Stop downloading, compiling, and uploading dead jes code [BT-84] (#6311)

build.sbt

@@ -208,13 +208,6 @@ lazy val googlePipelinesCommon = (project in backendRoot / "google" / "pipelines
   .dependsOn(services % "test->test")
   .dependsOn(common % "test->test")
 
-lazy val googlePipelinesV1Alpha2 = (project in backendRoot / "google" / "pipelines" / "v1alpha2")
-  .withLibrarySettings("cromwell-pipelines-v1-backend")
-  .dependsOn(googlePipelinesCommon)
-  .dependsOn(googlePipelinesCommon % "test->test")
-  .dependsOn(core % "test->test")
-  .dependsOn(common % "test->test")
-
 lazy val googlePipelinesV2Alpha1 = (project in backendRoot / "google" / "pipelines" / "v2alpha1")
   .withLibrarySettings("cromwell-pipelines-v2-alpha1-backend")
   .dependsOn(googlePipelinesCommon)
@@ -229,12 +222,6 @@ lazy val googlePipelinesV2Beta = (project in backendRoot / "google" / "pipelines
   .dependsOn(core % "test->test")
   .dependsOn(common % "test->test")
 
-// Legacy, inherits all its code from googlePipelinesV1Alpha2
-lazy val jesBackend = (project in backendRoot / "jes")
-  .withLibrarySettings("cromwell-jes-backend")
-  .dependsOn(googlePipelinesV1Alpha2)
-  .dependsOn(common % "test->test")
-
 lazy val awsBackend = (project in backendRoot / "aws")
   .withLibrarySettings("cromwell-aws-backend")
   .dependsOn(backend)
@@ -404,10 +391,8 @@ lazy val `cromwell-drs-localizer` = project
 lazy val server = project
   .withExecutableSettings("cromwell", serverDependencies)
   .dependsOn(engine)
-  .dependsOn(googlePipelinesV1Alpha2)
   .dependsOn(googlePipelinesV2Alpha1)
   .dependsOn(googlePipelinesV2Beta)
-  .dependsOn(jesBackend)
   .dependsOn(bcsBackend)
   .dependsOn(awsBackend)
   .dependsOn(tesBackend)
@@ -448,11 +433,9 @@ lazy val root = (project in file("."))
   .aggregate(ftpFileSystem)
   .aggregate(gcsFileSystem)
   .aggregate(googlePipelinesCommon)
-  .aggregate(googlePipelinesV1Alpha2)
   .aggregate(googlePipelinesV2Alpha1)
   .aggregate(googlePipelinesV2Beta)
   .aggregate(httpFileSystem)
-  .aggregate(jesBackend)
   .aggregate(languageFactoryCore)
   .aggregate(ossFileSystem)
   .aggregate(perf)

centaur/src/main/scala/centaur/test/Test.scala

@@ -10,7 +10,7 @@ import centaur.test.metadata.WorkflowFlatMetadata
 import centaur.test.metadata.WorkflowFlatMetadata._
 import centaur.test.submit.SubmitHttpResponse
 import centaur.test.workflow.Workflow
-import com.google.api.services.genomics.{Genomics, GenomicsScopes}
+import com.google.api.services.genomics.v2alpha1.{Genomics, GenomicsScopes}
 import com.google.api.services.storage.StorageScopes
 import com.google.auth.Credentials
 import com.google.auth.http.HttpCredentialsAdapter
@@ -384,7 +384,7 @@ object Operations extends StrictLogging {
     new Test[Unit] {
       def checkPAPIAborted(): IO[Unit] = {
         for {
-          operation <- IO { genomics.operations().get(jobId).execute() }
+          operation <- IO { genomics.projects().operations().get(jobId).execute() }
           done = operation.getDone
           operationError = Option(operation.getError)
           aborted = operationError.exists(_.getCode == 1) && operationError.exists(_.getMessage.startsWith("Operation canceled"))

project/Dependencies.scala

@@ -44,7 +44,6 @@ object Dependencies {
   private val googleCloudNioV = "0.61.0-alpha" // scala-steward:off
   private val googleCloudStorageV = "1.113.14"
   private val googleGaxGrpcV = "1.62.0"
-  private val googleGenomicsServicesV1ApiV = "v1alpha2-rev495-1.23.0"
   private val googleGenomicsServicesV2Alpha1ApiV = "v2alpha1-rev20210322-1.31.0"
   private val googleHttpClientApacheV = "2.1.2"
   private val googleHttpClientV = "1.38.0"
@@ -281,12 +280,6 @@ object Dependencies {
     "org.yaml" % "snakeyaml" % snakeyamlV % Test
   )
 
