Bug #17962


[arv-copy] blows up when copying a project with a registered workflow in it

Added by Ward Vandewege about 2 years ago. Updated almost 2 years ago.

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Trying to copy a test project from pirca to tordo.

First, the project contained only collections and container requests. The collections were copied, container requests ignored (as expected).

# on shell.tordo
$ arv-copy pirca-j7d0g-bbu5p6jsjjfokta
pirca-4zz18-ccifrmbm41a3z84: 0M / 0M 100.0% 
pirca-4zz18-aneymw4b20pwug0: 0M / 0M 100.0% 
pirca-4zz18-smataa81t834uug: 0M / 0M 100.0% 
pirca-4zz18-k03bijojmx1m3n1: 0M / 0M 100.0% 
pirca-4zz18-ldybp10d3adj60u: 0M / 0M 100.0% 
pirca-4zz18-nuz3ntrreffkanr: 0M / 0M 100.0% 
pirca-4zz18-3xsu89n5mbiy2l6: 0M / 0M 100.0% 
pirca-4zz18-ghfqhzbn8z9bghc: 0M / 0M 100.0% 
pirca-4zz18-uvwqkky5kjtthem: 0M / 0M 100.0% 
2021-08-02 15:17:03 arvados.arv-copy[26659] INFO: 
2021-08-02 15:17:03 arvados.arv-copy[26659] INFO: Success: created copy with uuid tordo-j7d0g-2s0oya2vzqps25h

Then, I copied a registered workflow into the project, and tried to copy it again:

$ arv-copy pirca-j7d0g-bbu5p6jsjjfokta
Traceback (most recent call last):
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 105, in stream
    return self._stream
AttributeError: 'SafeLoader' object has no attribute '_stream'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/bin/arv-copy", line 7, in <module>
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/arvados/commands/", line 144, in main
    result = copy_project(args.object_uuid, src_arv, dst_arv, args.project_uuid, args)
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/arvados/commands/", line 683, in copy_project
    copy_workflow(w["uuid"], src, dst, args)
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/arvados/commands/", line 291, in copy_workflow
    wf_def = yaml.safe_load(wf["definition"])
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 994, in safe_load
    return load(stream, SafeLoader, version)
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 947, in load
    loader = Loader(stream, version, preserve_quotes=preserve_quotes)
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 40, in __init__
    Scanner.__init__(self, loader=self)
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 82, in __init__
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 104, in reset_scanner
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 446, in fetch_stream_start
    mark = self.reader.get_mark()
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 180, in get_mark
    if is None:
  File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/", line 107, in stream
    raise YAMLStreamError('input stream needs to specified')
ruamel.yaml.error.YAMLStreamError: input stream needs to specified

Interestingly, this doesn't seem to happen all the time:

ward@shell:~$ dpkg -l |grep arv
ii  arvados-client                         2.3.0~dev20210803154620-1                   amd64        Arvados command line tool (beta)
ii  arvados-src                            2.3.0~dev20210803154620-1                   all          The Arvados source code
ii  libpam-arvados-go                      2.3.0~dev20210803154620-1                   amd64        Arvados PAM authentication module
ii  python3-arvados-cwl-runner             2.3.0~dev20210729201354-1                   amd64        Arvados Common Workflow Language runner
ii  python3-arvados-fuse                   2.3.0~dev20210726143205-1                   amd64        Arvados FUSE driver
ii  python3-arvados-python-client          2.3.0~dev20210726143205-1                   amd64        Arvados client library

ward@shell:~$ arv-copy pirca-j7d0g-qv5r6tyawa0fri3 --project-uuid ce8i5-j7d0g-3b990qlglr7cmse
pirca-4zz18-3ik849l082fqjcz: 0M / 0M 100.0% 
pirca-4zz18-xa0i7qjide8td5d: 156M / 156M 100.0% 
pirca-4zz18-n9os5bjq4ipwe7d: 23M / 23M 100.0% 
pirca-4zz18-xos3zqns62comjb: 94M / 94M 100.0% 
pirca-4zz18-ckim3zvdmbf3i05: 0M / 0M 100.0% 
pirca-4zz18-3n2p2xu20q42it0: 259M / 259M 100.0% 
2021-08-03 17:26:39 arvados.arv-copy[28298] INFO: 
2021-08-03 17:26:39 arvados.arv-copy[28298] INFO: Success: created copy with uuid ce8i5-j7d0g-fqjqh6cs9nezwey

Subtasks 1 (0 open1 closed)

Task #18038: Review 17962-check-wf-definitionResolvedPeter Amstutz11/17/2021


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