Examples with CodeType org.hl7.fhir.dstu2016may.model.CodeType used on opensource projects

Example 96 with CodeType

use of org.hl7.fhir.dstu2016may.model.CodeType in project pathling by aehrc.

the class ImportTest method buildImportParameters.

@SuppressWarnings("SameParameterValue")
@Nonnull
Parameters buildImportParameters(@Nonnull final URL jsonURL, @Nonnull final ResourceType resourceType, @Nonnull final ImportMode mode) {
    final Parameters parameters = buildImportParameters(jsonURL, resourceType);
    final ParametersParameterComponent sourceParam = parameters.getParameter().stream().filter(p -> p.getName().equals("source")).findFirst().orElseThrow();
    sourceParam.addPart().setName("mode").setValue(new CodeType(mode.getCode()));
    return parameters;
}

Example 97 with CodeType

use of org.hl7.fhir.dstu2016may.model.CodeType in project pathling by aehrc.

the class ImportTest method buildImportParameters.

@SuppressWarnings("SameParameterValue")
@Nonnull
Parameters buildImportParameters(@Nonnull final URL jsonURL, @Nonnull final ResourceType resourceType) {
    final Parameters parameters = new Parameters();
    final ParametersParameterComponent sourceParam = parameters.addParameter().setName("source");
    sourceParam.addPart().setName("resourceType").setValue(new CodeType(resourceType.toCode()));
    sourceParam.addPart().setName("url").setValue(new UrlType(jsonURL.toExternalForm()));
    return parameters;
}

Example 98 with CodeType

use of org.hl7.fhir.dstu2016may.model.CodeType 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 99 with CodeType

use of org.hl7.fhir.dstu2016may.model.CodeType in project pathling by aehrc.

the class DefaultTerminologyServiceTest method testTranslateForValidAndInvalidCodings.

@Test
void testTranslateForValidAndInvalidCodings() {
    // Response bundle:
    // [1]  CODING1_VERSION1 -> None
    // [2]  CODING2_VERSION1 -> { equivalent: CODING3_VERSION1, wider: CODING1_VERSION1}
    final Bundle responseBundle = new Bundle().setType(BundleType.BATCHRESPONSE);
    // entry with no mapping
    final Parameters noTranslation = new Parameters().addParameter("result", false);
    responseBundle.addEntry().setResource(noTranslation).getResponse().setStatus("200");
    // entry with two mappings
    final Parameters withTranslation = new Parameters().addParameter("result", true);
    final ParametersParameterComponent equivalentMatch = withTranslation.addParameter().setName("match");
    equivalentMatch.addPart().setName("equivalence").setValue(new CodeType("equivalent"));
    equivalentMatch.addPart().setName("concept").setValue(CODING3_VERSION1.toCoding());
    final ParametersParameterComponent widerMatch = withTranslation.addParameter().setName("match");
    widerMatch.addPart().setName("equivalence").setValue(new CodeType("wider"));
    widerMatch.addPart().setName("concept").setValue(CODING1_VERSION1.toCoding());
    responseBundle.addEntry().setResource(withTranslation).getResponse().setStatus("200");
    when(terminologyClient.batch(any())).thenReturn(responseBundle);
    final ConceptTranslator actualTranslator = terminologyService.translate(Arrays.asList(CODING1_VERSION1, CODING2_VERSION1, new SimpleCoding(SYSTEM1, null), new SimpleCoding(null, "code1"), new SimpleCoding(null, null), null), "uuid:concept-map", false, Collections.singletonList(ConceptMapEquivalence.EQUIVALENT));
    assertEquals(ConceptTranslatorBuilder.empty().put(CODING2_VERSION1, CODING3_VERSION1.toCoding()).build(), actualTranslator);
    // expected request bundle
    final Bundle requestBundle = new Bundle().setType(BundleType.BATCH);
    requestBundle.addEntry().setResource(new Parameters().addParameter("url", new UriType("uuid:concept-map")).addParameter("reverse", false).addParameter("coding", CODING1_VERSION1.toCoding())).getRequest().setMethod(HTTPVerb.POST).setUrl("ConceptMap/$translate");
    requestBundle.addEntry().setResource(new Parameters().addParameter("url", new UriType("uuid:concept-map")).addParameter("reverse", false).addParameter("coding", CODING2_VERSION1.toCoding())).getRequest().setMethod(HTTPVerb.POST).setUrl("ConceptMap/$translate");
    verify(terminologyClient).batch(deepEq(requestBundle));
    verifyNoMoreInteractions(terminologyClient);
}

Example 100 with CodeType

use of org.hl7.fhir.dstu2016may.model.CodeType in project kindling by HL7.

the class SpreadSheetReloader method parseStatus.

private void parseStatus(Element ed, String value) {
    ed.removeExtension(BuildExtensions.EXT_FMM_LEVEL);
    ed.removeExtension(BuildExtensions.EXT_STANDARDS_STATUS);
    ed.removeExtension(BuildExtensions.EXT_NORMATIVE_VERSION);
    if (!Utilities.noString(value) && value.contains("/")) {
        String[] p = value.split("\\/");
        if (Utilities.noString(p[0].trim())) {
            ed.removeExtension(BuildExtensions.EXT_FMM_LEVEL);
        } else {
            ed.addExtension(BuildExtensions.EXT_FMM_LEVEL, new IntegerType(p[0]));
        }
        if (p[1].contains(";")) {
            ed.addExtension(BuildExtensions.EXT_STANDARDS_STATUS, new CodeType(p[1].substring(0, p[1].indexOf(";"))));
            ed.addExtension(BuildExtensions.EXT_NORMATIVE_VERSION, new CodeType(p[1].substring(p[1].indexOf("from=") + 5)));
        } else {
            ed.addExtension(BuildExtensions.EXT_STANDARDS_STATUS, new CodeType(p[1]));
        }
    }
    sortExtensions(ed);
}