build: #16 add integration tests

GenomicDataInfrastructure · Mar 6, 2024 · 29fa9ba · 29fa9ba
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diff --git a/README.md b/README.md
@@ -33,16 +33,13 @@ Ensure you have [Maven](https://maven.apache.org/) and [GraalVM](https://www.gra
 sdk install java 21.0.2-graal
 sdk install maven 3.9.6
 echo -e "\nexport GRAALVM_HOME="$HOME/.sdkman/candidates/java/21.0.2-graal/" >> $HOME/.zprofile
+echo -e "\nryuk.container.privileged=true" >> $HOME/.testcontainers.properties
 ```
 
 ## Running the application in dev mode
 
 You can run your application in dev mode that enables live coding using:
 ```shell script
-cp .env.example .env
-docker compose build
-docker compose run --rm -e CMD="migrate;test-data" rems
-docker compose up -d
 mvn compile quarkus:dev
 ```
 
@@ -81,6 +78,16 @@ If you want to learn more about building native executables, please consult http
 
 All tests are automatically executed when you build a new package.
 
+## Running locally all the components
+
+Execute the commands below, if you want to test all the components, their integration and the native build.
+
+```shell script
+docker compose build
+docker compose run --rm -e CMD="migrate;test-data" rems
+docker compose up -d
+```
+
 ## License
 
 - All original source code is licensed under [Apache-2.0](./LICENSES/Apache-2.0.txt).

diff --git a/_http/rems/01_create_application.http b/_http/rems/01_create_application.http
@@ -6,7 +6,7 @@ POST http://localhost:3000/api/applications/create
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "catalogue-item-ids": [9]

diff --git a/_http/rems/02_retrieve_application.http b/_http/rems/02_retrieve_application.http
@@ -5,4 +5,4 @@
 GET http://rems:3000/api/applications/25
 Accept: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
diff --git a/_http/rems/03_accept_terms.http b/_http/rems/03_accept_terms.http
@@ -6,7 +6,7 @@ POST http://rems:3000/api/applications/accept-licenses
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "application-id": 28

diff --git a/_http/rems/04_add_member.http b/_http/rems/04_add_member.http
@@ -6,7 +6,7 @@ POST http://rems:3000/api/applications/invite-member
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "application-id": 28

diff --git a/_http/rems/05_remove_member.http b/_http/rems/05_remove_member.http
@@ -6,7 +6,7 @@ POST http://rems:3000/api/applications/uninvite-member
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "application-id": 28

diff --git a/_http/rems/06_attach_file.http b/_http/rems/06_attach_file.http
@@ -7,7 +7,7 @@ POST http://rems:3000/api/applications/add-attachment?application-id=28
 Accept: application/json
 Content-Type: multipart/form-data; boundary=MfnBoundry
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 --MfnBoundry
 Content-Disposition: form-data; name="file"; filename="06_dummy_attachment.txt"

diff --git a/_http/rems/07_remove_attachment.http b/_http/rems/07_remove_attachment.http
@@ -8,7 +8,7 @@ POST http://rems:3000/api/applications/save-draft
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "application-id": 28

diff --git a/_http/rems/08_update_duos.http b/_http/rems/08_update_duos.http
@@ -6,7 +6,7 @@ POST http://rems:3000/api/applications/save-draft
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "application-id": 28

diff --git a/_http/rems/09_save_forms.http b/_http/rems/09_save_forms.http
@@ -6,7 +6,7 @@ POST http://rems:3000/api/applications/save-draft
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "application-id": 28

diff --git a/_http/rems/10_submit_application.http b/_http/rems/10_submit_application.http
@@ -6,7 +6,7 @@ POST http://rems:3000/api/applications/submit
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "application-id" : 25

diff --git a/_http/rems/11_copy_as_new_application.http b/_http/rems/11_copy_as_new_application.http
@@ -6,7 +6,7 @@ POST http://localhost:3000/api/applications/copy-as-new
 Accept: application/json
 Content-Type: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
 
 {
     "application-id" : 25

diff --git a/_http/rems/12_my_applications.http b/_http/rems/12_my_applications.http
@@ -5,4 +5,4 @@
 GET http://rems:3000/api/my-applications
 Accept: application/json
 x-rems-api-key: 42
-x-rems-user-id: 52cacbab-c440-4385-9d5f-46aa4930b0e4
+x-rems-user-id: eb4123a3-b722-4798-9af5-8957f823657a
diff --git a/_http/rems/13_create_user.http b/_http/rems/13_create_user.http
@@ -8,7 +8,7 @@ x-rems-api-key: 42
 x-rems-user-id: owner
 
 {
-  "userid": "52cacbab-c440-4385-9d5f-46aa4930b0e4",
+  "userid": "eb4123a3-b722-4798-9af5-8957f823657a",
   "name": "CKAN Admin",
   "email": "[email protected]"
 }

diff --git a/keycloak/realms/ckan-realm.json b/keycloak/realms/ckan-realm.json
@@ -383,7 +383,7 @@
   "webAuthnPolicyPasswordlessAcceptableAaguids" : [ ],
