Merge pull request #59 from RADAR-base/release-0.9.0

Release 0.9.0
RADAR-base · Jul 13, 2022 · 49e6596 · 49e6596
2 parents d114455 + 7cc4370
commit 49e6596
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Showing 52 changed files with 257 additions and 195 deletions.
diff --git a/.github/workflows/scheduled_snyk.yaml b/.github/workflows/scheduled_snyk.yaml
@@ -8,21 +8,25 @@ jobs:
     env:
       REPORT_FILE: test.json
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
       - uses: snyk/actions/setup@master
+        with:
+          snyk-version: v1.931.0
 
-      - uses: actions/setup-java@v2
+      - uses: actions/setup-java@v3
         with:
-          distribution: zulu
+          distribution: temurin
           java-version: 11
 
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
       - name: Run Snyk
         env:
           SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
         run: >
           snyk test
           --configuration-matching='^runtimeClasspath$'
-          --configuration-matching='^compileClasspath$'
           --json-file-output=${{ env.REPORT_FILE }}
           --org=radar-base
           --sub-project=radar-jersey

diff --git a/.github/workflows/snyk.yaml b/.github/workflows/snyk.yaml
@@ -7,12 +7,14 @@ jobs:
   security:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
       - uses: snyk/actions/setup@master
+        with:
+          snyk-version: v1.931.0
 
-      - uses: actions/setup-java@v2
+      - uses: actions/setup-java@v3
         with:
-          distribution: zulu
+          distribution: temurin
           java-version: 11
 
       - name: Setup Gradle
@@ -24,7 +26,6 @@ jobs:
         run: >
           snyk test
           --configuration-matching='^runtimeClasspath$'
-          --configuration-matching='^compileClasspath$'
           --fail-on=upgradable
           --org=radar-base
           --sub-project=radar-jersey

diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ repositories {
 }
 
 dependencies {
-    api("org.radarbase:radar-jersey:0.8.3")
+    api("org.radarbase:radar-jersey:0.9.0")
 }
 ```
 

diff --git a/build.gradle.kts b/build.gradle.kts
@@ -13,7 +13,7 @@ plugins {
 
 allprojects {
     group = "org.radarbase"
-    version = "0.8.3"
+    version = "0.9.0"
 }
 
 subprojects {
@@ -43,12 +43,16 @@ subprojects {
         configurations["dokkaHtmlPlugin"]("org.jetbrains.dokka:kotlin-as-java-plugin:$dokkaVersion")
 
         val jacksonVersion: String by project
-        configurations["dokkaPlugin"](platform("com.fasterxml.jackson:jackson-bom:$jacksonVersion"))
-        configurations["dokkaRuntime"](platform("com.fasterxml.jackson:jackson-bom:$jacksonVersion"))
-
         val jsoupVersion: String by project
-        configurations["dokkaPlugin"]("org.jsoup:jsoup:$jsoupVersion")
-        configurations["dokkaRuntime"]("org.jsoup:jsoup:$jsoupVersion")
+        val kotlinVersion: String by project
+
+        sequenceOf("dokkaPlugin", "dokkaRuntime")
+            .map { configurations[it] }
+            .forEach { conf ->
+                conf(platform("com.fasterxml.jackson:jackson-bom:$jacksonVersion"))
+                conf("org.jsoup:jsoup:$jsoupVersion")
+                conf(platform("org.jetbrains.kotlin:kotlin-bom:$kotlinVersion"))
+            }
 
         val log4j2Version: String by project
         val testRuntimeOnly by configurations
@@ -208,5 +212,5 @@ nexusPublishing {
 }
 
 tasks.wrapper {
-    gradleVersion = "7.4.1"
+    gradleVersion = "7.4.2"
 }
diff --git a/gradle.properties b/gradle.properties
@@ -3,34 +3,36 @@ org.gradle.jvmargs=-Xmx2000m
 org.gradle.vfs.watch=true
 kotlin.code.style=official
 
-kotlinVersion=1.6.10
-dokkaVersion=1.6.10
-jsoupVersion=1.14.3
+kotlinVersion=1.7.10
+dokkaVersion=1.7.0
+jsoupVersion=1.15.2
 
-jerseyVersion=3.0.4
-grizzlyVersion=3.0.1
-okhttpVersion=4.9.3
+jerseyVersion=3.0.5
+grizzlyVersion=4.0.0
+okhttpVersion=4.10.0
 junitVersion=5.8.2
 hamcrestVersion=2.2
 mockitoKotlinVersion=4.0.0
 
-hk2Version=3.0.2
+hk2Version=3.0.3
 managementPortalVersion=0.8.1
-javaJwtVersion=3.19.0
-jakartaWsRsVersion=3.0.0
-jakartaAnnotationVersion=2.0.0
-jacksonVersion=2.13.2.20220324
+javaJwtVersion=4.0.0
+jakartaWsRsVersion=3.1.0
+jakartaAnnotationVersion=2.1.1
+jacksonVersion=2.13.3
 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
+log4j2Version=2.18.0
+jakartaXmlBindVersion=4.0.0
+jakartaJaxbCoreVersion=4.0.0
+jakartaJaxbRuntimeVersion=4.0.0
+jakartaValidationVersion=3.0.2
+hibernateValidatorVersion=7.0.4.Final
+glassfishJakartaElVersion=4.0.2
 jakartaActivation=2.1.0
-swaggerVersion=2.1.13
+swaggerVersion=2.2.1
 mustacheVersion=0.9.10
 
-hibernateVersion=5.6.7.Final
-liquibaseVersion=4.9.0
-postgresVersion=42.3.3
-h2Version=2.1.210
+hibernateVersion=6.1.1.Final
+liquibaseVersion=4.13.0
+postgresVersion=42.4.0
+h2Version=2.1.214
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/radar-jersey-hibernate/build.gradle.kts b/radar-jersey-hibernate/build.gradle.kts
@@ -14,8 +14,12 @@ dependencies {
     api("org.hibernate:hibernate-core:$hibernateVersion")
     runtimeOnly("org.hibernate:hibernate-c3p0:$hibernateVersion")
 
-    val javaxValidationVersion: String by project
-    implementation("javax.validation:validation-api:$javaxValidationVersion")
+    val jakartaValidationVersion: String by project
+    runtimeOnly("jakarta.validation:jakarta.validation-api:$jakartaValidationVersion")
+    val hibernateValidatorVersion: String by project
+    runtimeOnly("org.hibernate.validator:hibernate-validator:$hibernateValidatorVersion")
+    val glassfishJakartaElVersion: String by project
+    runtimeOnly("org.glassfish:jakarta.el:$glassfishJakartaElVersion")
 
     val slf4jVersion: String by project
     implementation("org.slf4j:slf4j-api:$slf4jVersion")

diff --git a/...-jersey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/DatabaseHealthMetrics.kt b/...-jersey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/DatabaseHealthMetrics.kt
@@ -1,26 +1,27 @@
 package org.radarbase.jersey.hibernate
 
 import jakarta.inject.Provider
+import jakarta.persistence.EntityManager
