Bug #17962
Updated by Ward Vandewege over 3 years ago
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).
<pre>
$ 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
</pre>
Then, I copied a registered workflow into the project, and tried to copy it again:
<pre>
$ 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/reader.py", 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>
main()
File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/arvados/commands/arv_copy.py", 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/arv_copy.py", 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/arv_copy.py", 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/main.py", 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/main.py", 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/loader.py", 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/scanner.py", line 82, in __init__
self.reset_scanner()
File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/scanner.py", line 104, in reset_scanner
self.fetch_stream_start()
File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/scanner.py", 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/reader.py", line 180, in get_mark
if self.stream is None:
File "/usr/share/python3/dist/python3-arvados-python-client/lib/python3.7/site-packages/ruamel/yaml/reader.py", line 107, in stream
raise YAMLStreamError('input stream needs to specified')
ruamel.yaml.error.YAMLStreamError: input stream needs to specified
</pre>
Interestingly, this doesn't seem to happen all the time:
<pre>
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
</pre>