Merge branch 'develop' into update/commons-io-2.17.0

.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# .git-blame-ignore-revs
+
+# scalafmt mass change
+3487e7a60194a66886572c899a6a93d7355dc376

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @broadinstitute/dsp-core-services

.github/workflows/format.yaml

@@ -0,0 +1,28 @@
+name: Check formatting for modified files with scalafmt
+
+on:
+  pull_request:
+    paths-ignore: ['**.md']
+
+jobs:
+  format:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: 17
+          cache: sbt
+
+      - name: Check formatting for modified files
+        run: |
+          sbt scalafmtCheckAll

.scalafmt.conf

@@ -1,15 +1,17 @@
-version = 2.4.2
+version = 3.8.3
 align = none
 align.openParenCallSite = true
 align.openParenDefnSite = true
 maxColumn = 120
 continuationIndent.defnSite = 2
 assumeStandardLibraryStripMargin = true
-danglingParentheses = true
+danglingParentheses.preset = true
 rewrite.rules = [SortImports, RedundantBraces, RedundantParens, SortModifiers]
-docstrings = JavaDoc
+docstrings.style = keep
 project.excludeFilters = [
   Dependencies.scala,
   Settings.scala,
   build.sbt
 ]
+runner.dialect = scala213
+project.git = true

build.sbt

@@ -6,23 +6,28 @@ version := "0.2"
 
 organization := "org.broadinstitute"
 
-scalaVersion := "2.13.10"
+scalaVersion := "2.13.15"
 
 val akkaV = "2.6.18"
 val akkaHttpV = "10.2.7"
 val slickV = "3.3.3"
-val workbenchGoogleV = "0.28-3ad3700"
-val scalaTestV = "3.2.11"
+
+val scalaTestV = "3.2.19"
+
+val workbenchLibsHash = "9254729"
+val workbenchGoogleV = s"0.32-$workbenchLibsHash"
+val workbenchNotificationsV = s"0.7-$workbenchLibsHash"
+
 
 resolvers ++= Seq(
   "Broad Artifactory Releases" at "https://broadinstitute.jfrog.io/broadinstitute/libs-release/",
   "Broad Artifactory Snapshots" at "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot/")
 
 libraryDependencies ++= Seq(
-  "org.webjars" % "swagger-ui" % "4.1.3",
+  "org.webjars" % "swagger-ui" % "5.17.14",
   "com.typesafe.scala-logging" %% "scala-logging" % "3.9.5",
   "com.typesafe.akka" %% "akka-http-spray-json" % "10.2.9",
-  "com.google.protobuf" % "protobuf-java" % "4.0.0-rc-2",
+  "com.google.protobuf" % "protobuf-java" % "4.29.0-RC1",
   "io.sentry" % "sentry" % "6.9.2",
   "io.sentry" % "sentry-logback" % "6.9.2",
   "org.broadinstitute.dsde.workbench" %%  "workbench-google" % workbenchGoogleV
@@ -32,7 +37,7 @@ libraryDependencies ++= Seq(
     exclude("org.bouncycastle", "bcprov-ext-jdk15on")
     exclude("org.bouncycastle", "bcutil-jdk15on")
     exclude("org.bouncycastle", "bcpkix-jdk15on"),
-  "org.broadinstitute.dsde.workbench" %% "workbench-notifications" % "0.7-9254729"
+  "org.broadinstitute.dsde.workbench" %% "workbench-notifications" % workbenchNotificationsV
     exclude("com.typesafe.akka", "akka-protobuf-v3_2.13")
     exclude("com.google.protobuf", "protobuf-java"),
   "com.typesafe.akka" %% "akka-http" % akkaHttpV,
@@ -46,19 +51,19 @@ libraryDependencies ++= Seq(
   "commons-io" % "commons-io" % "2.17.0",
   "commons-codec" % "commons-codec" % "1.15",
   "mysql" % "mysql-connector-java" % "8.0.28",
-  "org.liquibase" % "liquibase-core" % "4.7.1",
-  "org.hsqldb" % "hsqldb" % "2.6.1",
+  "org.liquibase" % "liquibase-core" % "4.30.0",
+  "org.hsqldb" % "hsqldb" % "2.7.4",
   "com.sendgrid" % "sendgrid-java" % "2.2.2",
-  "ch.qos.logback" % "logback-classic" % "1.4.14",
+  "ch.qos.logback" % "logback-classic" % "1.5.12",
   "org.broadinstitute.dsde.workbench" %% "sam-client" % "0.1-4cde1ff",
   "com.azure" % "azure-identity" % "1.12.2",
-  "com.azure" % "azure-core-management" % "1.15.0",
+  "com.azure" % "azure-core-management" % "1.15.5",
 //---------- Test libraries -------------------//
   "org.broadinstitute.dsde.workbench" %%  "workbench-google" % workbenchGoogleV % Test classifier "tests",
   "com.typesafe.akka" %% "akka-testkit" % akkaV % Test,
   "com.typesafe.akka" %% "akka-http-testkit" % akkaHttpV % Test,
   "org.scalatest" %% "scalatest" % scalaTestV % Test,
-  "org.mockito" %% "mockito-scala-scalatest" % "1.17.12" % Test,
+  "org.mockito" %% "mockito-scala-scalatest" % "1.17.37" % Test,
   "org.yaml" % "snakeyaml" % "1.33" % Test
 )
 