 import jakarta.ws.rs.core.Context
-import org.radarbase.jersey.hibernate.RadarEntityManagerFactory.Companion.connection
+import org.radarbase.jersey.hibernate.DatabaseInitialization.Companion.useConnection
 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 javax.persistence.EntityManager
 
 class DatabaseHealthMetrics(
         @Context private val entityManager: Provider<EntityManager>,
         @Context dbConfig: DatabaseConfig
 ): Metric(name = "db") {
     private val cachedStatus = CachedValue(
-            CacheConfig(
-                    refreshDuration = Duration.ofSeconds(dbConfig.healthCheckValiditySeconds),
-                    retryDuration = Duration.ofSeconds(dbConfig.healthCheckValiditySeconds),
-            ),
-            ::testConnection)
+        CacheConfig(
+            refreshDuration = Duration.ofSeconds(dbConfig.healthCheckValiditySeconds),
+            retryDuration = Duration.ofSeconds(dbConfig.healthCheckValiditySeconds),
+        ),
+        ::testConnection,
+    )
 
     override val status: HealthService.Status
         get() = cachedStatus.get { it == HealthService.Status.UP }
@@ -29,7 +30,7 @@ class DatabaseHealthMetrics(
         get() = mapOf("status" to status)
 
     private fun testConnection(): HealthService.Status = try {
-        entityManager.get().connection().close()
+        entityManager.get().useConnection { connection -> connection.close() }
         HealthService.Status.UP
     } catch (ex: Throwable) {
         HealthService.Status.DOWN

diff --git a/...jersey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/DatabaseInitialization.kt b/...jersey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/DatabaseInitialization.kt
@@ -1,5 +1,9 @@
 package org.radarbase.jersey.hibernate
 
+import jakarta.persistence.EntityManager
+import jakarta.persistence.EntityManagerFactory
+import jakarta.ws.rs.core.Context
+import jakarta.ws.rs.ext.Provider
 import liquibase.Contexts
 import liquibase.Liquibase
 import liquibase.database.DatabaseFactory
@@ -9,14 +13,12 @@ import org.glassfish.jersey.server.monitoring.ApplicationEvent
 import org.glassfish.jersey.server.monitoring.ApplicationEventListener
 import org.glassfish.jersey.server.monitoring.RequestEvent
 import org.glassfish.jersey.server.monitoring.RequestEventListener
-import org.radarbase.jersey.hibernate.RadarEntityManagerFactory.Companion.connection
+import org.hibernate.HibernateException
+import org.hibernate.Session
 import org.radarbase.jersey.hibernate.RadarEntityManagerFactoryFactory.Companion.useEntityManager
 import org.radarbase.jersey.hibernate.config.DatabaseConfig
 import org.slf4j.LoggerFactory
 import java.sql.Connection
-import javax.persistence.EntityManagerFactory
-import jakarta.ws.rs.core.Context
-import jakarta.ws.rs.ext.Provider
 
 @Provider
 class DatabaseInitialization(
@@ -27,9 +29,8 @@ class DatabaseInitialization(
     override fun onEvent(event: ApplicationEvent) {
         if (event.type != ApplicationEvent.Type.INITIALIZATION_APP_FINISHED) return
         try {
-            entityManagerFactory.get().useEntityManager {
-                // make first connection
-                it.connection().use { connection ->
+            entityManagerFactory.get().useEntityManager { em ->
+                em.useConnection { connection ->
                     if (dbConfig.liquibase.enable) {
                         initializeLiquibase(connection)
                     }
@@ -56,5 +57,11 @@ class DatabaseInitialization(
 
     companion object {
         private val logger = LoggerFactory.getLogger(DatabaseInitialization::class.java)
+
+        @Throws(HibernateException::class)
+        fun EntityManager.useConnection(work: (Connection) -> Unit) {
+            check(this is Session) { "Cannot use connection of EntityManager that is not a Hibernate Session" }
+            doWork(work)
+        }
     }
 }
diff --git a/radar-jersey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/HibernateRepository.kt b/radar-jersey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/HibernateRepository.kt
@@ -1,11 +1,11 @@
 package org.radarbase.jersey.hibernate
 
