WX-927 GCP Batch IAM scope fixes, GCSA tests

centaur/src/main/resources/standardTestCases/gcpbatch_papi_v2beta_gcsa.test

@@ -0,0 +1,17 @@
+name: gcpbatch_papi_v2beta_gcsa
+testFormat: WorkflowSuccess
+backends: [GCPBATCH-gcsa]
+
+files {
+  workflow: papi_v2_gcsa/gcpbatch_papi_v2_gcsa.wdl
+  options-dir: "Error: BA-6546 The environment variable CROMWELL_BUILD_RESOURCES_DIRECTORY must be set/export pointing to a valid path such as '${YOUR_CROMWELL_DIR}/target/ci/resources'"
+  options-dir: ${?CROMWELL_BUILD_RESOURCES_DIRECTORY}
+  options: ${files.options-dir}/papi_v2_gcsa.options.json
+}
+
+metadata {
+  workflowName: papi_v2_gcsa
+  status: Succeeded
+  "outputs.papi_v2_gcsa.email": "cromwell@broad-dsde-cromwell-dev.iam.gserviceaccount.com"
+  "outputs.papi_v2_gcsa.scopes": "https://www.googleapis.com/auth/bigquery https://www.googleapis.com/auth/cloud-platform https://www.googleapis.com/auth/cloudkms https://www.googleapis.com/auth/compute https://www.googleapis.com/auth/devstorage.full_control https://www.googleapis.com/auth/monitoring.write https://www.googleapis.com/auth/userinfo.email https://www.googleapis.com/auth/userinfo.profile"
+}

centaur/src/main/resources/standardTestCases/papi_v2_gcsa/gcpbatch_papi_v2_gcsa.wdl

@@ -0,0 +1,37 @@
+version 1.0
+
+workflow papi_v2_gcsa {
+    call get_token_info
+    output {
+        String email = get_token_info.json.email
+        String scopes = get_token_info.json.scopes
+        File service_account = get_token_info.service_account
+    }
+}
+
+# Confirm that even though the service account (SA) specified by the backend configuration creates the pipeline job,
+# instead the google compute service account (GCSA) workflow option is the actual account used to run the container.
+# https://cloud.google.com/genomics/reference/rest/Shared.Types/Metadata#VirtualMachine.FIELDS.service_account
+# https://cromwell.readthedocs.io/en/stable/wf_options/Google/#google-pipelines-api-workflow-options
+task get_token_info {
+    command <<<
+        apt-get install --assume-yes jq > /dev/null
+
+        curl --fail --silent \
+            'http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/?recursive=true' \
+            -H 'Metadata-Flavor: Google' > service_accounts.json
+
+        cat service_accounts.json | jq --monochrome-output \
+            '.default | {email, scopes: .scopes | sort | join(" ")}'
+    >>>
+
+    runtime {
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:slim"
+        backend: "GCPBATCH-gcsa"
+    }
+
+    output {
+        Object json = read_json(stdout())
+        File service_account = "service_accounts.json"
+    }
+}

centaur/src/main/resources/standardTestCases/papi_v2beta_gcsa.test

@@ -1,6 +1,6 @@
 name: papi_v2beta_gcsa
 testFormat: WorkflowSuccess
-backends: [papi-v2-gcsa, GCPBATCH_NEEDS_ALT]
+backends: [papi-v2-gcsa, GCPBATCH_ALT]
 
 files {
   workflow: papi_v2_gcsa/papi_v2_gcsa.wdl

src/ci/resources/gcp_batch_application.conf

@@ -23,6 +23,12 @@ backend {
         filesystems.gcs.auth = "requester_pays_service_account"
       }
     }
+    GCPBATCH-gcsa {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
+      config {
+        include "gcp_batch_provider_config.inc.conf"
+      }
+    }
     GCPBATCH-Virtual-Private-Cloud-Labels {
       actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
       config {

src/ci/resources/gcp_batch_shared_application.inc.conf

@@ -113,6 +113,24 @@ backend {
         include "dockerhub_provider_config_v2.inc.conf"
       }
     }
+    GCPBATCH-gcsa {
+      actor-factory = "REPLACEME!"
+      config {
+        # When importing: Remember to also include an appropriate provider_config.inc.conf here.
+
+        project = "user_error: google_project must be set in workflow options http://cromwell.readthedocs.io/en/develop/wf_options/Google/"
+        root = "user_error: jes_gcs_root must be set in workflow options http://cromwell.readthedocs.io/en/develop/wf_options/Google/"
+        genomics.compute-service-account = "user_error: google_compute_service_account must be set in workflow options http://cromwell.readthedocs.io/en/develop/wf_options/Google/"
+        genomics.auth = "google_compute_service_account"
+        filesystems.http {}
+        filesystems.drs.auth = "user_service_account"
+        filesystems.gcs.auth = "user_service_account"
+        filesystems.gcs.project = "user_error: user_service_account must be set in workflow options http://cromwell.readthedocs.io/en/develop/wf_options/Google/"
+
+        # Have the engine authenticate to docker.io. See BT-141 for more info.
+        include "dockerhub_provider_config_v2.inc.conf"
+      }
+    }
     GCPBATCHUSADockerhub {
       actor-factory = "REPLACEME!"
       config {

supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala

@@ -890,8 +890,7 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           rcFileOutputParameter = rcFileOutput,
           memoryRetryRCFileOutputParameter = memoryRetryRCFileOutput,
           logFileOutputParameter = logFileOutput
-        ),
-        List.empty
+        )
       )
 
