Examples with COMPLETED org.hl7.fhir.r4.model.Procedure.ProcedureStatus.COMPLETED used on opensource projects

Example 41 with COMPLETED

use of org.hl7.fhir.r4.model.Procedure.ProcedureStatus.COMPLETED in project fhir-bridge by ehrbase.

the class ProvideResourceAuditHandler method process.

@Override
public void process(Exchange exchange) throws Exception {
    RequestDetails requestDetails = getRequestDetails(exchange);
    AuditEvent auditEvent = new AuditEvent(new Coding("http://terminology.hl7.org/CodeSystem/audit-event-type", "rest", "RESTful Operation"), new InstantType(new Date()), getSource());
    getSubtype(requestDetails).ifPresent(auditEvent::addSubtype);
    getAction(requestDetails).ifPresent(auditEvent::setAction);
    Throwable ex = exchange.getProperty(Exchange.EXCEPTION_CAUGHT, Throwable.class);
    if (ex == null) {
        auditEvent.setOutcome(AuditEvent.AuditEventOutcome._0);
        auditEvent.setOutcomeDesc("Operation completed successfully");
    } else {
        auditEvent.setOutcome(AuditEvent.AuditEventOutcome._8);
        auditEvent.setOutcomeDesc("Operation failed: " + ex.getMessage());
    }
    auditEvent.addAgent(getAgent(exchange));
    getEntity(exchange, requestDetails).ifPresent(auditEvent::addEntity);
    MethodOutcome outcome = auditEventDao.create(auditEvent, requestDetails);
    LOG.debug("Created AuditEvent: id={}", outcome.getId());
}

Example 42 with COMPLETED

use of org.hl7.fhir.r4.model.Procedure.ProcedureStatus.COMPLETED in project odm2fhir by num-codex.

the class ImmunizationStatus method createImmunization.

@SuppressWarnings("fallthrough")
private Immunization createImmunization(ItemData immunizationCoding, ItemData dateCoding, ItemData textValue) {
    var immunization = (Immunization) new Immunization().addIdentifier(createIdentifier(IMMUNIZATION, immunizationCoding)).setOccurrence(createDateTimeType(dateCoding)).setMeta(createMeta(NUMStructureDefinition.IMMUNIZATION));
    var vaccineCodeableCoding = new CodeableConcept();
    var diseaseCodeableCoding = new CodeableConcept();
    for (var coding : createCodings(immunizationCoding)) {
        switch(coding.getCode()) {
            case // YES
            "410605003":
                immunization.setStatus(COMPLETED);
                break;
            case // NO
            "410594000":
                immunization.setStatus(NOTDONE);
                break;
            case // Answer = Sonstige/Other
            "385432009":
                diseaseCodeableCoding.addCoding(coding.setDisplay("Not applicable (qualifier value)"));
                if (!textValue.isEmpty()) {
                    diseaseCodeableCoding.setText(textValue.getValue());
                }
                break;
            case // UNKNOWN
            "261665006":
                // do not create FHIR-resources
                return new Immunization();
            // Influenza
            case "836377006":
            // Pneumokokken
            case "836398006":
            // BCG
            case "836402002":
            case // Covid19
            "1119349007":
                vaccineCodeableCoding.addCoding(coding);
                break;
            // cases for targetDisease
            case // Andere
            "64572001":
                if (!textValue.isEmpty()) {
                    diseaseCodeableCoding.setText(textValue.getValue());
                }
            // Influenza
            case "6142004":
            // Pneumokokken
            case "16814004":
            // BCG
            case "56717001":
            case // Covid19
            "840539006":
                diseaseCodeableCoding.addCoding(coding);
                break;
        }
    }
    if (vaccineCodeableCoding.isEmpty()) {
        // add No-Known-Immunuzations if no vaccineCode given
        vaccineCodeableCoding.addCoding(createCoding(NO_IMMUNIZATION_INFO_UV_IPS, "no-known-immunizations", "vaccineCode unknown"));
    }
    if (diseaseCodeableCoding.isEmpty()) {
        // add targetDisease unknown if none present
        diseaseCodeableCoding.addCoding(createCoding(SNOMED_CT, "64572001", "Disease (disorder)"));
    }
    immunization.setVaccineCode(vaccineCodeableCoding).addProtocolApplied(new ImmunizationProtocolAppliedComponent().setDoseNumber((StringType) new StringType().addExtension(DATA_ABSENT_FOR_UNKNOWN_REASON)).addTargetDisease(diseaseCodeableCoding));
    return immunization;
}

Example 43 with COMPLETED

use of org.hl7.fhir.r4.model.Procedure.ProcedureStatus.COMPLETED in project pathling by aehrc.

the class DockerImageTest method importDataAndQuery.

