Workflow output attach debug logging [BW-529] (#1376)

broadinstitute · Mar 8, 2021 · 7b30964 · 7b30964
1 parent d737b49
commit 7b30964
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Showing 2 changed files with 21 additions and 8 deletions.
diff --git a/core/src/main/scala/org/broadinstitute/dsde/rawls/jobexec/SubmissionMonitorActor.scala b/core/src/main/scala/org/broadinstitute/dsde/rawls/jobexec/SubmissionMonitorActor.scala
@@ -7,7 +7,7 @@ import akka.pattern._
 import com.google.api.client.auth.oauth2.Credential
 import com.typesafe.scalalogging.LazyLogging
 import nl.grons.metrics4.scala.Counter
-import org.broadinstitute.dsde.rawls.{RawlsException, RawlsFatalExceptionWithErrorReport}
+import org.broadinstitute.dsde.rawls.{RawlsException, RawlsFatalExceptionWithErrorReport, model}
 import org.broadinstitute.dsde.rawls.coordination.DataSourceAccess
 import org.broadinstitute.dsde.rawls.dataaccess._
 import org.broadinstitute.dsde.rawls.dataaccess.slick._
@@ -445,27 +445,36 @@ trait SubmissionMonitor extends FutureSupport with LazyLogging with RawlsInstrum
       logger.debug(s"attaching outputs for ${submissionId.toString}/${workflowRecord.externalId.getOrElse("MISSING_WORKFLOW")}: ${outputs}")
       logger.debug(s"output expressions for ${submissionId.toString}/${workflowRecord.externalId.getOrElse("MISSING_WORKFLOW")}: ${outputExpressionMap}")
 
-      val parsedExpressions = outputExpressionMap.map { case (outputName, outputExprStr) =>
+      val parsedExpressions: Seq[Try[OutputExpression]] = outputExpressionMap.map { case (outputName, outputExprStr) =>
         outputs.get(outputName) match {
           case None => Failure(new RawlsException(s"output named ${outputName} does not exist"))
           case Some(Right(uot: UnsupportedOutputType)) => Failure(new RawlsException(s"output named ${outputName} is not a supported type, received json u${uot.json.compactPrint}"))
           case Some(Left(output)) =>
             val entityTypeOpt = workflowRecord.workflowEntityId.flatMap(entitiesById.get).map(_.entityType)
             OutputExpression.build(outputExprStr, output, entityTypeOpt)
         }
-      }
+      }.toSeq
 
       if (parsedExpressions.forall(_.isSuccess)) {
-        val boundExpressions = parsedExpressions.collect { case Success(boe @ BoundOutputExpression(target, name, attr)) => boe }
+        val boundExpressions: Seq[BoundOutputExpression] = parsedExpressions.collect { case Success(boe @ BoundOutputExpression(target, name, attr)) => boe }
         val updates = updateEntityAndWorkspace(workflowRecord.workflowEntityId.map(id => Some(entitiesById(id))).getOrElse(None), workspace, boundExpressions)
+
+        val (optEntityUpdates, optWs) = updates
+        optEntityUpdates foreach { update: WorkflowEntityUpdate =>
+          logger.debug(s"Updating ${update.upserts.size} attributes for entity ${update.entityRef.entityName} of type ${update.entityRef.entityType} in ${submissionId.toString}/${workflowRecord.externalId.getOrElse("MISSING_WORKFLOW")}. First 100: ${update.upserts.take(100)}")
+        }
+        optWs foreach { workspace: Workspace =>
+          logger.debug(s"Updating ${workspace.attributes.size} workspace attributes in ${submissionId.toString}/${workflowRecord.externalId.getOrElse("MISSING_WORKFLOW")}. First 100: ${workspace.attributes.take(100)}")
+        }
+
         Left(updates)
       } else {
-        Right((workflowRecord, parsedExpressions.collect { case Failure(t) => AttributeString(t.getMessage) }.toSeq))
+        Right((workflowRecord, parsedExpressions.collect { case Failure(t) => AttributeString(t.getMessage) }))
       }
     }
   }
 
-  def updateEntityAndWorkspace(entity: Option[Entity], workspace: Workspace, workflowOutputs: Iterable[BoundOutputExpression]): (Option[WorkflowEntityUpdate], Option[Workspace]) = {
+  private def updateEntityAndWorkspace(entity: Option[Entity], workspace: Workspace, workflowOutputs: Iterable[BoundOutputExpression]): (Option[WorkflowEntityUpdate], Option[Workspace]) = {
     val entityUpsert = workflowOutputs.collect({ case BoundOutputExpression(ThisEntityTarget, attrName, attr) => (attrName, attr) })
     val workspaceAttributes = workflowOutputs.collect({ case BoundOutputExpression(WorkspaceTarget, attrName, attr) => (attrName, attr) })
 

diff --git a/core/src/main/scala/org/broadinstitute/dsde/rawls/jobexec/WorkflowSubmissionActor.scala b/core/src/main/scala/org/broadinstitute/dsde/rawls/jobexec/WorkflowSubmissionActor.scala
@@ -169,8 +169,10 @@ trait WorkflowSubmission extends FutureSupport with LazyLogging with MethodWiths
     } else {
       for {
         // we exclude workflows submitted by users that have exceeded the max workflows per user
-        excludedUsers <- dataAccess.workflowQuery.listSubmittersWithMoreWorkflowsThan(maxActiveWorkflowsPerUser, WorkflowStatuses.runningStatuses)
-        workflowRecs <- dataAccess.workflowQuery.findQueuedWorkflows(excludedUsers.map { case (submitter, count) => submitter }, SubmissionStatuses.terminalStatuses :+ SubmissionStatuses.Aborting).take(batchSize).result
+        excludedUsersMap <- dataAccess.workflowQuery.listSubmittersWithMoreWorkflowsThan(maxActiveWorkflowsPerUser, WorkflowStatuses.runningStatuses).map(_.toMap)
+        excludedUsers = excludedUsersMap.keys.toSeq
+        excludedStatuses = SubmissionStatuses.terminalStatuses :+ SubmissionStatuses.Aborting
+        workflowRecs: Seq[WorkflowRecord] <- dataAccess.workflowQuery.findQueuedWorkflows(excludedUsers, excludedStatuses).take(batchSize).result
         reservedRecs <- if (workflowRecs.isEmpty) {
             DBIO.successful(None)
           } else {
@@ -312,6 +314,8 @@ trait WorkflowSubmission extends FutureSupport with LazyLogging with MethodWiths
 
     val WorkflowBatch(workflowIds, submissionRec, workspaceRec) = batch
 
+    logger.info(s"Submitting batch of ${workflowIds.size} workflows for submission ${submissionRec.id} in workspace ${workspaceRec.namespace}/${workspaceRec.name} (${workspaceRec.id})")
+
     // implicitly passed to WorkflowComponent methods which update status
     implicit val wfStatusCounter = (status: WorkflowStatus) =>
       if (trackDetailedSubmissionMetrics) Option(workflowStatusCounter(workspaceSubmissionMetricBuilder(workspaceRec.toWorkspaceName, submissionRec.id))(status))