Merge pull request #57 from RADAR-base/release-0.8.2

Release 0.8.2

.github/workflows/main.yml

@@ -19,21 +19,13 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v2
         with:
+          distribution: zulu
           java-version: 11
 
-      - name: Cache
-        uses: actions/cache@v2
-        with:
-          # 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-
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
 
       # Compile the code
       - name: Compile code

.github/workflows/publish_snapshots.yml

@@ -21,21 +21,13 @@ jobs:
         id: is-snapshot
         run: grep 'version = ".*-SNAPSHOT"' build.gradle.kts
 
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v2
         with:
+          distribution: zulu
           java-version: 11
 
-      - name: Cache
-        uses: actions/cache@v2
-        with:
-          # 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-
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
 
       - name: Install gpg secret key
         run: |

.github/workflows/release.yml

@@ -14,21 +14,13 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v2
         with:
+          distribution: zulu
           java-version: 11
 
-      - name: Cache
-        uses: actions/cache@v2
-        with:
-          # 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-
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
 
       # Compile code
       - name: Compile code
@@ -50,4 +42,4 @@ jobs:
         env:
           OSSRH_USER: ${{ secrets.OSSRH_USER }}
           OSSRH_PASSWORD: ${{ secrets.OSSRH_PASSWORD }}
-        run: ./gradlew -Psigning.gnupg.keyName=CBEF2CF0 -Psigning.gnupg.executable=gpg -Psigning.gnupg.passphrase=${{ secrets.OSSRH_GPG_SECRET_KEY_PASSWORD }} publish closeAndReleaseSonatypeStagingRepository
+        run: ./gradlew -Psigning.gnupg.keyName=${{ secrets.OSSRH_GPG_SECRET_KEY_ID }} -Psigning.gnupg.executable=gpg -Psigning.gnupg.passphrase=${{ secrets.OSSRH_GPG_SECRET_KEY_PASSWORD }} publish closeAndReleaseSonatypeStagingRepository

.github/workflows/scheduled_snyk.yaml

@@ -9,13 +9,25 @@ jobs:
       REPORT_FILE: test.json
     steps:
       - uses: actions/checkout@master
-      - name: Run Snyk to check for vulnerabilities
-        uses: snyk/actions/gradle-jdk11@master
+      - uses: snyk/actions/setup@master
+
+      - uses: actions/setup-java@v2
+        with:
+          distribution: zulu
+          java-version: 11
+
+      - name: Run Snyk
         env:
           SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
-        with:
-          command: test
-          args: --json-file-output=${{ env.REPORT_FILE }}
+        run: >
+          snyk test
+          --configuration-matching='^runtimeClasspath$'
+          --configuration-matching='^compileClasspath$'
+          --json-file-output=${{ env.REPORT_FILE }}
+          --org=radar-base
+          --sub-project=radar-jersey
+          --sub-project=radar-jersey-hibernate
+
       - name: Report new vulnerabilities
         uses: thehyve/report-vulnerability@master
         with:

.github/workflows/snyk.yaml

@@ -7,10 +7,25 @@ jobs:
   security:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
-    - name: Run Snyk to check for vulnerabilities
-      uses: snyk/actions/gradle-jdk11@master
-      env:
-        SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
-      with:
-        args: --severity-threshold=high
+      - uses: actions/checkout@master
+      - uses: snyk/actions/setup@master
+
+      - uses: actions/setup-java@v2
+        with:
+          distribution: zulu
+          java-version: 11
+
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
+      - name: Run Snyk to check for vulnerabilities
+        env:
+          SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
+        run: >
+          snyk test
+          --configuration-matching='^runtimeClasspath$'
+          --configuration-matching='^compileClasspath$'
+          --fail-on=upgradable
+          --org=radar-base
+          --sub-project=radar-jersey
+          --sub-project=radar-jersey-hibernate

.gitignore

@@ -154,8 +154,5 @@ Desktop.ini
 ######################
 .eslintcache
 
-# output directory
-out/
-
 # don't ignore jars in /libs
 !libs/**/*.jar

.snyk

@@ -6,4 +6,9 @@ ignore:
     - '*':
         reason: No path to create alias
         expires: 2022-02-22T00:00:00.000Z
+  SNYK-JAVA-ORGJETBRAINSKOTLIN-2393744:
+    - '*':
+        reason: Not using Kotlin Files interface
+        expires: 2022-12-13T08:35:54.696Z
+        created: 2022-03-14T08:35:54.706Z
 patch: {}