@Test
void importDataAndQuery() throws JSONException {
    try {
        // Get the token endpoint from the CapabilityStatement.
        final CapabilityStatement capabilities = getCapabilityStatement();
        final String tokenUrl = capabilities.getRest().stream().findFirst().map(rest -> ((UriType) rest.getSecurity().getExtensionByUrl("http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris").getExtensionByUrl("token").getValue()).asStringValue()).orElseThrow();
        // Get an access token from the token endpoint.
        final HttpPost clientCredentialsGrant = new HttpPost(tokenUrl);
        final List<? extends NameValuePair> nameValuePairs = Arrays.asList(new BasicNameValuePair("grant_type", "client_credentials"), new BasicNameValuePair("client_id", CLIENT_ID), new BasicNameValuePair("client_secret", CLIENT_SECRET), new BasicNameValuePair("scope", REQUESTED_SCOPE));
        clientCredentialsGrant.setEntity(new UrlEncodedFormEntity(nameValuePairs));
        log.info("Requesting client credentials grant");
        final String accessToken;
        try (final CloseableHttpResponse response = (CloseableHttpResponse) httpClient.execute(clientCredentialsGrant)) {
            assertThat(response.getStatusLine().getStatusCode()).withFailMessage("Client credentials grant did not succeed").isEqualTo(200);
            final InputStream clientCredentialsStream = response.getEntity().getContent();
            final Gson gson = new GsonBuilder().setFieldNamingPolicy(FieldNamingPolicy.LOWER_CASE_WITH_UNDERSCORES).create();
            final ClientCredentialsResponse ccResponse = gson.fromJson(new InputStreamReader(clientCredentialsStream), ClientCredentialsResponse.class);
            accessToken = ccResponse.getAccessToken();
        }
        // Create a request to the $import operation, referencing the NDJSON files we have loaded into
        // the staging area.
        final InputStream requestStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("import/SystemTest/request.Parameters.json");
        assertThat(requestStream).isNotNull();
        final HttpPost importRequest = new HttpPost("http://localhost:8091/fhir/$import");
        importRequest.setEntity(new InputStreamEntity(requestStream));
        importRequest.addHeader("Content-Type", "application/json");
        importRequest.addHeader("Accept", "application/fhir+json");
        importRequest.addHeader("Authorization", "Bearer " + accessToken);
        log.info("Sending import request");
        final OperationOutcome importOutcome;
        try (final CloseableHttpResponse response = (CloseableHttpResponse) httpClient.execute(importRequest)) {
            final InputStream importResponseStream = response.getEntity().getContent();
            importOutcome = (OperationOutcome) jsonParser.parseResource(importResponseStream);
            assertThat(response.getStatusLine().getStatusCode()).withFailMessage(importOutcome.getIssueFirstRep().getDiagnostics()).isEqualTo(200);
        }
        assertThat(importOutcome.getIssueFirstRep().getDiagnostics()).isEqualTo("Data import completed successfully");
        log.info("Import completed successfully");
        final Parameters inParams = new Parameters();
        // Set subject resource parameter.
        final ParametersParameterComponent subjectResourceParam = new ParametersParameterComponent();
        subjectResourceParam.setName("subjectResource");
        subjectResourceParam.setValue(new CodeType("Patient"));
        // Add aggregation, number of patients.
        final ParametersParameterComponent aggregationParam = new ParametersParameterComponent();
        aggregationParam.setName("aggregation");
        aggregationParam.setValue(new StringType("count()"));
        // Add grouping, has the patient been diagnosed with a chronic disease?
        final ParametersParameterComponent groupingParam = new ParametersParameterComponent();
        groupingParam.setName("grouping");
        groupingParam.setValue(new StringType("reverseResolve(Condition.subject)" + ".code" + ".memberOf('http://snomed.info/sct?fhir_vs=ecl/" + "^ 32570581000036105 : " + "<< 263502005 = << 90734009')"));
        // Add filter, females only.
        final ParametersParameterComponent filterParam = new ParametersParameterComponent();
        filterParam.setName("filter");
        filterParam.setValue(new StringType("gender = 'female'"));
        inParams.getParameter().add(subjectResourceParam);
        inParams.getParameter().add(aggregationParam);
        inParams.getParameter().add(groupingParam);
        inParams.getParameter().add(filterParam);
        // Send a request to the `$aggregate` operation on the FHIR server.
        final String requestString = jsonParser.encodeResourceToString(inParams);
        final HttpPost queryRequest = new HttpPost("http://localhost:8091/fhir/Patient/$aggregate");
        queryRequest.setEntity(new StringEntity(requestString));
        queryRequest.addHeader("Content-Type", "application/fhir+json");
        queryRequest.addHeader("Accept", "application/fhir+json");
        queryRequest.addHeader("Authorization", "Bearer " + accessToken);
        log.info("Sending query request");
        try (final CloseableHttpResponse response = (CloseableHttpResponse) httpClient.execute(queryRequest)) {
            final int statusCode = response.getStatusLine().getStatusCode();
            final InputStream queryResponseStream = response.getEntity().getContent();
            if (statusCode == 200) {
                final StringWriter writer = new StringWriter();
                IOUtils.copy(queryResponseStream, writer, StandardCharsets.UTF_8);
                assertJson("responses/DockerImageTest/importDataAndQuery.Parameters.json", writer.toString());
            } else {
                captureLogs();
                final OperationOutcome opOutcome = (OperationOutcome) jsonParser.parseResource(queryResponseStream);
                assertEquals(200, statusCode, opOutcome.getIssueFirstRep().getDiagnostics());
            }
        }
    } catch (final Exception e) {
        captureLogs();
    } finally {
        stopContainer(dockerClient, fhirServerContainerId);
        fhirServerContainerId = null;
        getRuntime().removeShutdownHook(shutdownHook);
    }
}

