Merge pull request #26 from RADAR-base/release-0.6.0

Release 0.6.0
RADAR-base · Apr 14, 2021 · 02aa09c · 02aa09c
2 parents c3aee6e + aaa9df7
commit 02aa09c
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Showing 26 changed files with 110 additions and 97 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -28,10 +28,7 @@ jobs:
               with:
                   # Cache gradle directories
                   path: |
-                      ~/.gradle/caches/jars-3
-                      ~/.gradle/caches/modules-2/files-2.1/
-                      ~/.gradle/caches/modules-2/metadata-2.96/
-                      ~/.gradle/native
+                      ~/.gradle/caches
                       ~/.gradle/wrapper
                   # Key for restoring and saving the cache
                   key: ${{ runner.os }}-gradle

diff --git a/.github/workflows/publish_snapshots.yml b/.github/workflows/publish_snapshots.yml
@@ -17,6 +17,10 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
 
+      - name: Has SNAPSHOT version
+        id: is-snapshot
+        run: grep "version =\\? \\?'.*-SNAPSHOT'" build.gradle
+
       - uses: actions/setup-java@v1
         with:
           java-version: 11
@@ -26,10 +30,7 @@ jobs:
         with:
           # Cache gradle directories
           path: |
-            ~/.gradle/caches/jars-3
-            ~/.gradle/caches/modules-2/files-2.1/
-            ~/.gradle/caches/modules-2/metadata-2.96/
-            ~/.gradle/native
+            ~/.gradle/caches
             ~/.gradle/wrapper
           # Key for restoring and saving the cache
           key: ${{ runner.os }}-gradle

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -23,11 +23,8 @@ jobs:
               with:
                   # A list of files, directories, and wildcard patterns to cache and restore
                   path: |
-                      ~/.gradle/caches/jars-3
-                      ~/.gradle/caches/modules-2/files-2.1/
-                      ~/.gradle/caches/modules-2/metadata-2.96/
-                      ~/.gradle/native
-                      ~/.gradle/wrapper
+                    ~/.gradle/caches
+                    ~/.gradle/wrapper
                   # An explicit key for restoring and saving the cache
                   key: ${{ runner.os }}-gradle
 
@@ -51,4 +48,4 @@ 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
+              run: ./gradlew -Psigning.gnupg.keyName=CBEF2CF0 -Psigning.gnupg.executable=gpg -Psigning.gnupg.passphrase=${{ secrets.OSSRH_GPG_SECRET_KEY_PASSWORD }} publish closeAndReleaseSonatypeStagingRepository
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -1,14 +1,19 @@
+import com.github.benmanes.gradle.versions.updates.DependencyUpdatesTask
 import org.gradle.api.tasks.testing.logging.TestExceptionFormat.FULL
-import org.jetbrains.dokka.gradle.DokkaTask
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
-import com.github.benmanes.gradle.versions.updates.DependencyUpdatesTask
 
 plugins {
     kotlin("jvm") apply false
     `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"
+}
+
+allprojects {
+    group = "org.radarbase"
+    version = "0.6.0"
 }
 
 subprojects {
@@ -18,8 +23,6 @@ subprojects {
     apply(plugin = "org.jetbrains.dokka")
 
     val myproject = this
-    group = "org.radarbase"
-    version = "0.5.0"
 
     val githubRepoName = "RADAR-base/radar-jersey"
     val githubUrl = "https://github.com/$githubRepoName.git"
@@ -46,10 +49,14 @@ subprojects {
 
     repositories {
         mavenCentral()
-        jcenter()
-        maven(url = "https://dl.bintray.com/radar-cns/org.radarcns")
-        maven(url = "https://dl.bintray.com/radar-base/org.radarbase")
-        maven(url = "https://repo.thehyve.nl/content/repositories/snapshots")
+        // Temporary until Dokka is fully published on maven central.
+        // https://github.com/Kotlin/kotlinx.html/issues/81
+        maven(url = "https://maven.pkg.jetbrains.space/public/p/kotlinx-html/maven")
+    }
+
+    dependencies {
+        val dokkaVersion: String by project
+        configurations["dokkaHtmlPlugin"]("org.jetbrains.dokka:kotlin-as-java-plugin:$dokkaVersion")
     }
 
     val sourcesJar by tasks.registering(Jar::class) {
@@ -59,11 +66,6 @@ subprojects {
         dependsOn(classes)
     }
 
