Merge pull request #763 from RADAR-base/release-2.1.1

Release 2.1.1
RADAR-base · Mar 22, 2024 · 6a57c48 · 6a57c48
2 parents 008ff71 + 91b0dc6
commit 6a57c48
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -35,16 +35,17 @@ jobs:
           distribution: temurin
           java-version: 17
 
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
       - name: Cache
         uses: actions/cache@v3
         with:
           path: |
             ${{ steps.yarn-cache-dir-path.outputs.dir }}
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-java-${{ hashFiles('**/build.gradle', '**/gradle.properties', '**/yarn.lock', '.yarnrc.yml') }}
+          key: ${{ runner.os }}-node-${{ hashFiles('**/build.gradle', '**/gradle.properties', '**/yarn.lock', '.yarnrc.yml') }}
           restore-keys: |
-            ${{ runner.os }}-java-
+            ${{ runner.os }}-node-
 
       - name: Install Yarn dependencies
         run: yarn install
@@ -202,6 +203,16 @@ jobs:
             org.opencontainers.image.vendor=RADAR-base
             org.opencontainers.image.licenses=Apache-2.0
 
+#      # placeholder for testing
+#      - name: End to end tests (docker image)
+#        id: e2e-prod-docker
+#        run: |
+#          cp src/test/resources/config/keystore.p12 src/main/docker/etc/config
+#          ./gradlew -Pprod buildDocker -x test -x javadocJar
+#          docker-compose -f src/main/docker/app.yml up -d
+#          yarn run e2e-prod
+#          docker-compose -f src/main/docker/app.yml down -v
+
       # Temp fix
       # https://github.com/docker/build-push-action/issues/252
       # https://github.com/moby/buildkit/issues/1896

diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
@@ -33,29 +33,40 @@ jobs:
           distribution: temurin
           java-version: 17
 
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
       - name: Cache
         uses: actions/cache@v3
         with:
           path: |
             ${{ steps.yarn-cache-dir-path.outputs.dir }}
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-java-${{ hashFiles('**/build.gradle', '**/gradle.properties', '**/yarn.lock') }}
+          key: ${{ runner.os }}-rc-node-${{ hashFiles('**/build.gradle', '**/gradle.properties', '**/yarn.lock') }}
           restore-keys: |
-            ${{ runner.os }}-java-
+            ${{ runner.os }}-rc-node-
+            ${{ runner.os }}-node-
+
+      - name: Install Yarn dependencies
+        run: yarn install
+
+      - name: Yarn build
+        run: yarn build:prod
+
+      - name: Yarn check
+        run: yarn test
 
       # Compile the code
-      - name: Install dependencies
-        run: |
-          yarn install
+      - name: Compile java
+        run: ./gradlew assemble
 
-      - name: Run full end to end tests
+      - name: Run full production end to end tests
+        id: e2e
         run: |
           cp src/test/resources/config/keystore.p12 src/main/resources/config/keystore.p12
-          ./gradlew bootRun &>mp.log </dev/null &
-          yarn run wait-for-managementportal
-          ./gradlew generateOpenApiSpec
-          yarn e2e
+          docker-compose -f src/main/docker/postgresql.yml up -d
+          ./gradlew bootRun -Pprod -Pe2e-prod-test &>mp.log </dev/null &
+          yarn run e2e-prod
+          docker-compose -f src/main/docker/postgresql.yml down -v
           ./gradlew --stop
 
       - name: Upload screenshots of failed e2e tests

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -23,32 +23,22 @@ jobs:
         with:
           node-version: 16
 
-      - name: Get yarn cache directory path
-        id: yarn-cache-dir-path
-        run: echo "dir=.yarn/cache" >> $GITHUB_OUTPUT
-
       - uses: actions/setup-java@v3
         with:
           distribution: temurin
           java-version: 17
 
-      - name: Cache
-        uses: actions/cache@v3
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
         with:
-          path: |
-            ${{ steps.yarn-cache-dir-path.outputs.dir }}
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-java-${{ hashFiles('**/build.gradle', '**/gradle.properties', '**/yarn.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-java-
+          cache-disabled: true
 
