Merge pull request #17 from RADAR-base/release-0.3.1

Release 0.3.1

README.md

@@ -11,7 +11,7 @@ repositories {
 }
 
 dependencies {
-    api("org.radarbase:radar-jersey:0.2.4")
+    api("org.radarbase:radar-jersey:0.3.1")
 }
 ```
 
@@ -54,7 +54,8 @@ class MyEnhancerFactory(private val config: MyConfigClass): EnhancerFactory {
             MyResourceEnhancer(),
             // RADAR OAuth2 enhancement
             ConfigLoader.Enhancers.radar(AuthConfig(
-                    managementPortalUrl = "http://...",
+                    managementPortal = MPConfig(
+                        url = "http://..."),
                     jwtResourceName = "res_MyResource")),
             // Use ManagementPortal OAuth implementation
             ConfigLoader.Enhancers.managementPortal,
@@ -83,7 +84,15 @@ class MyEnhancerFactory(private val config: MyConfigClass): EnhancerFactory {
     }
 }
 ```
-Ensure that a class implementing `org.radarbase.jersey.auth.ProjectService` is added to the binder.
+Ensure that a class implementing `org.radarbase.jersey.auth.ProjectService` is added to the binder. This is done automatically if you configure a `MPConfig.clientId` and `MPConfig.clientSecret`. Then the projects will be fetched from ManagementPortal.
+
+The following variables will be fetched from environment variables if set:\
+`MANAGEMENT_PORTAL_CLIENT_ID` sets `AuthConfig.managementPortal.clientId`\
+`MANAGEMENT_PORTAL_CLIENT_SECRET` sets `AuthConfig.managementPortal.clientSecret`\
+`AUTH_KEYSTORE_PASSWORD` sets `AuthConfig.jwtKeystorePassword`\
+`DATABASE_URL` sets `DatabaseConfig.url`\
+`DATABASE_USER` sets `DatabaseConfig.user`\
+`DATABASE_PASSWORD` sets `DatabaseConfig.password`
 