-    dependencies {
-        val dokkaVersion: String by project
-        configurations["dokkaHtmlPlugin"]("org.jetbrains.dokka:kotlin-as-java-plugin:$dokkaVersion")
-    }
-
     val dokkaJar by tasks.registering(Jar::class) {
         from("$buildDir/dokka/javadoc")
         archiveClassifier.set("javadoc")
@@ -103,15 +105,10 @@ subprojects {
             }
         }
 
-        tasks.withType<DokkaTask> {
-            logging.level = LogLevel.QUIET
-        }
-
         val assemble by tasks
         assemble.dependsOn(sourcesJar)
         assemble.dependsOn(dokkaJar)
 
-
         publishing {
             publications {
                 create<MavenPublication>("mavenJar") {
@@ -161,27 +158,6 @@ subprojects {
                     }
                 }
             }
-            repositories {
-                fun Project.propertyOrEnv(propertyName: String, envName: String): String? {
-                    return if (hasProperty(propertyName)) {
-                        property(propertyName)?.toString()
-                    } else {
-                        System.getenv(envName)
-                    }
-                }
-
-                maven {
-                    name = "OSSRH"
-                    credentials {
-                        username = propertyOrEnv("ossrh.user", "OSSRH_USER")
-                        password = propertyOrEnv("ossrh.password", "OSSRH_PASSWORD")
-                    }
-
-                    val releasesRepoUrl = uri("https://oss.sonatype.org/service/local/staging/deploy/maven2/")
-                    val snapshotsRepoUrl = uri("https://oss.sonatype.org/content/repositories/snapshots/")
-                    url = if (version.toString().endsWith("SNAPSHOT")) snapshotsRepoUrl else releasesRepoUrl
-                }
-            }
         }
 
         signing {
@@ -197,6 +173,23 @@ subprojects {
     }
 }
 
+fun Project.propertyOrEnv(propertyName: String, envName: String): String? {
+    return if (hasProperty(propertyName)) {
+        property(propertyName)?.toString()
+    } else {
+        System.getenv(envName)
+    }
+}
+
+nexusPublishing {
+    repositories {
+        sonatype {
+            username.set(propertyOrEnv("ossrh.user", "OSSRH_USER"))
+            password.set(propertyOrEnv("ossrh.password", "OSSRH_PASSWORD"))
+        }
+    }
+}
+
 tasks.wrapper {
-    gradleVersion = "6.8.3"
+    gradleVersion = "7.0"
 }
diff --git a/gradle.properties b/gradle.properties
@@ -3,27 +3,28 @@ org.gradle.jvmargs=-Xmx2000m
 org.gradle.vfs.watch=true
 kotlin.code.style=official
 
-kotlinVersion=1.4.30
-dokkaVersion=1.4.20
+kotlinVersion=1.4.32
+dokkaVersion=1.4.30
 
 jerseyVersion=3.0.1
 grizzlyVersion=3.0.0
 okhttpVersion=4.9.1
 junitVersion=5.7.1
 
 hk2Version=2.6.1
-managementPortalVersion=0.6.4
+managementPortalVersion=0.7.0
+javaJwtVersion=3.12.0
 jakartaWsRsVersion=3.0.0
 jakartaAnnotationVersion=2.0.0
-jacksonVersion=2.12.1
+jacksonVersion=2.12.3
 slf4jVersion=1.7.30
 jakartaXmlBindVersion=3.0.0
 jakartaJaxbCoreVersion=3.0.0
 jakartaJaxbRuntimeVersion=3.0.0
-jakartaActivation=2.0.0
+jakartaActivation=2.0.1
 swaggerVersion=2.1.7
 
-hibernateVersion=5.4.28.Final
-liquibaseVersion=4.3.1
+hibernateVersion=5.4.30.Final
+liquibaseVersion=4.3.3
 postgresVersion=42.2.19
 h2Version=1.4.200
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-6.8.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.0-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/radar-jersey/build.gradle.kts b/radar-jersey/build.gradle.kts
@@ -10,9 +10,12 @@ dependencies {
     api(kotlin("stdlib-jdk8", version=kotlinVersion))
 
     val managementPortalVersion: String by project
-    api("org.radarcns:radar-auth:$managementPortalVersion")
+    api("org.radarbase:radar-auth:$managementPortalVersion")
     api("org.radarbase:managementportal-client:$managementPortalVersion")
 
