Specify events when pulling fields from REDCap

.github/workflows/main.yml

@@ -0,0 +1,36 @@
+# Continuous integration, including test and integration test
+name: CI
+
+# Run in main and dev branches and in all pull requests to those branches
+on:
+  push:
+    branches: [ master, dev ]
+  pull_request:
+    branches: [ master, dev ]
+
+jobs:
+  # Build and test the code
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 17
+
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
+      # Compile the code
+      - name: Compile code
+        run: ./gradlew assemble
+
+      # Gradle check
+      - name: Check
+        run: ./gradlew check

Dockerfile

@@ -10,7 +10,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-FROM openjdk:14 as builder
+FROM openjdk:17 as builder
 
 RUN mkdir /code
 WORKDIR /code

build.gradle

@@ -5,176 +5,167 @@ plugins {
     id 'checkstyle'
     id 'jacoco'
     id 'application'
-    id 'org.jetbrains.kotlin.jvm' version '1.3.72'
+    id 'org.jetbrains.kotlin.jvm' version '1.5.21'
 }
 
-group 'org.radarbase'
-version '1.0.2-SNAPSHOT'
+group = 'org.radarbase'
+version = '1.0.5-SNAPSHOT'
 
-mainClassName = 'org.radarbase.redcap.webapp.GrizzlyServer'
-
-targetCompatibility = '11'
-sourceCompatibility = '11'
+application {
+    mainClass = 'org.radarbase.redcap.webapp.GrizzlyServer'
+}
 
-configurations {
-    codacy
-    provided
-    compile.extendsFrom provided
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(11)
+    }
 }
 
 repositories {
     mavenCentral()
 }
 
 sourceSets {
-    main.kotlin.srcDirs += 'src/main/kotlin'
-    main.java.srcDirs += 'src/main/kotlin'
-
-    test.kotlin.srcDirs += 'src/test/kotlin'
-    test.java.srcDirs += 'src/test/kotlin'
-
+    main {
+        java {
+            srcDirs += 'src/main/kotlin'
+        }
+        kotlin {
+            srcDirs += 'src/main/kotlin'
+        }
+    }
+    test {
+        java {
+            srcDirs += 'src/test/kotlin'
+        }
+        kotlin {
+            srcDirs += 'src/test/kotlin'
+        }
+    }
     integrationTest {
         java {
-            compileClasspath += main.output + test.output + test.compileClasspath
-            runtimeClasspath += main.output + test.output + test.compileClasspath + test.runtimeClasspath + main.runtimeClasspath
-            srcDir file('src/integration-test/kotlin')
+            srcDirs += 'src/integration-test/kotlin'
+            compileClasspath += sourceSets.main.output + sourceSets.test.output + configurations.testRuntimeClasspath
+            runtimeClasspath += output + compileClasspath + configurations.testRuntimeClasspath
+        }
+        resources {
+            srcDirs += 'src/integration-test/resources'
         }
-        resources.srcDir file('src/integration-test/resources')
     }
 }
 
+configurations {
+    codacy
+    provided
+    compileClasspath {
+        extendsFrom(provided)
+    }
+}
 
-ext.apacheCommonsIoVersion = '2.5'
-ext.apacheCommonsLangVersion = '3.6'
-ext.jerseyVersion = '2.30.1'
-ext.jerseymediaVersion = '2.30.1'
-ext.junitVersion = '4.12'
-ext.logbackVersion = '1.2.3'
-ext.okhttp3Version = '3.8.1'
-ext.radarOauthClientVersion = '0.8.0'
-ext.grizzlyVersion = '2.4.4'
-ext.jacksonVersion = '2.11.2'
+ext {
+    apacheCommonsIoVersion = '2.5'
+    apacheCommonsLangVersion = '3.6'
+    jerseyVersion = '2.30.1'
+    jerseymediaVersion = '2.30.1'
+    junitVersion = '4.12'
+    logbackVersion = '1.2.3'
+    okhttp3Version = '4.9.3'
+    radarOauthClientVersion = '0.8.0'
+    grizzlyVersion = '2.4.4'
+    jacksonVersion = '2.11.2'
+}
 
