Add CdsHook tests and documentation

README.md

@@ -483,7 +483,11 @@ The server may be configured with subscription support by enabling properties in
 
 ## Enabling Clinical Reasoning
 
-Set `hapi.fhir.cr_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [Clinical Quality Language](https://cql.hl7.org/) on this server.
+Set `hapi.fhir.cr_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [Clinical Quality Language](https://cql.hl7.org/) on this server. An alternate settings file, [cds.application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/cds.application.yaml), exists with the Clinical Reasoning module enabled and default settings that have been found to work with most CDS and dQM test cases.
+
+## Enabling CDS Hooks
+
+Set `hapi.fhir.cdshooks.enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [CDS Hooks](https://cds-hooks.org/) on this server. The Clinical Reasoning module must also be enabled because this implementation of CDS Hooks includes [CDS on FHIR](https://build.fhir.org/clinicalreasoning-cds-on-fhir.html). An example CDS Service using CDS on FHIR is available in the CdsHooksServletIT test class.
 
 ## Enabling MDM (EMPI)
 

src/test/java/ca/uhn/fhir/jpa/starter/CdsHooksServletIT.java

@@ -0,0 +1,141 @@
+package ca.uhn.fhir.jpa.starter;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.cr.config.RepositoryConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
+import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
+import com.google.gson.Gson;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.util.EntityUtils;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.web.server.LocalServerPort;
+
+import java.io.IOException;
+import java.util.concurrent.TimeUnit;
+
+import static org.awaitility.Awaitility.await;
+import static org.hamcrest.Matchers.equalTo;
+import static org.junit.jupiter.api.Assertions.*;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
+ classes = {
+ Application.class,
+ NicknameServiceConfig.class,
+ RepositoryConfig.class,
+ CdsHooksConfig.class
+ }, properties = {
+ "spring.profiles.include=storageSettingsTest",
+ "spring.datasource.url=jdbc:h2:mem:dbr4",
+ "hapi.fhir.enable_repository_validating_interceptor=true",
+ "hapi.fhir.fhir_version=r4",
+ "hapi.fhir.cr.enabled=true",
+ "hapi.fhir.cr.caregaps.section_author=Organization/alphora-author",
+ "hapi.fhir.cr.caregaps.reporter=Organization/alphora",
+ "hapi.fhir.cdshooks.enabled=true",
+ "spring.main.allow-bean-definition-overriding=true"})
+class CdsHooksServletIT implements IServerSupport {
+ private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CdsHooksServletIT.class);
+ private final FhirContext ourCtx = FhirContext.forR4Cached();
+ private final IParser ourParser = ourCtx.newJsonParser();
+ private IGenericClient ourClient;
+ private String ourCdsBase;
+
+ @Autowired
+ DaoRegistry myDaoRegistry;
+
+ @Autowired
+ ICdsServiceRegistry myCdsServiceRegistry;
+
+ @LocalServerPort
+ private int port;
+
+ @BeforeEach
+ void beforeEach() {
+ ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+ ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
+ String ourServerBase = "http:https://localhost:" + port + "/fhir/";
+ ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
+ ourCdsBase = "http:https://localhost:" + port + "/cds-services";
+ }
+
+ private JsonArray getCdsServices() throws IOException {
+ var response = callCdsServicesDiscovery();
+ String result = EntityUtils.toString(response.getEntity());
+ Gson gsonResponse = new Gson();
+ JsonObject services = gsonResponse.fromJson(result, JsonObject.class);
+ return !services.has("services") ? new JsonArray() : services.get("services").getAsJsonArray();
+ }
+
+ private CloseableHttpResponse callCdsServicesDiscovery() {
+ try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
+ HttpGet request = new HttpGet(ourCdsBase);
+ request.addHeader("Content-Type", "application/json");
+ return httpClient.execute(request);
+ } catch (IOException ioe) {
+ fail(ioe.getMessage());
+ return null;
+ }
+ }
+
+ @Test
+ void testGetCdsServices() {
+ var response = callCdsServicesDiscovery();
+ assertEquals(200, response.getStatusLine().getStatusCode());
+ }
+
+ @Test
+ void testCdsHooks() throws IOException, InterruptedException {
+ loadBundle("r4/HelloWorld-Bundle.json", ourCtx, ourClient);
+ await().atMost(10000, TimeUnit.MILLISECONDS).until(() -> getCdsServices().size(), equalTo(1));
+ var cdsRequest = "{\n" +
+ " \"hookInstance\": \"12345\",\n" +
+ " \"hook\": \"patient-view\",\n" +
+ " \"context\": {\n" +
+ " \"userId\": \"Practitioner/example\",\n" +
+ " \"patientId\": \"Patient/example-hello-world\"\n" +
+ " },\n" +
+ " \"prefetch\": {\n" +
+ " \"item1\": {\n" +
+ " \"resourceType\": \"Patient\",\n" +
+ " \"id\": \"example-hello-world\",\n" +
+ " \"gender\": \"male\",\n" +
+ " \"birthDate\": \"2000-01-01\"\n" +
+ " }\n" +
+ " }\n" +
+ "}";
+ try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
+ HttpPost request = new HttpPost(ourCdsBase + "/hello-world");
+ request.setEntity(new StringEntity(cdsRequest));
+ request.addHeader("Content-Type", "application/json");
+
+ CloseableHttpResponse httpResponse = httpClient.execute(request);
+ String result = EntityUtils.toString(httpResponse.getEntity());
+ Gson gsonResponse = new Gson();
+ JsonObject response = gsonResponse.fromJson(result, JsonObject.class);
+ assertNotNull(response);
+ JsonArray cards = response.getAsJsonArray("cards");
+ assertEquals(1, cards.size());
+ assertEquals("\"Hello World!\"", cards.get(0).getAsJsonObject().get("summary").toString());
+ } catch (IOException ioe) {
+ fail(ioe.getMessage());
+ }
+ }
+}

