Merge pull request #245 from RADAR-base/release-4.4.0

Release 4.4.0
RADAR-base · Oct 30, 2023 · 6867f5d · 6867f5d
2 parents dae59b2 + 7ed4f5e
commit 6867f5d
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Showing 52 changed files with 999 additions and 653 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -15,12 +15,8 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[*.kt]
-ktlint_standard_no-wildcard-imports=disabled
-
 [*.md]
 trim_trailing_whitespace = false
 
 [*.{json,yaml,yml}]
-indent_style = space
 indent_size = 2
diff --git a/authorizer-app-backend/Dockerfile b/authorizer-app-backend/Dockerfile
@@ -10,15 +10,17 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-FROM --platform=$BUILDPLATFORM gradle:7.6-jdk17 as builder
+FROM --platform=$BUILDPLATFORM gradle:8.3-jdk17 as builder
 
 RUN mkdir /code
 WORKDIR /code
 
 ENV GRADLE_USER_HOME=/code/.gradlecache \
     GRADLE_OPTS="-Djdk.lang.Process.launchMechanism=vfork -Dorg.gradle.vfs.watch=false"
 
+COPY ./buildSrc /code/buildSrc
 COPY ./build.gradle.kts ./settings.gradle.kts ./gradle.properties /code/
+COPY ./buildSrc /code/buildSrc
 COPY authorizer-app-backend/build.gradle.kts  /code/authorizer-app-backend/
 RUN gradle downloadDependencies copyDependencies startScripts
 

diff --git a/authorizer-app-backend/build.gradle.kts b/authorizer-app-backend/build.gradle.kts
@@ -1,86 +1,41 @@
-import org.gradle.api.tasks.testing.logging.TestExceptionFormat.FULL
-import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
-
 plugins {
     application
-    kotlin("jvm")
-    id("org.jetbrains.kotlin.plugin.noarg")
-    id("org.jetbrains.kotlin.plugin.jpa")
-    id("org.jetbrains.kotlin.plugin.allopen")
+    kotlin("plugin.serialization")
+    kotlin("plugin.noarg")
+    kotlin("plugin.jpa")
+    kotlin("plugin.allopen")
 }
 
 application {
     mainClass.set("org.radarbase.authorizer.Main")
-    applicationDefaultJvmArgs = listOf(
-        "-Djava.security.egd=file:/dev/./urandom",
-        "-Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager",
-    )
-}
-
-repositories {
-    maven(url = "https://oss.sonatype.org/content/repositories/snapshots")
 }
 
 dependencies {
     api(kotlin("stdlib-jdk8"))
     implementation(kotlin("reflect"))
 
-    val radarJerseyVersion: String by project
-    implementation("org.radarbase:radar-jersey:$radarJerseyVersion")
-    implementation("org.radarbase:radar-jersey-hibernate:$radarJerseyVersion") {
-        val postgresVersion: String by project
-        runtimeOnly("org.postgresql:postgresql:$postgresVersion")
+    implementation("org.radarbase:radar-jersey:${Versions.radarJersey}")
+    implementation("org.radarbase:radar-jersey-hibernate:${Versions.radarJersey}") {
+        runtimeOnly("org.postgresql:postgresql:${Versions.postgresql}")
     }
+    implementation("org.radarbase:radar-commons-kotlin:${Versions.radarCommons}")
 
-    val slf4jVersion: String by project
-    implementation("org.slf4j:slf4j-api:$slf4jVersion")
-
-    val okhttpVersion: String by project
-    implementation("com.squareup.okhttp3:okhttp:$okhttpVersion")
+    implementation("redis.clients:jedis:${Versions.jedis}")
 
-    val jedisVersion: String by project
-    implementation("redis.clients:jedis:$jedisVersion")
+    implementation(enforcedPlatform("io.ktor:ktor-bom:${Versions.ktor}"))
+    implementation("io.ktor:ktor-client-core")
+    implementation("io.ktor:ktor-client-auth")
+    implementation("io.ktor:ktor-client-cio")
+    implementation("io.ktor:ktor-client-content-negotiation")
+    implementation("io.ktor:ktor-serialization-kotlinx-json")
 
