WX-728 Add configurable WSM client to Cromwell

centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json

@@ -0,0 +1,3 @@
+{
+  "fileChecksum.inputFile": "https://<storage-account>.blob.core.windows.net/cromwell/user-inputs/inputFile.txt"
+}

centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl

@@ -0,0 +1,20 @@
+task md5 {
+    File inputFile
+    command {
+        echo "`date`: Running checksum on ${inputFile}..."
+        md5sum ${inputFile} > md5sum.txt
+        echo "`date`: Checksum is complete."
+    }
+    output {
+        File result = "md5sum.txt"
+    }
+    runtime {
+        docker: 'ubuntu:18.04'
+        preemptible: true
+    }
+}
+
+workflow fileChecksum {
+    File inputFile
+    call md5 { input: inputFile=inputFile}
+}

filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

@@ -19,6 +19,8 @@ import scala.util.{Failure, Success, Try}
 import com.azure.resourcemanager.storage.models.StorageAccountKey
 import com.typesafe.scalalogging.LazyLogging
 
+import java.util.UUID
+
 case class FileSystemAPI() {
   def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
   def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = FileSystems.newFileSystem(uri, config.asJava)
@@ -82,31 +84,32 @@ case class BlobFileSystemManager(
 sealed trait BlobTokenGenerator {def generateAccessToken: Try[AzureSasCredential]}
 object BlobTokenGenerator {
   def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId]): BlobTokenGenerator = {
-    createBlobTokenGenerator(container, endpoint, None, None, subscription)
+    NativeBlobTokenGenerator(container, endpoint, subscription)
   }
-  def createBlobTokenGenerator(container: BlobContainerName,
-                               endpoint: EndpointURL,
-                               workspaceId: Option[WorkspaceId],
-                               workspaceManagerURL: Option[WorkspaceManagerURL],
-                               subscription: Option[SubscriptionId]
-                              ): BlobTokenGenerator = {
-     (container: BlobContainerName, endpoint: EndpointURL, workspaceId, workspaceManagerURL) match {
-       case (container, endpoint, None, None) =>
-         NativeBlobTokenGenerator(container, endpoint, subscription)
-       case (container, endpoint, Some(workspaceId), Some(workspaceManagerURL)) =>
-         WSMBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerURL)
-       case _ =>
-         throw new Exception("Arguments provided do not match any available BlobTokenGenerator implementation.")
-     }
+  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: WorkspaceId, workspaceManagerClient: WorkspaceManagerApiClientProvider): BlobTokenGenerator = {
+    WSMBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerClient)
   }
-  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL): BlobTokenGenerator = createBlobTokenGenerator(container, endpoint, None)
-  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: Option[WorkspaceId], workspaceManagerURL: Option[WorkspaceManagerURL]): BlobTokenGenerator =
-      createBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerURL, None)
 
 }
 
-case class WSMBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: WorkspaceId, workspaceManagerURL: WorkspaceManagerURL) extends BlobTokenGenerator {
-  def generateAccessToken: Try[AzureSasCredential] = Failure(new NotImplementedError)
+case class WSMBlobTokenGenerator(
+  container: BlobContainerName,
+  endpoint: EndpointURL,
+  workspaceId: WorkspaceId,
+  wsmClient: WorkspaceManagerApiClientProvider) extends BlobTokenGenerator {
+
+  def generateAccessToken: Try[AzureSasCredential] = Try {
+    val token = wsmClient.getControlledAzureResourceApi.createAzureStorageContainerSasToken(
+      UUID.fromString(workspaceId.value),
+      UUID.fromString("00001111-2222-3333-aaaa-bbbbccccdddd"),
+      null,
+      null,
+      null,
+      null
+    ).getToken // TODO `null` items may be required, investigate in WX-696
+
+    new AzureSasCredential(token) // TODO Does `signature` actually mean token? save for WX-696
+  }
 }
 
 case class NativeBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobTokenGenerator {

filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala

@@ -24,9 +24,17 @@ final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Co
   val workspaceId: Option[WorkspaceId] = instanceConfig.as[Option[String]]("workspace-id").map(WorkspaceId)
   val expiryBufferMinutes: Long = instanceConfig.as[Option[Long]]("expiry-buffer-minutes").getOrElse(10)
   val workspaceManagerURL: Option[WorkspaceManagerURL] = singletonConfig.config.as[Option[String]]("workspace-manager-url").map(WorkspaceManagerURL)
+  val b2cToken: Option[String] = instanceConfig.as[Option[String]]("b2cToken")
+
+  val blobTokenGenerator: BlobTokenGenerator = (workspaceManagerURL, b2cToken, workspaceId) match {
+    case (Some(url), Some(token), Some(workspaceId)) =>
+      val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(url, token)
+      // parameterizing client instead of URL to make injecting mock client possible
+      BlobTokenGenerator.createBlobTokenGenerator(container, endpoint, workspaceId, wsmClient)
+    case _ =>
+      BlobTokenGenerator.createBlobTokenGenerator(container, endpoint, subscription)
+  }
 
-  val blobTokenGenerator: BlobTokenGenerator = BlobTokenGenerator.createBlobTokenGenerator(
-    container, endpoint, workspaceId, workspaceManagerURL, subscription)
   val fsm: BlobFileSystemManager = BlobFileSystemManager(container, endpoint, expiryBufferMinutes, blobTokenGenerator)
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {

filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala

@@ -0,0 +1,32 @@
+package cromwell.filesystems.blob
+
+import bio.terra.workspace.api.ControlledAzureResourceApi
+import bio.terra.workspace.client.ApiClient
+
+/**
+  * Represents a way to get various workspace manager clients
+  *
+  * Pared down from `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.WorkspaceManagerApiClientProvider`
+  *
+  * For testing, create an anonymous subclass as in `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.HttpWorkspaceManagerDAOSpec`
+  */
+trait WorkspaceManagerApiClientProvider {
+  def getApiClient: ApiClient
+
+  def getControlledAzureResourceApi: ControlledAzureResourceApi
+
+}
+
+class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL, token: String) extends WorkspaceManagerApiClientProvider {
+  def getApiClient: ApiClient = {
+    val client: ApiClient = new ApiClient()
+    client.setBasePath(baseWorkspaceManagerUrl.value)
+    client.setAccessToken(token)
+
+    client
+  }
+
+  def getControlledAzureResourceApi: ControlledAzureResourceApi =
+    new ControlledAzureResourceApi(getApiClient)
+
+}

filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala

@@ -27,8 +27,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
   it should "parse configs for a functioning factory" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
     val container = BlobContainerName("storageContainer")
-    val workspaceId = WorkspaceId("mockWorkspaceId")
-    val workspaceManagerURL = WorkspaceManagerURL("https://test.ws.org")
+    val workspaceId = WorkspaceId("B0BAFE77-0000-0000-0000-000000000000")
+    val workspaceManagerURL = WorkspaceManagerURL("https://wsm.example.com")
     val instanceConfig = ConfigFactory.parseString(
       s"""
       |container = "$container"

project/Dependencies.scala

@@ -59,7 +59,12 @@ object Dependencies {
   private val hsqldbV = "2.6.1"
   private val http4sV = "0.21.31" // this release is EOL. We need to upgrade further for cats3. https://http4s.org/versions/
   private val jacksonV = "2.13.3"
+  private val jakartaActivationV = "1.2.1"
+  private val jakartaAnnotationV = "1.3.5"
+  private val jakartaInjectV = "2.6.1"
+  private val jakartaXmlBindApiV = "2.3.2"
   private val janinoV = "3.1.7"
+  private val jerseyV = "2.32" // Use a jersey compatible with WSM. See notes in wsmDependencies below.
   private val jsr305V = "3.0.2"
   private val junitV = "4.13.2"
   private val kindProjectorV = "0.13.2"
@@ -172,6 +177,16 @@ object Dependencies {
     "com.google.api-client" % "google-api-client-jackson2" % googleApiClientV
       exclude("com.google.guava", "guava-jdk5"),
     "com.google.cloud" % "google-cloud-resourcemanager" % googleCloudResourceManagerV,
+    /*
+    The google-cloud-java dependencies have similar issues with using an older javax.* vs. jakarta.* as guice.
+    google-cloud-java is still using javax.annotation and guice is sticking with javax.inject:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/google-cloud-java/blob/v0.201.0/google-cloud-jar-parent/pom.xml#L131-L136
+
+     Globally use of jakarta instead of javax until Google does themselves.
+     The javax.annotation exclusion is below in cromwellExcludeDependencies.
+     */
+    "jakarta.annotation" % "jakarta.annotation-api" % jakartaAnnotationV,
   )
 
