✅ test: Replace embedded database with MongoDB test container for onF…

…hir unit tests
srdc · May 22, 2024 · 2b28d43 · 2b28d43
1 parent 6afbfd5
commit 2b28d43
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Showing 4 changed files with 45 additions and 8 deletions.
diff --git a/tofhir-engine/pom.xml b/tofhir-engine/pom.xml
@@ -263,6 +263,12 @@
             <artifactId>kafka</artifactId>
             <scope>test</scope>
         </dependency>
+        <!-- For MongoDB test container -->
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>mongodb</artifactId>
+            <scope>test</scope>
+        </dependency>
         <!-- onFhir test container-->
         <dependency>
             <groupId>org.testcontainers</groupId>

diff --git a/tofhir-engine/src/test/scala/io/tofhir/OnFhirTestContainer.scala b/tofhir-engine/src/test/scala/io/tofhir/OnFhirTestContainer.scala
@@ -2,7 +2,7 @@ package io.tofhir
 
 import io.onfhir.client.OnFhirNetworkClient
 import io.tofhir.engine.Execution.actorSystem
-import org.testcontainers.containers.GenericContainer
+import org.testcontainers.containers.{GenericContainer, MongoDBContainer, Network}
 import org.testcontainers.containers.wait.strategy.Wait
 import org.testcontainers.utility.DockerImageName
 
@@ -18,8 +18,19 @@ object OnFhirTestContainer {
   private val TIMEOUT_SECONDS = 180 // Timeout in seconds for container startup
 
   private lazy val container: GenericContainer[_] = {
+    // initialize a Testcontainers network
+    val network = Network.newNetwork()
+    // Start a MongoDB container and attach it to the created network
+    new MongoDBContainer("mongo:7.0")
+      .withNetwork(network)
+      .withNetworkAliases("mongoDB")
+      .start()
+    // Create a generic container for onFHIR
     val container: GenericContainer[Nothing] = new GenericContainer(DockerImageName.parse("srdc/onfhir:r5")).withExposedPorts(ONFHIR_TESTCONTAINER_PORT)
-    container.addEnv("DB_EMBEDDED", "true")
+    container.withNetwork(network) // attach the onFHIR container to the same network
+    container.withNetworkAliases("onFhir")
+    container.addEnv("DB_EMBEDDED", "false") // disable embedded database
+    container.addEnv("DB_HOST", s"mongoDB:27017") // connect to MongoDB
     container.addEnv("SERVER_PORT", ONFHIR_TESTCONTAINER_PORT.toString)
     container.addEnv("SERVER_BASE_URI", "fhir")
     container.addEnv("FHIR_ROOT_URL", s"http://${container.getHost}:$ONFHIR_TESTCONTAINER_PORT/fhir")

diff --git a/tofhir-server/pom.xml b/tofhir-server/pom.xml
@@ -221,6 +221,12 @@
             <artifactId>testcontainers</artifactId>
             <scope>test</scope>
         </dependency>
+        <!-- For MongoDB test container -->
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>mongodb</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>junit-jupiter</artifactId>

diff --git a/tofhir-server/src/test/scala/io/tofhir/server/BaseEndpointTest.scala b/tofhir-server/src/test/scala/io/tofhir/server/BaseEndpointTest.scala
@@ -18,9 +18,10 @@ import org.json4s.jackson.Serialization.writePretty
 import org.scalatest.BeforeAndAfterAll
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.wordspec.AnyWordSpec
-import org.testcontainers.containers.GenericContainer
+import org.testcontainers.containers.{GenericContainer, MongoDBContainer}
 import org.testcontainers.containers.wait.strategy.Wait
 import org.testcontainers.junit.jupiter.Container
+import org.testcontainers.containers.Network
 import org.testcontainers.utility.DockerImageName
 
 import java.io.File
@@ -36,6 +37,8 @@ trait BaseEndpointTest extends AnyWordSpec with Matchers with ScalatestRouteTest
   // route endpoint
   var route: Route = _
 
+  private val ONFHIR_TESTCONTAINER_PORT = 8081 // Port number of the OnFhir instance to be created for testing.
+
   // Instance of OnFhirNetworkClient initialized with onFhir container
   lazy val onFhirClient: OnFhirNetworkClient = initializeOnFhirClient()
 
@@ -44,11 +47,22 @@ trait BaseEndpointTest extends AnyWordSpec with Matchers with ScalatestRouteTest
    * */
   def initializeOnFhirClient(): OnFhirNetworkClient = {
     @Container
-    val container: GenericContainer[Nothing] = new GenericContainer(DockerImageName.parse("srdc/onfhir:r5")).withExposedPorts(8081);
-    container.addEnv("DB_EMBEDDED", "true");
-    container.addEnv("SERVER_PORT", "8081");
-    container.addEnv("SERVER_BASE_URI", "fhir");
-    container.addEnv("FHIR_ROOT_URL", s"http://${container.getHost}:8081/fhir")
+    // initialize a Testcontainers network
+    val network = Network.newNetwork()
+    // Start a MongoDB container and attach it to the created network
+    new MongoDBContainer("mongo:7.0")
+      .withNetwork(network)
+      .withNetworkAliases("mongoDB")
+      .start()
+    // Create a generic container for onFHIR
+    val container: GenericContainer[Nothing] = new GenericContainer(DockerImageName.parse("srdc/onfhir:r5")).withExposedPorts(ONFHIR_TESTCONTAINER_PORT)
+    container.withNetwork(network) // attach the onFHIR container to the same network
+    container.withNetworkAliases("onFhir")
+    container.addEnv("DB_EMBEDDED", "false") // disable embedded database
+    container.addEnv("DB_HOST", s"mongoDB:27017") // connect to MongoDB
+    container.addEnv("SERVER_PORT", ONFHIR_TESTCONTAINER_PORT.toString)
+    container.addEnv("SERVER_BASE_URI", "fhir")
+    container.addEnv("FHIR_ROOT_URL", s"http://${container.getHost}:$ONFHIR_TESTCONTAINER_PORT/fhir")
     // The default startup timeout of 60 seconds is not sufficient for OnFhir, as it utilizes an embedded
     // MongoDB, which requires additional initialization time. Therefore, we increase the timeout to 3 minutes (180 seconds).
     container.waitingFor(Wait.forHttp("/fhir/metadata").forStatusCode(200).withStartupTimeout(Duration.ofSeconds(180)))