Arvados

$ arvados-cwl-runner --debug xxxx1-7fd4e-redactedredacte --fasta_file keep/shared/redact\ redacte/redactedred/reda\ redactedre\ r/test_fasta.fa --stdout_name "test1" 

INFO /usr/bin/arvados-cwl-runner 2.3.2, arvados-python-client 2.3.2, cwltool 3.1.20211107152837
INFO Resolved 'xxxx1-7fd4e-REDACTEDREDACTE' to 'arvwf:xxxx1-7fd4e-REDACTEDREDACTE#main'
DEBUG Parsed job order from command line: {
    "id": "xxxx1-7fd4e-REDACTEDREDACTE",
    "fasta_file": {
        "class": "File",
        "location": "file:///home/redacted/keep/shared/redact%20redacte/redactedred/reda%20redactedre%20r/test_fasta.fa" 
    },
    "stdout_name": "test1" 
}
INFO Using cluster xxxx1 (https://workbench2.xxxx1.redactedredacted.redacted/)
ERROR Unhandled error:
  name 'file' is not defined
Traceback (most recent call last):
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/cwltool/main.py", line 1302, in main
    (out, status) = real_executor(
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/arvados_cwl/executor.py", line 564, in arv_executor
    job_order = upload_job_order(self, "%s input" % runtimeContext.name,
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/arvados_cwl/runner.py", line 557, in upload_job_order
    jobmapper = upload_dependencies(arvrunner,
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/arvados_cwl/runner.py", line 395, in upload_dependencies
    mapper = ArvPathMapper(arvrunner, sc, "",
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/arvados_cwl/pathmapper.py", line 64, in __init__
    super(ArvPathMapper, self).__init__(referenced_files, input_basedir, None)
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/cwltool/pathmapper.py", line 70, in __init__
    self.setup(dedup(referenced_files), basedir)
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/arvados_cwl/pathmapper.py", line 184, in setup
    self.visit(srcobj, uploadfiles)
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/arvados_cwl/pathmapper.py", line 87, in visit
    st = arvados.commands.run.statfile("", ab,
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/arvados/commands/run.py", line 108, in statfile
    (pdh, branch) = is_in_collection(sp[0], sp[1])
  File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.8/site-packages/arvados/commands/run.py", line 68, in is_in_collection
    with file(fn, 'r') as f:
NameError: name 'file' is not defined