   val spiDependencies: List[ModuleID] = List(
@@ -197,6 +212,36 @@ object Dependencies {
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
   )
 
+  val wsmDependencies: List[ModuleID] = List(
+    "bio.terra" % "workspace-manager-client" % "0.254.452-SNAPSHOT"
+      exclude("com.sun.activation", "jakarta.activation"),
+    /*
+    1. WSM is looking for the rs-api under javax.*.
+
+    Jersey 3.x switched to jakarta.ws.rs-api 3.x. If one uses jakarta's rs-api, 3.x will automatically evict 2.x.
+
+    However, jakarta's rs-api 2.x provides packages javax.* while 3.x provides jakarta.* instead.
+     - https://javadoc.io/doc/jakarta.ws.rs/jakarta.ws.rs-api/2.1.6/javax/ws/rs/package-summary.html
+     - https://javadoc.io/doc/jakarta.ws.rs/jakarta.ws.rs-api/3.1.0/jakarta.ws.rs/module-summary.html
+
+    TODO: Perhaps coordinate with the WSM team to use the jakarta 3.x rs-api and jakarta.* instead of javax.*.
+
+    2. Use the exact version of jersey that WSM is using.
+
+    Jersey libraries cannot be mixed and matched as the various modules cannot be mixed and matched.
+    For example jersey-client 2.32 is not compatible with jersey-common 2.37.
+
+    If needed one may also explicitly enumerate the list of jersey artifacts and explicitly set the versions similar to
+    catsDepeendencies, akkaHttpDependencies, etc.
+     - https://broadinstitute.jfrog.io/ui/repos/tree/PomView/libs-snapshot-local/bio/terra/workspace-manager-client/0.254.452-SNAPSHOT/workspace-manager-client-0.254.452-20221114.190249-1.pom
+     - https://github.com/eclipse-ee4j/jersey/blob/2.32/core-client/src/main/java/org/glassfish/jersey/client/ClientExecutorProvidersConfigurator.java#L139
+     - https://github.com/eclipse-ee4j/jersey/blob/2.37/core-client/src/main/java/org/glassfish/jersey/client/ClientExecutorProvidersConfigurator.java#L136-L137
+     */
+    "org.glassfish.jersey.inject" % "jersey-hk2" % jerseyV
+      exclude("com.sun.activation", "jakarta.activation"),
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
+  )
+
   val implFtpDependencies = List(
     "commons-net" % "commons-net" % commonNetV,
     "io.github.andrebeat" %% "scala-pool" % scalaPoolV,
@@ -256,7 +301,11 @@ object Dependencies {
   )
 
   private val liquibaseDependencies = List(
+    // The XML bind API replacement below may be removed when this ticket is addressed:
+    // https://github.com/liquibase/liquibase/issues/2991
     "org.liquibase" % "liquibase-core" % liquibaseV
+      exclude("javax.xml.bind", "jaxb-api"),
+    "jakarta.xml.bind" % "jakarta.xml.bind-api" % jakartaXmlBindApiV,
   )
 
