{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/rawls/pulls/comments/63772326","id":63772326,"diff_hunk":"@@ -0,0 +1,244 @@\n+package org.broadinstitute.dsde.rawls.jobexec\n+\n+import java.util.UUID\n+\n+import akka.actor._\n+import akka.pattern._\n+import com.google.api.client.auth.oauth2.Credential\n+import com.typesafe.scalalogging.LazyLogging\n+import org.broadinstitute.dsde.rawls.{RawlsExceptionWithErrorReport, RawlsException}\n+import org.broadinstitute.dsde.rawls.dataaccess._\n+import org.broadinstitute.dsde.rawls.dataaccess.slick._\n+import org.broadinstitute.dsde.rawls.jobexec.WorkflowSubmissionActor._\n+import org.broadinstitute.dsde.rawls.model._\n+import org.broadinstitute.dsde.rawls.util.{MethodWiths, FutureSupport}\n+import _root_.slick.dbio.DBIOAction\n+import _root_.slick.dbio.Effect.Read\n+import spray.http.{StatusCodes, OAuth2BearerToken}\n+import spray.json._\n+import spray.httpx.SprayJsonSupport._\n+\n+\n+import scala.concurrent.{Future, ExecutionContext}\n+import scala.concurrent.duration.FiniteDuration\n+import scala.util.{Success, Failure}\n+\n+\n+object WorkflowSubmissionActor {\n+  def props(dataSource: SlickDataSource,\n+            methodRepoDAO: MethodRepoDAO,\n+            googleServicesDAO: GoogleServicesDAO,\n+            executionServiceDAO: ExecutionServiceDAO,\n+            batchSize: Int,\n+            credential: Credential,\n+            pollInterval: FiniteDuration): Props = {\n+    Props(new WorkflowSubmissionActor(dataSource, methodRepoDAO, googleServicesDAO, executionServiceDAO, batchSize, credential, pollInterval))\n+  }\n+\n+  sealed trait WorkflowSubmissionMessage\n+  case object ScheduleNextWorkflowQuery extends WorkflowSubmissionMessage\n+  case object LookForWorkflows extends WorkflowSubmissionMessage\n+  case class SubmitWorkflowBatch(workflowIds: Seq[Long]) extends WorkflowSubmissionMessage\n+\n+}\n+\n+class WorkflowSubmissionActor(val dataSource: SlickDataSource,\n+                              val methodRepoDAO: MethodRepoDAO,\n+                              val googleServicesDAO: GoogleServicesDAO,\n+                              val executionServiceDAO: ExecutionServiceDAO,\n+                              val batchSize: Int,\n+                              val credential: Credential,\n+                              val pollInterval: FiniteDuration) extends Actor with WorkflowSubmission with LazyLogging {\n+\n+  import context._\n+\n+  self ! ScheduleNextWorkflowQuery\n+\n+  override def receive = {\n+    case ScheduleNextWorkflowQuery =>\n+      scheduleNextWorkflowQuery\n+\n+    case LookForWorkflows =>\n+      getUnlaunchedWorkflowBatch() pipeTo self\n+\n+    case SubmitWorkflowBatch(workflowIds) =>\n+      submitWorkflowBatch(workflowIds) pipeTo self\n+\n+    case Status.Failure(t) =>\n+      logger.error(t.getMessage)\n+      scheduleNextWorkflowQuery\n+  }\n+\n+  def scheduleNextWorkflowQuery: Cancellable = {\n+    system.scheduler.scheduleOnce(pollInterval, self, LookForWorkflows)\n+  }\n+}\n+\n+trait WorkflowSubmission extends FutureSupport with LazyLogging with MethodWiths {\n+  val dataSource: SlickDataSource\n+  val methodRepoDAO: MethodRepoDAO\n+  val googleServicesDAO: GoogleServicesDAO\n+  val executionServiceDAO: ExecutionServiceDAO\n+  val batchSize: Int\n+  val credential: Credential\n+  val pollInterval: FiniteDuration\n+\n+  import dataSource.dataAccess.driver.api._\n+\n+  //Get a blob of unlaunched workflows, flip their status, and queue them for submission.\n+  def getUnlaunchedWorkflowBatch()(implicit executionContext: ExecutionContext): Future[WorkflowSubmissionMessage] = {\n+    val unlaunchedWfOptF = dataSource.inTransaction { dataAccess =>\n+      //grab a bunch of unsubmitted workflows\n+      dataAccess.workflowQuery.findUnsubmittedWorkflows().take(batchSize).result flatMap { wfRecs =>\n+        if (wfRecs.isEmpty) {\n+          DBIO.successful(wfRecs)\n+        } else {\n+          //they should also all have the same submission ID\n+          val wfsWithASingleSubmission = wfRecs.filter(_.submissionId == wfRecs.head.submissionId)\n+          dataAccess.workflowQuery.batchUpdateStatus(wfsWithASingleSubmission, WorkflowStatuses.Launching).map(_ => wfsWithASingleSubmission)\n+        }\n+      }\n+    }\n+\n+    unlaunchedWfOptF.map {\n+      // submit the batch we found\n+      case workflowRecs if workflowRecs.nonEmpty => SubmitWorkflowBatch(workflowRecs.map(_.id))\n+\n+      // if we didn't find any then look again in a little bit\n+      case _ => ScheduleNextWorkflowQuery\n+\n+    } recover {\n+      // if we found some but another actor reserved the first look again immediately\n+      case t: RawlsConcurrentModificationException => LookForWorkflows\n+    }\n+  }\n+\n+  def buildWorkflowOpts(workspace: WorkspaceRecord, submissionId: UUID, user: RawlsUser, token: String, billingProject: RawlsBillingProject) = {\n+    ExecutionServiceWorkflowOptions(\n+      