+    val javaJwtVersion: String by project
+    implementation("com.auth0:java-jwt:$javaJwtVersion")
+
     val jakartaWsRsVersion: String by project
     api("jakarta.ws.rs:jakarta.ws.rs-api:$jakartaWsRsVersion")
     val jakartaAnnotationVersion: String by project

diff --git a/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/Auth.kt b/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/Auth.kt
@@ -10,10 +10,10 @@
 package org.radarbase.jersey.auth
 
 import com.fasterxml.jackson.databind.JsonNode
+import org.radarbase.auth.authorization.Permission
+import org.radarbase.auth.token.RadarToken
 import org.radarbase.jersey.exception.HttpBadRequestException
 import org.radarbase.jersey.exception.HttpForbiddenException
-import org.radarcns.auth.authorization.Permission
-import org.radarcns.auth.token.RadarToken
 import org.slf4j.LoggerFactory
 
 interface Auth {
@@ -143,9 +143,14 @@ interface Auth {
             get() = methodName.isAuthMethodName || declaringClass.isAuthClass
 
         private val String.isAuthMethodName: Boolean
-            get() = startsWith("logPermission") || startsWith("checkPermission")
+            get() = startsWith("logPermission")
+                || startsWith("checkPermission")
+                || startsWith("invoke")
 
         private val Class<*>.isAuthClass: Boolean
-            get() = isInstance(Auth::class.java) || isAnonymousClass || isLocalClass
+            get() = isInstance(Auth::class.java)
+                    || isAnonymousClass
+                    || isLocalClass
+                    || simpleName == "ReflectionHelper"
     }
 }
diff --git a/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/AuthValidator.kt b/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/AuthValidator.kt
@@ -9,8 +9,8 @@
 
 package org.radarbase.jersey.auth
 
+import org.radarbase.auth.exception.TokenValidationException
 import org.radarbase.jersey.auth.filter.AuthenticationFilter
-import org.radarcns.auth.exception.TokenValidationException
 import jakarta.ws.rs.container.ContainerRequestContext
 import kotlin.jvm.Throws
 

diff --git a/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/NeedsPermission.kt b/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/NeedsPermission.kt
@@ -9,7 +9,7 @@
 
 package org.radarbase.jersey.auth
 
-import org.radarcns.auth.authorization.Permission
+import org.radarbase.auth.authorization.Permission
 
 /**
  * Indicates that a method needs an authenticated user that has a certain permission.

diff --git a/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/disabled/DisabledAuth.kt b/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/disabled/DisabledAuth.kt
@@ -2,9 +2,9 @@ package org.radarbase.jersey.auth.disabled
 
 import com.fasterxml.jackson.databind.JsonNode
 import com.fasterxml.jackson.databind.node.NullNode
+import org.radarbase.auth.authorization.Permission
+import org.radarbase.auth.token.RadarToken
 import org.radarbase.jersey.auth.Auth
-import org.radarcns.auth.authorization.Permission
-import org.radarcns.auth.token.RadarToken
 import java.util.*
 
 /** Authorization that grants permission to all resources. */

diff --git a/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/filter/AuthenticationFilter.kt b/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/filter/AuthenticationFilter.kt
@@ -9,10 +9,10 @@
 
 package org.radarbase.jersey.auth.filter
 
+import org.radarbase.auth.exception.TokenValidationException
 import org.radarbase.jersey.auth.AuthValidator
 import org.radarbase.jersey.auth.Authenticated
 import org.radarbase.jersey.exception.HttpUnauthorizedException
-import org.radarcns.auth.exception.TokenValidationException
 import jakarta.annotation.Priority
 import jakarta.inject.Singleton
 import jakarta.ws.rs.Priorities

diff --git a/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/filter/PermissionFilter.kt b/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/filter/PermissionFilter.kt
@@ -9,11 +9,11 @@
 
 package org.radarbase.jersey.auth.filter
 
+import org.radarbase.auth.authorization.Permission
 import org.radarbase.jersey.auth.Auth
 import org.radarbase.jersey.auth.NeedsPermission
 import org.radarbase.jersey.exception.HttpForbiddenException
 import org.radarbase.jersey.service.ProjectService
-import org.radarcns.auth.authorization.Permission
 import jakarta.ws.rs.container.ContainerRequestContext
 import jakarta.ws.rs.container.ContainerRequestFilter
 import jakarta.ws.rs.container.ResourceInfo