docker/build.sh

@@ -89,7 +89,7 @@ fi
 function make_jar()
 {
 	echo "building thurloe jar..."
-	docker run --rm -v $PWD:/working -v jar-cache:/root/.ivy -v jar-cache:/root/.ivy2 sbtscala/scala-sbt:openjdk-17.0.2_1.7.2_2.13.10 /working/docker/install.sh /working
+	docker run --rm -v $PWD:/working -v jar-cache:/root/.ivy -v jar-cache:/root/.ivy2 sbtscala/scala-sbt:eclipse-temurin-17.0.13_11_1.10.5_2.13.15 /working/docker/install.sh /working
 }
 
 function docker_cmd()

docker/build_jar.sh

@@ -10,7 +10,7 @@ echo "building thurloe jar..."
 
 docker run --rm -v $PWD:/working \
 -v jar-cache:/root/.ivy \
--v jar-cache:/root/.ivy2 sbtscala/scala-sbt:openjdk-17.0.2_1.7.2_2.13.10 /working/docker/install.sh /working
+-v jar-cache:/root/.ivy2 sbtscala/scala-sbt:eclipse-temurin-17.0.13_11_1.10.5_2.13.15 /working/docker/install.sh /working
 
 
 EXIT_CODE=$?

project/build.properties

@@ -1 +1 @@
-sbt.version=1.6.2
+sbt.version=1.10.5

project/plugins.sbt

@@ -1,13 +1,13 @@
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "2.3.0")
 
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.5")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.2.2")
 
-addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.4.6")
+addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.2")
 
 addSbtPlugin(
-  "com.github.cb372" % "sbt-explicit-dependencies" % "0.2.16"
+  "com.github.cb372" % "sbt-explicit-dependencies" % "0.3.1"
 ) // Use `unusedCompileDependencies` to see unused dependencies
 
-addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % "0.9.34")
+addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % "0.13.0")
 
