Merge branch 'develop' into AN-333-drs-retry

.github/workflows/cromwell_unit_tests.yml

@@ -22,6 +22,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3 # checkout the cromwell repo
+    - uses: sbt/setup-sbt@v1
     - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
       with:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}

.github/workflows/docker_build_test.yml

@@ -25,6 +25,7 @@ jobs:
           repository: broadinstitute/cromwell
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
           path: cromwell
+      - uses: sbt/setup-sbt@v1
       - uses: actions/setup-java@v4
         with:
           distribution: 'temurin'

.github/workflows/integration_tests.yml

@@ -93,9 +93,9 @@ jobs:
             friendly_name: Centaur Engine Upgrade Local with MySQL 5.7
           - build_type: referenceDiskManifestBuilderApp
             friendly_name: Reference Disk Manifest Builder App
-          - build_type: centaurSlurm
-            build_mysql: 5.7
-            friendly_name: "Centaur Slurm with MySQL 5.7"
+#          - build_type: centaurSlurm
+#            build_mysql: 5.7
+#            friendly_name: "Centaur Slurm with MySQL 5.7"
           - build_type: centaurBlob
             build_mysql: 5.7
             friendly_name: Centaur Blob
@@ -114,6 +114,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 120
     steps:
+    - uses: sbt/setup-sbt@v1
     - uses: actions/checkout@v3 # checkout the cromwell repo
       with:
         ref: ${{ inputs.target-branch }}

.github/workflows/scalafmt-check.yml

@@ -19,6 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 20
     steps:
+      - uses: sbt/setup-sbt@v1
       - uses: actions/checkout@v3
         with:
           ref: ${{ inputs.target-branch }}

.github/workflows/trivy.yml

@@ -17,6 +17,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
+      - uses: sbt/setup-sbt@v1
 
       # fetch SBT package
       - uses: actions/setup-java@v4

engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala

@@ -347,7 +347,8 @@ class MetadataBuilderActorSpec
     val subWorkflow1aId = WorkflowId(UUID.fromString("1a1a1a1a-f76d-4af3-b371-5ba580916729"))
     val subWorkflow1bId = WorkflowId(UUID.fromString("1b1b1b1b-f76d-4af3-b371-5ba580916729"))
 
-    val workflowState = WorkflowSucceeded
+    val workflowSucceededState = WorkflowSucceeded
+    val workflowRunningState = WorkflowRunning
 
     val mainEvents = List(
       MetadataEvent(MetadataKey(mainWorkflowId, Option(MetadataJobKey("wfMain", None, 1)), "subWorkflowId"),
@@ -391,19 +392,25 @@ class MetadataBuilderActorSpec
     class TestReadDatabaseMetadataWorkerActorForCost extends ReadDatabaseMetadataWorkerActor(defaultTimeout, 1000000) {
       override def receive: Receive = {
         case GetCost(wfId) if wfId == mainWorkflowId =>
-          sender() ! CostResponse(mainWorkflowId, workflowState, MetadataLookupResponse(mainQuery, mainEvents))
+          sender() ! CostResponse(mainWorkflowId, workflowRunningState, MetadataLookupResponse(mainQuery, mainEvents))
           ()
         case GetCost(wfId) if wfId == subWorkflow1Id =>
-          sender() ! CostResponse(subWorkflow1Id, workflowState, MetadataLookupResponse(sub1Query, sub1Events))
+          sender() ! CostResponse(subWorkflow1Id, workflowSucceededState, MetadataLookupResponse(sub1Query, sub1Events))
           ()
         case GetCost(wfId) if wfId == subWorkflow2Id =>
-          sender() ! CostResponse(subWorkflow2Id, workflowState, MetadataLookupResponse(sub2Query, sub2Events))
+          sender() ! CostResponse(subWorkflow2Id, workflowSucceededState, MetadataLookupResponse(sub2Query, sub2Events))
           ()
         case GetCost(wfId) if wfId == subWorkflow1aId =>
-          sender() ! CostResponse(subWorkflow1aId, workflowState, MetadataLookupResponse(sub1aQuery, sub1aEvents))
+          sender() ! CostResponse(subWorkflow1aId,
+                                  workflowSucceededState,
+                                  MetadataLookupResponse(sub1aQuery, sub1aEvents)
+          )
           ()
         case GetCost(wfId) if wfId == subWorkflow1bId =>
-          sender() ! CostResponse(subWorkflow1bId, workflowState, MetadataLookupResponse(sub1bQuery, sub1bEvents))
+          sender() ! CostResponse(subWorkflow1bId,
+                                  workflowSucceededState,
+                                  MetadataLookupResponse(sub1bQuery, sub1bEvents)
+          )
           ()
         case _ => ()
       }
@@ -414,7 +421,7 @@ class MetadataBuilderActorSpec
          |"cost": 7,
          |"currency": "USD",
          |"id": "${mainWorkflowId}",
-         |"status": "${workflowState.toString}",
+         |"status": "${workflowRunningState.toString}",
          |"errors": ["Couldn't find valid vmCostPerHour for call1aA.-1.1"]
          |}""".stripMargin
 

