toil-cwl-runner cannot parse default if parent workflow does not provide input

Error log:

WARNING:toil.leader:9/C/job6PDNtG    WARNING:toil.resource:Can't globalize module ModuleDescriptor(dirPath='/home/johnsoni/virtualenvs/pipeline_1.2.6/lib/python2.7/site-packages', name='toil.cwl.cwltoil', fromVirtualEnv=True).
WARNING:toil.leader:9/C/job6PDNtG    DEBUG:toil.resource:Module dir is /home/johnsoni/virtualenvs/pipeline_1.2.6/lib/python2.7/site-packages
WARNING:toil.leader:9/C/job6PDNtG    WARNING:toil.resource:Can't globalize module ModuleDescriptor(dirPath='/home/johnsoni/virtualenvs/pipeline_1.2.6/lib/python2.7/site-packages', name='toil.cwl.cwltoil', fromVirtualEnv=True).
WARNING:toil.leader:9/C/job6PDNtG    DEBUG:toil.fileStore:LOG-TO-MASTER: Job 4/O/jobqSOorG/g/tmpQUrbBM-_serialiseJob-stream used 0.00% (1.5 KB [1536B] used, 10.0 GB [10737418240B] requested) at the end of its run.
WARNING:toil.leader:9/C/job6PDNtG    Traceback (most recent call last):
WARNING:toil.leader:9/C/job6PDNtG      File "/home/johnsoni/virtualenvs/pipeline_1.2.6/lib/python2.7/site-packages/toil/worker.py", line 324, in workerScript
WARNING:toil.leader:9/C/job6PDNtG        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)
WARNING:toil.leader:9/C/job6PDNtG      File "/home/johnsoni/virtualenvs/pipeline_1.2.6/lib/python2.7/site-packages/toil/job.py", line 1351, in _runner
WARNING:toil.leader:9/C/job6PDNtG        returnValues = self._run(jobGraph, fileStore)
WARNING:toil.leader:9/C/job6PDNtG      File "/home/johnsoni/virtualenvs/pipeline_1.2.6/lib/python2.7/site-packages/toil/job.py", line 1296, in _run
WARNING:toil.leader:9/C/job6PDNtG        return self.run(fileStore)
WARNING:toil.leader:9/C/job6PDNtG      File "/home/johnsoni/virtualenvs/pipeline_1.2.6/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 917, in run
WARNING:toil.leader:9/C/job6PDNtG        jobobj[key][0]] is None:
WARNING:toil.leader:9/C/job6PDNtG    KeyError: u'bam_compression_level'
WARNING:toil.leader:9/C/job6PDNtG    ERROR:toil.worker:Exiting the worker because of a failed job on host jx21
WARNING:toil.leader:9/C/job6PDNtG    WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'CWLWorkflow' 9/C/job6PDNtG with ID 9/C/job6PDNtG to 0
DEBUG:toil.leader:Added job: 'CWLWorkflow' 9/C/job6PDNtG to active jobs
DEBUG:toil.leader:Built the jobs list, currently have 1 jobs to update and 0 jobs issued

I believe that these lines from cwltoil.py:

                            if "default" in inp:
                                if key in jobobj:
                                    if isinstance(jobobj[key][1], Promise):
                                        d = copy.copy(inp["default"])
                                        jobobj[key] = DefaultWithSource(
                                            d, jobobj[key])
                                    else:
                                        if jobobj[key][1][
                                                jobobj[key][0]] is None:
                                            d = copy.copy(inp["default"])
                                            jobobj[key] = (
                                                "default", {"default": d})
                                else:
                                    d = copy.copy(inp["default"])
                                    jobobj[key] = ("default", {"default": d})

Should be change to:

                                        if hasattr(jobobj[key][1], jobobj[key][0]) and \
                                            and jobobj[key][1][jobobj[key][0]] is None:
                                                ...

but it’s a bit hard to understand the difference between jobobj[key][0] and jobobj[key][1]

┆Issue is synchronized with this Jira Task ┆Issue Number: TOIL-425

[ionox0]

I edited the title of this issue as I’ve found a minimally-reproducible example:

tool.cwl:

cwlVersion: v1.0

class: CommandLineTool

baseCommand: echo

inputs:

  input_one:
    type: int?
    inputBinding:
      position: 2

outputs: []

subworkflow.cwl:

cwlVersion: v1.0

class: Workflow

inputs:

  one: int?

outputs: []

steps:

  step_one:
    run: ./tool.cwl
    in:
      input_one:
        source: one
        default: 2
    out: []

parent_workflow.cwl:

cwlVersion: v1.0

class: Workflow

requirements:
  SubworkflowFeatureRequirement: {}

inputs:

  one: int?

outputs: []

steps:

  step_one:
    run: ./child.cwl
    in: []
#      one:
#        source: one
#        default: 1
    out: []

The difference between this workflow passing and failing is based on the presence of the input one in the parent workflow, and without it the following error occurs:

WARNING:toil.leader:c/r/jobqzOvP3    Traceback (most recent call last):
WARNING:toil.leader:c/r/jobqzOvP3      File "/Users/johnsoni/.virtualenvs/toil/lib/python2.7/site-packages/toil/worker.py", line 324, in workerScript
WARNING:toil.leader:c/r/jobqzOvP3        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)
WARNING:toil.leader:c/r/jobqzOvP3      File "/Users/johnsoni/.virtualenvs/toil/lib/python2.7/site-packages/toil/job.py", line 1351, in _runner
WARNING:toil.leader:c/r/jobqzOvP3        returnValues = self._run(jobGraph, fileStore)
WARNING:toil.leader:c/r/jobqzOvP3      File "/Users/johnsoni/.virtualenvs/toil/lib/python2.7/site-packages/toil/job.py", line 1296, in _run
WARNING:toil.leader:c/r/jobqzOvP3        return self.run(fileStore)
WARNING:toil.leader:c/r/jobqzOvP3      File "/Users/johnsoni/.virtualenvs/toil/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 917, in run
WARNING:toil.leader:c/r/jobqzOvP3        jobobj[key][0]] is None:
WARNING:toil.leader:c/r/jobqzOvP3    KeyError: u'one'
WARNING:toil.leader:c/r/jobqzOvP3    ERROR:toil.worker:Exiting the worker because of a failed job on host lski2427
WARNING:toil.leader:c/r/jobqzOvP3    WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'CWLWorkflow' c/r/jobqzOvP3 with ID c/r/jobqzOvP3 to 0

It is not present with cwltool, which runs successfully

[mr-c]

assigned to myself