diff --git a/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/jwt/EcdsaJwtTokenValidator.kt b/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/jwt/EcdsaJwtTokenValidator.kt
@@ -15,10 +15,10 @@ import com.auth0.jwt.algorithms.Algorithm
 import com.auth0.jwt.exceptions.AlgorithmMismatchException
 import com.auth0.jwt.exceptions.JWTVerificationException
 import com.auth0.jwt.exceptions.SignatureVerificationException
+import org.radarbase.auth.exception.ConfigurationException
 import org.radarbase.jersey.auth.Auth
 import org.radarbase.jersey.auth.AuthConfig
 import org.radarbase.jersey.auth.AuthValidator
-import org.radarcns.auth.exception.ConfigurationException
 import org.slf4j.Logger
 import org.slf4j.LoggerFactory
 import java.nio.file.Files

diff --git a/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/jwt/JwtAuth.kt b/radar-jersey/src/main/kotlin/org/radarbase/jersey/auth/jwt/JwtAuth.kt
@@ -12,11 +12,11 @@ package org.radarbase.jersey.auth.jwt
 import com.auth0.jwt.interfaces.DecodedJWT
 import com.fasterxml.jackson.databind.JsonNode
 import com.fasterxml.jackson.databind.node.NullNode
+import org.radarbase.auth.authorization.Permission
+import org.radarbase.auth.authorization.Permission.Entity
+import org.radarbase.auth.token.JwtRadarToken
+import org.radarbase.auth.token.RadarToken
 import org.radarbase.jersey.auth.Auth
-import org.radarcns.auth.authorization.Permission
-import org.radarcns.auth.authorization.Permission.Entity
-import org.radarcns.auth.token.JwtRadarToken
-import org.radarcns.auth.token.RadarToken
 
 /**
  * Parsed JWT for validating authorization of data contents.

diff --git a/...jersey/src/main/kotlin/org/radarbase/jersey/auth/managementportal/ManagementPortalAuth.kt b/...jersey/src/main/kotlin/org/radarbase/jersey/auth/managementportal/ManagementPortalAuth.kt
@@ -11,10 +11,10 @@ package org.radarbase.jersey.auth.managementportal
 
 import com.auth0.jwt.interfaces.DecodedJWT
 import com.fasterxml.jackson.databind.JsonNode
+import org.radarbase.auth.authorization.Permission.MEASUREMENT_CREATE
+import org.radarbase.auth.token.JwtRadarToken
+import org.radarbase.auth.token.RadarToken
 import org.radarbase.jersey.auth.Auth
-import org.radarcns.auth.authorization.Permission.MEASUREMENT_CREATE
-import org.radarcns.auth.token.JwtRadarToken
-import org.radarcns.auth.token.RadarToken
 
 /**
  * Parsed JWT for validating authorization of data contents.

diff --git a/.../main/kotlin/org/radarbase/jersey/auth/managementportal/ManagementPortalTokenValidator.kt b/.../main/kotlin/org/radarbase/jersey/auth/managementportal/ManagementPortalTokenValidator.kt
@@ -10,10 +10,10 @@
 package org.radarbase.jersey.auth.managementportal
 
 import com.auth0.jwt.JWT
+import org.radarbase.auth.authentication.TokenValidator
+import org.radarbase.auth.exception.TokenValidationException
 import org.radarbase.jersey.auth.Auth
 import org.radarbase.jersey.auth.AuthValidator
-import org.radarcns.auth.authentication.TokenValidator
-import org.radarcns.auth.exception.TokenValidationException
 import org.slf4j.LoggerFactory
 import jakarta.ws.rs.container.ContainerRequestContext
 import jakarta.ws.rs.core.Context

diff --git a/...ersey/src/main/kotlin/org/radarbase/jersey/auth/managementportal/TokenValidatorFactory.kt b/...ersey/src/main/kotlin/org/radarbase/jersey/auth/managementportal/TokenValidatorFactory.kt
@@ -9,9 +9,9 @@
 
 package org.radarbase.jersey.auth.managementportal
 
+import org.radarbase.auth.authentication.TokenValidator
+import org.radarbase.auth.config.TokenVerifierPublicKeyConfig
 import org.radarbase.jersey.auth.AuthConfig
-import org.radarcns.auth.authentication.TokenValidator
-import org.radarcns.auth.config.TokenVerifierPublicKeyConfig
 import java.net.URI
 import java.util.function.Supplier
 import jakarta.ws.rs.core.Context