README.md

@@ -11,7 +11,7 @@ repositories {
 }
 
 dependencies {
-    api("org.radarbase:radar-jersey:0.8.1")
+    api("org.radarbase:radar-jersey:0.8.2")
 }
 ```
 
@@ -52,7 +52,7 @@ class MyEnhancerFactory(private val config: MyConfigClass): EnhancerFactory {
     override fun createEnhancers(): List<JerseyResourceEnhancer> {
         val authConfig = AuthConfig(
             managementPortal = MPConfig(
-                url = "http://...",
+                url = "https://...",
             ),
             jwtResourceName = "res_MyResource",
         )
@@ -114,7 +114,7 @@ fun main(args: Array<String>) {
 
 Errors are handled by adding the `ConfigLoader.Enhancers.httpException` enhancer. This adds error handling for `org.radarbase.jersey.exception.HttpApplicationException` exceptions 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.
+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 shorthand code for the specific error, and an optional `detailedMessage` for a human-readable message.
 
 Any other uncaught exceptions can be handled by adding the `ConfigLoader.Enhancers.generalException`.
 
@@ -143,8 +143,10 @@ 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:1.7.32")
+    val logbackVersion: String by project
+    runtimeOnly("ch.qos.logback:logback-classic:$logbackVersion")
+    val slf4jVersion: String by project
+    implementation("org.slf4j:jul-to-slf4j:$slf4jVersion")
 }
 ```
 

build.gradle.kts

@@ -7,13 +7,13 @@ plugins {
     `maven-publish`
     signing
     id("org.jetbrains.dokka") apply false
-    id("com.github.ben-manes.versions") version "0.41.0"
+    id("com.github.ben-manes.versions") version "0.42.0"
     id("io.github.gradle-nexus.publish-plugin") version "1.1.0"
 }
 
 allprojects {
     group = "org.radarbase"
-    version = "0.8.1"
+    version = "0.8.2"
 }
 
 subprojects {
@@ -46,6 +46,18 @@ subprojects {
         configurations["dokkaPlugin"](platform("com.fasterxml.jackson:jackson-bom:$jacksonVersion"))
         configurations["dokkaRuntime"](platform("com.fasterxml.jackson:jackson-bom:$jacksonVersion"))
 
+        val jacksonKotlinModuleVersion: String by project
+        configurations["dokkaPlugin"]("com.fasterxml.jackson.module:jackson-module-kotlin:$jacksonKotlinModuleVersion") {
+            version {
+                strictly(jacksonKotlinModuleVersion)
+            }
+        }
+        configurations["dokkaRuntime"]("com.fasterxml.jackson.module:jackson-module-kotlin:$jacksonKotlinModuleVersion") {
+            version {
+                strictly(jacksonKotlinModuleVersion)
+            }
+        }
+
         val jsoupVersion: String by project
         configurations["dokkaPlugin"]("org.jsoup:jsoup:$jsoupVersion")
         configurations["dokkaRuntime"]("org.jsoup:jsoup:$jsoupVersion")
@@ -78,8 +90,8 @@ subprojects {
     tasks.withType<KotlinCompile> {
         kotlinOptions {
             jvmTarget = "11"
-            apiVersion = "1.5"
-            languageVersion = "1.5"
+            apiVersion = "1.6"
+            languageVersion = "1.6"
         }
     }
 
@@ -128,7 +140,7 @@ subprojects {
                         licenses {
                             license {
                                 name.set("The Apache Software License, Version 2.0")
-                                url.set("http://www.apache.org/licenses/LICENSE-2.0.txt")
+                                url.set("https://www.apache.org/licenses/LICENSE-2.0.txt")
                                 distribution.set("repo")
                             }
                         }
@@ -152,7 +164,7 @@ subprojects {
                         }
                         organization {
                             name.set("RADAR-base")
-                            url.set("http://radar-base.org")
+                            url.set("https://radar-base.org")
                         }
                         scm {
                             connection.set("scm:git:$githubUrl")
@@ -208,5 +220,5 @@ nexusPublishing {
 }
 
