Examples with IParser org.hl7.fhir.r5.formats.IParser used on opensource projects

Example 91 with IParser

use of org.hl7.fhir.r5.formats.IParser in project beneficiary-fhir-data by CMSgov.

the class OutpatientClaimTransformerV2Test method before.

@BeforeEach
public void before() {
    claim = generateClaim();
    ExplanationOfBenefit genEob = OutpatientClaimTransformerV2.transform(new MetricRegistry(), claim, Optional.empty());
    IParser parser = fhirContext.newJsonParser();
    String json = parser.encodeResourceToString(genEob);
    eob = parser.parseResource(ExplanationOfBenefit.class, json);
}

Example 92 with IParser

use of org.hl7.fhir.r5.formats.IParser in project health-patterns by LinuxForHealth.

the class DeIdentifier method postResource.

/**
 * Posts the given Resource to the FHIR server
 *
 * @param fhirResource the resource to post
 * @return the FHIR response of executing the POST operation
 * @throws DeIdentifierException if there is a problem posting the resource
 */
@SuppressWarnings("unchecked")
private String postResource(JsonNode fhirResource) throws DeIdentifierException {
    System.out.println("Initializing FHIR create resource...");
    IParser parser = fhirClient.getFhirContext().newJsonParser();
    // We don't know exactly what type of Resource we are going to POST to FHiR and the FHIR requires
    // that when parsing a Resource a concrete class is used, so we load the concrete type reflexively
    ClassLoader classLoader = this.getClass().getClassLoader();
    Class<? extends Resource> aClass = null;
    String resourceType = getResourceType(fhirResource);
    try {
        aClass = (Class<? extends Resource>) classLoader.loadClass("org.hl7.fhir.r4.model." + resourceType);
    } catch (ClassNotFoundException e) {
        throw new DeIdentifierException("A Resource of type '" + resourceType + "' could not be found in the current HAPI FHIR JAR: " + e.getMessage(), e);
    }
    Resource resource = parser.parseResource(aClass, fhirResource.toString());
    MethodOutcome outcome;
    try {
        outcome = fhirClient.create().resource(resource).encodedJson().execute();
    } catch (BaseServerResponseException e) {
        throw new DeIdentifierException("The FHIR transaction could not be executed: " + e.getMessage(), e);
    }
    System.out.println("FHIR create resource done!");
    return outcome.getId().toString();
}

Example 93 with IParser

use of org.hl7.fhir.r5.formats.IParser in project health-patterns by LinuxForHealth.

the class CohortService method getPatientsForCohort.

/**
 * Gets the FHIR response with the patients that matched the cohort defined by the given library ID.
 *
 * @param libraryID the library ID
 * @param patientsSubset the subset of patients over which to execute the cohort
 * @param reverseMatch run the CQL such that only the patients that don't match it are returned
 * @return the FHIR JSON response (a Bundle) with all the patients that matched
 * @throws CQLExecutionException if there is a problem executing the library
 */
public String getPatientsForCohort(String libraryID, List<String> patientsSubset, boolean reverseMatch) throws CQLExecutionException {
    List<String> cohortPatients = getPatientIdsForCohort(libraryID, patientsSubset, reverseMatch);
    if (cohortPatients == null) {
        return null;
    }
    String theSearchUrl = fhir.getServerBase() + "/Patient?_id=" + String.join(",", cohortPatients);
    Bundle cohortBundle = fhir.search().byUrl(theSearchUrl).returnBundle(Bundle.class).execute();
    IParser parser = fhir.getFhirContext().newJsonParser();
    String serialized = parser.encodeResourceToString(cohortBundle);
    return serialized;
}

Example 94 with IParser

use of org.hl7.fhir.r5.formats.IParser in project BridgeServer2 by Sage-Bionetworks.

the class CRCController method postAppointment.

@PutMapping("/v1/cuimc/appointments")
public ResponseEntity<StatusMessage> postAppointment() {
    App app = httpBasicAuthentication();
    IParser parser = FHIR_CONTEXT.newJsonParser();
    JsonNode data = parseJson(JsonNode.class);
    Appointment appointment = parser.parseResource(Appointment.class, data.toString());
    String userId = findUserId(appointment);
    // They send appointment when it is booked, cancelled, or (rarely) enteredinerror.
    AccountStates state = TESTS_SCHEDULED;
    String apptStatus = data.get("status").asText();
    if ("entered-in-error".equals(apptStatus)) {
        deleteReportAndUpdateState(app, userId);
        return ResponseEntity.ok(new StatusMessage("Appointment deleted."));
    } else if ("cancelled".equals(apptStatus)) {
        state = TESTS_CANCELLED;
    }
    // Columbia wants us to call back to them to get information about the location.
    // And UI team wants geocoding of location to render a map.
    String locationString = findLocation(appointment);
    if (locationString != null) {
        AccountId accountId = parseAccountId(app.getIdentifier(), userId);
        Account account = accountService.getAccount(accountId).orElseThrow(() -> new EntityNotFoundException(Account.class));
        addLocation(data, account, locationString);
    }
    int status = writeReportAndUpdateState(app, userId, data, APPOINTMENT_REPORT, state, true);
    if (status == 200) {
        return ResponseEntity.ok(new StatusMessage("Appointment updated (status = " + apptStatus + ")."));
    }
    return ResponseEntity.created(URI.create("/v1/cuimc/appointments/" + userId)).body(new StatusMessage("Appointment created (status = " + apptStatus + ")."));
}

Example 95 with IParser

use of org.hl7.fhir.r5.formats.IParser in project BridgeServer2 by Sage-Bionetworks.

the class CRCController method postObservation.

@PutMapping("/v1/cuimc/observations")
public ResponseEntity<StatusMessage> postObservation() {
    App app = httpBasicAuthentication();
    IParser parser = FHIR_CONTEXT.newJsonParser();
    JsonNode data = parseJson(JsonNode.class);
    Observation observation = parser.parseResource(Observation.class, data.toString());
    AccountStates state = TESTS_AVAILABLE;
    // There are two conditions under which the type of report is considered to be unknown. Either the code
    // is for a test other than the serum test, or the result value is not recognized by our client application,
    // and that's also treated as an unknown type of report.
    String code = getObservationCoding(observation);
    String valueString = getObservationValue(observation);
    if (code == null || valueString == null || !SERUM_TEST_CODES.contains(code) || !SERUM_TEST_STATES.contains(valueString)) {
        state = TESTS_AVAILABLE_TYPE_UNKNOWN;
        LOG.warn("CRC observation in unknown format: code=" + code + ", valueString=" + valueString);
    }
    String userId = findUserId(observation.getSubject());
    int status = writeReportAndUpdateState(app, userId, data, OBSERVATION_REPORT, state, true);
    if (status == 200) {
        return ResponseEntity.ok(new StatusMessage("Observation updated."));
    }
    return ResponseEntity.created(URI.create("/v1/cuimc/observations/" + userId)).body(new StatusMessage("Observation created."));
}