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Bug #18835

Updated by Ward Vandewege about 2 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>

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