       - name: Compile code
         run: ./gradlew assemble
 
       # Upload it to GitHub
       - name: Upload to GitHub
-        uses: AButler/[email protected]
+        uses: AButler/[email protected].2
         with:
           files: '*/build/libs/*'
           repo-token: ${{ secrets.GITHUB_TOKEN }}

diff --git a/CODEOWNERS b/CODEOWNERS
@@ -1 +1 @@
-*       @nivemaham @blootsvoets
+*       @nivemaham @blootsvoets @bdegraaf1234 @peyman-mohtashami
diff --git a/README.md b/README.md
@@ -21,7 +21,7 @@ Management Portal is an application which is used to manage clinical studies for
 - [Testing](#testing)
   * [Client tests](#client-tests)
   * [Other tests](#other-tests)
-- [Using Docker to simplify development (optional)](#using-docker-to-simplify-development--optional-)
+- [Using Docker to simplify development (optional)](#using-docker-to-simplify-development-optional)
 - [Documentation](#documentation)
 - [Client libraries](#client-libraries)
 
@@ -49,7 +49,7 @@ docker-compose files.
 3. Now, we can start the stack with `docker-compose -f src/main/docker/management-portal.yml up -d`.
 
 This will start a Postgres database and ManagementPortal. The default password for the `admin`
-account is `admin`.
+account is `admin`. An angular live development server to access the managementportal can be started using the `yarn start` command (see [Development](#development)).
 
 ### Build from source
 
@@ -68,15 +68,14 @@ You must install and configure the following dependencies on your machine to run
 main differences between the profiles. Configure the application using the property file at `src/main/resources/config/application-<profile>.yml`.Read more about configurations [here](#configuration)
 
 5. Run ManagementPortal by running `./gradlew bootRun -Pprod` or `./gradlew bootRun -Pdev`. Development mode will start an in
-memory database and ManagementPortal. 
+memory database and ManagementPortal. An angular live development server to access the managementportal can be started using the `yarn start` command (see [Development](#development)).
 6. You can log in to the application using `admin:admin`. Please don't forgot to change the password of `admin`, if you are using the application on production environment.
 
 
 |                                  | Development     | Production                        |
 |----------------------------------|-----------------|-----------------------------------|
 | Database type                    | In-memory       | Postgres                          |
 | Demo data loaded                 | Yes             | No                                |
-| Context path of the application  | `/`             | `/managementportal`               |
 
 
 
@@ -249,6 +248,8 @@ auto-refreshes when files change on your hard drive.
 
 Then open <http://localhost:8081/> to start the interface and sign in with admin/admin.
 
+### Managing dependencies
+
 [Yarn][] is also used to manage CSS and JavaScript dependencies used in this application. You can upgrade dependencies by
 specifying a newer version in [package.json](package.json). You can also run `yarn update` and `yarn install` to manage dependencies.
 Add the `help` flag on any command to see how you can use it. For example, `yarn help update`.
@@ -294,15 +295,15 @@ To launch your application's tests, run:
 
 ### Client tests
 
-Unit tests are run by [Karma][] and written with [Jasmine][]. They're located in [src/test/javascript/](src/test/javascript/) and can be run with:
+Unit tests are run by [Karma][] and written with [Jasmine][]. They're located in `src/test/javascript/` and can be run with:
 
     yarn test
 
 UI end-to-end tests are powered by [Cypress][], which is built on top of WebDriverJS. They're located in [src/test/javascript/e2e](src/test/javascript/e2e)
 and can be run by starting Spring Boot in one terminal (`./gradlew bootRun`) and running the tests (`yarn run e2e`) in a second one.
 ### Other tests
 
-Performance tests are run by [Gatling][] and written in Scala. They're located in [src/test/gatling](src/test/gatling) and can be run with:
+Performance tests are run by [Gatling][] and written in Scala. They're located in `src/test/gatling` and can be run with:
 
     ./gradlew gatlingRunAll
 

diff --git a/angular.json b/angular.json
@@ -136,9 +136,7 @@
           },
           "configurations": {
             "production": {
-              "devServerTarget": "management-portal:serve:production",
-              "watch": false,
-              "headless": true
+              "devServerTarget": "management-portal:serve:production"
             }
           }
         }

diff --git a/build.gradle b/build.gradle
@@ -21,8 +21,10 @@ plugins {
     id "io.github.gradle-nexus.publish-plugin" version "1.3.0"
     id("com.github.ben-manes.versions") version "0.47.0"
     id 'org.jetbrains.kotlin.jvm' version "1.9.10"
+    id "org.jetbrains.kotlin.kapt" version "1.9.10"
     id 'org.jetbrains.kotlin.plugin.serialization' version '1.9.10' apply false
     id 'org.jetbrains.dokka' version "1.8.20"
+    id "org.jetbrains.kotlin.plugin.allopen" version "1.9.10"
 }
 
 apply plugin: 'org.springframework.boot'
@@ -32,7 +34,7 @@ apply plugin: 'io.spring.dependency-management'
 
 allprojects {
     group 'org.radarbase'
-    version '2.1.0' // project version
+    version '2.1.1' // project version
 
