Merge pull request #46 from RADAR-base/release-0.6.1

Release 0.6.1

.github/workflows/main.yml

@@ -24,14 +24,16 @@ jobs:
                   java-version: 11
 
             - name: Cache
-              uses: actions/cache@v2.0.0
+              uses: actions/cache@v2
               with:
                   # Cache gradle directories
                   path: |
                       ~/.gradle/caches
                       ~/.gradle/wrapper
                   # Key for restoring and saving the cache
-                  key: ${{ runner.os }}-gradle
+                  key: ${{ runner.os }}-gradle-${{ hashFiles("**/*.gradle.kts", "gradle.properties" }}
+                  restore-keys: |
+                    ${{ runner.os }}-gradle-
 
             # Compile the code
             - name: Compile code

.github/workflows/publish_snapshots.yml

@@ -19,21 +19,23 @@ jobs:
 
       - name: Has SNAPSHOT version
         id: is-snapshot
-        run: grep "version =\\? \\?'.*-SNAPSHOT'" build.gradle
+        run: grep 'version = ".*-SNAPSHOT"' build.gradle.kts
 
       - uses: actions/setup-java@v1
         with:
           java-version: 11
 
       - name: Cache
-        uses: actions/cache@v2.0.0
+        uses: actions/cache@v2
         with:
           # Cache gradle directories
           path: |
             ~/.gradle/caches
             ~/.gradle/wrapper
           # Key for restoring and saving the cache
-          key: ${{ runner.os }}-gradle
+          key: ${{ runner.os }}-gradle-${{ hashFiles("**/*.gradle.kts", "gradle.properties" }}
+          restore-keys: |
+            ${{ runner.os }}-gradle-
 
       - name: Install gpg secret key
         run: |

.github/workflows/release.yml

@@ -19,14 +19,16 @@ jobs:
                   java-version: 11
 
             - name: Cache
-              uses: actions/cache@v2.0.0
+              uses: actions/cache@v2
               with:
-                  # A list of files, directories, and wildcard patterns to cache and restore
-                  path: |
-                    ~/.gradle/caches
-                    ~/.gradle/wrapper
-                  # An explicit key for restoring and saving the cache
-                  key: ${{ runner.os }}-gradle
+                # Cache gradle directories
+                path: |
+                  ~/.gradle/caches
+                  ~/.gradle/wrapper
+                # Key for restoring and saving the cache
+                key: ${{ runner.os }}-gradle-${{ hashFiles("**/*.gradle.kts", "gradle.properties" }}
+                restore-keys: |
+                  ${{ runner.os }}-gradle-
 
             # Compile code
             - name: Compile code

README.md

@@ -7,11 +7,11 @@ Library to facilitate using with a Jersey-based REST API. This includes OAuth 2.
 Add this library to your project using the following Gradle configuration:
 ```gradle
 repositories {
-    maven { url "https://dl.bintray.com/radar-base/org.radarbase" }
+    mavenCentral()
 }
 
 dependencies {
-    api("org.radarbase:radar-jersey:0.5.0")
+    api("org.radarbase:radar-jersey:0.6.1")
 }
 ```
 
@@ -110,3 +110,40 @@ fun main(args: Array<String>) {
 This package adds some error handling. Specifically, `org.radarbase.jersey.exception.HttpApplicationException` and its subclasses can be used and extended to serve detailed error messages with customized logging and HTML templating. They can be thrown from any resource.
 