   "webAuthnPolicyPasswordlessExtraOrigins" : [ ],
   "users" : [ {
-    "id" : "52cacbab-c440-4385-9d5f-46aa4930b0e4",
+    "id" : "eb4123a3-b722-4798-9af5-8957f823657a",
     "createdTimestamp" : 1703107576892,
     "username" : "ckan_admin",
     "enabled" : true,

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
   xmlns="http://maven.apache.org/POM/4.0.0"
   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
   <modelVersion>4.0.0</modelVersion>
-  <groupId>lu.lnds.daam</groupId>
+  <groupId>io.github.genomicdatainfrastructure</groupId>
   <artifactId>gdi-userportal-access-management-service</artifactId>
   <version>0.0.0</version>
   <name>gdi-userportal-access-management-service</name>
@@ -22,6 +22,8 @@
     <quarkus.platform.version>3.8.1</quarkus.platform.version>
     <skipITs>true</skipITs>
     <surefire-plugin.version>3.2.5</surefire-plugin.version>
+    <surefire.version>3.0.0-M7</surefire.version>
+    <quarkus-wiremock.version>1.3.0</quarkus-wiremock.version>
   </properties>
   <dependencyManagement>
     <dependencies>
@@ -69,14 +71,6 @@
       <groupId>io.quarkus</groupId>
       <artifactId>quarkus-rest-client-reactive-jackson</artifactId>
     </dependency>
-    <dependency>
-      <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-oidc-client-reactive-filter</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-security</artifactId>
-    </dependency>
     <dependency>
       <groupId>io.quarkiverse.openapi.generator</groupId>
       <artifactId>quarkus-openapi-generator</artifactId>
@@ -105,10 +99,38 @@
     <dependency>
       <groupId>io.quarkus</groupId>
       <artifactId>quarkus-junit5-mockito</artifactId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>io.quarkus</groupId>
+      <artifactId>quarkus-test-keycloak-server</artifactId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>io.quarkiverse.wiremock</groupId>
+      <artifactId>quarkus-wiremock</artifactId>
+      <version>${quarkus-wiremock.version}</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>io.quarkiverse.wiremock</groupId>
+      <artifactId>quarkus-wiremock-test</artifactId>
+      <version>${quarkus-wiremock.version}</version>
+      <scope>test</scope>
     </dependency>
   </dependencies>
   <build>
     <plugins>
+      <plugin>
+        <artifactId>maven-surefire-plugin</artifactId>
+        <version>${surefire.version}</version>
+        <configuration>
+          <systemPropertyVariables>
+            <java.util.logging.manager>org.jboss.logmanager.LogManager</java.util.logging.manager>
+            <maven.home>${maven.home}</maven.home>
+          </systemPropertyVariables>
+        </configuration>
+      </plugin>
       <plugin>
         <groupId>${quarkus.platform.group-id}</groupId>
         <artifactId>quarkus-maven-plugin</artifactId>
@@ -156,7 +178,8 @@
         </executions>
         <configuration>
           <systemPropertyVariables>
-            <native.image.path>${project.build.directory}/${project.build.finalName}-runner</native.image.path>
+            <native.image.path>${project.build.directory}/${project.build.finalName}-runner
+            </native.image.path>
             <java.util.logging.manager>org.jboss.logmanager.LogManager</java.util.logging.manager>
             <maven.home>${maven.home}</maven.home>
           </systemPropertyVariables>

diff --git a/...nds/daam/api/ApplicationQueryApiImpl.java → ...ure/daam/api/ApplicationQueryApiImpl.java b/...nds/daam/api/ApplicationQueryApiImpl.java → ...ure/daam/api/ApplicationQueryApiImpl.java
@@ -1,21 +1,18 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
-package lu.lnds.daam.api;
-
-import static lu.lnds.daam.security.PostAuthenticationFilter.USER_ID_CLAIM;
+package io.github.genomicdatainfrastructure.daam.api;
 
+import io.github.genomicdatainfrastructure.daam.model.ListedApplication;
+import io.github.genomicdatainfrastructure.daam.model.RetrievedApplication;
+import io.github.genomicdatainfrastructure.daam.security.PostAuthenticationFilter;
+import io.github.genomicdatainfrastructure.daam.services.ListApplicationsService;
 import io.quarkus.oidc.runtime.OidcJwtCallerPrincipal;
-import io.quarkus.security.Authenticated;
 import io.quarkus.security.identity.SecurityIdentity;
 import java.io.File;
 import java.util.List;
 import lombok.RequiredArgsConstructor;
-import lu.lnds.daam.model.ListedApplication;
-import lu.lnds.daam.model.RetrievedApplication;
-import lu.lnds.daam.services.ListApplicationsService;
 
-@Authenticated
 @RequiredArgsConstructor
 public class ApplicationQueryApiImpl implements ApplicationQueryApi {
 
@@ -25,7 +22,8 @@ public class ApplicationQueryApiImpl implements ApplicationQueryApi {
   @Override
   public List<ListedApplication> listApplicationsV1() {