     // The comment on the previous line is only there to identify the project version line easily
     // with a sed command, to auto-update the version number with the prepare-release-branch.sh
@@ -147,9 +149,10 @@ if (project.hasProperty('prod')) {
 ext.findbugAnnotationVersion = '3.0.2'
 
 dependencies {
+    implementation("org.jetbrains.kotlin:kotlin-reflect:${kotlin_version}")
     implementation("tech.jhipster:jhipster-framework:${jhipster_server_version}")
     implementation("tech.jhipster:jhipster-dependencies:${jhipster_server_version}")
-    implementation("io.micrometer:micrometer-core")
+    implementation("io.micrometer:micrometer-core:${micrometer_version}")
     runtimeOnly "com.fasterxml.jackson.datatype:jackson-datatype-jsr310"
     implementation "com.fasterxml.jackson.datatype:jackson-datatype-hibernate5"
     implementation "com.fasterxml.jackson.dataformat:jackson-dataformat-csv"
@@ -169,28 +172,29 @@ dependencies {
     runtimeOnly ("org.springframework.boot:spring-boot-starter-data-jpa") {
         exclude group: 'org.hibernate', module: 'hibernate-entitymanager'
     }
-    implementation "org.hibernate:hibernate-core"
-    implementation "org.hibernate:hibernate-envers"
-    implementation 'org.hibernate:hibernate-validator:8.0.0.Final'
-
-    runtimeOnly "org.postgresql:postgresql:${postgresql_version}"
-    runtimeOnly "org.hsqldb:hsqldb:${hsqldb_version}"
-
-    runtimeOnly "org.springframework.boot:spring-boot-starter-security"
     implementation "org.springframework.security:spring-security-data"
 
     implementation("org.springframework.boot:spring-boot-starter-web") {
         exclude module: 'spring-boot-starter-tomcat'
     }
+    runtimeOnly "org.springframework.boot:spring-boot-starter-security"
     implementation ("org.springframework.boot:spring-boot-starter-undertow")
+
+    implementation "org.hibernate:hibernate-core"
+    implementation "org.hibernate:hibernate-envers"
+    implementation "org.hibernate:hibernate-validator:${hibernate_validator_version}"
+
+    runtimeOnly "org.postgresql:postgresql:${postgresql_version}"
+    runtimeOnly "org.hsqldb:hsqldb:${hsqldb_version}"
+
     // Fix vulnerabilities
     runtimeOnly("io.undertow:undertow-websockets-jsr:2.2.25.Final")
     runtimeOnly("io.undertow:undertow-servlet:2.2.25.Final")
     runtimeOnly("io.undertow:undertow-core:2.2.25.Final")
 
     implementation "org.springframework.boot:spring-boot-starter-thymeleaf"
-    runtimeOnly("org.thymeleaf:thymeleaf-spring5:${thymeleaf_version}")
     runtimeOnly("org.thymeleaf:thymeleaf:${thymeleaf_version}")
+    runtimeOnly("org.thymeleaf:thymeleaf-spring5:${thymeleaf_version}")
     implementation("org.springframework:spring-context-support")
     implementation("org.springframework.session:spring-session-hazelcast")
 
@@ -201,6 +205,9 @@ dependencies {
     implementation project(':radar-auth')
     implementation "org.springframework.data:spring-data-envers"
 
+    implementation "org.mockito:mockito-core:$mockito_version"
+    implementation "org.mockito.kotlin:mockito-kotlin:${mockito_kotlin_version}"
+
     runtimeOnly("jakarta.xml.bind:jakarta.xml.bind-api:${javax_xml_bind_version}")
     runtimeOnly("org.glassfish.jaxb:jaxb-core:${javax_jaxb_core_version}")
     runtimeOnly("org.glassfish.jaxb:jaxb-runtime:${javax_jaxb_runtime_version}")
@@ -217,14 +224,20 @@ dependencies {
     testImplementation "org.springframework.boot:spring-boot-test"
     testImplementation "org.assertj:assertj-core:${assertj_version}"
     testImplementation "org.junit.jupiter:junit-jupiter-api"
-    testImplementation "org.mockito:mockito-core:$mockito_version"
+    testImplementation "org.mockito.kotlin:mockito-kotlin:${mockito_kotlin_version}"
     testImplementation "com.mattbertolini:liquibase-slf4j:${liquibase_slf4j_version}"
     testImplementation "org.hamcrest:hamcrest-library"
     testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine"
 
     annotationProcessor("org.springframework.boot:spring-boot-configuration-processor")
 }
 
