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Sbpack 2020.10.5 Fails when there's a url in the cwl. Older versions don't #12

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violetbrina opened this issue May 20, 2021 · 0 comments · Fixed by #15 or #16
Closed

Sbpack 2020.10.5 Fails when there's a url in the cwl. Older versions don't #12

violetbrina opened this issue May 20, 2021 · 0 comments · Fixed by #15 or #16

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@violetbrina
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For sbpack 2020.10.5 packing where the run: points to a url fails:

sbpack v2020.10.05
Upload CWL apps to any Seven Bridges powered platform
(c) Seven Bridges 2020

Traceback (most recent call last):
  File "/Users/srispin/.local/bin/sbpack", line 8, in <module>
    sys.exit(main())
  File "/Users/srispin/.local/pipx/venvs/sbpack/lib/python3.8/site-packages/sbpack/pack.py", line 356, in main
    cwl = pack(cwl_path, filter_non_sbg_tags=args.filter_non_sbg_tags)
  File "/Users/srispin/.local/pipx/venvs/sbpack/lib/python3.8/site-packages/sbpack/pack.py", line 318, in pack
    cwl = pack_process(cwl, full_url)
  File "/Users/srispin/.local/pipx/venvs/sbpack/lib/python3.8/site-packages/sbpack/pack.py", line 65, in pack_process
    cwl = resolve_steps(cwl, base_url, user_defined_types)
  File "/Users/srispin/.local/pipx/venvs/sbpack/lib/python3.8/site-packages/sbpack/pack.py", line 201, in resolve_steps
    v["run"], new_base_url = lib.load_linked_file(
  File "/Users/srispin/.local/pipx/venvs/sbpack/lib/python3.8/site-packages/sbpack/lib.py", line 132, in load_linked_file
    new_url = resolved_path(base_url, link)
  File "/Users/srispin/.local/pipx/venvs/sbpack/lib/python3.8/site-packages/sbpack/lib.py", line 125, in resolved_path
    new_url = urllib.parse.ParseResult(link_url)
TypeError: __new__() missing 5 required positional arguments: 'netloc', 'path', 'params', 'query', and 'fragment'

Where as, in an older version I get no issues (2020.6.18)
sbpack cavatica mwonge/mwtest/graphene-sage-hg19 graphene-sage.hg19.cwl

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