cqframework · rob-reynolds · May 8, 2022 · May 6, 2022 · May 7, 2022
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -12,7 +12,6 @@
 			"projectName": "cqf-ruler-server",
 			"vmArgs": [
 				"-XX:TieredStopAtLevel=1",
-				"-Xverify:none",
 				"-Dspring.main.lazy-initialization=true",
 				"-Ddebug=true",
 				"-Dloader.debug=true"
@@ -32,23 +31,6 @@
 				"$Runtime"
 			]
 		},
-		{
-			"type": "java",
-			"name": "Attach",
-			"request": "attach",
-			"hostName": "localhost",
-			"port": "5005",
-			"stepFilters": {
-				"classNameFilters": [
-					"java.*",
-					"javax.*",
-					"com.sun.*",
-					"sun.*",
-					"sunw.*",
-					"org.omg.*"
-				]
-			}
-		},
 		{
 			"type": "java",
 			"name": "Launch Server DSTU3 (Live Reload)",
@@ -57,7 +39,6 @@
 			"projectName": "cqf-ruler-server",
 			"vmArgs": [
 				"-XX:TieredStopAtLevel=1",
-				"-Xverify:none",
 				"-Dspring.main.lazy-initialization=true",
 				"-Ddebug=true",
 				"-Dloader.debug=true",

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -6,7 +6,6 @@
 			"name": "test-config",
 			"vmArgs": [
 				"-XX:TieredStopAtLevel=1",
-				"-Xverify:none",
 				"-Dspring.main.lazy-initialization=true"
 			]
 		},

diff --git a/core/pom.xml b/core/pom.xml
@@ -1,6 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0"
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<parent>
 		<groupId>org.opencds.cqf.ruler</groupId>
@@ -16,7 +15,6 @@
 			<artifactId>javaee-api</artifactId>
 			<version>8.0.1</version>
 		</dependency>
-
 		<dependency>
 			<groupId>org.opencds.cqf.ruler</groupId>
 			<artifactId>cqf-ruler-external</artifactId>

diff --git a/core/src/main/java/org/opencds/cqf/ruler/Application.java b/core/src/main/java/org/opencds/cqf/ruler/Application.java
@@ -1,7 +1,6 @@
 package org.opencds.cqf.ruler;
 
 import org.opencds.cqf.ruler.config.BeanFinderConfig;
-import org.opencds.cqf.ruler.config.ServerProperties;
 import org.opencds.cqf.ruler.config.TesterUIConfig;
 import org.opencds.cqf.ruler.external.FhirTesterConfig;
 import org.opencds.cqf.ruler.external.annotations.OnEitherVersion;
@@ -69,9 +68,4 @@ public ServletRegistrationBean<Server> hapiServletRegistration() {
 
 		return servletRegistrationBean;
 	}
-
-	@Bean
-	public ServerProperties serverProperties() {
-		return new ServerProperties();
-	}
 }
diff --git a/core/src/test/java/org/opencds/cqf/ruler/ExampleServerDstu2IT.java b/core/src/test/java/org/opencds/cqf/ruler/ExampleServerDstu2IT.java
@@ -15,22 +15,21 @@
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 
-
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
-  {
-    "spring.batch.job.enabled=false",
-    "hapi.fhir.fhir_version=dstu2",
-    "spring.datasource.url=jdbc:h2:mem:dbr2"
-  })
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = {
+		"spring.batch.job.enabled=false",
+		"hapi.fhir.fhir_version=dstu2",
+		"spring.datasource.url=jdbc:h2:mem:dbr2",
+		"spring.flyway.enabled=false"
+})
 public class ExampleServerDstu2IT {
 
 	private IGenericClient ourClient;
 	private FhirContext ourCtx;
 
-  @LocalServerPort
-  private int port;
+	@LocalServerPort
+	private int port;
 
-  @Test
+	@Test
 	void testCreateAndRead() {
 
 		String methodName = "testCreateResourceConditional";
@@ -42,11 +41,10 @@ void testCreateAndRead() {
 		assertEquals(methodName, pt2.getName().get(0).getFamily().get(0).getValue());
 	}
 