 dependencies {
-    implementation group: 'ch.qos.logback', name: 'logback-classic', version: logbackVersion
-    runtimeOnly group: 'org.glassfish.jersey.media', name: 'jersey-media-json-jackson', version: jerseymediaVersion
-
-    implementation group: 'org.glassfish.jersey.containers', name: 'jersey-container-servlet', version: jerseyVersion
-    implementation group: 'org.glassfish.jersey.inject', name: 'jersey-hk2', version: jerseyVersion
-
-    implementation group: 'org.glassfish.grizzly', name: 'grizzly-http-server', version: grizzlyVersion
-    implementation group: 'org.glassfish.jersey.containers', name: 'jersey-container-grizzly2-http', version: jerseyVersion
-
-    implementation group: 'org.radarbase', name: 'oauth-client-util', version: radarOauthClientVersion
-
-    implementation group: 'commons-io', name: 'commons-io', version: apacheCommonsIoVersion
-    implementation group: 'org.apache.commons', name: 'commons-lang3', version: apacheCommonsLangVersion
-
-    implementation group: 'com.squareup.okhttp3', name: 'okhttp', version: okhttp3Version
-
+    implementation "ch.qos.logback:logback-classic:$logbackVersion"
+    runtimeOnly "org.glassfish.jersey.media:jersey-media-json-jackson:$jerseymediaVersion"
+    implementation "org.glassfish.jersey.containers:jersey-container-servlet:$jerseyVersion"
+    implementation "org.glassfish.jersey.inject:jersey-hk2:$jerseyVersion"
+    implementation "org.glassfish.grizzly:grizzly-http-server:$grizzlyVersion"
+    implementation "org.glassfish.jersey.containers:jersey-container-grizzly2-http:$jerseyVersion"
+    implementation "org.radarbase:oauth-client-util:$radarOauthClientVersion"
+    implementation "commons-io:commons-io:$apacheCommonsIoVersion"
+    implementation "org.apache.commons:commons-lang3:$apacheCommonsLangVersion"
+    implementation "com.squareup.okhttp3:okhttp:$okhttp3Version"
     implementation "org.jetbrains.kotlin:kotlin-stdlib-jdk8"
     implementation "org.jetbrains.kotlin:kotlin-reflect"
-    implementation "com.fasterxml.jackson.module:jackson-module-kotlin:${jacksonVersion}"
-    implementation "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:${jacksonVersion}"
+    implementation "com.fasterxml.jackson.module:jackson-module-kotlin:$jacksonVersion"
+    implementation "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:$jacksonVersion"
     implementation "org.json:json:20170516"
-
-    testImplementation group: 'junit', name: 'junit', version: junitVersion
+    testImplementation "junit:junit:$junitVersion"
     testImplementation "com.nhaarman.mockitokotlin2:mockito-kotlin:2.2.0"
 }
 
-//---------------------------------------------------------------------------//
-// Style checking                                                            //
-//---------------------------------------------------------------------------//
 checkstyle {
-    // codacy version
-    toolVersion '6.16'
-    ignoreFailures false
-
-    // ignore tests
+    toolVersion = '8.46'
+    ignoreFailures = false
     sourceSets = [sourceSets.main, sourceSets.test, sourceSets.integrationTest]
 }
 
 pmd {
-    // pmd version
-    toolVersion = '6.0.0'
+    toolVersion = '6.44.0'
     ignoreFailures = false
-
     sourceSets = [sourceSets.main, sourceSets.test, sourceSets.integrationTest]
-
     consoleOutput = true
-
     ruleSets = []
     ruleSetFiles = files("config/pmd/ruleset.xml")
 }
 
-pmdTest {
+tasks.named('pmdTest') {
     ruleSetFiles = files("config/pmd/test_ruleset.xml")
 }
 
-
-//---------------------------------------------------------------------------//
-// Build system metadata                                                     //
-//---------------------------------------------------------------------------//
 idea {
     module {
         downloadSources = true
     }
 }
 
-gradle.projectsEvaluated {
-    tasks.withType(JavaCompile) {
-        options.compilerArgs << "-Xlint:unchecked" << "-Xlint:deprecation"
-    }
+tasks.withType(JavaCompile) {
+    options.compilerArgs.addAll(['-Xlint:unchecked', '-Xlint:deprecation'])
 }
 
-wrapper {
-    gradleVersion = '6.4'
+tasks.named('wrapper') {
+    gradleVersion = '7.4'
 }
 
 tasks.withType(Tar) {
     compression = Compression.GZIP
-    extension("tar")
+    extension = "tar"
 }
 
-//---------------------------------------------------------------------------//
-// Testing                                                                   //
-//---------------------------------------------------------------------------//
-
 test {
     testLogging {
-        // Show that tests are run in the command-line output
-        events "skipped", "failed"
+        events("skipped", "failed")
     }
 }
 