-    val log4j2Version: String by project
-    runtimeOnly("org.apache.logging.log4j:log4j-core:$log4j2Version")
-    runtimeOnly("org.apache.logging.log4j:log4j-slf4j2-impl:$log4j2Version")
-    runtimeOnly("org.apache.logging.log4j:log4j-jul:$log4j2Version")
-
-    val junitVersion: String by project
-    testImplementation("org.junit.jupiter:junit-jupiter:$junitVersion")
-    testImplementation("org.hamcrest:hamcrest-all:1.3")
-
-    val mockitoKotlinVersion: String by project
-    testImplementation("org.mockito.kotlin:mockito-kotlin:$mockitoKotlinVersion")
-
-    val jerseyVersion: String by project
-    testImplementation("org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:$jerseyVersion")
-}
-
-tasks.withType<KotlinCompile> {
-    kotlinOptions {
-        jvmTarget = "17"
-        apiVersion = "1.7"
-        languageVersion = "1.7"
-    }
-}
-
-tasks.withType<JavaCompile> {
-    options.release.set(17)
-}
-
-tasks.withType<Test> {
-    useJUnitPlatform()
-    testLogging {
-        events("passed", "skipped", "failed")
-        showStandardStreams = true
-        exceptionFormat = FULL
-    }
-    systemProperty("java.util.logging.manager", "org.apache.logging.log4j.jul.LogManager")
+    testImplementation("org.hamcrest:hamcrest:${Versions.hamcrest}")
+    testImplementation("org.mockito.kotlin:mockito-kotlin:${Versions.mockitoKotlin}")
+    testImplementation("org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:${Versions.jersey}")
 }
 
 allOpen {
-    annotation("javax.persistence.Entity")
-    annotation("javax.persistence.MappedSuperclass")
-    annotation("javax.persistence.Embeddable")
+    annotation("jakarta.persistence.Entity")
+    annotation("jakarta.persistence.MappedSuperclass")
+    annotation("jakarta.persistence.Embeddable")
 }
diff --git a/authorizer-app-backend/src/main/java/org/radarbase/authorizer/api/ApiDeclarations.kt b/authorizer-app-backend/src/main/java/org/radarbase/authorizer/api/ApiDeclarations.kt
@@ -16,27 +16,48 @@
 
 package org.radarbase.authorizer.api
 
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties
-import com.fasterxml.jackson.annotation.JsonProperty
+import kotlinx.serialization.SerialName
+import kotlinx.serialization.Serializable
 import java.time.Instant
 
-@JsonIgnoreProperties(ignoreUnknown = true)
+@Serializable
 data class RestOauth2AccessToken(
-    @JsonProperty("access_token") val accessToken: String,
-    @JsonProperty("refresh_token") val refreshToken: String? = null,
-    @JsonProperty("expires_in") val expiresIn: Int = 0,
-    @JsonProperty("token_type") val tokenType: String? = null,
-    @JsonProperty("user_id") val externalUserId: String? = null,
+    @SerialName("access_token")
+    val accessToken: String,
+    @SerialName("refresh_token")
+    val refreshToken: String? = null,
+    @SerialName("expires_in")
+    val expiresIn: Int = 0,
+    @SerialName("token_type")
+    val tokenType: String? = null,
+    @SerialName("user_id")
+    val externalUserId: String? = null,
 )
 
+@Serializable
 data class RestOauth1AccessToken(
-    @JsonProperty("oauth_token") val token: String,
-    @JsonProperty("oauth_token_secret") val tokenSecret: String? = null,
-    @JsonProperty("oauth_verifier") val tokenVerifier: String? = null,
+    @SerialName("oauth_token")
+    val token: String,
+    @SerialName("oauth_token_secret")
+    val tokenSecret: String? = null,
+    @SerialName("oauth_verifier")
+    val tokenVerifier: String? = null,
 )
 
+@Serializable
 data class RestOauth1UserId(
-    @JsonProperty("userId") val userId: String,
+    @SerialName("userId")
+    val userId: String,
+)
+
+@Serializable
+data class OuraAuthUserId(
+    val age: Int,
+    val weight: Float,
+    val height: Float,
+    val gender: String,
+    val email: String,
+    @SerialName("user_id") val userId: String,
 )
 
 data class SignRequestParams(

diff --git a/authorizer-app-backend/src/main/java/org/radarbase/authorizer/api/RestSourceUserMapper.kt b/authorizer-app-backend/src/main/java/org/radarbase/authorizer/api/RestSourceUserMapper.kt
@@ -19,11 +19,12 @@ package org.radarbase.authorizer.api
 import jakarta.ws.rs.core.Context
 import org.radarbase.authorizer.doa.entity.RestSourceUser
 import org.radarbase.jersey.service.managementportal.RadarProjectService
+import org.radarbase.kotlin.coroutines.forkJoin
 
 class RestSourceUserMapper(
     @Context private val projectService: RadarProjectService,
 ) {
-    fun fromEntity(user: RestSourceUser): RestSourceUserDTO {
+    suspend fun fromEntity(user: RestSourceUser): RestSourceUserDTO {
         val mpUser = user.projectId?.let { p ->
             user.userId?.let { u -> projectService.subject(p, u) }
         }
@@ -48,8 +49,8 @@ class RestSourceUserMapper(
         )
     }
 
