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

Example 36 with Account

use of org.hl7.fhir.dstu3.model.Account 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 37 with Account

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

the class FhirStu3 method basicInfo.

/**
 * Map the given Person to a FHIR Patient resource, and add it to the given Bundle.
 *
 * @param person The Person
 * @param bundle The Bundle to add to
 * @param stopTime Time the simulation ended
 * @return The created Entry
 */
@SuppressWarnings("rawtypes")
private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long stopTime) {
    Patient patientResource = new Patient();
    patientResource.addIdentifier().setSystem("https://github.com/synthetichealth/synthea").setValue((String) person.attributes.get(Person.ID));
    Code mrnCode = new Code("http://hl7.org/fhir/v2/0203", "MR", "Medical Record Number");
    patientResource.addIdentifier().setType(mapCodeToCodeableConcept(mrnCode, "http://hl7.org/fhir/v2/0203")).setSystem("http://hospital.smarthealthit.org").setValue((String) person.attributes.get(Person.ID));
    Code ssnCode = new Code("http://hl7.org/fhir/identifier-type", "SB", "Social Security Number");
    patientResource.addIdentifier().setType(mapCodeToCodeableConcept(ssnCode, "http://hl7.org/fhir/identifier-type")).setSystem("http://hl7.org/fhir/sid/us-ssn").setValue((String) person.attributes.get(Person.IDENTIFIER_SSN));
    if (person.attributes.get(Person.IDENTIFIER_DRIVERS) != null) {
        Code driversCode = new Code("http://hl7.org/fhir/v2/0203", "DL", "Driver's License");
        patientResource.addIdentifier().setType(mapCodeToCodeableConcept(driversCode, "http://hl7.org/fhir/v2/0203")).setSystem("urn:oid:2.16.840.1.113883.4.3.25").setValue((String) person.attributes.get(Person.IDENTIFIER_DRIVERS));
    }
    if (person.attributes.get(Person.IDENTIFIER_PASSPORT) != null) {
        Code passportCode = new Code("http://hl7.org/fhir/v2/0203", "PPN", "Passport Number");
        patientResource.addIdentifier().setType(mapCodeToCodeableConcept(passportCode, "http://hl7.org/fhir/v2/0203")).setSystem(SHR_EXT + "passportNumber").setValue((String) person.attributes.get(Person.IDENTIFIER_PASSPORT));
    }
    if (person.attributes.get(Person.CONTACT_EMAIL) != null) {
        ContactComponent contact = new ContactComponent();
        HumanName contactName = new HumanName();
        contactName.setUse(HumanName.NameUse.OFFICIAL);
        contactName.addGiven((String) person.attributes.get(Person.CONTACT_GIVEN_NAME));
        contactName.setFamily((String) person.attributes.get(Person.CONTACT_FAMILY_NAME));
        contact.setName(contactName);
        contact.addTelecom().setSystem(ContactPointSystem.EMAIL).setUse(ContactPointUse.HOME).setValue((String) person.attributes.get(Person.CONTACT_EMAIL));
        patientResource.addContact(contact);
    }
    // We do not yet account for mixed race
    Extension raceExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-race");
    String race = (String) person.attributes.get(Person.RACE);
    String raceDisplay;
    switch(race) {
        case "white":
            raceDisplay = "White";
            break;
        case "black":
            raceDisplay = "Black or African American";
            break;
        case "asian":
            raceDisplay = "Asian";
            break;
        case "native":
            raceDisplay = "American Indian or Alaska Native";
            break;
        case "hawaiian":
            raceDisplay = "Native Hawaiian or Other Pacific Islander";
            break;
        default:
            raceDisplay = "Other";
            break;
    }
    String raceNum = (String) raceEthnicityCodes.get(race);
    Extension raceCodingExtension = new Extension("ombCategory");
    Coding raceCoding = new Coding();
    if (raceDisplay.equals("Other")) {
        raceCoding.setSystem("http://hl7.org/fhir/v3/NullFlavor");
        raceCoding.setCode("UNK");
        raceCoding.setDisplay("Unknown");
    } else {
        raceCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
        raceCoding.setCode(raceNum);
        raceCoding.setDisplay(raceDisplay);
    }
    raceCodingExtension.setValue(raceCoding);
    raceExtension.addExtension(raceCodingExtension);
    Extension raceTextExtension = new Extension("text");
    raceTextExtension.setValue(new StringType(raceDisplay));
    raceExtension.addExtension(raceTextExtension);
    patientResource.addExtension(raceExtension);
    // We do not yet account for mixed ethnicity