-task downloadApplicationDependencies {
-    description "Pre-downloads application dependencies"
-    configurations.compileClasspath.files
-    configurations.runtimeClasspath.files
+tasks.register('downloadApplicationDependencies') {
+    description = "Pre-downloads application dependencies"
+    doLast {
+        configurations.compileClasspath.getFiles()
+        configurations.runtimeClasspath.getFiles()
+    }
 }
 
-task integrationTest(type: Test, dependsOn: ['installMP', 'copyConf']) {
+tasks.register('integrationTest', Test) {
     description = "Run integration tests (located in src/integrationTest/...)."
-
+    dependsOn('installMP', 'copyConf')
     testClassesDirs = sourceSets.integrationTest.output.classesDirs
     classpath = sourceSets.integrationTest.runtimeClasspath
-
-    // Don't run specific test classes as they will be run by the Test Suite
-    exclude '**/*IntegratorTest*'
-    exclude '**/*MpClientTest*'
-    exclude '**/*EntryPointTest*'
-    // This is not needed, but I like to see which tests have run
+    exclude("**/*IntegratorTest*", "**/*MpClientTest*", "**/*EntryPointTest*")
     testLogging {
-        events "skipped", "failed", "passed", "STANDARD_OUT", "STANDARD_ERROR"
+        events("skipped", "failed", "passed", "STANDARD_OUT", "STANDARD_ERROR")
     }
 }
 
-integrationTest.finalizedBy 'removeLock'
+tasks.named('integrationTest') {
+    finalizedBy('removeLock')
+}
 
-ext.sudoLinux = System.properties['os.name'].toLowerCase().contains('linux') ? ['sudo'] : []
-ext.lock = 'src/integration-test/.RUNNING_INSTANCE_LOCK'
+def sudoLinux = System.properties['os.name'].toLowerCase().contains('linux') ? ['sudo'] : []
+def lock = 'src/integration-test/.RUNNING_INSTANCE_LOCK'
 
-task installMP(type: Exec) {
+tasks.register('installMP', Exec) {
     doFirst {
         def lockFile = new File(lock)
         if (lockFile.exists()) {
@@ -183,44 +174,33 @@ task installMP(type: Exec) {
             lockFile.createNewFile()
         }
     }
-
-    workingDir 'src/integration-test/'
+    workingDir = file('src/integration-test/')
     standardInput = System.in
-    commandLine sudoLinux + ['docker-compose', 'up', '-d', '--build', '--force-recreate']
-
+    commandLine = sudoLinux + ['docker-compose', 'up', '-d', '--build', '--force-recreate']
     doLast {
-        // wait until the managementportal is ready
-        sleep(60_000)
+        Thread.sleep(60_000)
     }
 }
 
-task removeLock(type: Exec) {
-
-    workingDir 'src/integration-test/'
-    commandLine sudoLinux + ['docker-compose', 'down']
-
+tasks.register('removeLock', Exec) {
+    workingDir = file('src/integration-test/')
+    commandLine = sudoLinux + ['docker-compose', 'down']
     doLast {
         new File(lock).delete()
     }
 }
 
-task copyConf(type: Copy) {
-    from "src/integration-test/resources/radar.yml"
-    into "/usr/local/etc/radar-redcap-int/"
-
+tasks.register('copyConf', Copy) {
+    from = "src/integration-test/resources/radar.yml"
+    into = "/usr/local/etc/radar-redcap-int/"
     filter { String line ->
         line.replace("  base_url: http://managementportal-app:8090/",
-                "  base_url: http://localhost:8090/")
+                     "  base_url: http://localhost:8090/")
     }
 }
 
-compileKotlin {
+tasks.withType(org.jetbrains.kotlin.gradle.tasks.KotlinCompile) {
     kotlinOptions {
         jvmTarget = "11"
     }
 }
-compileTestKotlin {
-    kotlinOptions {
-        jvmTarget = "11"
-    }
-}

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.4-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.4-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/integration-test/kotlin/org/radarbase/redcap/EntryPointTest.kt

@@ -28,7 +28,7 @@ class EntryPointTest {
         Assert.assertNotNull(response)
         // This is because the the app fails to update redcap form as there is no actual redcap instance.
         // So the request times out with an exception
-        Assert.assertEquals(500, response.code().toLong())
+        Assert.assertEquals(500, response.code)
 
         // But we can verify if the corresponding subject creation in MP works fine.
         val subject: Subject? =