   private val akkaDependencies = List(
@@ -323,15 +372,24 @@ object Dependencies {
   private val googleCloudDependencies = List(
     "io.grpc" % "grpc-core" % grpcV,
     "com.google.guava" % "guava" % guavaV,
+    /*
+    The google-cloud-nio has the same problems with an ancient inject as guice:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/java-storage-nio/blob/v0.124.20/google-cloud-nio/pom.xml#L49-L53
+
+     Force use of jakarta instead of javax until Google does themselves.
+     */
     "com.google.cloud" % "google-cloud-nio" % googleCloudNioV
       exclude("com.google.api.grpc", "grpc-google-common-protos")
       exclude("com.google.cloud.datastore", "datastore-v1-protos")
+      exclude("javax.inject", "javax.inject")
       exclude("org.apache.httpcomponents", "httpclient"),
     "org.broadinstitute.dsde.workbench" %% "workbench-google" % workbenchGoogleV
       exclude("com.google.apis", "google-api-services-genomics"),
     "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV,
     "com.google.apis" % "google-api-services-cloudkms" % googleCloudKmsV
-      exclude("com.google.guava", "guava-jdk5")
+      exclude("com.google.guava", "guava-jdk5"),
+    "org.glassfish.hk2.external" % "jakarta.inject" % jakartaInjectV,
   ) ++ googleGenomicsV2Alpha1Dependency ++ googleLifeSciencesV2BetaDependency
 
   private val dbmsDependencies = List(
@@ -407,7 +465,7 @@ object Dependencies {
     List("scalatest", "mysql", "mariadb", "postgresql")
       .map(name => "com.dimafeng" %% s"testcontainers-scala-$name" % testContainersScalaV % Test)
 
-  val blobFileSystemDependencies: List[ModuleID] = azureDependencies
+  val blobFileSystemDependencies: List[ModuleID] = azureDependencies ++ wsmDependencies
 
   val s3FileSystemDependencies: List[ModuleID] = junitDependencies
 
@@ -431,6 +489,8 @@ object Dependencies {
   val languageFactoryDependencies = List(
     "com.softwaremill.sttp" %% "core" % sttpV,
     "com.softwaremill.sttp" %% "async-http-client-backend-cats" % sttpV
+      exclude("com.sun.activation", "javax.activation"),
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   )
 
   val draft2LanguageFactoryDependencies = List(
@@ -452,10 +512,16 @@ object Dependencies {
   - https://www.slf4j.org/legacy.html#jclOverSLF4J
    */
   val owlApiDependencies = List(
+    // This whole section (incl. javax->jakarta issues) is probably going to be removed when CWL support is removed
+    // For now, replace javax usage with jakarta.
     "net.sourceforge.owlapi" % "owlapi-distribution" % owlApiV
+      exclude("javax.inject", "javax.inject")
+      exclude("javax.xml.bind", "jaxb-api")
       exclude("org.apache.httpcomponents", "httpclient-osgi")
       exclude("org.apache.httpcomponents", "httpcore-osgi")
       exclude("org.slf4j", "jcl-over-slf4j"),
+    "org.glassfish.hk2.external" % "jakarta.inject" % jakartaInjectV,
+    "jakarta.xml.bind" % "jakarta.xml.bind-api" % jakartaXmlBindApiV,
     "org.apache.httpcomponents" % "httpclient-cache" % apacheHttpClientV,
     "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV
   )
@@ -480,7 +546,9 @@ object Dependencies {
   val coreDependencies: List[ModuleID] = List(
     "com.google.auth" % "google-auth-library-oauth2-http" % googleOauth2V,
     "com.chuusai" %% "shapeless" % shapelessV,
+    // NOTE: See scalameter comment under engineDependencies
     "com.storm-enroute" %% "scalameter" % scalameterV % Test
+      exclude("com.fasterxml.jackson.module", "jackson-module-scala_2.13")
       exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.github.scopt" %% "scopt" % scoptV,
   ) ++ akkaStreamDependencies ++ configDependencies ++ catsDependencies ++ circeDependencies ++
@@ -507,9 +575,22 @@ object Dependencies {
   val engineDependencies: List[ModuleID] = List(
     "commons-codec" % "commons-codec" % commonsCodecV,
     "commons-io" % "commons-io" % commonsIoV,
+    /*
+    Maybe ScalaMeter should be used, but is anyone?
+
+    For now keep its dependencies from breaking jackson for other libraries. If someone wants to use it they can
+    re-fight with dependency-hell at that point.
+
+    Avoid:
+    "com.fasterxml.jackson.databind.JsonMappingException: Scala module 2.11.3 requires Jackson Databind
+    version >= 2.11.0 and < 2.12.0":
+     - https://scalameter.github.io/home/gettingstarted/0.7/sbt/index.html
+     - https://github.com/FasterXML/jackson-module-scala/blob/jackson-module-scala-2.11.3/src/main/scala/com/fasterxml/jackson/module/scala/JacksonModule.scala#L53-L62
+     */
     "com.storm-enroute" %% "scalameter" % scalameterV
       exclude("com.fasterxml.jackson.core", "jackson-databind")
       exclude("com.fasterxml.jackson.module", "jackson-module-scala")
+      exclude("com.fasterxml.jackson.module", "jackson-module-scala_2.13")
       exclude("org.scala-tools.testing", "test-interface")
       exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.fasterxml.jackson.core" % "jackson-databind" % jacksonV,
@@ -525,11 +606,24 @@ object Dependencies {
   val serverDependencies: List[ModuleID] = slf4jBindingDependencies
 