     var principal = (OidcJwtCallerPrincipal) identity.getPrincipal();
-    return listApplicationsService.listApplications(principal.getClaim(USER_ID_CLAIM));
+    return listApplicationsService.listApplications(principal.getClaim(
+        PostAuthenticationFilter.USER_ID_CLAIM));
   }
 
   @Override
@@ -36,6 +34,7 @@ public RetrievedApplication retrieveApplicationV1(String id) {
   @Override
   public File retrieveAttachmentFromApplicationV1(String id, String attachmentId) {
     throw new UnsupportedOperationException(
-        "Unimplemented method 'retrieveAttachmentFromApplicationV1'");
+        "Unimplemented method 'retrieveAttachmentFromApplicationV1'"
+    );
   }
 }
diff --git a/...am/security/PostAuthenticationFilter.java → ...am/security/PostAuthenticationFilter.java b/...am/security/PostAuthenticationFilter.java → ...am/security/PostAuthenticationFilter.java
@@ -1,8 +1,9 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
-package lu.lnds.daam.security;
+package io.github.genomicdatainfrastructure.daam.security;
 
+import io.github.genomicdatainfrastructure.daam.services.CreateRemsUserService;
 import io.quarkus.oidc.runtime.OidcJwtCallerPrincipal;
 import io.quarkus.security.identity.SecurityIdentity;
 import jakarta.annotation.Priority;
@@ -11,7 +12,6 @@
 import jakarta.ws.rs.container.ContainerRequestContext;
 import jakarta.ws.rs.container.ContainerRequestFilter;
 import jakarta.ws.rs.ext.Provider;
-import lu.lnds.daam.services.CreateRemsUserService;
 
 @Provider
 @Priority(Priorities.AUTHENTICATION)
@@ -25,8 +25,9 @@ public class PostAuthenticationFilter implements ContainerRequestFilter {
   private final CreateRemsUserService createRemsUserService;
 
   @Inject
-  public PostAuthenticationFilter(
-      SecurityIdentity identity, CreateRemsUserService createRemsUserService) {
+  public PostAuthenticationFilter(SecurityIdentity identity,
+      CreateRemsUserService createRemsUserService
+  ) {
     this.identity = identity;
     this.createRemsUserService = createRemsUserService;
   }

diff --git a/.../daam/services/CreateRemsUserService.java → .../daam/services/CreateRemsUserService.java b/.../daam/services/CreateRemsUserService.java → .../daam/services/CreateRemsUserService.java
@@ -1,12 +1,12 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
-package lu.lnds.daam.services;
+package io.github.genomicdatainfrastructure.daam.services;
 
+import io.github.genomicdatainfrastructure.daam.remote.rems.api.RemsUsersApi;
+import io.github.genomicdatainfrastructure.daam.remote.rems.model.CreateUserCommand;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
-import lu.lnds.daam.remote.rems.api.RemsUsersApi;
-import lu.lnds.daam.remote.rems.model.CreateUserCommand;
 import org.eclipse.microprofile.config.inject.ConfigProperty;
 import org.eclipse.microprofile.rest.client.inject.RestClient;
 
@@ -21,7 +21,8 @@ public class CreateRemsUserService {
   public CreateRemsUserService(
       @ConfigProperty(name = "quarkus.rest-client.rems_yaml.api-key") String remsApiKey,
       @ConfigProperty(name = "quarkus.rest-client.rems_yaml.bot-user") String remsBotUser,
-      @RestClient RemsUsersApi usersApi) {
+      @RestClient RemsUsersApi usersApi
+  ) {
     this.remsApiKey = remsApiKey;
     this.remsBotUser = remsBotUser;
     this.usersApi = usersApi;

diff --git a/...aam/services/ListApplicationsService.java → ...aam/services/ListApplicationsService.java b/...aam/services/ListApplicationsService.java → ...aam/services/ListApplicationsService.java
@@ -1,14 +1,14 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
-package lu.lnds.daam.services;
+package io.github.genomicdatainfrastructure.daam.services;
 
+import io.github.genomicdatainfrastructure.daam.model.ListedApplication;
+import io.github.genomicdatainfrastructure.daam.remote.rems.api.RemsApplicationsApi;
+import io.github.genomicdatainfrastructure.daam.remote.rems.model.ApplicationOverview;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
 import java.util.List;
-import lu.lnds.daam.model.ListedApplication;
-import lu.lnds.daam.remote.rems.api.RemsApplicationsApi;
-import lu.lnds.daam.remote.rems.model.ApplicationOverview;
 import org.eclipse.microprofile.config.inject.ConfigProperty;
 import org.eclipse.microprofile.rest.client.inject.RestClient;
 
@@ -21,7 +21,8 @@ public class ListApplicationsService {
   @Inject
   public ListApplicationsService(
       @ConfigProperty(name = "quarkus.rest-client.rems_yaml.api-key") String remsApiKey,
-      @RestClient RemsApplicationsApi applicationsApi) {
+      @RestClient RemsApplicationsApi applicationsApi
+  ) {
     this.remsApiKey = remsApiKey;
     this.applicationsApi = applicationsApi;
   }

diff --git a/src/main/java/lu/lnds/daam/services/CreateApplicationService.java b/src/main/java/lu/lnds/daam/services/CreateApplicationService.java