 This factory can then be specified in your main method, by adding it to your `MyConfigClass` definition:
 ```kotlin

build.gradle

@@ -5,13 +5,13 @@ plugins {
 
 allprojects {
     group = 'org.radarbase'
-    version = '0.3.0'
+    version = '0.3.1'
 
     ext {
-        jerseyVersion = "2.31"
+        jerseyVersion = "2.32"
         grizzlyVersion = "2.4.4"
-        okhttpVersion = "4.8.1"
-        junitVersion = "5.6.2"
+        okhttpVersion = "4.9.0"
+        junitVersion = "5.7.0"
     }
 }
 
@@ -24,7 +24,7 @@ ext {
     website = 'http://radar-base.org'
 
     hk2Version = "2.6.1"
-    managementPortalVersion = "0.5.8"
+    managementPortalVersion = "0.6.0"
     jakartaWsRsVersion = "2.1.6"
     jakartaAnnotationVersion = "1.3.5"
     jacksonVersion = "2.11.2"
@@ -105,7 +105,7 @@ test {
 }
 
 wrapper {
-    gradleVersion = "6.6"
+    gradleVersion = "6.6.1"
 }
 
 apply from: "gradle/publishing.gradle"

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.6-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.6.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

radar-jersey-hibernate/src/README.md

@@ -1,6 +1,6 @@
 # radar-jersey-hibernate
 
-Extension module of radar-jersey to use Hibernate in a Jersey project. Default database configuration is for PostgreSQL, but any JDBC driver compatible with Hibernate can be used. The module is activated by adding `HibernateResourceEnhancer` to your `EnhancerFactory` with a given database configuration. When this is done, `Provider<EntityManager>` can be injected via the `Context` annotation.
+Extension module `radar-jersey-hibernate` of radar-jersey to use Hibernate in a Jersey project. Default database configuration is for PostgreSQL, but any JDBC driver compatible with Hibernate can be used. The module is activated by adding `HibernateResourceEnhancer` to your `EnhancerFactory` with a given database configuration. When this is done, `Provider<EntityManager>` can be injected via the `Context` annotation.
 
 To make full use if the module, let any database-using classes extend `HibernateRepository`. Any database operations must be wrapped in a `transact { doSomething() }` or `createTransaction { doSomething() }.use { result -> doSomething result }`. Both closures have EntityManager as `this` object, meaning that `createQuery` and derivatives should be called without referencing an additional `EntityManager`.
 

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

@@ -1,5 +1,7 @@
 package org.radarbase.jersey.hibernate.config
 
+import org.radarbase.jersey.config.ConfigLoader.copyEnv
+
 
 data class DatabaseConfig(
         /** Classes that can be used in Hibernate queries. */
@@ -12,7 +14,12 @@ data class DatabaseConfig(
         val properties: Map<String, String> = emptyMap(),
         val liquibase: LiquibaseConfig = LiquibaseConfig(),
         val healthCheckValiditySeconds: Long = 60
-)
+) {
+    fun withEnv(): DatabaseConfig = this
+            .copyEnv("DATABASE_URL") { copy(url = it) }
+            .copyEnv("DATABASE_USER") { copy(user = it) }
+            .copyEnv("DATABASE_PASSWORD") { copy(password = it) }
+}
 
 data class LiquibaseConfig(
         val enable: Boolean = true,

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

@@ -18,7 +18,7 @@ class HibernateResourceEnhancer(
     override val classes: Array<Class<*>> = arrayOf(DatabaseInitialization::class.java)
 
     override fun AbstractBinder.enhance() {
-        bind(databaseConfig)
+        bind(databaseConfig.withEnv())
                 .to(DatabaseConfig::class.java)
 
         bind(DatabaseHealthMetrics::class.java)

src/main/kotlin/org/radarbase/jersey/auth/AuthConfig.kt

@@ -10,6 +10,8 @@
 package org.radarbase.jersey.auth
 
 import com.fasterxml.jackson.annotation.JsonIgnore
+import org.radarbase.jersey.config.ConfigLoader.copyEnv
+import org.radarbase.jersey.config.ConfigLoader.copyOnChange
 import java.time.Duration
 
 data class AuthConfig(
@@ -29,7 +31,11 @@ data class AuthConfig(
         val jwtKeystoreAlias: String? = null,
         /** Key password for the key alias in the p12 keystore. */
         val jwtKeystorePassword: String? = null,
-        )
+) {
+    fun withEnv(): AuthConfig = this
+            .copyOnChange(managementPortal, { it.withEnv() }) { copy(managementPortal = it) }
+            .copyEnv("AUTH_KEYSTORE_PASSWORD") { copy(jwtKeystorePassword = it) }
+}
 
 data class MPConfig(
         /** URL for the current service to find the ManagementPortal installation. */
@@ -43,10 +49,14 @@ data class MPConfig(
         /** Interval after which the list of subjects in a project should be refreshed (minutes). */
         val syncParticipantsIntervalMin: Long = 5,
 ) {
-        /** Interval after which the list of projects should be refreshed. */