+allOpen {
+    annotation("org.springframework.stereotype.Component")
+    annotation("org.springframework.boot.test.context.SpringBootTest")
+    annotation("org.springframework.web.bind.annotation.RestController")
+}
+
 dependencyManagement {
     imports {
         mavenBom "com.fasterxml.jackson:jackson-bom:$jackson_version"

diff --git a/cypress.json b/cypress.json
@@ -7,5 +7,5 @@
   "screenshotsFolder": "src/test/javascript/e2e/cypress/screenshots",
   "pluginsFile": false,
   "fixturesFolder": false,
-  "baseUrl": "http://localhost:9000"
+  "baseUrl": "http://localhost:8081"
 }
diff --git a/gradle.properties b/gradle.properties
@@ -2,12 +2,12 @@ rootProject.name=management-portal
 profile=dev
 assertj_version=3.23.1
 jhipster_server_version=7.9.3
-hazelcast_version=5.2.4
+hazelcast_version=5.2.5
 hazelcast_hibernate_version=5.1.0
 hikaricp_version=5.0.1
 liquibase_slf4j_version=4.1.0
 liquibase_version=4.22.0
-postgresql_version=42.6.0
+postgresql_version=42.6.1
 springdoc_version=1.6.15
 spring_boot_version=2.7.15
 spring_framework_version=5.3.27
@@ -16,20 +16,28 @@ thymeleaf_version=3.1.2.RELEASE
 spring_session_version=2021.2.0
 gatling_version=3.8.4
 mapstruct_version=1.5.5.Final
-jackson_version=2.15.2
+jackson_version=2.16.1
 javax_xml_bind_version=2.3.3
 javax_jaxb_core_version=2.3.0.1
 javax_jaxb_runtime_version=2.3.8
 javax_activation=1.1.1
 mockito_version=4.8.1
+mockito_kotlin_version=5.1.0
 slf4j_version=2.0.7
 logback_version=1.4.11
 oauth_jwt_version=4.4.0
 junit_version=5.10.0
 okhttp_version=4.10.0
 hsqldb_version=2.7.2
-coroutines_version=1.7.3
-ktor_version=2.3.3
+coroutines_version=1.8.0
+ktor_version=2.3.9
+radar_commons_version=1.0.0
+hamcrest_version=2.2
+wiremock_version=3.0.1
+kotlin_version=1.9.10
+micrometer_version=1.12.3
+hibernate_orm_version=6.4.4.Final
+hibernate_validator_version=8.0.0.Final
 
 kotlin.code.style=official
 org.gradle.vfs.watch=true

diff --git a/gradle/docker.gradle b/gradle/docker.gradle
@@ -12,9 +12,5 @@ task buildDocker(type: Exec, dependsOn: bootWar) {
             include "*.war*"
         }
     }
-    if (OperatingSystem.current().isWindows()) {
-        commandLine 'cmd', '/c', 'docker', 'image', 'build', '-f', 'build/docker/Dockerfile', '-t', 'managementportal', 'build/docker/'
-    } else {
-        commandLine 'docker', 'image', 'build', '-f', 'build/docker/Dockerfile', '-t', 'managementportal', 'build/docker/'
-    }
+    commandLine 'docker', 'image', 'build', '-f', 'build/docker/Dockerfile', '-t', 'managementportal', 'build/docker/'
 }
diff --git a/gradle/mapstruct.gradle b/gradle/mapstruct.gradle
@@ -1,5 +1,5 @@
 
 dependencies {
     implementation group: 'org.mapstruct', name: 'mapstruct', version: mapstruct_version
-    annotationProcessor group: 'org.mapstruct', name: 'mapstruct-processor', version: mapstruct_version
+    kapt group: 'org.mapstruct', name: 'mapstruct-processor', version: mapstruct_version
 }
diff --git a/gradle/profile_dev.gradle b/gradle/profile_dev.gradle
@@ -12,6 +12,10 @@ if (project.hasProperty('no-liquibase')) {
     profiles += ',no-liquibase'
 }
 
+if (project.hasProperty('e2e-prod-test')) {
+    profiles += ',e2e-prod-test'
+}
+
 bootRun {
     args = []
     systemProperty "spring.profiles.active", profiles
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		* @nivemaham @blootsvoets
		* @nivemaham @blootsvoets @bdegraaf1234 @peyman-mohtashami