    Extension ethnicityExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");
    String ethnicity = (String) person.attributes.get(Person.ETHNICITY);
    String ethnicityDisplay;
    if (ethnicity.equals("hispanic")) {
        ethnicity = "hispanic";
        ethnicityDisplay = "Hispanic or Latino";
    } else {
        ethnicity = "nonhispanic";
        ethnicityDisplay = "Not Hispanic or Latino";
    }
    String ethnicityNum = (String) raceEthnicityCodes.get(ethnicity);
    Extension ethnicityCodingExtension = new Extension("ombCategory");
    Coding ethnicityCoding = new Coding();
    ethnicityCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
    ethnicityCoding.setCode(ethnicityNum);
    ethnicityCoding.setDisplay(ethnicityDisplay);
    ethnicityCodingExtension.setValue(ethnicityCoding);
    ethnicityExtension.addExtension(ethnicityCodingExtension);
    Extension ethnicityTextExtension = new Extension("text");
    ethnicityTextExtension.setValue(new StringType(ethnicityDisplay));
    ethnicityExtension.addExtension(ethnicityTextExtension);
    patientResource.addExtension(ethnicityExtension);
    String firstLanguage = (String) person.attributes.get(Person.FIRST_LANGUAGE);
    Map languageMap = (Map) languageLookup.get(firstLanguage);
    Code languageCode = new Code((String) languageMap.get("system"), (String) languageMap.get("code"), (String) languageMap.get("display"));
    List<PatientCommunicationComponent> communication = new ArrayList<PatientCommunicationComponent>();
    communication.add(new PatientCommunicationComponent(mapCodeToCodeableConcept(languageCode, (String) languageMap.get("system"))));
    patientResource.setCommunication(communication);
    HumanName name = patientResource.addName();
    name.setUse(HumanName.NameUse.OFFICIAL);
    name.addGiven((String) person.attributes.get(Person.FIRST_NAME));
    name.setFamily((String) person.attributes.get(Person.LAST_NAME));
    if (person.attributes.get(Person.NAME_PREFIX) != null) {
        name.addPrefix((String) person.attributes.get(Person.NAME_PREFIX));
    }
    if (person.attributes.get(Person.NAME_SUFFIX) != null) {
        name.addSuffix((String) person.attributes.get(Person.NAME_SUFFIX));
    }
    if (person.attributes.get(Person.MAIDEN_NAME) != null) {
        HumanName maidenName = patientResource.addName();
        maidenName.setUse(HumanName.NameUse.MAIDEN);
        maidenName.addGiven((String) person.attributes.get(Person.FIRST_NAME));
        maidenName.setFamily((String) person.attributes.get(Person.MAIDEN_NAME));
        if (person.attributes.get(Person.NAME_PREFIX) != null) {
            maidenName.addPrefix((String) person.attributes.get(Person.NAME_PREFIX));
        }
        if (person.attributes.get(Person.NAME_SUFFIX) != null) {
            maidenName.addSuffix((String) person.attributes.get(Person.NAME_SUFFIX));
        }
    }
    Extension mothersMaidenNameExtension = new Extension("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");
    String mothersMaidenName = (String) person.attributes.get(Person.NAME_MOTHER);
    mothersMaidenNameExtension.setValue(new StringType(mothersMaidenName));
    patientResource.addExtension(mothersMaidenNameExtension);
    long birthdate = (long) person.attributes.get(Person.BIRTHDATE);
    patientResource.setBirthDate(new Date(birthdate));
    Extension birthSexExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
    if (person.attributes.get(Person.GENDER).equals("M")) {
        patientResource.setGender(AdministrativeGender.MALE);
        birthSexExtension.setValue(new CodeType("M"));
    } else if (person.attributes.get(Person.GENDER).equals("F")) {
        patientResource.setGender(AdministrativeGender.FEMALE);
        birthSexExtension.setValue(new CodeType("F"));
    }
    patientResource.addExtension(birthSexExtension);
    String state = (String) person.attributes.get(Person.STATE);
    Address addrResource = patientResource.addAddress();
    addrResource.addLine((String) person.attributes.get(Person.ADDRESS)).setCity((String) person.attributes.get(Person.CITY)).setPostalCode((String) person.attributes.get(Person.ZIP)).setState(state);
    if (COUNTRY_CODE != null) {
        addrResource.setCountry(COUNTRY_CODE);
    }
    Address birthplace = new Address();
    birthplace.setCity((String) person.attributes.get(Person.BIRTH_CITY)).setState((String) person.attributes.get(Person.BIRTH_STATE)).setCountry((String) person.attributes.get(Person.BIRTH_COUNTRY));
    Extension birthplaceExtension = new Extension("http://hl7.org/fhir/StructureDefinition/birthPlace");