+import jakarta.inject.Provider
+import jakarta.persistence.EntityManager
+import jakarta.persistence.EntityTransaction
 import org.radarbase.jersey.exception.HttpInternalServerException
 import org.radarbase.jersey.hibernate.config.CloseableTransaction
 import org.slf4j.LoggerFactory
-import jakarta.inject.Provider
-import javax.persistence.EntityManager
-import javax.persistence.EntityTransaction
 
 open class HibernateRepository(
         private val entityManagerProvider: Provider<EntityManager>

diff --git a/...sey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/RadarEntityManagerFactory.kt b/...sey-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/RadarEntityManagerFactory.kt
@@ -1,12 +1,10 @@
 package org.radarbase.jersey.hibernate
 
+import jakarta.persistence.EntityManager
+import jakarta.persistence.EntityManagerFactory
 import jakarta.ws.rs.core.Context
 import org.glassfish.jersey.internal.inject.DisposableSupplier
-import org.hibernate.internal.SessionImpl
 import org.slf4j.LoggerFactory
-import java.sql.Connection
-import javax.persistence.EntityManager
-import javax.persistence.EntityManagerFactory
 
 class RadarEntityManagerFactory(
         @Context private val emf: EntityManagerFactory
@@ -26,7 +24,5 @@ class RadarEntityManagerFactory(
 
     companion object {
         private val logger = LoggerFactory.getLogger(RadarEntityManagerFactory::class.java)
-
-        fun EntityManager.connection(): Connection = unwrap(SessionImpl::class.java).connection()
     }
 }
diff --git a/...ernate/src/main/kotlin/org/radarbase/jersey/hibernate/RadarEntityManagerFactoryFactory.kt b/...ernate/src/main/kotlin/org/radarbase/jersey/hibernate/RadarEntityManagerFactoryFactory.kt
@@ -1,14 +1,14 @@
 package org.radarbase.jersey.hibernate
 
+import jakarta.persistence.EntityManager
+import jakarta.persistence.EntityManagerFactory
+import jakarta.ws.rs.core.Context
 import org.glassfish.jersey.internal.inject.DisposableSupplier
 import org.hibernate.jpa.HibernatePersistenceProvider
 import org.radarbase.jersey.hibernate.config.DatabaseConfig
 import org.radarbase.jersey.hibernate.config.RadarPersistenceInfo
 import org.slf4j.LoggerFactory
 import java.util.*
-import javax.persistence.EntityManager
-import javax.persistence.EntityManagerFactory
-import jakarta.ws.rs.core.Context
 
 /**
  * Creates EntityManagerFactory using Hibernate. When an [EntityManagerFactory] is created,

diff --git a/...y-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/config/CloseableTransaction.kt b/...y-hibernate/src/main/kotlin/org/radarbase/jersey/hibernate/config/CloseableTransaction.kt
@@ -1,7 +1,7 @@
 package org.radarbase.jersey.hibernate.config
 
+import jakarta.persistence.EntityTransaction
 import java.io.Closeable
-import javax.persistence.EntityTransaction
 
 interface CloseableTransaction : Closeable {
     val transaction: EntityTransaction

diff --git a/...ernate/src/main/kotlin/org/radarbase/jersey/hibernate/config/HibernateResourceEnhancer.kt b/...ernate/src/main/kotlin/org/radarbase/jersey/hibernate/config/HibernateResourceEnhancer.kt
@@ -1,5 +1,8 @@
 package org.radarbase.jersey.hibernate.config
 
+import jakarta.inject.Singleton
+import jakarta.persistence.EntityManager
+import jakarta.persistence.EntityManagerFactory
 import org.glassfish.jersey.internal.inject.AbstractBinder
 import org.glassfish.jersey.process.internal.RequestScoped
 import org.radarbase.jersey.enhancer.JerseyResourceEnhancer
@@ -8,9 +11,6 @@ import org.radarbase.jersey.hibernate.DatabaseInitialization
 import org.radarbase.jersey.hibernate.RadarEntityManagerFactory
 import org.radarbase.jersey.hibernate.RadarEntityManagerFactoryFactory
 import org.radarbase.jersey.service.HealthService
-import jakarta.inject.Singleton
-import javax.persistence.EntityManager
-import javax.persistence.EntityManagerFactory
 
 class HibernateResourceEnhancer(
         private val databaseConfig: DatabaseConfig
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,7 +11,7 @@ repositories { @@
     }
     dependencies {
-        api("org.radarbase:radar-jersey:0.8.3")
+        api("org.radarbase:radar-jersey:0.9.0")
     }
     ```
@@ Expand Down @@