Update Clinical Reasoning plugin (#692)
* Reproducing issues with CR/HAPI cds-hooks processing * Add new $questionnaire operation * Update StarterIpsConfig.java * Update pom.xml * Fixes for configuration properties * Update VS Code launch properties * Fixes for CQL logging * Update pom.xml * Remove unused threaded option * Update to 7.1.7 * Fix some CR defaults * Update to new snapshot * Update pom.xml * Fix test settings * Do not make prefetch calls if all items are present * Add alternative application.yaml for CDS settings. * Add CdsHook tests and documentation * Comment out custom prefetch until it is more mature * Removal of DataEndpoint parameter is not longer needed * Fix debug logging setting being overwritten * Revert change * Remove unused class * Adding Rec10 Test * Disable test until fixed * fix tests --------- Co-authored-by: c-schuler <hoofschu@gmail.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
This commit is contained in:
Brenin Rhodes
GitHub
242
src/test/java/ca/uhn/fhir/jpa/starter/CdsHooksServletIT.java
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242
src/test/java/ca/uhn/fhir/jpa/starter/CdsHooksServletIT.java
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@@ -0,0 +1,242 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.cr.config.RepositoryConfig;
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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 ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
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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.Test;
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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 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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@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
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classes = {
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Application.class,
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NicknameServiceConfig.class,
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RepositoryConfig.class,
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CdsHooksConfig.class,
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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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"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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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 * 1000);
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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 && !cdsServicesJson.getServices().isEmpty()) {
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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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return response.getEntity().getContentLength() > 21 || 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, InterruptedException {
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loadBundle("r4/HelloWorld-Bundle.json", ourCtx, ourClient);
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await().atMost(10000, TimeUnit.MILLISECONDS).until(() -> hasCdsServices());
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var cdsRequest = "{\n" +
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" \"hookInstance\": \"12345\",\n" +
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" \"hook\": \"patient-view\",\n" +
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" \"context\": {\n" +
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" \"userId\": \"Practitioner/example\",\n" +
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" \"patientId\": \"Patient/example-hello-world\"\n" +
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" },\n" +
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" \"prefetch\": {\n" +
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" \"item1\": {\n" +
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" \"resourceType\": \"Patient\",\n" +
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" \"id\": \"example-hello-world\",\n" +
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" \"gender\": \"male\",\n" +
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" \"birthDate\": \"2000-01-01\"\n" +
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" }\n" +
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" }\n" +
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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(() -> hasCdsServices());
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var fhirServer = " \"fhirServer\": " + "\"" + ourServerBase + "\"" + ",\n";
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var cdsRequest = "{\n" +
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" \"hookInstance\": \"055b009c-4a7d-4db4-a35e-0e5198918ed1\",\n" +
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" \"hook\": \"order-sign\",\n" +
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fhirServer +
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" \"context\": {\n" +
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" \"patientId\": \"example-rec-10-order-sign-illicit-POS-Cocaine-drugs\",\n" +
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" \"userId\": \"COREPRACTITIONER1\",\n" +
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" \"draftOrders\": {\n" +
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" \"resourceType\": \"Bundle\",\n" +
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" \"entry\": [\n" +
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" {\n" +
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" \"resource\": {\n" +
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" \"resourceType\": \"MedicationRequest\",\n" +
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" \"id\": \"request-123\",\n" +
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" \"status\": \"draft\",\n" +
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" \"subject\": {\n" +
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" \"reference\": \"Patient/example-rec-10-order-sign-illicit-POS-Cocaine-drugs\"\n" +
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" },\n" +
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" \"authoredOn\": \"2024-03-27\",\n" +
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" \"dosageInstruction\": [\n" +
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" {\n" +
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" \"timing\": {\n" +
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" \"repeat\": {\n" +
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" \"frequency\": 1,\n" +
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" \"period\": 1,\n" +
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" \"periodUnit\": \"d\"\n" +
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" }\n" +
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" },\n" +
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" \"doseAndRate\": [\n" +
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" {\n" +
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" \"doseQuantity\": {\n" +
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" \"value\": 1,\n" +
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" \"system\": \"http://unitsofmeasure.org\",\n" +
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" \"code\": \"{pill}\"\n" +
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" }\n" +
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" }\n" +
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" ]\n" +
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" }\n" +
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" ],\n" +
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" \"dispenseRequest\": {\n" +
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" \"expectedSupplyDuration\": {\n" +
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" \"value\": 90,\n" +