Example 44 with COMPLETED

use of org.hl7.fhir.r4.model.Procedure.ProcedureStatus.COMPLETED in project org.hl7.fhir.core by hapifhir.

the class MedicationDispense10_50 method convertMedicationDispenseStatus.

public static org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes> convertMedicationDispenseStatus(org.hl7.fhir.dstu2.model.Enumeration<org.hl7.fhir.dstu2.model.MedicationDispense.MedicationDispenseStatus> src) throws FHIRException {
    if (src == null)
        return null;
    org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes> tgt = new org.hl7.fhir.r5.model.Enumeration<>(new MedicationDispenseStatusCodesEnumFactory());
    ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().copyElement(src, tgt);
    switch(src.getValue()) {
        case COMPLETED:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.COMPLETED);
            break;
        case ENTEREDINERROR:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.ENTEREDINERROR);
            break;
        case INPROGRESS:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.INPROGRESS);
            break;
        case NULL:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.NULL);
            break;
        case ONHOLD:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.ONHOLD);
            break;
        case STOPPED:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.STOPPED);
            break;
    }
    return tgt;
}

Example 45 with COMPLETED

use of org.hl7.fhir.r4.model.Procedure.ProcedureStatus.COMPLETED in project org.hl7.fhir.core by hapifhir.

the class MedicationDispense40_50 method convertMedicationStatus.

private static org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes> convertMedicationStatus(org.hl7.fhir.r4.model.Enumeration<org.hl7.fhir.r4.model.MedicationDispense.MedicationDispenseStatus> src) {
    if (src == null)
        return null;
    org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes> tgt = new org.hl7.fhir.r5.model.Enumeration<>(new MedicationDispenseStatusCodesEnumFactory());
    ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().copyElement(src, tgt);
    switch(src.getValue()) {
        case CANCELLED:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.CANCELLED);
            break;
        case COMPLETED:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.COMPLETED);
            break;
        case DECLINED:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.DECLINED);
            break;
        case ENTEREDINERROR:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.ENTEREDINERROR);
            break;
        case INPROGRESS:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.INPROGRESS);
            break;
        case NULL:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.NULL);
            break;
        case ONHOLD:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.ONHOLD);
            break;
        case PREPARATION:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.PREPARATION);
            break;
        case STOPPED:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.STOPPED);
            break;
        case UNKNOWN:
            tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusCodes.UNKNOWN);
            break;
    }
    return tgt;
}