services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala

@@ -35,17 +35,43 @@ object MetadataBuilderActor {
   case object IdleData extends MetadataBuilderActorData
   final case class HasWorkData(target: ActorRef, originalRequest: BuildMetadataJsonAction)
       extends MetadataBuilderActorData
+
+  // Classes extending this trait are used to track state when the actor has launched child
+  // actors to collect metadata for subworkflows. This class aggregates data as it comes in,
+  // and builds the complete output when all subworkflow data is present. There's one child
+  // class for plain metadata queries and one for cost queries.
+  sealed trait EventsCollectorData extends MetadataBuilderActorData {
+    val target: ActorRef
+    val originalRequest: BuildMetadataJsonAction
+    val originalQuery: MetadataQuery
+    val originalEvents: Seq[MetadataEvent]
+    val subWorkflowsMetadata: Map[String, JsValue]
+    val waitFor: Int
+
+    def isComplete = subWorkflowsMetadata.size == waitFor
+  }
+
   final case class HasReceivedEventsData(target: ActorRef,
                                          originalRequest: BuildMetadataJsonAction,
                                          originalQuery: MetadataQuery,
                                          originalEvents: Seq[MetadataEvent],
                                          subWorkflowsMetadata: Map[String, JsValue],
                                          waitFor: Int
-  ) extends MetadataBuilderActorData {
+  ) extends EventsCollectorData {
     def withSubWorkflow(id: String, metadata: JsValue) =
       this.copy(subWorkflowsMetadata = subWorkflowsMetadata + ((id, metadata)))
+  }
 
-    def isComplete = subWorkflowsMetadata.size == waitFor
+  final case class HasReceivedCostEventsData(target: ActorRef,
+                                             originalRequest: BuildMetadataJsonAction,
+                                             originalQuery: MetadataQuery,
+                                             originalEvents: Seq[MetadataEvent],
+                                             originalStatus: WorkflowState,
+                                             subWorkflowsMetadata: Map[String, JsValue],
+                                             waitFor: Int
+  ) extends EventsCollectorData {
+    def withSubWorkflow(id: String, metadata: JsValue) =
+      this.copy(subWorkflowsMetadata = subWorkflowsMetadata + ((id, metadata)))
   }
 
   def props(readMetadataWorkerMaker: () => Props,
@@ -432,7 +458,7 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props,
   }
 
   when(WaitingForSubWorkflowCost) {
-    case Event(mbr: MetadataJsonResponse, data: HasReceivedEventsData) =>
+    case Event(mbr: MetadataJsonResponse, data: HasReceivedCostEventsData) =>
       processSubWorkflowCost(mbr, data)
     case Event(failure: MetadataServiceFailure, data: HasReceivedEventsData) =>
       data.target ! FailedMetadataJsonResponse(data.originalRequest, failure.reason)
@@ -482,7 +508,7 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props,
         failAndDie(new Exception(message), data.target, data.originalRequest)
     }
 