 To serve custom HTML error messages for error codes 400 to 599, add a Mustache template to the classpath in directory `org/radarbase/jersey/exception/mapper/<code>.html`. You can use special cases `4xx.html` and `5xx.html` as a catch-all template. The templates can use variables `status` for the HTTP status code, `code` for short-hand code for the specific error, and an optional `detailedMessage` for a human-readable message.
+
+## Logging
+
+To enable logging with radar-jersey, please set the following configurations. For new projects, the default should be Log4j 2. A configuration file is included in the classpath. First include the following dependencies:
+
+```kotlin
+dependencies {
+    // To enable logging either use log4j
+    val log4j2Version: String by project
+    runtimeOnly("org.apache.logging.log4j:log4j-slf4j-impl:$log4j2Version")
+    runtimeOnly("org.apache.logging.log4j:log4j-api:$log4j2Version")
+    runtimeOnly("org.apache.logging.log4j:log4j-jul:$log4j2Version")
+
+}
+```
+
+Then before any other command is made, set:
+```kotlin
+// Initialize logging with log4j2
+System.setProperty("java.util.logging.manager", "org.apache.logging.log4j.jul.LogManager")
+```
+Execute this statement before ANY logging or logging initialization code has been called, for example in the `init` of a companion object of the main class. Alternatively, set it as a Java system property in the command line, i.e. `-Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager`. 
+
+If Logback is used instead, import the following dependencies to gradle:
+
+```kotlin
+dependencies {
+    runtimeOnly("ch.qos.logback:logback-classic:1.2.3")
+    implementation("org.slf4j:jul-to-slf4j:1.7.30")
+}
+```
+
+Then before any logging code has been called, set:
+```kotlin
+SLF4JBridgeHandler.removeHandlersForRootLogger()
+SLF4JBridgeHandler.install()
+```

build.gradle.kts

@@ -7,16 +7,32 @@ plugins {
     `maven-publish`
     signing
     id("org.jetbrains.dokka") apply false
-    id("com.github.ben-manes.versions") version "0.36.0" apply false
-    id("io.github.gradle-nexus.publish-plugin") version "1.0.0"
+    id("com.github.ben-manes.versions") version "0.38.0"
+    id("io.github.gradle-nexus.publish-plugin") version "1.1.0"
+}
+
+fun isNonStable(version: String): Boolean {
+    val stableKeyword = listOf("RELEASE", "FINAL", "GA").any { version.toUpperCase().contains(it) }
+    val regex = "^[0-9,.v-]+(-r)?$".toRegex()
+    val isStable = stableKeyword || regex.matches(version)
+    return isStable.not()
 }
 
 allprojects {
     group = "org.radarbase"
-    version = "0.6.0"
+    version = "0.6.1"
+
+    afterEvaluate {
+        tasks.withType<DependencyUpdatesTask> {
+            rejectVersionIf {
+                isNonStable(candidate.version)
+            }
+        }
+    }
 }
 
 subprojects {
+    apply(plugin = "kotlin")
     apply(plugin = "maven-publish")
     apply(plugin = "signing")
     apply(plugin = "com.github.ben-manes.versions")
@@ -34,19 +50,6 @@ subprojects {
         set("githubIssueUrl", githubIssueUrl)
     }
 
-    fun isNonStable(version: String): Boolean {
-        val stableKeyword = listOf("RELEASE", "FINAL", "GA").any { version.toUpperCase().contains(it) }
-        val regex = "^[0-9,.v-]+(-r)?$".toRegex()
-        val isStable = stableKeyword || regex.matches(version)
-        return isStable.not()
-    }
-
-    tasks.named<DependencyUpdatesTask>("dependencyUpdates").configure {
-        rejectVersionIf {
-            isNonStable(candidate.version)
-        }
-    }
-
     repositories {
         mavenCentral()
         // Temporary until Dokka is fully published on maven central.
@@ -57,6 +60,12 @@ subprojects {
     dependencies {
         val dokkaVersion: String by project
         configurations["dokkaHtmlPlugin"]("org.jetbrains.dokka:kotlin-as-java-plugin:$dokkaVersion")
+
+        val log4j2Version: String by project
+        val testRuntimeOnly by configurations
+        testRuntimeOnly("org.apache.logging.log4j:log4j-slf4j-impl:$log4j2Version")
+        testRuntimeOnly("org.apache.logging.log4j:log4j-api:$log4j2Version")
+        testRuntimeOnly("org.apache.logging.log4j:log4j-jul:$log4j2Version")
     }
 
     val sourcesJar by tasks.registering(Jar::class) {
@@ -89,6 +98,7 @@ subprojects {
                 exceptionFormat = FULL
             }
             useJUnitPlatform()
+            systemProperty("java.util.logging.manager", "org.apache.logging.log4j.jul.LogManager")
         }
 
         tasks.withType<Tar> {
@@ -191,5 +201,5 @@ nexusPublishing {
 }
 
 tasks.wrapper {
-    gradleVersion = "7.0"
+    gradleVersion = "7.0.2"
 }

gradle.properties

@@ -3,28 +3,29 @@ org.gradle.jvmargs=-Xmx2000m
 org.gradle.vfs.watch=true
 kotlin.code.style=official
 