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java

@@ -152,13 +152,6 @@ private int loadDataFromDirectory(String theDirectoryName) throws IOException {
  return count;
  }
 
- private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
- String json = stringFromResource(theLocation);
- Bundle bundle = (Bundle) theCtx.newJsonParser().parseResource(json);
- Bundle result = theClient.transaction().withBundle(bundle).execute();
- return result;
- }
-
  @Test
  void testWebsocketSubscription() throws Exception {
  /*

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -131,13 +131,6 @@ public void testCQLEvaluateMeasureEXM130() throws IOException {
  assertEquals(measureUrl + "|0.0.003", report.getMeasure());
  }
 
- private org.hl7.fhir.r4.model.Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
- String json = stringFromResource(theLocation);
- org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) theCtx.newJsonParser().parseResource(json);
- org.hl7.fhir.r4.model.Bundle result = theClient.transaction().withBundle(bundle).execute();
- return result;
- }
-
  public Parameters runCqlExecution(Parameters parameters) {
 
  var results = ourClient.operation().onServer()

src/test/java/ca/uhn/fhir/jpa/starter/IServerSupport.java

@@ -3,8 +3,10 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.core.io.DefaultResourceLoader;
 import org.springframework.core.io.Resource;
@@ -28,6 +30,12 @@ default IBaseResource loadResource(String theLocation, FhirContext theFhirContex
  }
  }
 
+ default IBaseBundle loadBundle(String theLocation, FhirContext theFhirContext, IGenericClient theClient) throws IOException {
+ String json = stringFromResource(theLocation);
+ IBaseBundle bundle = (IBaseBundle) theFhirContext.newJsonParser().parseResource(json);
+ return theClient.transaction().withBundle(bundle).execute();
+ }
+
  default String stringFromResource(String theLocation) throws IOException {
  InputStream is = null;
  if (theLocation.startsWith(File.separator)) {