device         The device to add.
 * @return The added Entry.
 */
private static BundleEntryComponent device(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, HealthRecord.Device device) {
    Device deviceResource = new Device();
    if (USE_US_CORE_IG) {
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-implantable-device");
        deviceResource.setMeta(meta);
    }
    deviceResource.addUdiCarrier().setDeviceIdentifier(device.deviceIdentifier).setCarrierHRF(device.udi);
    deviceResource.setStatus(FHIRDeviceStatus.ACTIVE);
    deviceResource.setDistinctIdentifier(device.deviceIdentifier);
    if (device.manufacturer != null) {
        deviceResource.setManufacturer(device.manufacturer);
    }
    if (device.model != null) {
        deviceResource.setModelNumber(device.model);
    }
    deviceResource.setManufactureDate(new Date(device.manufactureTime));
    deviceResource.setExpirationDate(new Date(device.expirationTime));
    deviceResource.setLotNumber(device.lotNumber);
    deviceResource.setSerialNumber(device.serialNumber);
    deviceResource.addDeviceName().setName(device.codes.get(0).display).setType(DeviceNameType.USERFRIENDLYNAME);
    deviceResource.setType(mapCodeToCodeableConcept(device.codes.get(0), SNOMED_URI));
    deviceResource.setPatient(new Reference(personEntry.getFullUrl()));
    return newEntry(rand, bundle, deviceResource);
}

Example 44 with Device

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

the class FHIRSTU3ExporterTest method testFHIRSTU3Export.

@Test
public void testFHIRSTU3Export() throws Exception {
    TestHelper.loadTestProperties();
    Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
    Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());
    FhirContext ctx = FhirStu3.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    FhirValidator validator = ctx.newValidator();
    validator.setValidateAgainstStandardSchema(true);
    validator.setValidateAgainstStandardSchematron(true);
    ValidationResources validationResources = new ValidationResources();
    List<String> errors = ParallelTestingService.runInParallel((person) -> {
        List<String> validationErrors = new ArrayList<String>();
        TestHelper.exportOff();
        Config.set("exporter.fhir_stu3.export", "true");
        Config.set("exporter.fhir.use_shr_extensions", "true");
        FhirStu3.TRANSACTION_BUNDLE = person.randBoolean();
        String fhirJson = FhirStu3.convertToFHIRJson(person, System.currentTimeMillis());
        // (these should have been converted into URIs)
        if (fhirJson.contains("SNOMED-CT")) {
            validationErrors.add("JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
        }
        // let's crack open the Bundle and validate
        // each individual entry.resource to get context-sensitive error
        // messages...
        Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
        for (BundleEntryComponent entry : bundle.getEntry()) {
            ValidationResult eresult = validator.validateWithResult(entry.getResource());
            if (!eresult.isSuccessful()) {
                for (SingleValidationMessage emessage : eresult.getMessages()) {
                    boolean valid = false;
                    if (emessage.getMessage().contains("@ Observation obs-7")) {
                        /*
               * The obs-7 invariant basically says that Observations should have values, unless
               * they are made of components. This test replaces an invalid XPath expression
               * that was causing correct instances to fail validation.
               */
                        valid = validateObs7((Observation) entry.getResource());
                    } else if (emessage.getMessage().contains("@ Condition con-4")) {
                        /*
               * The con-4 invariant says "If condition is abated, then clinicalStatus must be
               * either inactive, resolved, or remission" which is very clear and sensical.
               * However, the XPath expression does not evaluate correctly for valid instances,
               * so we must manually validate.
               */
                        valid = validateCon4((Condition) entry.getResource());
                    } else if (emessage.getMessage().contains("@ MedicationRequest mps-1")) {
                        /*
               * The mps-1 invariant says MedicationRequest.requester.onBehalfOf can only be
               * specified if MedicationRequest.requester.agent is practitioner or device.
               * But the invariant is poorly written and does not correctly handle references
               * starting with "urn:uuid"
               */
                        // ignore this error
                        valid = true;
                    } else if (emessage.getMessage().contains("per-1: If present, start SHALL have a lower value than end")) {
                        /*
               * The per-1 invariant does not account for daylight savings time... so, if the
               * daylight savings switch happens between the start and end, the validation
               * fails, even if it is valid.
               */
                        // ignore this error
                        valid = true;
                    }
                    if (!valid) {
                        System.out.println(parser.encodeResourceToString(entry.getResource()));
                        System.out.println("ERROR: " + emessage.getMessage());
                        validationErrors.add(emessage.getMessage());
                    }
                }
            }
            // Check ExplanationOfBenefit Resources against BlueButton
            if (entry.getResource().fhirType().equals("ExplanationOfBenefit")) {
                ValidationResult bbResult = validationResources.validateSTU3(entry.getResource());
                for (SingleValidationMessage message : bbResult.getMessages()) {
                    if (message.getMessage().contains("extension https://bluebutton.cms.gov/assets")) {
                        /*
               * The instance validator complains about the BlueButton extensions, ignore
               */
                        continue;
                    } else if (message.getSeverity() == ResultSeverityEnum.ERROR) {
                        if (!(message.getMessage().contains("Element 'ExplanationOfBenefit.id': minimum required = 1, but only found 0") || message.getMessage().contains("Could not verify slice for profile"))) {
                            // For some reason the validator is not detecting the IDs on the resources,
                            // even though they appear to be present while debugging and during normal
                            // operations.
                            System.out.println(message.getSeverity() + ": " + message.getMessage());
                            Assert.fail(message.getSeverity() + ": " + message.getMessage());
                        }
                    }
                }
            }
        }
        if (!validationErrors.isEmpty()) {
            FailedExportHelper.dumpInfo("FHIRSTU3", fhirJson, validationErrors, person);
        }
        return validationErrors;
    });
    assertTrue("Validation of exported FHIR bundle failed: " + String.join("|", errors), errors.size() == 0);
}

Example 45 with Device

use of org.hl7.fhir.dstu3.model.Device in project java-docs-samples by GoogleCloudPlatform.

the class DeviceRegistryExample method listDevices.

// [END iot_clear_registry]
// [START iot_list_devices]
/**
 * Print all of the devices in this registry to standard out.
 */
protected static void listDevices(String projectId, String cloudRegion, String registryName) throws GeneralSecurityException, IOException {
    GoogleCredentials credential = GoogleCredentials.getApplicationDefault().createScoped(CloudIotScopes.all());
    JsonFactory jsonFactory = JacksonFactory.getDefaultInstance();
    HttpRequestInitializer init = new HttpCredentialsAdapter(credential);
    final CloudIot service = new CloudIot.Builder(GoogleNetHttpTransport.newTrustedTransport(), jsonFactory, init).setApplicationName(APP_NAME).build();
    final String registryPath = String.format("projects/%s/locations/%s/registries/%s", projectId, cloudRegion, registryName);
    List<Device> devices = service.projects().locations().registries().devices().list(registryPath).execute().getDevices();
    if (devices != null) {
        System.out.println("Found " + devices.size() + " devices");
        for (Device d : devices) {
            System.out.println("Id: " + d.getId());
            if (d.getConfig() != null) {
                // Note that this will show the device config in Base64 encoded format.
                System.out.println("Config: " + d.getConfig().toPrettyString());
            }
            System.out.println();
        }
    } else {
        System.out.println("Registry has no devices.");
    }
}