-
 	@BeforeEach
 	void beforeEach() {
 
-    ourCtx = FhirContext.forCached(FhirVersionEnum.DSTU2);
+		ourCtx = FhirContext.forCached(FhirVersionEnum.DSTU2);
 		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
 		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
 		String ourServerBase = "http://localhost:" + port + "/fhir/";

diff --git a/core/src/test/java/org/opencds/cqf/ruler/ExampleServerDstu3IT.java b/core/src/test/java/org/opencds/cqf/ruler/ExampleServerDstu3IT.java
@@ -16,13 +16,13 @@
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 
-
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = {
 		"spring.datasource.url=jdbc:h2:mem:dbr3",
 		"hapi.fhir.fhir_version=dstu3",
 		"hapi.fhir.subscription.websocket_enabled=true",
 		"hapi.fhir.allow_external_references=true",
 		"hapi.fhir.allow_placeholder_references=true",
+		"spring.flyway.enabled=false"
 })
 
 public class ExampleServerDstu3IT {

diff --git a/core/src/test/java/org/opencds/cqf/ruler/ExampleServerR4IT.java b/core/src/test/java/org/opencds/cqf/ruler/ExampleServerR4IT.java
@@ -24,18 +24,19 @@
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.util.BundleUtil;
 
-
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
-	{
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = {
 		"spring.batch.job.enabled=false",
 		"spring.datasource.url=jdbc:h2:mem:dbr4",
 		"hapi.fhir.enable_repository_validating_interceptor=true",
 		"hapi.fhir.fhir_version=r4",
 		"hapi.fhir.subscription.websocket_enabled=true",
 		"hapi.fhir.mdm_enabled=true",
-		//Override is currently required when using MDM as the construction of the MDM beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment
-		"spring.main.allow-bean-definition-overriding=true"
-	})
+		// Override is currently required when using MDM as the construction of the MDM
+		// beans are ambiguous as they are constructed multiple places. This is evident
+		// when running in a spring boot environment
+		"spring.main.allow-bean-definition-overriding=true",
+		"spring.flyway.enabled=false"
+})
 public class ExampleServerR4IT {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);
 	private IGenericClient ourClient;
@@ -44,7 +45,6 @@ public class ExampleServerR4IT {
 	@LocalServerPort
 	private int port;
 
-
 	@Test
 	@Order(0)
 	void testCreateAndRead() {
@@ -63,99 +63,109 @@ void testCreateAndRead() {
 
 		// Wait until the MDM message has been processed
 		// await().until(() -> {
-		// 	sleep(1000);
-		// 	return getGoldenResourcePatient() != null;
+		// sleep(1000);
+		// return getGoldenResourcePatient() != null;
 		// });
 		// Patient goldenRecord = getGoldenResourcePatient();
 
 		// // Verify that a golden record Patient was created
-		// assertNotNull(goldenRecord.getMeta().getTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD"));
+		// assertNotNull(goldenRecord.getMeta().getTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status",
+		// "GOLDEN_RECORD"));
 	}
 
 	@SuppressWarnings("unused")
 	private List<Patient> getPatients() {
-		Bundle bundle = ourClient.search().forResource(Patient.class).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
+		Bundle bundle = ourClient.search().forResource(Patient.class)
+				.cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
 		List<Patient> retVal = BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Patient.class);
 		retVal.sort(comparing(o -> ((Patient) o).getMeta().getLastUpdated()).reversed());
 		return retVal;
 	}
 
 	// private Patient getGoldenResourcePatient() {
-	// 	Bundle bundle = ourClient.search()
-	// 		.forResource(Patient.class)
-	// 		.withTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD")
-	// 		.cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
-	// 	if (bundle.getEntryFirstRep() != null) {
-	// 		return (Patient) bundle.getEntryFirstRep().getResource();
-	// 	} else {
-	// 		return null;
-	// 	}
+	// Bundle bundle = ourClient.search()
+	// .forResource(Patient.class)
+	// .withTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status",
+	// "GOLDEN_RECORD")
+	// .cacheControl(new
+	// CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
+	// if (bundle.getEntryFirstRep() != null) {
+	// return (Patient) bundle.getEntryFirstRep().getResource();
+	// } else {
+	// return null;
+	// }
 	// }
 