-        @JsonIgnore
-        val syncProjectsInterval: Duration = Duration.ofMinutes(syncProjectsIntervalMin)
-        /** Interval after which the list of subjects in a project should be refreshed. */
-        @JsonIgnore
-        val syncParticipantsInterval: Duration = Duration.ofMinutes(syncParticipantsIntervalMin)
+    /** Interval after which the list of projects should be refreshed. */
+    @JsonIgnore
+    val syncProjectsInterval: Duration = Duration.ofMinutes(syncProjectsIntervalMin)
+    /** Interval after which the list of subjects in a project should be refreshed. */
+    @JsonIgnore
+    val syncParticipantsInterval: Duration = Duration.ofMinutes(syncParticipantsIntervalMin)
+
+    fun withEnv(): MPConfig = this
+            .copyEnv("MANAGEMENT_PORTAL_CLIENT_ID") { copy(clientId = it) }
+            .copyEnv("MANAGEMENT_PORTAL_CLIENT_SECRET") { copy(clientSecret = it) }
 }

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

@@ -114,4 +114,13 @@ object ConfigLoader {
         val httpException = HttpExceptionResourceEnhancer()
         val generalException = GeneralExceptionResourceEnhancer()
     }
+
+    inline fun <T> T.copyEnv(key: String, doCopy: T.(String?) -> T): T = copyOnChange<T, String?>(null, { System.getenv(key) }, doCopy)
+
+    inline fun <T, V> T.copyOnChange(original: V, modification: (V) -> V, doCopy: T.(V) -> T): T {
+        val newValue = modification(original)
+        return if (newValue != original) {
+            doCopy(newValue)
+        } else this
+    }
 }

src/main/kotlin/org/radarbase/jersey/config/ManagementPortalResourceEnhancer.kt

@@ -28,6 +28,7 @@ import javax.inject.Singleton
  */
 class ManagementPortalResourceEnhancer(private val config: AuthConfig) : JerseyResourceEnhancer {
     override fun AbstractBinder.enhance() {
+        val config = config.withEnv()
         bindFactory(TokenValidatorFactory::class.java)
                 .to(TokenValidator::class.java)
                 .`in`(Singleton::class.java)

src/main/kotlin/org/radarbase/jersey/config/RadarJerseyResourceEnhancer.kt

@@ -43,7 +43,7 @@ class RadarJerseyResourceEnhancer(
     }
 
     override fun AbstractBinder.enhance() {
-        bind(config)
+        bind(config.withEnv())
                 .to(AuthConfig::class.java)
 
         bind(OkHttpClient().newBuilder()
@@ -59,7 +59,7 @@ class RadarJerseyResourceEnhancer(
         // Bind factories.
         bindFactory(AuthFactory::class.java)
                 .proxy(true)
-                .proxyForSameScope(false)
+                .proxyForSameScope(true)
                 .to(Auth::class.java)
                 .`in`(RequestScoped::class.java)
     }

src/test/kotlin/org/radarbase/jersey/auth/AuthConfigTest.kt

@@ -0,0 +1,53 @@
+package org.radarbase.jersey.auth
+
+import org.hamcrest.MatcherAssert.assertThat
+import org.hamcrest.Matchers.equalTo
+import org.hamcrest.Matchers.not
+import org.junit.jupiter.api.Test
+import java.util.*
+
+internal class AuthConfigTest {
+    @Test
+    fun testEnv() {
+        val config = AuthConfig(jwtResourceName = "res_test")
+
+        setEnv(mapOf(
+                "AUTH_KEYSTORE_PASSWORD" to "test",
+                "MANAGEMENT_PORTAL_CLIENT_ID" to "clId",
+                "MANAGEMENT_PORTAL_CLIENT_SECRET" to "clSecret",
+        ))
+        val newConfig = config.withEnv()
+        assertThat(newConfig, not(equalTo(config)))
+        assertThat(newConfig, equalTo(
+                config.copy(
+                        managementPortal = config.managementPortal.copy(
+                                clientId = "clId",
+                                clientSecret = "clSecret",
+                        ),
+                        jwtKeystorePassword = "test",
+                )))
+    }
+
+    @Suppress("UNCHECKED_CAST")
+    @Throws(Exception::class)
+    fun setEnv(newenv: Map<String, String>) {
+        try {
+            val processEnvironmentClass = Class.forName("java.lang.ProcessEnvironment")
+            processEnvironmentClass.putAll(null, "theEnvironment", newenv)
+            processEnvironmentClass.putAll(null, "theCaseInsensitiveEnvironment", newenv)
+        } catch (e: NoSuchFieldException) {
+            Collections::class.java.declaredClasses
+                    .filter { "java.util.Collections\$UnmodifiableMap" == it.name }
+                    .forEach { it.putAll(System.getenv(), "m", newenv) }
+        }
+    }
+
+    @Suppress("UNCHECKED_CAST")
+    private fun Class<*>.putAll(obj: Any?, fieldName: String, map: Map<String, String>) {
+        getDeclaredField(fieldName)
+                .apply { isAccessible = true }
+                .let { it.get(obj) as MutableMap<String, String> }
+                .putAll(map)
+
+    }
+}