s\"gs://${workspace.bucketName}/${submissionId}\",\n+      workspace.namespace,\n+      user.userEmail.value,\n+      token,\n+      billingProject.cromwellAuthBucketUrl\n+    )\n+  }\n+\n+  def getWdl(methodConfig: MethodConfiguration)(implicit executionContext: ExecutionContext): ReadWriteAction[String] = {\n+    withMethod(methodConfig.methodRepoMethod.methodNamespace, methodConfig.methodRepoMethod.methodName, methodConfig.methodRepoMethod.methodVersion, getUserInfo(credential)) { method =>\n+      withWdl(method) { wdl =>\n+        DBIO.successful(wdl)\n+      }\n+    }\n+  }\n+\n+  def getWorkflowRecordBatch(workflowIds: Seq[Long], dataAccess: DataAccess)(implicit executionContext: ExecutionContext) = {\n+    dataAccess.workflowQuery.findWorkflowByIds(workflowIds).result map { wfRecs =>\n+      val submissionId = wfRecs.head.submissionId\n+      if( !wfRecs.forall(_.submissionId == submissionId) ) {\n+        throw new RawlsExceptionWithErrorReport(ErrorReport(StatusCodes.InternalServerError, \"Workflow batch has different 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Sending workflows to Cromwell asynchronously","user":{"login":"helgridly","id":775136,"avatar_url":"https://avatars.githubusercontent.com/u/775136?v=3","gravatar_id":"","url":"https://api.github.com/users/helgridly","html_url":"https://github.com/helgridly","followers_url":"https://api.github.com/users/helgridly/followers","following_url":"https://api.github.com/users/helgridly/following{/other_user}","gists_url":"https://api.github.com/users/helgridly/gists{/gist_id}","starred_url":"https://api.github.com/users/helgridly/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/helgridly/subscriptions","organizations_url":"https://api.github.com/users/helgridly/orgs","repos_url":"https://api.github.com/users/helgridly/repos","events_url":"https://api.github.com/users/helgridly/events{/privacy}","received_events_url":"https://api.github.com/users/helgridly/received_events","type":"User","site_admin":false},"body":"\r\n- [ ] **Submitter**: Rebase to develop. DO NOT SQUASH\r\n- [ ] **Submitter**: Make sure Swagger is updated if API changes\r\n- [ ] **Submitter**: Make sure documentation for code is complete\r\n- [ ] **Submitter**: Make sure liquibase is updated if appropriate\r\n- [ ] **Submitter**: Review code comments; remove done TODOs, create stories for remaining TODOs\r\n- [ ] **Submitter**: Include the JIRA issue number in the PR description\r\n- [ ] **Submitter**: Add description or comments on the PR explaining the hows/whys (if not obvious)\r\n- [ ] Tell ![](http://i.imgur.com/9dLzbPd.png) that the PR exists if he wants to look at it **(apply requires_doge label)**\r\n- [ ] Anoint a lead reviewer (LR). **Assign PR to LR**\r\n- [ ] **LR**: Initial review by LR and others.\r\n- [ ] Comment / review / update cycle:\r\n  * Rest of team may comments on PR at will\r\n  * **LR assigns to submitter** for feedback fixes\r\n  * Submitter updates documentation as needed\r\n  * Submitter rebases to develop again if necessary\r\n  * Submitter makes further commits. DO NOT SQUASH. **Reassign to LR** for further feedback\r\n- [ ] ![](http://i.imgur.com/9dLzbPd.png) sign off\r\n- [ ] **LR** sign off\r\n- [ ] **Assign to submitter** to finalize\r\n- [ ] **Submitter**: Squash commits, rebase if necessary\r\n- [ ] **Submitter**: Verify all tests go green, including CI tests\r\n- [ ] **Submitter**: Merge to develop \r\n- [ ] **Submitter**: Delete branch after merge\r\n- [ ] **Submitter**: Check configuration files in Jenkins in case they need changes\r\n- [ ] **Submitter**: **Test this change works on dev environment after deployment**. YOU own getting it fixed if dev isn't working for ANY reason!\r\n- [ ] **Submitter**: Verify swagger UI on dev environment still works after deployment\r\n- [ ] **Submitter**: Inform other teams of any API changes via hipchat and/or email\r\n- [ ] **Submitter**: Mark JIRA issue as resolved once this checklist is completed\r\n","created_at":"2016-05-17T18:24:56Z","updated_at":"2016-05-18T20:06:06Z","closed_at":null,"merged_at":null,"merge_commit_sha":"0d504cbb53ea5fe9222433b9061e498296a95e93","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/rawls/pulls/429/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/rawls/pulls/429/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/rawls/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/rawls/issues/429/comments","statuses_url":"https://api.github.com/repos/broadinstitute/rawls/statuses/ac01d814b7bcb06914792839c2ef5cedad1d145b","head":{"label":"broadinstitute:606_workflow_submission_actor","ref":"606_workflow_submission_actor","sha":"ac01d814b7bcb06914792839c2ef5cedad1d145b","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":34129770,"name":"rawls","full_name":"broadinstitute/rawls","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/rawls","description":"Rawls 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