Defined() does not work on undefined keys in object.

[rhpvorderman]

In the following code snippet:

    scatter(centrifuge in centrifugeList){
        call centrifugeDownload {
            input:
              centrifugeOutput= centrifuge.outputDir,
              domain=centrifuge.domain,
              database=if defined(centrifuge.database) then centrifuge.database else "refseq"
              }
        }
    }

The centrifugeList is a list of dictionaries. The resulting centrifuge object may or may not have a key database.

Expected behaviour:

database defaults to "refseq" if no database key is present in the dictionary. It will use the database key if it exists.

Observed behaviour:

java.lang.RuntimeException: Evaluating if defined(centrifuge.database) then centrifuge.database else "refseq" failed: Could not find key database in WdlObject
        at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.$anonfun$processRunnable$2(ExpressionKey.scala:36)
        at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.$anonfun$processRunnable$2$adapted(ExpressionKey.scala:31)
        at scala.Function1.$anonfun$andThen$1(Function1.scala:52)
        at cats.data.Validated.fold(Validated.scala:14)
        at cats.data.Validated.bimap(Validated.scala:109)
        at cats.data.Validated.map(Validated.scala:152)
        at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.processRunnable(ExpressionKey.scala:31)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$anonfun$processRunnableTaskCallInputExpression$4(WorkflowExecutionActor.scala:452)
        at scala.util.Either.flatMap(Either.scala:338)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$anonfun$processRunnableTaskCallInputExpression$2(WorkflowExecutionActor.scala:449)
        at scala.util.Either.flatMap(Either.scala:338)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$anonfun$processRunnableTaskCallInputExpression$1(WorkflowExecutionActor.scala:448)
        at scala.util.Either.flatMap(Either.scala:338)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.processRunnableTaskCallInputExpression(WorkflowExecutionActor.scala:447)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$anonfun$startRunnableNodes$4(WorkflowExecutionActor.scala:421)
        at cats.instances.ListInstances$$anon$1.$anonfun$traverse$2(list.scala:65)
        at cats.instances.ListInstances$$anon$1.loop$2(list.scala:58)
        at cats.instances.ListInstances$$anon$1.$anonfun$foldRight$2(list.scala:60)
        at cats.Eval$Call$.cats$Eval$Call$$loop(Eval.scala:267)
        at cats.Eval$Call.value(Eval.scala:257)
        at cats.instances.ListInstances$$anon$1.traverse(list.scala:64)
        at cats.instances.ListInstances$$anon$1.traverse(list.scala:12)
        at cats.Traverse$Ops.traverse(Traverse.scala:19)
        at cats.Traverse$Ops.traverse$(Traverse.scala:19)
        at cats.Traverse$ToTraverseOps$$anon$3.traverse(Traverse.scala:19)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.cromwell$engine$workflow$lifecycle$execution$WorkflowExecutionActor$$startRunnableNodes(WorkflowExecutionActor.scala:416)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:148)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:146)
        at scala.PartialFunction$OrElse.apply(PartialFunction.scala:168)
        at akka.actor.FSM.processEvent(FSM.scala:668)
        at akka.actor.FSM.processEvent$(FSM.scala:662)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowExecutionActor.scala:41)
        at akka.actor.LoggingFSM.processEvent(FSM.scala:801)
        at akka.actor.LoggingFSM.processEvent$(FSM.scala:783)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.processEvent(WorkflowExecutionActor.scala:41)
        at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:659)
        at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:653)
        at akka.actor.Actor.aroundReceive(Actor.scala:514)
        at akka.actor.Actor.aroundReceive$(Actor.scala:512)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$Timers$$super$aroundReceive(WorkflowExecutionActor.scala:41)
        at akka.actor.Timers.aroundReceive(Timers.scala:40)
        at akka.actor.Timers.aroundReceive$(Timers.scala:36)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.aroundReceive(WorkflowExecutionActor.scala:41)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
        at akka.actor.ActorCell.invoke(ActorCell.scala:496)
        at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
        at akka.dispatch.Mailbox.run(Mailbox.scala:224)
        at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
        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)

[cjllanwarne]

@rhpvorderman great comment, I don't think there's an especially nice workaround to this right now.

This is caused because defined operates on optional values (eg File?) whereas object member accesses either returns a value, or fail the workflow. We could fix this in a couple of ways:

• Change member access to always return optional values. This would have the side effect of forcing subsequent usages to handle the optional result even if you know the object has that key.
• Add a hasKey(object, key) method for objects, roughly equivalent to how you're trying to use defined.
• Maybe adding a getPath(object, path) method that returns an optional value which is set if the path exists in the object, or empty if it isn't.

And with my apologies, I'm now going to immediately redirect you elsewhere...

Since any of the above suggestions would require a change to the WDL spec, I suggest you open this as a new issue in that repo. Once the change is accepted there I'll be able to make a new issue here to implement the change in Cromwell.

[cjllanwarne]

One other comment, I'd suggest you check out (and maybe vote on) the proposed addition of structs in this PR in openWDL: https://github.com/openwdl/wdl/pull/160

If the PR passes, it's possible your problem might be fixed without needing further spec changes. You'll be able to define a Centrifuge struct like this:

struct Centrifuge {
  String? database
  # ... other fields
}

If you had this then the defined method would be able to key off the database field (which would always have a value, either set to a string, or set to a null).

This isn't part of the WDL spec yet, but it's very close, so watch out for it!

[rhpvorderman]

Thank you @cjllanwarne . A Struct would be indeed a nicer way to fix this as you can define all the items. An object can then be used for simpler things. Extra methods just add clutter. I will check it out.

EDIT: on second thought, best to leave this issue open until structs are actually there.

[rhpvorderman]

Structs are there.