-    fun fromRestSourceUsers(records: List<RestSourceUser>, page: Page?) = RestSourceUsers(
-        users = records.map(::fromEntity),
+    suspend fun fromRestSourceUsers(records: List<RestSourceUser>, page: Page?) = RestSourceUsers(
+        users = records.forkJoin { fromEntity(it) },
         metadata = page,
     )
 }
diff --git a/...izer-app-backend/src/main/java/org/radarbase/authorizer/config/AuthorizerServiceConfig.kt b/...izer-app-backend/src/main/java/org/radarbase/authorizer/config/AuthorizerServiceConfig.kt
@@ -1,7 +1,9 @@
 package org.radarbase.authorizer.config
 
-import okhttp3.HttpUrl
-import okhttp3.HttpUrl.Companion.toHttpUrlOrNull
+import io.ktor.http.URLBuilder
+import io.ktor.http.Url
+import io.ktor.http.appendPathSegments
+import io.ktor.http.takeFrom
 import org.radarbase.authorizer.enhancer.ManagementPortalEnhancerFactory
 import org.radarbase.jersey.enhancer.EnhancerFactory
 import java.net.URI
@@ -18,26 +20,20 @@ data class AuthorizerServiceConfig(
     val tokenExpiryTimeInMinutes: Long = 15,
     val persistentTokenExpiryInMin: Long = 3.days.inWholeMinutes,
 ) {
-    val callbackUrl: HttpUrl by lazy {
+    val callbackUrl: Url by lazy {
         val frontendBaseUrlBuilder = when {
-            frontendBaseUri != null -> frontendBaseUri.toHttpUrlOrNull()?.newBuilder()
-            advertisedBaseUri != null -> {
-                advertisedBaseUri.toHttpUrlOrNull()?.let { advertisedUrl ->
-                    advertisedUrl.newBuilder().apply {
-                        advertisedUrl.pathSegments.asReversed()
-                            .forEachIndexed { idx, segment ->
-                                if (segment.isEmpty() || segment == "backend") {
-                                    removePathSegment(advertisedUrl.pathSize - 1 - idx)
-                                }
-                            }
-                        addPathSegment("authorizer")
-                    }
+            frontendBaseUri != null -> URLBuilder().takeFrom(frontendBaseUri)
+            advertisedBaseUri != null -> URLBuilder().apply {
+                takeFrom(advertisedBaseUri)
+                pathSegments = buildList(pathSegments.size) {
+                    addAll(pathSegments.dropLastWhile { it.isEmpty() || it == "backend" })
+                    add("authorizer")
                 }
             }
-            else -> null
+            else -> throw IllegalStateException("Frontend URL parameter is not a valid HTTP URL.")
         }
-        checkNotNull(frontendBaseUrlBuilder) { "Frontend URL parameter $frontendBaseUri is not a valid HTTP URL." }
-            .addPathSegment("users:new")
+        frontendBaseUrlBuilder
+            .appendPathSegments("users:new")
             .build()
     }
 }
diff --git a/authorizer-app-backend/src/main/java/org/radarbase/authorizer/config/RestSourceClient.kt b/authorizer-app-backend/src/main/java/org/radarbase/authorizer/config/RestSourceClient.kt
@@ -1,7 +1,7 @@
 package org.radarbase.authorizer.config
 
 import org.radarbase.jersey.config.ConfigLoader.copyEnv
-import java.util.*
+import java.util.Locale
 