-  def processSubWorkflowCost(metadataResponse: MetadataJsonResponse, data: HasReceivedEventsData) =
+  def processSubWorkflowCost(metadataResponse: MetadataJsonResponse, data: HasReceivedCostEventsData) =
     metadataResponse match {
       case SuccessfulMetadataJsonResponse(GetCost(workflowId), js) =>
         val subId: WorkflowId = workflowId
@@ -491,7 +517,7 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props,
         if (newData.isComplete) {
           buildCostAndStop(
             data.originalQuery.workflowId,
-            extractFromJsAs[JsString](js, "status").map(_.value).getOrElse(""), // should never be empty
+            data.originalStatus,
             data.originalEvents,
             newData.subWorkflowsMetadata,
             data.target,
@@ -579,7 +605,7 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props,
 
     if (subWorkflowIds.isEmpty)
       // If no subworkflows found, just build cost data
-      buildCostAndStop(id, status.toString, metadataResponse.eventList, Map.empty, target, originalRequest)
+      buildCostAndStop(id, status, metadataResponse.eventList, Map.empty, target, originalRequest)
     else {
       // Otherwise spin up a metadata builder actor for each sub workflow
       subWorkflowIds foreach { subId =>
@@ -591,18 +617,19 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props,
         )
         subMetadataBuilder ! GetCost(WorkflowId.fromString(subId))
       }
-      goto(WaitingForSubWorkflowCost) using HasReceivedEventsData(target,
-                                                                  originalRequest,
-                                                                  metadataResponse.query,
-                                                                  metadataResponse.eventList,
-                                                                  Map.empty,
-                                                                  subWorkflowIds.size
+      goto(WaitingForSubWorkflowCost) using HasReceivedCostEventsData(target,
+                                                                      originalRequest,
+                                                                      metadataResponse.query,
+                                                                      metadataResponse.eventList,
+                                                                      status,
+                                                                      Map.empty,
+                                                                      subWorkflowIds.size
       )
     }
   }
 
   def buildCostAndStop(id: WorkflowId,
-                       status: String,
+                       status: WorkflowState,
                        eventsList: Seq[MetadataEvent],
                        expandedValues: Map[String, JsValue],
                        target: ActorRef,
@@ -644,7 +671,7 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props,
     val resp = JsObject(
       Map(
         WorkflowMetadataKeys.Id -> JsString(id.toString),
-        WorkflowMetadataKeys.Status -> JsString(status),
+        WorkflowMetadataKeys.Status -> JsString(status.toString),
         "currency" -> JsString(DefaultCurrency.getCurrencyCode),
         "cost" -> JsNumber(callCost + subworkflowCost),
         "errors" -> JsArray(costErrors ++ subworkflowErrors)

src/ci/bin/test.inc.sh

@@ -543,7 +543,9 @@ cromwell::private::pip_install() {
 
 cromwell::private::upgrade_pip() {
     sudo apt-get install -y python3-pip
-    cromwell::private::pip_install pip --upgrade
+    # as of ubuntu 23 need to pass --user flag
+    # https://mail.openvswitch.org/pipermail/ovs-dev/2024-June/414969.html
+    cromwell::private::pip_install pip --upgrade --user pip
     cromwell::private::pip_install requests[security] --ignore-installed
 }
 

supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/authentication/PipelinesApiVMAuthentication.scala

@@ -6,18 +6,6 @@ import common.validation.ErrorOr._
 import common.validation.Validation._
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.core.DockerCredentials
-import spray.json.{JsString, JsValue}
-
-/**
- * Interface for Authentication information that can be included as a json object in the file uploaded to GCS
- * upon workflow creation and used in the VM.
- */
-sealed trait PipelinesApiAuthObject {
-  def context: String
-  def map: Map[String, JsValue]
-
-  def toMap: Map[String, Map[String, JsValue]] = Map(context -> map)
-}
 
 object PipelinesApiDockerCredentials {
 
@@ -53,10 +41,3 @@ case class PipelinesApiDockerCredentials(override val token: String,
                                          override val keyName: Option[String],
                                          override val authName: Option[String]
 ) extends DockerCredentials(token = token, keyName = keyName, authName = authName)
-    with PipelinesApiAuthObject {
-
-  override val context = "docker"
-  override val map = Map(
-    "token" -> JsString(token)
-  )
-}