Fixes needed to run tutorial

[denis-yuen]

I was using cromwell-0.16.jar

The most common issue was without the declarations it would result in messages like:

$ java -jar cromwell-0.16.jar run hello.wdl hello.json
[2016-02-01 17:12:22,721] [info] RUN sub-command
[2016-02-01 17:12:22,726] [info]   WDL file: hello.wdl
[2016-02-01 17:12:22,726] [info]   Inputs: hello.json
[2016-02-01 17:12:22,858] [info] Slf4jLogger started
[2016-02-01 17:12:22,883] [info] SingleWorkflowRunnerActor: launching workflow
[2016-02-01 17:12:23,241] [info] Running with database db.url = jdbc:hsqldb:mem:76a7a3c4-4518-4249-8e74-1ee6df7bd650;shutdown=false;hsqldb.tx=mvcc
[2016-02-01 17:12:23,567] [info] WorkflowManagerActor submitWorkflow input id = None, effective id = 6cfab9e1-96d6-494a-8f9b-ee849ef12a1c
[2016-02-01 17:12:23,579] [info] WorkflowManagerActor Found no workflows to restart.
[2016-02-01 17:12:23,893] [info] WorkflowActor [6cfab9e1]: Start message received
[2016-02-01 17:12:23,953] [info] SingleWorkflowRunnerActor: workflow ID 6cfab9e1-96d6-494a-8f9b-ee849ef12a1c
[2016-02-01 17:12:23,954] [info] WorkflowActor [6cfab9e1]: ExecutionStoreCreated(Start) message received
[2016-02-01 17:12:23,962] [info] WorkflowActor [6cfab9e1]: Beginning transition from Submitted to Running.
[2016-02-01 17:12:23,963] [warn] SingleWorkflowRunnerActor: received unexpected message: CurrentState(Actor[akka://cromwell-system/user/WorkflowManagerActor/WorkflowActor-6cfab9e1-96d6-494a-8f9b-ee849ef12a1c#-586069509],Submitted)
[2016-02-01 17:12:23,964] [info] WorkflowActor [6cfab9e1]: transitioning from Submitted to Running.
[2016-02-01 17:12:23,964] [info] SingleWorkflowRunnerActor: transitioning to Running
[2016-02-01 17:12:23,966] [info] WorkflowActor [6cfab9e1]: starting calls: test.hello
[2016-02-01 17:12:23,967] [info] WorkflowActor [6cfab9e1]: persisting status of hello to Starting.
[2016-02-01 17:12:23,974] [info] WorkflowActor [6cfab9e1:hello]: Call caching 'readFromCache' is turned off, starting call
[2016-02-01 17:12:24,97] [info] WorkflowActor [6cfab9e1]: no inputs for call 'hello'
[2016-02-01 17:12:24,98] [info] WorkflowActor [6cfab9e1]: created call actor for hello.
[2016-02-01 17:12:24,103] [info] WorkflowActor [6cfab9e1]: persisting status of hello to Running.
[2016-02-01 17:12:24,123] [error] CallActor [6cfab9e1:hello]: Failing call: Could not find declaration for name
java.lang.UnsupportedOperationException: Could not find declaration for name
    at wdl4s.command.ParameterCommandPart.instantiate(ParameterCommandPart.scala:40)
    at wdl4s.Task$$anonfun$instantiateCommand$1$$anonfun$apply$2.apply(Task.scala:93)
    at wdl4s.Task$$anonfun$instantiateCommand$1$$anonfun$apply$2.apply(Task.scala:93)
    at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245)
    at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245)
    at scala.collection.Iterator$class.foreach(Iterator.scala:742)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1194)
    at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
    at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
    at scala.collection.TraversableLike$class.map(TraversableLike.scala:245)
    at scala.collection.AbstractTraversable.map(Traversable.scala:104)
    at wdl4s.Task$$anonfun$instantiateCommand$1.apply(Task.scala:93)
    at wdl4s.Task$$anonfun$instantiateCommand$1.apply(Task.scala:93)
    at scala.util.Try$.apply(Try.scala:192)
    at wdl4s.Task.instantiateCommand(Task.scala:93)
    at wdl4s.Call.instantiateCommandLine(Call.scala:104)
    at cromwell.engine.backend.Backend$class.instantiateCommand(Backend.scala:71)
    at cromwell.engine.backend.local.LocalBackend.instantiateCommand(LocalBackend.scala:112)
    at cromwell.engine.backend.local.LocalBackend$$anonfun$execute$1.apply(LocalBackend.scala:126)
    at cromwell.engine.backend.local.LocalBackend$$anonfun$execute$1.apply(LocalBackend.scala:124)
    at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
    at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
    at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
    at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
    at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
    at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
    at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
    at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
[2016-02-01 17:12:24,124] [info] WorkflowActor [6cfab9e1]: persisting status of hello to Failed.
[2016-02-01 17:12:24,126] [info] WorkflowActor [6cfab9e1]: Beginning transition from Running to Failed.
[2016-02-01 17:12:24,135] [info] WorkflowActor [6cfab9e1]: transitioning from Running to Failed.
[2016-02-01 17:12:24,135] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2016-02-01 17:12:24,136] [error] Workflow 6cfab9e1-96d6-494a-8f9b-ee849ef12a1c transitioned to state Failed
java.lang.Throwable: Workflow 6cfab9e1-96d6-494a-8f9b-ee849ef12a1c transitioned to state Failed
    at cromwell.engine.workflow.SingleWorkflowRunnerActor$RunnerData.addFailure(SingleWorkflowRunnerActor.scala:42)
    at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:88)
    at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:78)
    at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
    at akka.actor.FSM$class.processEvent(FSM.scala:604)
    at cromwell.engine.workflow.SingleWorkflowRunnerActor.akka$actor$LoggingFSM$$super$processEvent(SingleWorkflowRunnerActor.scala:53)
    at akka.actor.LoggingFSM$class.processEvent(FSM.scala:734)
    at cromwell.engine.workflow.SingleWorkflowRunnerActor.processEvent(SingleWorkflowRunnerActor.scala:53)
    at akka.actor.FSM$class.akka$actor$FSM$$processMsg(FSM.scala:598)
    at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:592)
    at akka.actor.Actor$class.aroundReceive(Actor.scala:467)
    at cromwell.engine.workflow.SingleWorkflowRunnerActor.aroundReceive(SingleWorkflowRunnerActor.scala:53)
    at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
    at akka.actor.ActorCell.invoke(ActorCell.scala:487)
    at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238)
    at akka.dispatch.Mailbox.run(Mailbox.scala:220)
    at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
    at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
    at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
    at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
    at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Workflow 6cfab9e1-96d6-494a-8f9b-ee849ef12a1c transitioned to state Failed

[scottfrazer]

This change raised an eyebrow... I'm pretty sure it should work the way it was originally. I'll take a look. Did you change this because it was broken for you or because you preferred this style over what was there?

[denis-yuen]

I wasn't sure, but thought maybe that was the intent of the section. It looked like the example under modifying-task-outputs was precisely the same as referencing-files-on-disk, so I thought maybe there was a copy-paste error and a change like that was intended to demonstrate referencing files on disk.

[scottfrazer]

I see, well thanks for this contribution! I'll merge soon

[pgrosu]

Probably the link to Draft 2 Language Specification (open) in the README.md file might need some updating as well, since it gave me a 404 error for some time.

[scottfrazer]

Thanks @pgrosu