-kotlinVersion=1.4.32
-dokkaVersion=1.4.30
+kotlinVersion=1.5.0
+dokkaVersion=1.4.32
 
-jerseyVersion=3.0.1
+jerseyVersion=3.0.2
 grizzlyVersion=3.0.0
 okhttpVersion=4.9.1
-junitVersion=5.7.1
+junitVersion=5.7.2
 
 hk2Version=2.6.1
-managementPortalVersion=0.7.0
-javaJwtVersion=3.12.0
+managementPortalVersion=0.7.1
+javaJwtVersion=3.16.0
 jakartaWsRsVersion=3.0.0
 jakartaAnnotationVersion=2.0.0
 jacksonVersion=2.12.3
 slf4jVersion=1.7.30
-jakartaXmlBindVersion=3.0.0
-jakartaJaxbCoreVersion=3.0.0
-jakartaJaxbRuntimeVersion=3.0.0
+log4j2Version=2.14.1
+jakartaXmlBindVersion=3.0.1
+jakartaJaxbCoreVersion=3.0.1
+jakartaJaxbRuntimeVersion=3.0.1
 jakartaActivation=2.0.1
-swaggerVersion=2.1.7
+swaggerVersion=2.1.9
 
-hibernateVersion=5.4.30.Final
-liquibaseVersion=4.3.3
-postgresVersion=42.2.19
+hibernateVersion=5.4.31.Final
+liquibaseVersion=4.3.5
+postgresVersion=42.2.20
 h2Version=1.4.200

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.0-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.0.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

radar-jersey-hibernate/build.gradle.kts

@@ -36,6 +36,4 @@ dependencies {
     testImplementation("org.hamcrest:hamcrest-all:1.3")
     val okhttpVersion: String by project
     testImplementation("com.squareup.okhttp3:okhttp:$okhttpVersion")
-
-    testRuntimeOnly("ch.qos.logback:logback-classic:1.2.3")
 }

radar-jersey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/DatabaseInitialization.kt

@@ -20,20 +20,20 @@ import jakarta.ws.rs.ext.Provider
 
 @Provider
 class DatabaseInitialization(
-        @Context private val entityManagerFactory: jakarta.inject.Provider<EntityManagerFactory>,
-        @Context private val dbConfig: DatabaseConfig,
+    @Context private val entityManagerFactory: jakarta.inject.Provider<EntityManagerFactory>,
+    @Context private val dbConfig: DatabaseConfig,
 ) : ApplicationEventListener {
+
     override fun onEvent(event: ApplicationEvent) {
-        logger.info("Application state: {}", event.type)
         if (event.type != ApplicationEvent.Type.INITIALIZATION_APP_FINISHED) return
         try {
             entityManagerFactory.get().useEntityManager {
-                    // make first connection
-                    it.connection().use { connection ->
-                        if (dbConfig.liquibase.enable) {
-                            initializeLiquibase(connection)
-                        }
+                // make first connection
+                it.connection().use { connection ->
+                    if (dbConfig.liquibase.enable) {
+                        initializeLiquibase(connection)
                     }
+                }
             }
         } catch (ex: Throwable) {
             throw IllegalStateException("Cannot initialize database.", ex)
@@ -43,11 +43,13 @@ class DatabaseInitialization(
     private fun initializeLiquibase(connection: Connection) {
         logger.info("Initializing Liquibase")
         val database = DatabaseFactory.getInstance()
-                .findCorrectDatabaseImplementation(
-                        JdbcConnection(connection))
-        Liquibase(dbConfig.liquibase.changelogs, ClassLoaderResourceAccessor(), database).use {
-            it.update(null as Contexts?)
-        }
+            .findCorrectDatabaseImplementation(JdbcConnection(connection))
+
+        Liquibase(
+            dbConfig.liquibase.changelogs,
+            ClassLoaderResourceAccessor(),
+            database,
+        ).use { it.update(null as Contexts?) }
     }
 
     override fun onRequest(requestEvent: RequestEvent?): RequestEventListener? = null

radar-jersey-hibernate/src/test/kotlin/org/radarbase/jersey/hibernate/HibernateTest.kt