    birthplaceExtension.setValue(birthplace);
    patientResource.addExtension(birthplaceExtension);
    if (person.attributes.get(Person.MULTIPLE_BIRTH_STATUS) != null) {
        patientResource.setMultipleBirth(new IntegerType((int) person.attributes.get(Person.MULTIPLE_BIRTH_STATUS)));
    } else {
        patientResource.setMultipleBirth(new BooleanType(false));
    }
    patientResource.addTelecom().setSystem(ContactPoint.ContactPointSystem.PHONE).setUse(ContactPoint.ContactPointUse.HOME).setValue((String) person.attributes.get(Person.TELECOM));
    String maritalStatus = ((String) person.attributes.get(Person.MARITAL_STATUS));
    if (maritalStatus != null) {
        Code maritalStatusCode = new Code("http://hl7.org/fhir/v3/MaritalStatus", maritalStatus, maritalStatus);
        patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://hl7.org/fhir/v3/MaritalStatus"));
    } else {
        Code maritalStatusCode = new Code("http://hl7.org/fhir/v3/MaritalStatus", "S", "Never Married");
        patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://hl7.org/fhir/v3/MaritalStatus"));
    }
    Point2D.Double coord = person.getLonLat();
    if (coord != null) {
        Extension geolocation = addrResource.addExtension();
        geolocation.setUrl("http://hl7.org/fhir/StructureDefinition/geolocation");
        geolocation.addExtension("latitude", new DecimalType(coord.getY()));
        geolocation.addExtension("longitude", new DecimalType(coord.getX()));
    }
    if (!person.alive(stopTime)) {
        patientResource.setDeceased(convertFhirDateTime((Long) person.attributes.get(Person.DEATHDATE), true));
    }
    String generatedBySynthea = "Generated by <a href=\"https://github.com/synthetichealth/synthea\">Synthea</a>." + "Version identifier: " + Utilities.SYNTHEA_VERSION + " . " + "  Person seed: " + person.getSeed() + "  Population seed: " + person.populationSeed;
    patientResource.setText(new Narrative().setStatus(NarrativeStatus.GENERATED).setDiv(new XhtmlNode(NodeType.Element).setValue(generatedBySynthea)));
    if (USE_SHR_EXTENSIONS) {
        patientResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-entity-Patient"));
        // Patient profile requires race, ethnicity, birthsex,
        // MothersMaidenName, FathersName, Person-extension
        patientResource.addExtension().setUrl(SHR_EXT + "shr-actor-FictionalPerson-extension").setValue(new BooleanType(true));
        String fathersName = (String) person.attributes.get(Person.NAME_FATHER);
        Extension fathersNameExtension = new Extension(SHR_EXT + "shr-entity-FathersName-extension", new HumanName().setText(fathersName));
        patientResource.addExtension(fathersNameExtension);
        String ssn = (String) person.attributes.get(Person.IDENTIFIER_SSN);
        Extension ssnExtension = new Extension(SHR_EXT + "shr-demographics-SocialSecurityNumber-extension", new StringType(ssn));
        patientResource.addExtension(ssnExtension);
        Basic personResource = new Basic();
        // the only required field on this patient resource is code
        Coding fixedCode = new Coding("http://standardhealthrecord.org/fhir/basic-resource-type", "shr-entity-Person", "shr-entity-Person");
        personResource.setCode(new CodeableConcept().addCoding(fixedCode));
        Meta personMeta = new Meta();
        personMeta.addProfile(SHR_EXT + "shr-entity-Person");
        personResource.setMeta(personMeta);
        BundleEntryComponent personEntry = newEntry(person, bundle, personResource);
        patientResource.addExtension().setUrl(SHR_EXT + "shr-entity-Person-extension").setValue(new Reference(personEntry.getFullUrl()));
    }
    // DALY and QALY values
    // we only write the last(current) one to the patient record
    Double dalyValue = (Double) person.attributes.get("most-recent-daly");
    Double qalyValue = (Double) person.attributes.get("most-recent-qaly");
    if (dalyValue != null) {
        Extension dalyExtension = new Extension(SYNTHEA_EXT + "disability-adjusted-life-years");
        DecimalType daly = new DecimalType(dalyValue);
        dalyExtension.setValue(daly);
        patientResource.addExtension(dalyExtension);
        Extension qalyExtension = new Extension(SYNTHEA_EXT + "quality-adjusted-life-years");
        DecimalType qaly = new DecimalType(qalyValue);
        qalyExtension.setValue(qaly);
        patientResource.addExtension(qalyExtension);
    }
    return newEntry(bundle, patientResource, (String) person.attributes.get(Person.ID));
}