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" \"unit\": \"days\",\n" +
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" \"system\": \"http://unitsofmeasure.org\",\n" +
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" \"code\": \"d\"\n" +
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" }\n" +
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" },\n" +
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" \"intent\": \"order\",\n" +
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" \"category\": {\n" +
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" \"coding\": [\n" +
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" {\n" +
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" \"system\": \"http://terminology.hl7.org/CodeSystem/medicationrequest-category\",\n" +
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" \"code\": \"community\"\n" +
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" }\n" +
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" ]\n" +
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" },\n" +
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" \"medicationCodeableConcept\": {\n" +
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" \"coding\": [\n" +
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" {\n" +
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" \"system\": \"http://www.nlm.nih.gov/research/umls/rxnorm\",\n" +
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" \"code\": \"1049502\",\n" +
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" \"display\": \"12 HR oxycodone hydrochloride 10 MG Extended Release Oral Tablet\"\n" +
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" }\n" +
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" ]\n" +
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" }\n" +
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" }\n" +
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" }\n" +
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" ]\n" +
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" }\n" +
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" }\n" +
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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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@@ -152,13 +152,6 @@ class ExampleServerDstu3IT implements IServerSupport {
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return count;
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}
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private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
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String json = stringFromResource(theLocation);
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Bundle bundle = (Bundle) theCtx.newJsonParser().parseResource(json);
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Bundle result = theClient.transaction().withBundle(bundle).execute();
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return result;
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}
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@Test
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void testWebsocketSubscription() throws Exception {
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/*
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@@ -62,8 +62,8 @@ import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
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//"hapi.fhir.subscription.websocket_enabled=true",
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//"hapi.fhir.mdm_enabled=true",
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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.cr.caregaps.section_author=Organization/alphora-author",
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"hapi.fhir.cr.caregaps.reporter=Organization/alphora",
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"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
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"hapi.fhir.implementationguides.dk-core.version=1.1.0",
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"hapi.fhir.auto_create_placeholder_reference_targets=true",
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@@ -131,13 +131,6 @@ class ExampleServerR4IT implements IServerSupport {
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assertEquals(measureUrl + "|0.0.003", report.getMeasure());
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}
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private org.hl7.fhir.r4.model.Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
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String json = stringFromResource(theLocation);
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org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) theCtx.newJsonParser().parseResource(json);
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org.hl7.fhir.r4.model.Bundle result = theClient.transaction().withBundle(bundle).execute();
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return result;
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}
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public Parameters runCqlExecution(Parameters parameters) {
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var results = ourClient.operation().onServer()
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@@ -275,8 +268,8 @@ class ExampleServerR4IT implements IServerSupport {
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@Test
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void testCareGaps() throws IOException {
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var reporter = crProperties.getCareGapsReporter();
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var author = crProperties.getCareGapsSectionAuthor();
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var reporter = crProperties.getCareGaps().getReporter();
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var author = crProperties.getCareGaps().getSection_author();
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assertTrue(reporter.equals("Organization/alphora"));
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assertTrue(author.equals("Organization/alphora-author"));
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@@ -3,8 +3,10 @@ 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.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import com.google.common.base.Charsets;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.springframework.core.io.DefaultResourceLoader;
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import org.springframework.core.io.Resource;
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@@ -28,6 +30,12 @@ public interface IServerSupport {
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}
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}
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default IBaseBundle loadBundle(String theLocation, FhirContext theFhirContext, IGenericClient theClient) throws IOException {
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String json = stringFromResource(theLocation);
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IBaseBundle bundle = (IBaseBundle) theFhirContext.newJsonParser().parseResource(json);
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return theClient.transaction().withBundle(bundle).execute();
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}
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default String stringFromResource(String theLocation) throws IOException {
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InputStream is = null;
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if (theLocation.startsWith(File.separator)) {
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309
src/test/resources/r4/HelloWorld-Bundle.json
Normal file
309
src/test/resources/r4/HelloWorld-Bundle.json
Normal file
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
Reference in New Issue
Block a user