 	// @Test
 	// @Order(1)
 	// public void testWebsocketSubscription() throws Exception {
-	// 	/*
-	// 	 * Create subscription
-	// 	 */
-	// 	Subscription subscription = new Subscription();
-	// 	subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
-	// 	subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
-	// 	subscription.setCriteria("Observation?status=final");
-
-	// 	Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
-	// 	channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
-	// 	channel.setPayload("application/json");
-	// 	subscription.setChannel(channel);
-
-	// 	MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
-	// 	IIdType mySubscriptionId = methodOutcome.getId();
-
-	// 	// Wait for the subscription to be activated
-	// 	await().until(() -> activeSubscriptionCount() == 3);
-
-	// 	/*
-	// 	 * Attach websocket
-	// 	 */
-
-	// 	WebSocketClient myWebSocketClient = new WebSocketClient();
-	// 	SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
-
-	// 	myWebSocketClient.start();
-	// 	URI echoUri = new URI("ws://localhost:" + port + "/websocket");
-	// 	ClientUpgradeRequest request = new ClientUpgradeRequest();
-	// 	ourLog.info("Connecting to : {}", echoUri);
-	// 	Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
-	// 	Session session = connection.get(2, TimeUnit.SECONDS);
-
-	// 	ourLog.info("Connected to WS: {}", session.isOpen());
-
-	// 	/*
-	// 	 * Create a matching resource
-	// 	 */
-	// 	Observation obs = new Observation();
-	// 	obs.setStatus(Observation.ObservationStatus.FINAL);
-	// 	ourClient.create().resource(obs).execute();
-
-	// 	// Give some time for the subscription to deliver
-	// 	sleep(2000);
-
-	// 	/*
-	// 	 * Ensure that we receive a ping on the websocket
-	// 	 */
-	// 	waitForSize(1, () -> mySocketImplementation.myPingCount);
-
-	// 	/*
-	// 	 * Clean up
-	// 	 */
-	// 	ourClient.delete().resourceById(mySubscriptionId).execute();
+	// /*
+	// * Create subscription
+	// */
+	// Subscription subscription = new Subscription();
+	// subscription.setReason("Monitor new neonatal function (note, age will be
+	// determined by the monitor)");
+	// subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
+	// subscription.setCriteria("Observation?status=final");
+
+	// Subscription.SubscriptionChannelComponent channel = new
+	// Subscription.SubscriptionChannelComponent();
+	// channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
+	// channel.setPayload("application/json");
+	// subscription.setChannel(channel);
+
+	// MethodOutcome methodOutcome =
+	// ourClient.create().resource(subscription).execute();
+	// IIdType mySubscriptionId = methodOutcome.getId();
+
+	// // Wait for the subscription to be activated
+	// await().until(() -> activeSubscriptionCount() == 3);
+
+	// /*
+	// * Attach websocket
+	// */
+
+	// WebSocketClient myWebSocketClient = new WebSocketClient();
+	// SocketImplementation mySocketImplementation = new
+	// SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
+
+	// myWebSocketClient.start();
+	// URI echoUri = new URI("ws://localhost:" + port + "/websocket");
+	// ClientUpgradeRequest request = new ClientUpgradeRequest();
+	// ourLog.info("Connecting to : {}", echoUri);
+	// Future<Session> connection =
+	// myWebSocketClient.connect(mySocketImplementation, echoUri, request);
+	// Session session = connection.get(2, TimeUnit.SECONDS);
+
+	// ourLog.info("Connected to WS: {}", session.isOpen());
+
+	// /*
+	// * Create a matching resource
+	// */
+	// Observation obs = new Observation();
+	// obs.setStatus(Observation.ObservationStatus.FINAL);
+	// ourClient.create().resource(obs).execute();
+
+	// // Give some time for the subscription to deliver
+	// sleep(2000);
+
+	// /*
+	// * Ensure that we receive a ping on the websocket
+	// */
+	// waitForSize(1, () -> mySocketImplementation.myPingCount);
+
+	// /*
+	// * Clean up
+	// */
+	// ourClient.delete().resourceById(mySubscriptionId).execute();
 	// }
 
 	// private int activeSubscriptionCount() {
-	// 	return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
+	// return
+	// ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new
+	// CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
 	// }
 
-
 	@BeforeEach
 	void beforeEach() {
 
@@ -164,7 +174,7 @@ void beforeEach() {
 		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
 		String ourServerBase = "http://localhost:" + port + "/fhir/";
 		ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
-//		ourClient.registerInterceptor(new LoggingInterceptor(false));
+		// ourClient.registerInterceptor(new LoggingInterceptor(false));
 	}
 
 	@BeforeAll