-addDependencyTreePlugin
+addDependencyTreePlugin

src/main/resources/application.conf

@@ -9,6 +9,10 @@ akka.http {
   }
 }
 
+auth {
+  googleClientId = ""
+}
+
 swagger {
   docsPath = "swagger/thurloe.yaml"
   uiVersion = "2.1.1"

src/main/scala/thurloe/Main.scala

@@ -41,10 +41,9 @@ object Main extends App {
   val routes = new ThurloeServiceActor(samDao)
 
   for {
-    binding <- Http().newServerAt("0.0.0.0", 8000).bind(routes.route).recover {
-      case t: Throwable =>
-        system.log.error("FATAL - failure starting http server", t)
-        throw t
+    binding <- Http().newServerAt("0.0.0.0", 8000).bind(routes.route).recover { case t: Throwable =>
+      system.log.error("FATAL - failure starting http server", t)
+      throw t
     }
     _ = system.log.info("Thurloe now available for all your key/value pair and notification needs.")
     _ <- binding.whenTerminated
@@ -56,7 +55,8 @@ object Main extends App {
 
     val pem =
       GoogleCredentialModes.Pem(WorkbenchEmail(gcsConfig.getString("clientEmail")),
-                                new File(gcsConfig.getString("pathToPem")))
+                                new File(gcsConfig.getString("pathToPem"))
+      )
     val pubSubDAO = new HttpGooglePubSubDAO(
       gcsConfig.getString("appName"),
       pem,

src/main/scala/thurloe/crypto/Encryption.scala

@@ -52,10 +52,12 @@ case object Aes256Cbc {
     }
 
   final def decrypt(encryptedBytes: EncryptedBytes, secretKey: SecretKey): Try[Array[Byte]] =
-    validateLength("Secret key", secretKey.key, keySize) validateAnotherLength ("Initialization vector", encryptedBytes.iv, blockSize) map {
-      _ =>
-        val cipher = init(Cipher.DECRYPT_MODE, secretKey.key, encryptedBytes.iv)
-        cipher.doFinal(encryptedBytes.cipherText)
+    validateLength("Secret key", secretKey.key, keySize) validateAnotherLength ("Initialization vector",
+                                                                                encryptedBytes.iv,
+                                                                                blockSize
+    ) map { _ =>
+      val cipher = init(Cipher.DECRYPT_MODE, secretKey.key, encryptedBytes.iv)
+      cipher.doFinal(encryptedBytes.cipherText)
     }
 }
 

src/main/scala/thurloe/dataaccess/HttpSamDAO.scala

@@ -37,9 +37,9 @@ class HttpSamDAO(config: Config, cloudServiceAuthTokenProvider: CloudServiceAuth
   protected def adminApi(samApiClient: ApiClient) = new AdminApi(samApiClient)
 
   override def getUserById(userId: String): List[sam.model.User] =
-    try {
+    try
       adminApi(getApiClient).adminGetUsersByQuery(userId, userId, userId, 5).asScala.toList
-    } catch {
+    catch {
       case e: Exception =>
         logger.warn(s"Sam user not found: $userId", e)
         List.empty

src/main/scala/thurloe/dataaccess/HttpSendGridDAO.scala

@@ -32,7 +32,7 @@ class HttpSendGridDAO(samDao: SamDAO) extends SendGridDAO with LazyLogging {
     }
   }
 
-  //Looks up a KVP, converting empty values or missing KVPs into None
+  // Looks up a KVP, converting empty values or missing KVPs into None
   private def lookupNonEmptyKeyValuePair(userId: String, key: String) =
     dataAccess
       .lookup(samDao, userId, key)
@@ -42,7 +42,7 @@ class HttpSendGridDAO(samDao: SamDAO) extends SendGridDAO with LazyLogging {
       }
       .recover(_ => None)
 
