Bug #9659
Updated by Brett Smith over 8 years ago
It appears that the cwl documentation may be out of sync with latest arvados-cwl-runner code updates. <pre>$ <pre> ~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --debug bwa-mem.cwl bwa-mem-input.yml /data/scratch/brett/cwl/bin/arvados-cwl-runner /home/radhika/venv/bin/arvados-cwl-runner 1.0.20160717133709, arvados-python-client 0.1.20160627200331, cwltool 1.0.20160714182449 2016-07-26 20:44:32 arvados.arv-run[29762] 2016-07-21 19:43:30 arvados.arv-run[13106] INFO: Upload local files: "bwa-mem.cwl" 2016-07-26 20:44:33 arvados.arv-run[29762] 2016-07-21 19:43:30 arvados.arv-run[13106] INFO: Uploaded to qr1hi-4zz18-rbnsxtxmyjshh87 Using collection 9tee4-4zz18-1om5a5o9jxspigw 2016-07-26 20:44:33 arvados.cwl-runner[29762] 2016-07-21 19:43:30 arvados.cwl-runner[13106] ERROR: Caught unhandled exception, marking pipeline as failed. Error was: 'UploadFile' object has no attribute 'keepref' Traceback (most recent call last): File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/__init__.py", line 190, in arvExecutor runnable.run(**kwargs) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/arvjob.py", line 216, in run job_spec = self.arvados_job_spec(*args, **kwargs) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/arvjob.py", line 202, in arvados_job_spec workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/runner.py", line 85, in arvados_job_spec **kwargs) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/pathmapper.py", line 26, in __init__ super(ArvPathMapper, self).__init__(referenced_files, input_basedir, None) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/cwltool/pathmapper.py", line 90, in __init__ self.setup(referenced_files, basedir) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/pathmapper.py", line 92, in setup self._pathmap[src] = MapperEnt("keep:" + st.keepref, st.fn, "File") AttributeError: 'UploadFile' object has no attribute 'keepref' Workflow error, try again with --debug for more information: Workflow failed. Traceback (most recent call last): File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/cwltool/main.py", line 707, in main **vars(args)) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/__init__.py", line 222, in arvExecutor raise WorkflowException("Workflow failed.") WorkflowException: Workflow failed. </pre>