@@ -79,7 +79,6 @@ internal class HibernateTest {
                     override fun writeTo(sink: BufferedSink) {
                         sink.writeUtf8("{\"name\": \"a\"}")
                     }
-
                 })
                 .url("http://localhost:9091/projects")
                 .build()).execute().use { response ->

radar-jersey/build.gradle.kts

@@ -68,8 +68,6 @@ dependencies {
     val junitVersion: String by project
     testImplementation("org.junit.jupiter:junit-jupiter:$junitVersion")
     testImplementation("org.hamcrest:hamcrest-all:1.3")
-
-    testRuntimeOnly("ch.qos.logback:logback-classic:1.2.3")
 }
 
 tasks.processResources {

radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/Auth.kt

@@ -146,6 +146,7 @@ interface Auth {
             get() = startsWith("logPermission")
                 || startsWith("checkPermission")
                 || startsWith("invoke")
+                || startsWith("internal")
 
         private val Class<*>.isAuthClass: Boolean
             get() = isInstance(Auth::class.java)

radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/filter/AuthenticationFilter.kt

@@ -29,7 +29,7 @@ import jakarta.ws.rs.ext.Provider
 @Priority(Priorities.AUTHENTICATION)
 @Singleton
 class AuthenticationFilter(
-        @Context private val validator: AuthValidator
+    @Context private val validator: AuthValidator,
 ) : ContainerRequestFilter {
 
     override fun filter(requestContext: ContainerRequestContext) {

radar-jersey/src/main/kotlin/org/radarbase/jersey/config/ConfigLoader.kt

@@ -4,7 +4,6 @@ import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory
 import com.fasterxml.jackson.module.kotlin.KotlinModule
 import io.swagger.v3.oas.models.OpenAPI
-import io.swagger.v3.oas.models.info.Info
 import org.glassfish.jersey.internal.inject.AbstractBinder
 import org.glassfish.jersey.server.ResourceConfig
 import org.radarbase.jersey.auth.AuthConfig
@@ -118,6 +117,7 @@ object ConfigLoader {
         val health = HealthResourceEnhancer()
         val httpException = HttpExceptionResourceEnhancer()
         val generalException = GeneralExceptionResourceEnhancer()
+        val utility = UtilityResourceEnhancer()
         fun swagger(openApi: OpenAPI, resourcePackages: Set<String>? = null) = SwaggerResourceEnhancer(openApi, resourcePackages)
     }
 

radar-jersey/src/main/kotlin/org/radarbase/jersey/config/DisabledAuthorizationResourceEnhancer.kt

@@ -21,7 +21,7 @@ import jakarta.inject.Singleton
 class DisabledAuthorizationResourceEnhancer : JerseyResourceEnhancer {
     override fun AbstractBinder.enhance() {
         bind(DisabledAuthValidator::class.java)
-                .to(AuthValidator::class.java)
-                .`in`(Singleton::class.java)
+            .to(AuthValidator::class.java)
+            .`in`(Singleton::class.java)
     }
 }

radar-jersey/src/main/kotlin/org/radarbase/jersey/config/EcdsaResourceEnhancer.kt

@@ -24,7 +24,7 @@ import jakarta.inject.Singleton
 class EcdsaResourceEnhancer : JerseyResourceEnhancer {
     override fun AbstractBinder.enhance() {
         bind(EcdsaJwtTokenValidator::class.java)
-                .to(AuthValidator::class.java)
-                .`in`(Singleton::class.java)
+            .to(AuthValidator::class.java)
+            .`in`(Singleton::class.java)
     }
 }

radar-jersey/src/main/kotlin/org/radarbase/jersey/config/GeneralExceptionResourceEnhancer.kt

@@ -6,6 +6,7 @@ import org.radarbase.jersey.exception.mapper.WebApplicationExceptionMapper
 /** Add WebApplicationException and any exception handling. */
 class GeneralExceptionResourceEnhancer: JerseyResourceEnhancer {
     override val classes: Array<Class<*>> = arrayOf(
-            UnhandledExceptionMapper::class.java,
-            WebApplicationExceptionMapper::class.java)
+        UnhandledExceptionMapper::class.java,
+        WebApplicationExceptionMapper::class.java,
+    )
 }