-  // The v1 dependency has been cloned in the broad artifactory so that we can have the 2 versions co-exist in the same jar
-  private val googleGenomicsV1Dependency = List(
-    "org.broadinstitute" % "cromwell-google-api-services-genomics" % googleGenomicsServicesV1ApiV
-      exclude("com.google.guava", "guava-jdk5")
-  )
-
   private val googleGenomicsV2Alpha1Dependency = List(
     "com.google.apis" % "google-api-services-genomics" % googleGenomicsServicesV2Alpha1ApiV
       exclude("com.google.guava", "guava-jdk5")
@@ -333,7 +326,7 @@ object Dependencies {
     "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV,
     "com.google.apis" % "google-api-services-cloudkms" % googleCloudKmsV
       exclude("com.google.guava", "guava-jdk5")
-  ) ++ googleGenomicsV1Dependency ++ googleGenomicsV2Alpha1Dependency ++ googleLifeSciencesV2BetaDependency
+  ) ++ googleGenomicsV2Alpha1Dependency ++ googleLifeSciencesV2BetaDependency
 
   private val aliyunOssDependencies = List(
     "com.aliyun.oss" % "aliyun-sdk-oss" % aliyunOssV

services/src/main/scala/cromwell/services/healthmonitor/impl/workbench/WorkbenchHealthMonitorServiceActor.scala

@@ -83,10 +83,8 @@ abstract class WorkbenchHealthMonitorServiceActor(val serviceConfig: Config, glo
       genomicsChecker = if (actorFactoryName.contains("v2beta")) {
         val location = papiConfig.as[String]("genomics.location")
         GenomicsCheckerV2Beta(googleConfig.applicationName, googleAuth, endpointUrl, location, credentials, papiProjectId)
-      } else if (actorFactoryName.contains("v2alpha1")) {
-        GenomicsCheckerV2Alpha1(googleConfig.applicationName, googleAuth, endpointUrl, credentials, papiProjectId)
       } else {
-        GenomicsCheckerV1(googleConfig.applicationName, googleAuth, endpointUrl, credentials, papiProjectId)
+        GenomicsCheckerV2Alpha1(googleConfig.applicationName, googleAuth, endpointUrl, credentials, papiProjectId)
       }
       checked <- genomicsChecker.check
     } yield checked
@@ -109,25 +107,6 @@ object WorkbenchHealthMonitorServiceActor {
     def check: Future[Unit]
   }
 
-  case class GenomicsCheckerV1(applicationName: String,
-                               authMode: GoogleAuthMode,
-                               endpointUrl: URL,
-                               credentials: Credentials,
-                               papiProjectId: String)(implicit val ec: ExecutionContext) extends GenomicsChecker {
-    val genomics = new com.google.api.services.genomics.Genomics.Builder(
-      GoogleAuthMode.httpTransport,
-      GoogleAuthMode.jsonFactory,
-      httpInitializer(credentials))
-      .setApplicationName(applicationName)
-      .setRootUrl(endpointUrl.toString)
-      .build
-
-    override def check = Future {
-      genomics.pipelines().list().setProjectId(papiProjectId).setPageSize(1).execute()
-      ()
-    }
-  }
-
   case class GenomicsCheckerV2Beta(applicationName: String,
                                    authMode: GoogleAuthMode,
                                    endpointUrl: URL,

supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActor.scala

@@ -5,7 +5,7 @@ import com.google.api.client.http.{HttpRequest, HttpResponse}
 import com.google.api.services.cloudkms.v1.model.EncryptRequest
 import com.google.api.services.cloudkms.v1.{CloudKMS, CloudKMSScopes}
 import com.google.api.services.cloudresourcemanager.CloudResourceManager
-import com.google.api.services.genomics.GenomicsScopes
+import com.google.api.services.genomics.v2alpha1.GenomicsScopes
 import com.google.api.services.lifesciences.v2beta.CloudLifeSciencesScopes
 import com.google.api.services.storage.StorageScopes
 import com.google.auth.Credentials
@@ -65,10 +65,6 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
       CloudLifeSciencesScopes.CLOUD_PLATFORM,
       GenomicsScopes.GENOMICS,
       /*
-      Genomics Pipelines API v1alpha2 requires the COMPUTE scope. Does not seem to be required for either v2alpha1 or v2beta.
-       */
-      GenomicsScopes.COMPUTE,
-      /*
       Used to write so-called "auth" files. The `gcsAuthFilePath` could probably be refactored such that *this* created
       `genomicsCredentials` doesn't actually need DEVSTORAGE_FULL_CONTROL, but it's also not clear how the magic
       Genomics Pipelines API parameter "__extra_config_gcs_path" works nor where it's documented.