This exposed a different bug with URI quoting filenames:
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr Traceback (most recent call last):
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/arvados_cwl/crunch_script.py", line 140, in run
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr runner.arv_executor(t, job_order_object, args, logger=logger)
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/arvados_cwl/__init__.py", line 559, in arv_executor
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr runtimeContext)
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/arvados_cwl/arvtool.py", line 42, in job
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr builder = self._init_job(joborder, builderargs)
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/cwltool/process.py", line 594, in _init_job
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr fill_in_defaults(self.tool[u"inputs"], job, fs_access)
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/cwltool/process.py", line 392, in fill_in_defaults
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr visit_class(job, ("File",), functools.partial(add_sizes, fsaccess))
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/cwltool/utils.py", line 223, in visit_class
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr visit_class(rec[d], cls, op)
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/cwltool/utils.py", line 221, in visit_class
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr op(rec)
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/cwltool/process.py", line 369, in add_sizes
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr obj["size"] = fsaccess.size(obj["location"])
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr File "/usr/lib/python2.7/dist-packages/arvados_cwl/fsaccess.py", line 149, in size
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr raise IOError(errno.EINVAL, "Not a path to a file %s" % (fn))
2018-08-13_18:36:52 2tlax-8i9sb-vg3zchxctq1q4mk 29781 0 stderr IOError: [Errno 22] Not a path to a file keep:6bf7c0d0f95d3ca89ce7a1d64ea4ff0a+56/item%20%231.txt