 tasks.wrapper {
-    gradleVersion = "7.3.3"
+    gradleVersion = "7.4.1"
 }

gradle.properties

@@ -7,30 +7,31 @@ kotlinVersion=1.6.10
 dokkaVersion=1.6.10
 jsoupVersion=1.14.3
 
-jerseyVersion=3.0.3
+jerseyVersion=3.0.4
 grizzlyVersion=3.0.1
 okhttpVersion=4.9.3
 junitVersion=5.8.2
 hamcrestVersion=2.2
 mockitoKotlinVersion=4.0.0
 
 hk2Version=3.0.2
-managementPortalVersion=0.8.0
-javaJwtVersion=3.18.2
+managementPortalVersion=0.8.1
+javaJwtVersion=3.18.3
 jakartaWsRsVersion=3.0.0
 jakartaAnnotationVersion=2.0.0
-jacksonVersion=2.12.6
-slf4jVersion=1.7.32
-log4j2Version=2.17.1
+jacksonVersion=2.13.2
+jacksonKotlinModuleVersion=2.13.1
+slf4jVersion=1.7.36
+log4j2Version=2.17.2
 jakartaXmlBindVersion=3.0.1
 jakartaJaxbCoreVersion=3.0.2
 jakartaJaxbRuntimeVersion=3.0.2
 javaxValidationVersion=2.0.1.Final
-jakartaActivation=2.0.1
-swaggerVersion=2.1.12
+jakartaActivation=2.1.0
+swaggerVersion=2.1.13
 mustacheVersion=0.9.10
 
-hibernateVersion=5.6.3.Final
-liquibaseVersion=4.6.2
-postgresVersion=42.3.1
-h2Version=2.0.206
+hibernateVersion=5.6.5.Final
+liquibaseVersion=4.8.0
+postgresVersion=42.3.3
+h2Version=2.1.210

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

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

@@ -1,16 +1,15 @@
 package org.radarbase.jersey.hibernate
 
+import jakarta.inject.Provider
+import jakarta.ws.rs.core.Context
 import org.radarbase.jersey.hibernate.RadarEntityManagerFactory.Companion.connection
 import org.radarbase.jersey.hibernate.config.DatabaseConfig
 import org.radarbase.jersey.service.HealthService
 import org.radarbase.jersey.service.HealthService.Metric
 import org.radarbase.jersey.util.CacheConfig
 import org.radarbase.jersey.util.CachedValue
 import java.time.Duration
-import jakarta.inject.Provider
-import javax.persistence.Cache
 import javax.persistence.EntityManager
-import jakarta.ws.rs.core.Context
 
 class DatabaseHealthMetrics(
         @Context private val entityManager: Provider<EntityManager>,

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

@@ -1,13 +1,12 @@
 package org.radarbase.jersey.hibernate
 
+import jakarta.ws.rs.core.Context
 import org.glassfish.jersey.internal.inject.DisposableSupplier
-import org.hibernate.engine.spi.SharedSessionContractImplementor
 import org.hibernate.internal.SessionImpl
 import org.slf4j.LoggerFactory
-import jakarta.inject.Provider
+import java.sql.Connection
 import javax.persistence.EntityManager
 import javax.persistence.EntityManagerFactory
-import jakarta.ws.rs.core.Context
 
 class RadarEntityManagerFactory(
         @Context private val emf: EntityManagerFactory
@@ -28,6 +27,6 @@ class RadarEntityManagerFactory(
     companion object {
         private val logger = LoggerFactory.getLogger(RadarEntityManagerFactory::class.java)
 
-        fun EntityManager.connection() = unwrap(SessionImpl::class.java).connection()
+        fun EntityManager.connection(): Connection = unwrap(SessionImpl::class.java).connection()
     }
 }

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

@@ -36,7 +36,7 @@ class RadarEntityManagerFactoryFactory(
 
         /**
          * Use an EntityManager for the duration of [method]. No reference of the passed
-         * [EntityManager] should be returned back, either directly or indirectly.
+         * [EntityManager] should be returned, either directly or indirectly.
          */
         @Suppress("unused")
         inline fun <T> EntityManagerFactory.useEntityManager(method: (EntityManager) -> T): T {