Dockstore CLI Fails Launching a WDL with Imports

Bug Report

The following checker workflow has WDL imports. You get an NPE when you try to launch it:

dockstore workflow launch --entry github.com/DataBiosphere/topmed-workflows/u_of_Michigan_alignment_pipeline_wdl_checker:1.29.0 --json foo.json
15:15:23.562 [main] ERROR io.dockstore.client.cli.ArgumentUtility - Could not get WDL imports: null
15:15:23.567 [main] ERROR io.dockstore.client.cli.ArgumentUtility - java.lang.NullPointerException
	at wdl4s.wdl.WdlNamespace$.apply(WdlNamespace.scala:216)
	at wdl4s.wdl.WdlNamespace$$anonfun$wdl4s$wdl$WdlNamespace$$load$1.apply(WdlNamespace.scala:179)
	at wdl4s.wdl.WdlNamespace$$anonfun$wdl4s$wdl$WdlNamespace$$load$1.apply(WdlNamespace.scala:179)
	at scala.util.Try$.apply(Try.scala:192)
	at wdl4s.wdl.WdlNamespace$.wdl4s$wdl$WdlNamespace$$load(WdlNamespace.scala:178)
	at wdl4s.wdl.WdlNamespace$$anonfun$20.apply(WdlNamespace.scala:209)
	at wdl4s.wdl.WdlNamespace$$anonfun$20.apply(WdlNamespace.scala:207)
	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
	at scala.collection.immutable.List.foreach(List.scala:392)
	at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
	at scala.collection.immutable.List.map(List.scala:296)
	at wdl4s.wdl.WdlNamespace$.apply(WdlNamespace.scala:207)
	at wdl4s.wdl.WdlNamespace$$anonfun$wdl4s$wdl$WdlNamespace$$load$1.apply(WdlNamespace.scala:179)
	at wdl4s.wdl.WdlNamespace$$anonfun$wdl4s$wdl$WdlNamespace$$load$1.apply(WdlNamespace.scala:179)
	at scala.util.Try$.apply(Try.scala:192)
	at wdl4s.wdl.WdlNamespace$.wdl4s$wdl$WdlNamespace$$load(WdlNamespace.scala:178)
	at wdl4s.wdl.WdlNamespace$.loadUsingSource(WdlNamespace.scala:175)
	at wdl4s.wdl.WdlNamespaceWithWorkflow$.load(WdlNamespace.scala:555)
	at io.dockstore.common.Bridge.getInputFiles(Bridge.scala:91)
	at io.github.collaboratory.wdl.WDLClient.launch(WDLClient.java:151)
	at io.dockstore.client.cli.nested.WorkflowClient.launch(WorkflowClient.java:436)
	at io.dockstore.client.cli.nested.AbstractEntryClient.processEntryCommands(AbstractEntryClient.java:226)
	at io.dockstore.client.cli.Client.run(Client.java:706)
	at io.dockstore.client.cli.Client.main(Client.java:608)```
Here is the foo.json, used as an input:

 "checkerWorkflow.input_cram_file": "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/input_files/NWD176325.25reads.cram",
"checkerWorkflow.input_crai_file": "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/input_files/NWD176325.25reads.cram.crai",
  "checkerWorkflow.inputTruthCRAMFile": "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner_checker/truth_NWD176325.25reads.cram",
  "checkerWorkflow.ref_alt":  "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/hs38DH.fa.alt",
  "checkerWorkflow.ref_bwt":  "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/hs38DH.fa.bwt",
  "checkerWorkflow.ref_pac":  "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/hs38DH.fa.pac",
  "checkerWorkflow.ref_ann":  "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/hs38DH.fa.ann",
  "checkerWorkflow.ref_amb":  "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/hs38DH.fa.amb",
  "checkerWorkflow.ref_sa":  "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/hs38DH.fa.sa",
  "checkerWorkflow.ref_fasta":  "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/hs38DH.fa",
  "checkerWorkflow.ref_fasta_index":  "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/hs38DH.fa.fai",
  "checkerWorkflow.dbSNP_vcf": "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/Homo_sapiens_assembly38.dbsnp138.vcf.gz",
  "checkerWorkflow.dbSNP_vcf_index": "https://storage.googleapis.com/topmed_workflow_testing/topmed_aligner/reference_files/hg38/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi",
  "checkerWorkflow.docker_image": "statgen/alignment:1.0.0"
}```



┆Issue is synchronized with this [Jira Bug](https://ucsc-cgl.atlassian.net/browse/DOCK-95)
┆Issue Number: DOCK-95
┆Sprint: Backlog
┆Issue Type: Bug

[coverbeck]

Verified this with staging, using Cromwell 36.

My ~/.dockstore/config settings:

server-url: https://staging.dockstore.org/api
cromwell-version: 36

And I did an EXPORT DOCKSTORE_VERSION=1.5.3

The workflow failed at the very end, running on a Mac, due to a known problem with the workflow that Walt is going to look into, but it is unrelated to the provisioning that this bug fixes. Here’s the output when running the Java program:

[2018-12-05 11:51:14,99] [info] BackgroundConfigAsyncJobExecutionActor [abbd26efcheckerWorkflow.checkerTask:NA:1]: job id: 70032
[2018-12-05 11:51:15,00] [info] BackgroundConfigAsyncJobExecutionActor [abbd26efcheckerWorkflow.checkerTask:NA:1]: Status change from - to WaitingForReturnCode
[2018-12-05 11:52:48,39] [info] BackgroundConfigAsyncJobExecutionActor [abbd26efcheckerWorkflow.checkerTask:NA:1]: Status change from WaitingForReturnCode to Done
[2018-12-05 11:52:49,37] [error] WorkflowManagerActor Workflow abbd26ef-a445-48ec-b1e5-6b6a19604a61 failed (during ExecutingWorkflowState): Job checkerWorkflow.checkerTask:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /Users/charlesoverbeck/tmp/cromwell-executions/checkerWorkflow/abbd26ef-a445-48ec-b1e5-6b6a19604a61/call-checkerTask/execution/stderr.
 [samfaipath] build FASTA index...
md5sum: WARNING: 1 computed checksum did NOT match

[coverbeck]

cc: @wshands

I think this workflow doesn’t work with Cromwell 30.2. I think I ran it successfully with Cromwell 36. Will try later today. Sorry for the confusion.