* Add Elasticsearch configuration section to application.yaml * Add configuration for reindexing resources upon search parameter change * Add Elasticsearch client configuration for testing * Update logback dependencies because of a security issue and enable resource filtering in pom.xml * Add application name and tester configuration to application.yaml. Refactor hibernate properties * Add custom Elasticsearch configuration to create ElasticsearchClient bean * Add index prefix configuration for Elasticsearch indices * Fix Elasticsearch URI format in test initialization * Refactor ElasticsearchConfig for improved readability and code style consistency (spotless:apply) * Refactor ElasticsearchConfig for improved readability and code style consistency (spotless:apply) * Update index prefix in application.yaml for Elasticsearch configuration * Enhance index prefix validation and add sanitization method for Elasticsearch index names * Merged with master in upstream * Refactor ElasticsearchBootSvcImpl and ElasticsearchConfig for improved readability (mvn spotless) * Comment out custom_content_path in application.yaml for clarity * - Refactor application.yaml for improved structure and readability; - Add PostgresLucenePatientIT integration test; and - Update testcontainers dependencies to avoid compatibility issues with newer Docker APIs. * Refactor PostgresLucenePatientIT to use external configuration file for test properties * Add integration tests for PostgreSQL and Elasticsearch with dynamic configuration * Increase socket timeout in CdsHooksServletIT for improved stability during tests * Remove deprecated tester configuration from application.yaml
255 lines
9.1 KiB
Java
255 lines
9.1 KiB
Java
package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
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import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig;
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import ca.uhn.fhir.parser.IParser;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
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import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
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import com.google.gson.Gson;
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import com.google.gson.JsonArray;
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import com.google.gson.JsonObject;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.client.methods.HttpPost;
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import org.apache.http.entity.StringEntity;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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import org.apache.http.util.EntityUtils;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.api.Test;
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import org.opencds.cqf.fhir.cr.hapi.config.CrCdsHooksConfig;
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import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
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import org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.boot.test.context.SpringBootTest;
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import org.springframework.boot.test.web.server.LocalServerPort;
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import org.springframework.test.context.ActiveProfiles;
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import java.io.IOException;
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import java.util.concurrent.TimeUnit;
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import static org.awaitility.Awaitility.await;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.fail;
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@ActiveProfiles("test")
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@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, NicknameServiceConfig.class, RepositoryConfig.class, TestCdsHooksConfig.class, CrCdsHooksConfig.class, StarterCdsHooksConfig.class},
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properties = {
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"spring.profiles.include=storageSettingsTest",
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"spring.datasource.url=jdbc:h2:mem:dbr4",
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"spring.jpa.properties.hibernate.search.backend.directory.type=local-heap",
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"hapi.fhir.enable_repository_validating_interceptor=true",
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"hapi.fhir.fhir_version=r4",
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"hapi.fhir.cr.enabled=true",
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"hapi.fhir.cr.caregaps.section_author=Organization/alphora-author",
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"hapi.fhir.cr.caregaps.reporter=Organization/alphora",
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"hapi.fhir.cdshooks.enabled=true",
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"spring.main.allow-bean-definition-overriding=true",
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"server.max-http-request-header-size=16KB"})
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class CdsHooksServletIT implements IServerSupport {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CdsHooksServletIT.class);
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private final FhirContext ourCtx = FhirContext.forR4Cached();
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private final IParser ourParser = ourCtx.newJsonParser();
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private IGenericClient ourClient;
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private String ourCdsBase;
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@Autowired
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DaoRegistry myDaoRegistry;
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@Autowired
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ICdsServiceRegistry myCdsServiceRegistry;
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@LocalServerPort
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private int port;
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private String ourServerBase;
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@BeforeEach
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void beforeEach() {
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ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
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ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 3000);
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ourServerBase = "http://localhost:" + port + "/fhir/";
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ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
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ourCdsBase = "http://localhost:" + port + "/cds-services";
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var cdsServicesJson = myCdsServiceRegistry.getCdsServicesJson();
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if (cdsServicesJson != null && cdsServicesJson.getServices() != null) {
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var services = cdsServicesJson.getServices();
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for (int i = 0; i < services.size(); i++) {
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myCdsServiceRegistry.unregisterService(services.get(i).getId(), "CR");
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}
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}
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}
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private Boolean hasCdsServices() throws IOException {
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var response = callCdsServicesDiscovery();
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// NOTE: this is looking for a response that indicates there are CDS services available.
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// And empty response looks like: {"services": []}
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// Looking at the actual response string consumes the InputStream which has side effects, making it tricky to compare the actual contents.
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// Hence, the test just looks at the length to make this determination.