 data class RestSourceClient(
     val sourceType: String,

diff --git a/authorizer-app-backend/src/main/java/org/radarbase/authorizer/doa/RegistrationRepository.kt b/authorizer-app-backend/src/main/java/org/radarbase/authorizer/doa/RegistrationRepository.kt
@@ -8,21 +8,23 @@ import org.radarbase.authorizer.config.AuthorizerConfig
 import org.radarbase.authorizer.doa.entity.RegistrationState
 import org.radarbase.authorizer.doa.entity.RestSourceUser
 import org.radarbase.authorizer.util.Hmac256Secret
-import org.radarbase.authorizer.util.Hmac256Secret.Companion.encodeToBase64
-import org.radarbase.authorizer.util.Hmac256Secret.Companion.randomize
+import org.radarbase.authorizer.util.encodeToBase64
+import org.radarbase.authorizer.util.randomize
 import org.radarbase.jersey.hibernate.HibernateRepository
+import org.radarbase.jersey.service.AsyncCoroutineService
 import java.time.Instant
 import kotlin.time.Duration.Companion.minutes
 
 class RegistrationRepository(
     @Context private val config: AuthorizerConfig,
     @Context em: Provider<EntityManager>,
-) : HibernateRepository(em) {
+    @Context asyncService: AsyncCoroutineService,
+) : HibernateRepository(em, asyncService) {
 
     private val tokenExpiryTime = config.service.tokenExpiryTimeInMinutes.minutes
     private val persistentTokenExpiryTime = config.service.persistentTokenExpiryInMin.minutes
 
-    fun generate(
+    suspend fun generate(
         user: RestSourceUser,
         secret: Hmac256Secret?,
         persistent: Boolean,
@@ -53,11 +55,11 @@ class RegistrationRepository(
             }
     }
 
-    operator fun get(token: String): RegistrationState? = transact {
+    suspend fun get(token: String): RegistrationState? = transact {
         find(RegistrationState::class.java, token)
     }
 
-    fun cleanUp(): Int = transact {
+    suspend fun cleanUp(): Int = transact {
         val cb = criteriaBuilder
 
         // create delete
@@ -70,15 +72,11 @@ class RegistrationRepository(
         createQuery(deleteQuery).executeUpdate()
     }
 
-    operator fun minusAssign(token: String) = remove(token)
-
-    operator fun minusAssign(registrationState: RegistrationState) = remove(registrationState)
-
-    fun remove(registrationState: RegistrationState): Unit = transact {
+    suspend fun remove(registrationState: RegistrationState): Unit = transact {
         remove(registrationState)
     }
 
-    fun remove(token: String): Unit = transact {
+    suspend fun remove(token: String): Unit = transact {
         val state = find(RegistrationState::class.java, token)
         remove(state)
     }

diff --git a/...orizer-app-backend/src/main/java/org/radarbase/authorizer/doa/RestSourceUserRepository.kt b/...orizer-app-backend/src/main/java/org/radarbase/authorizer/doa/RestSourceUserRepository.kt
@@ -23,20 +23,20 @@ import org.radarbase.authorizer.doa.entity.RestSourceUser
 import java.time.Instant
 
 interface RestSourceUserRepository {
-    fun create(user: RestSourceUserDTO): RestSourceUser
-    fun updateToken(token: RestOauth2AccessToken?, user: RestSourceUser): RestSourceUser
-    fun read(id: Long): RestSourceUser?
-    fun update(userId: Long, user: RestSourceUserDTO): RestSourceUser
-    fun query(
+    suspend fun create(user: RestSourceUserDTO): RestSourceUser
+    suspend fun updateToken(token: RestOauth2AccessToken?, user: RestSourceUser): RestSourceUser
+    suspend fun read(id: Long): RestSourceUser?
+    suspend fun update(userId: Long, user: RestSourceUserDTO): RestSourceUser
+    suspend fun query(
         page: Page,
         projectIds: List<String>,
         sourceType: String? = null,
         search: String?,
         userIds: List<String>,
         isAuthorized: Boolean?,
     ): Pair<List<RestSourceUser>, Page>
-    fun queryAllWithElapsedEndDate(sourceType: String? = null): List<RestSourceUser>
-    fun delete(user: RestSourceUser)
-    fun reset(user: RestSourceUser, startDate: Instant, endDate: Instant?): RestSourceUser
-    fun findByExternalId(externalId: String, sourceType: String): RestSourceUser?
+    suspend fun queryAllWithElapsedEndDate(sourceType: String? = null): List<RestSourceUser>
+    suspend fun delete(user: RestSourceUser)
+    suspend fun reset(user: RestSourceUser, startDate: Instant, endDate: Instant?): RestSourceUser
+    suspend fun findByExternalId(externalId: String, sourceType: String): RestSourceUser?
 }