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Access to optional variables in conditionals broken for WDL 1.0 (works w draft-2)

See original GitHub issue

I’ve attached two workflows that are essentially the same, one that conforms to draft-2 and the other that conforms to 1.0. The former runs fine (Cromwell v40), the latter one fails. It looks like there’s a regression in handling the following situation:

task bar {
  input {
    Array[Array[String]]? baz
  }
  command <<<
  echo ~{ if defined(baz) then write_tsv(baz) else 'no file' }
  >>>
  ...
}

Error:

```java
Failed to process task definition 'bar' (reason 1 of 1): Failed to process expression 'if defined(baz) then write_tsv(baz) else ""' (reason 1 of 1): Invalid parameter 'IdentifierLookup(baz)'. Expected 'Array[Array[String]]' but got 'Array[Array[String]]?'
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.cromwell$engine$workflow$lifecycle$materialization$MaterializeWorkflowDescriptorActor$$workflowInitializationFailed(MaterializeWorkflowDescriptorActor.scala:215)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:185)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:180)
        at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
        at akka.actor.FSM.processEvent(FSM.scala:684)
        at akka.actor.FSM.processEvent$(FSM.scala:681)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.akka$actor$LoggingFSM$$super$processEvent(MaterializeWorkflowDescriptorActor.scala:136)
        at akka.actor.LoggingFSM.processEvent(FSM.scala:820)
        at akka.actor.LoggingFSM.processEvent$(FSM.scala:802)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.processEvent(MaterializeWorkflowDescriptorActor.scala:136)
        at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:678)
        at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:672)
        at akka.actor.Actor.aroundReceive(Actor.scala:517)
        at akka.actor.Actor.aroundReceive$(Actor.scala:515)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.aroundReceive(MaterializeWorkflowDescriptorActor.scala:136)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
        at akka.actor.ActorCell.invoke(ActorCell.scala:557)
        at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
        at akka.dispatch.Mailbox.run(Mailbox.scala:225)
        at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
        at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

Issue Analytics

State:
Created 4 years ago
Comments:16 (2 by maintainers)

Top GitHub Comments

1reaction

jdidioncommented, Jul 10, 2019

It works now, thank you. I’m going to remove my email address from the previous comment.

0reactions

gemmalamcommented, Jul 10, 2019

@jdidion I’ve added you. Let me know if you still need help with access.

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