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// The actual response has newlines in it which vary in size on some systems, but a value of 25 seems to work across linux/mac/windows
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// to ensure the response actually contains CDS services in it
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return response.getEntity().getContentLength() > 25 || response.getEntity().isChunked();
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}
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private CloseableHttpResponse callCdsServicesDiscovery() {
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try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
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HttpGet request = new HttpGet(ourCdsBase);
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request.addHeader("Content-Type", "application/json");
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return httpClient.execute(request);
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} catch (IOException ioe) {
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fail(ioe.getMessage());
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return null;
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}
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}
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@Test
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void testGetCdsServices() {
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var response = callCdsServicesDiscovery();
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assertEquals(200, response.getStatusLine().getStatusCode());
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}
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@Test
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void testCdsHooks() throws IOException {
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loadBundle("r4/HelloWorld-Bundle.json", ourCtx, ourClient);
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await().atMost(10000, TimeUnit.MILLISECONDS).until(this::hasCdsServices);
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var cdsRequest = """
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{
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"hookInstance": "12345",
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"hook": "patient-view",
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"context": {
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"userId": "Practitioner/example",
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"patientId": "Patient/example-hello-world"
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},
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"prefetch": {
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"item1": {
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"resourceType": "Patient",
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"id": "example-hello-world",
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"gender": "male",
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"birthDate": "2000-01-01"
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}
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}
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}""";
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try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
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HttpPost request = new HttpPost(ourCdsBase + "/hello-world");
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request.setEntity(new StringEntity(cdsRequest));
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request.addHeader("Content-Type", "application/json");
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CloseableHttpResponse httpResponse = httpClient.execute(request);
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String result = EntityUtils.toString(httpResponse.getEntity());
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Gson gsonResponse = new Gson();
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JsonObject response = gsonResponse.fromJson(result, JsonObject.class);
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assertNotNull(response);
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JsonArray cards = response.getAsJsonArray("cards");
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assertEquals(1, cards.size());
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assertEquals("\"Hello World!\"", cards.get(0).getAsJsonObject().get("summary").toString());
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} catch (IOException ioe) {
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fail(ioe.getMessage());
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}
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}
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@Test
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void testRec10() throws IOException {
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loadBundle("r4/opioidcds-10-order-sign-bundle.json", ourCtx, ourClient);
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await().atMost(20000, TimeUnit.MILLISECONDS).until(this::hasCdsServices);
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var fhirServer = " \"fhirServer\": " + "\"" + ourServerBase + "\"" + ",\n";
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var cdsRequest = """
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{
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"hookInstance": "055b009c-4a7d-4db4-a35e-0e5198918ed1",
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"hook": "order-sign",
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""" + fhirServer + """
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"context": {
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"patientId": "example-rec-10-order-sign-illicit-POS-Cocaine-drugs",
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"userId": "COREPRACTITIONER1",
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"draftOrders": {
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"resourceType": "Bundle",
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"entry": [
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{
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"resource": {
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"resourceType": "MedicationRequest",
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"id": "request-123",
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"status": "draft",
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"subject": {
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"reference": "Patient/example-rec-10-order-sign-illicit-POS-Cocaine-drugs"
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},
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"authoredOn": "2024-03-27",
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"dosageInstruction": [
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{
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"timing": {
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"repeat": {
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"frequency": 1,
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"period": 1,
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"periodUnit": "d"
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}
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},
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"doseAndRate": [
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{
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"doseQuantity": {
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"value": 1,
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"system": "http://unitsofmeasure.org",
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"code": "{pill}"
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}
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}
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]
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}
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],
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"dispenseRequest": {
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"expectedSupplyDuration": {
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"value": 90,
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"unit": "days",
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"system": "http://unitsofmeasure.org",
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"code": "d"
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}
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},
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"intent": "order",
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"category": [
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{
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/medicationrequest-category",
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"code": "community"
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}
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]
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}
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],
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"medicationCodeableConcept": {
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"coding": [
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{
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"system": "http://www.nlm.nih.gov/research/umls/rxnorm",
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"code": "1049502",
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"display": "12 HR oxycodone hydrochloride 10 MG Extended Release Oral Tablet"
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}
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]
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}
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}
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}
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]
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}
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}
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}
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""";
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try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
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HttpPost request = new HttpPost(ourCdsBase + "/opioidcds-10-order-sign");
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request.setEntity(new StringEntity(cdsRequest));
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request.addHeader("Content-Type", "application/json");
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CloseableHttpResponse httpResponse = httpClient.execute(request);
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String result = EntityUtils.toString(httpResponse.getEntity());
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Gson gsonResponse = new Gson();
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JsonObject response = gsonResponse.fromJson(result, JsonObject.class);
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assertNotNull(response);
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JsonArray cards = response.getAsJsonArray("cards");
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assertEquals(0, cards.size());
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//assertEquals("\"Hello World!\"", cards.get(0).getAsJsonObject().get("summary").toString());
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} catch (IOException ioe) {
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fail(ioe.getMessage());
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}
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}
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}
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