   val cromiamDependencies: List[ModuleID] = List(
+    /*
+    sttp 1.x was last released in 2019
+    See above comment regarding "cats-effect, fs2, http4s, and sttp" all needing to update together.
+    For now, replace sttp 1.x's com.sun.activation usage with the jakarta version.
+
+    NOTE when upgrading: sttp 3.x no longer requires an async-http-client-backend-future so jakarta.activation can
+    probably be removed from the dependencies:
+     - https://sttp.softwaremill.com/en/v3/backends/future.html#using-async-http-client
+     - https://sttp.softwaremill.com/en/v2/backends/future.html#using-async-http-client
+     - https://sttp.softwaremill.com/en/v1/backends/asynchttpclient.html
+     */
     "com.softwaremill.sttp" %% "core" % sttpV,
-    "com.softwaremill.sttp" %% "async-http-client-backend-future" % sttpV,
+    "com.softwaremill.sttp" %% "async-http-client-backend-future" % sttpV
+      exclude("com.sun.activation", "javax.activation"),
     "com.typesafe.scala-logging" %% "scala-logging" % scalaLoggingV,
     "org.broadinstitute.dsde.workbench" %% "workbench-model" % workbenchModelV,
-    "org.broadinstitute.dsde.workbench" %% "workbench-util" % workbenchUtilV
+    "org.broadinstitute.dsde.workbench" %% "workbench-util" % workbenchUtilV,
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   ) ++ akkaHttpDependencies ++ swaggerUiDependencies ++ slf4jBindingDependencies
 
   val wes2cromwellDependencies: List[ModuleID] = coreDependencies ++ akkaHttpDependencies
@@ -736,5 +830,15 @@ object Dependencies {
   val cromwellExcludeDependencies: List[ExclusionRule] = List(
     // Replaced with jcl-over-slf4j
     ExclusionRule("commons-logging", "commons-logging"),
+    /*
+    The google-cloud-java dependencies have similar issues with using an older javax.* vs. jakarta.* as guice.
+    google-cloud-java is still using javax.annotation and guice is sticking with javax.inject:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/google-cloud-java/blob/v0.201.0/google-cloud-jar-parent/pom.xml#L131-L136
+
+     Globally use of jakarta instead of javax until Google does themselves.
+     The jakarta.annotation inclusion is above in googleApiClientDependencies.
+     */
+    ExclusionRule("javax.annotation", "javax.annotation-api"),
   )
 }

project/Publishing.scala

@@ -150,6 +150,10 @@ object Publishing {
     "Broad Artifactory" at
       "https://broadinstitute.jfrog.io/broadinstitute/libs-release/"
 
+  private val broadArtifactoryResolverSnap: Resolver =
+    "Broad Artifactory Snapshots" at
+      "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/"
+
   // https://stackoverflow.com/questions/9819965/artifactory-snapshot-filename-handling
   private val buildTimestamp = System.currentTimeMillis() / 1000
 
@@ -159,6 +163,7 @@ object Publishing {
 
   val additionalResolvers = List(
     broadArtifactoryResolver,
+    broadArtifactoryResolverSnap,
     Resolver.sonatypeRepo("releases")
   )