Example 38 with Account

use of org.hl7.fhir.dstu3.model.Account in project BridgeServer2 by Sage-Bionetworks.

the class CRCControllerTest method operationMissingIdentifiers.

@Test(expectedExceptions = BadRequestException.class, expectedExceptionsMessageRegExp = "Could not find Bridge user ID.")
public void operationMissingIdentifiers() throws Exception {
    when(mockRequest.getHeader(AUTHORIZATION)).thenReturn(AUTHORIZATION_HEADER_VALUE);
    when(mockAccountService.authenticate(any(), any())).thenReturn(account);
    when(mockAccountService.getAccount(ACCOUNT_ID)).thenReturn(Optional.of(account));
    Observation observation = new Observation();
    String json = FHIR_CONTEXT.newJsonParser().encodeResourceToString(observation);
    mockRequestBody(mockRequest, json);
    controller.postObservation();
}

Example 39 with Account

use of org.hl7.fhir.dstu3.model.Account in project BridgeServer2 by Sage-Bionetworks.

the class CRCControllerTest method postAppointmentFailsWhenLocationCallFails.

@Test
public void postAppointmentFailsWhenLocationCallFails() throws Exception {
    when(mockRequest.getHeader(AUTHORIZATION)).thenReturn(AUTHORIZATION_HEADER_VALUE);
    when(mockAccountService.authenticate(any(), any())).thenReturn(account);
    when(mockAccountService.getAccount(ACCOUNT_ID)).thenReturn(Optional.of(account));
    // mockGetGeocoding();
    DateRangeResourceList<? extends ReportData> results = new DateRangeResourceList<>(ImmutableList.of());
    doReturn(results).when(mockReportService).getParticipantReport(APP_ID, TEST_USER_ID, APPOINTMENT_REPORT, HEALTH_CODE, JAN1, JAN2);
    Appointment appointment = new Appointment();
    appointment.setStatus(BOOKED);
    // add a wrong participant to verify we go through them all and look for ours
    addAppointmentParticipantComponent(appointment, "Location/foo");
    addAppointmentSageId(appointment, TEST_USER_ID);
    String json = FHIR_CONTEXT.newJsonParser().encodeResourceToString(appointment);
    mockRequestBody(mockRequest, json);
    HttpResponse mockResponse = mock(HttpResponse.class);
    doReturn(mockResponse).when(controller).post(any(), any(), any());
    StatusLine mockStatusLine = mock(StatusLine.class);
    when(mockResponse.getStatusLine()).thenReturn(mockStatusLine);
    when(mockStatusLine.getStatusCode()).thenReturn(400);
    HttpEntity mockEntity = mock(HttpEntity.class);
    when(mockResponse.getEntity()).thenReturn(mockEntity);
    when(mockEntity.getContent()).thenReturn(IOUtils.toInputStream("This was an error.", UTF_8));
    ResponseEntity<StatusMessage> retValue = controller.postAppointment();
    assertEquals(retValue.getBody().getMessage(), "Appointment created (status = booked).");
    assertEquals(retValue.getStatusCodeValue(), 201);
    verify(mockAppender).doAppend(loggingEventCaptor.capture());
    final LoggingEvent loggingEvent = loggingEventCaptor.getValue();
    assertEquals(loggingEvent.getLevel(), Level.WARN);
    assertEquals(loggingEvent.getFormattedMessage(), "Error retrieving location, id = foo, status = 400, response body = This was an error.");
}

Example 40 with Account

use of org.hl7.fhir.dstu3.model.Account in project BridgeServer2 by Sage-Bionetworks.

the class CRCControllerTest method procedureMissingIdentifiers.

@Test(expectedExceptions = BadRequestException.class, expectedExceptionsMessageRegExp = "Could not find Bridge user ID.")
public void procedureMissingIdentifiers() throws Exception {
    when(mockRequest.getHeader(AUTHORIZATION)).thenReturn(AUTHORIZATION_HEADER_VALUE);
    when(mockAccountService.authenticate(any(), any())).thenReturn(account);
    when(mockAccountService.getAccount(ACCOUNT_ID)).thenReturn(Optional.of(account));
    ProcedureRequest procedure = new ProcedureRequest();
    String json = FHIR_CONTEXT.newJsonParser().encodeResourceToString(procedure);
    mockRequestBody(mockRequest, json);
    controller.postProcedureRequest();
}