-  //There are two cases that need to be handled when looking up the preferred contact email:
+  // There are two cases that need to be handled when looking up the preferred contact email:
   // 1) If the contactEmail is not present at all, the DB query will throw an exception. So that needs to be handled.
   // 2) If the contactEmail is present but blank, it also needs to be ignored. Thurloe accepts arbitrary key/value pairs
   //    and makes no guarantees about what the data might look like, so a blank value or invalid email is a valid case.
@@ -54,12 +54,13 @@ class HttpSendGridDAO(samDao: SamDAO) extends SendGridDAO with LazyLogging {
   //      how profiles are populated.
   def lookupPreferredEmail(userId: WorkbenchUserId): Future[WorkbenchEmail] =
     lookupNonEmptyKeyValuePair(userId.value, "contactEmail") flatMap {
-      case Some(kvp) => Future.successful(WorkbenchEmail(kvp.keyValuePair.value)) //contactEmail was found and non-empty
+      case Some(kvp) =>
+        Future.successful(WorkbenchEmail(kvp.keyValuePair.value)) // contactEmail was found and non-empty
       case None =>
         logger.info(s"Failed to get stored contactEmail for ${userId.value}. Defaulting to account email for user.")
         lookupNonEmptyKeyValuePair(userId.value, "email") flatMap {
           case Some(kvp) =>
-            Future.successful(WorkbenchEmail(kvp.keyValuePair.value)) //account email was found and non-empty
+            Future.successful(WorkbenchEmail(kvp.keyValuePair.value)) // account email was found and non-empty
           case None => Future.failed(new KeyNotFoundException(userId.value, "email"))
         }
     }

src/main/scala/thurloe/dataaccess/SendGridDAO.scala

@@ -36,7 +36,8 @@ trait SendGridDAO {
                 new NotificationException(StatusCodes.BadRequest,
                                           "No recipient specified",
                                           Seq.empty,
-                                          notification.notificationId)
+                                          notification.notificationId
+                )
               )
             )
         )
@@ -45,12 +46,12 @@ trait SendGridDAO {
         Future.traverse(_)(lookupPreferredEmail).map(replyToEmails => Option(replyToEmails))
       } getOrElse Future.successful(None)
 
-      val emailSubstitutionsFuture = Future.traverse(notification.emailLookupSubstitutions.toList) {
-        case (key, id) => lookupPreferredEmail(id).map(email => key -> email.value)
+      val emailSubstitutionsFuture = Future.traverse(notification.emailLookupSubstitutions.toList) { case (key, id) =>
+        lookupPreferredEmail(id).map(email => key -> email.value)
       }
 
-      val nameSubstitutionsFuture = Future.traverse(notification.nameLookupSubstitution.toList) {
-        case (key, id) => lookupUserName(id).map(name => key -> name)
+      val nameSubstitutionsFuture = Future.traverse(notification.nameLookupSubstitution.toList) { case (key, id) =>
+        lookupUserName(id).map(name => key -> name)
       }
 
       val recipientFirstNameSubstitutionFuture = notification.userId match {
@@ -82,7 +83,8 @@ trait SendGridDAO {
   def createEmail(toAddress: WorkbenchEmail,
                   replyTos: Option[Set[WorkbenchEmail]],
                   notificationId: String,
-                  substitutions: Map[String, String] = Map.empty): SendGrid.Email = {
+                  substitutions: Map[String, String] = Map.empty
+  ): SendGrid.Email = {
     val email = new SendGrid.Email()
 
     email.addTo(toAddress.value)
@@ -115,8 +117,8 @@ trait SendGridDAO {
 case class NotificationException(statusCode: StatusCode,
                                  message: String,
                                  recipients: Seq[String],
-                                 notificationId: String)
-    extends Exception {
+                                 notificationId: String
+) extends Exception {
   override def getMessage =
     s"Error message: [${message}], recipients: [${recipients.mkString(",")}], notificationId: [${notificationId}]"
 }

src/main/scala/thurloe/dataaccess/auth/CloudServiceAuthTokenProvider.scala

@@ -24,7 +24,8 @@ object CloudServiceAuthTokenProvider {
       val gcsConfig = config.getConfig("gcs")
       val pem =
         GoogleCredentialModes.Pem(WorkbenchEmail(gcsConfig.getString("clientEmail")),
-                                  new File(gcsConfig.getString("pathToPem")))
+                                  new File(gcsConfig.getString("pathToPem"))
+        )
 
       new GcpAuthTokenProvider(pem)
     }