Bug #18835
Updated by Ward Vandewege almost 3 years ago
<pre>
$ 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
</pre>