     })

supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala

@@ -59,8 +59,7 @@ object GcpBatchRequestFactory {
     detritusInputParameters: DetritusInputParameters,
     jobInputParameters: List[GcpBatchInput],
     jobOutputParameters: List[GcpBatchOutput],
-    detritusOutputParameters: DetritusOutputParameters,
-    literalInputParameters: List[GcpBatchLiteralInput]
+    detritusOutputParameters: DetritusOutputParameters
   ) {
     lazy val fileInputParameters: List[GcpBatchInput] = jobInputParameters ++ detritusInputParameters.all
     lazy val fileOutputParameters: List[GcpBatchOutput] = detritusOutputParameters.all ++ jobOutputParameters
@@ -94,13 +93,7 @@ object GcpBatchRequestFactory {
                                       vpcNetworkAndSubnetworkProjectLabels: Option[VpcAndSubnetworkProjectLabelValues],
                                       dockerhubCredentials: (String, String)
   ) {
-    def literalInputs = inputOutputParameters.literalInputParameters
-
-    def inputParameters = inputOutputParameters.fileInputParameters
-
     def outputParameters = inputOutputParameters.fileOutputParameters
-
-    def allParameters = inputParameters ++ outputParameters
   }
 
 }

supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala

@@ -1,5 +1,9 @@
 package cromwell.backend.google.batch.api
 
+import com.google.api.services.bigquery.BigqueryScopes
+import com.google.api.services.compute.ComputeScopes
+import com.google.api.services.oauth2.Oauth2Scopes
+import com.google.api.services.storage.StorageScopes
 import com.google.cloud.batch.v1.AllocationPolicy._
 import com.google.cloud.batch.v1.LogsPolicy.Destination
 import com.google.cloud.batch.v1.{
@@ -169,7 +173,20 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
 
     // set parent for metadata storage of job information
     lazy val parent = s"projects/${createParameters.projectId}/locations/${data.gcpBatchParameters.region}"
-    val gcpSa = ServiceAccount.newBuilder.setEmail(createParameters.computeServiceAccount).build
+    val scopes = List(
+      ComputeScopes.COMPUTE,
+      StorageScopes.DEVSTORAGE_FULL_CONTROL,
+      GoogleCloudScopes.KmsScope,
+      // Profile and Email scopes are requirements for interacting with DRS Resolvers
+      Oauth2Scopes.USERINFO_EMAIL,
+      Oauth2Scopes.USERINFO_PROFILE,
+      // Monitoring scope as POC
+      GoogleCloudScopes.MonitoringWrite,
+      // Allow read/write with BigQuery
+      BigqueryScopes.BIGQUERY
+    ).asJava
+
+    val gcpSa = ServiceAccount.newBuilder.setEmail(createParameters.computeServiceAccount).addAllScopes(scopes).build
 
     // make zones path
     val zones = toZonesPath(runtimeAttributes.zones)

supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GoogleCloudScopes.scala

@@ -0,0 +1,25 @@
+package cromwell.backend.google.batch.api
+
+/**
+  * Google cloud scopes that don't have constants defined elsewhere in Google Cloud Java API.
+  */
+object GoogleCloudScopes {
+
+  /**
+    * More restricted version of com.google.api.services.cloudkms.v1.CloudKMSScopes.CLOUD_PLATFORM
+    * Could use that scope to keep things simple, but docs say to use a more restricted scope:
+    *
+    *   https://cloud.google.com/kms/docs/accessing-the-api#google_compute_engine
+    *
+    * For some reason this scope isn't listed as a constant under CloudKMSScopes.
+    */
+  val KmsScope = "https://www.googleapis.com/auth/cloudkms"
+
+  /**
+    * Scope to write metrics to Stackdriver Monitoring API.
+    * Used by the monitoring action.
+    *
+    * For some reason we couldn't find this scope within Google libraries
+    */
+  val MonitoringWrite = "https://www.googleapis.com/auth/monitoring.write"
+}

supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala

@@ -79,6 +79,3 @@ final case class GcpBatchDirectoryOutput(name: String,
                                          secondary: Boolean,
                                          override val contentType: Option[ContentType] = None
 ) extends GcpBatchOutput
-
-// TODO: Remove when support for V1 is stopped, this is only used to pass the extra_param auth file
-final case class GcpBatchLiteralInput(name: String, value: String)