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Doesn't seem to run with my public workflows -- am I doing something wrong? #14

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hexylena opened this issue Feb 20, 2024 · 0 comments

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@hexylena
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$ ghevaluator -u https://usegalaxy.eu/u/helena-rasche/h/cwl-target-history-1 -w https://usegalaxy.eu/u/helena-rasche/w/genome-annotation-with-prokka-feb-2020-imported-from-uploaded-file -a $GALAXY_API_KEY -o out
Traceback (most recent call last):
  File "/home/user/arbeit/galaxy/training-material/.direnv/python-3.11/lib64/python3.11/site-packages/requests/models.py", line 971, in json
    return complexjson.loads(self.text, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib64/python3.11/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib64/python3.11/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib64/python3.11/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 5 column 1 (char 4)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/arbeit/galaxy/training-material/.direnv/python-3.11/bin/ghevaluator", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/user/arbeit/galaxy/training-material/.direnv/python-3.11/lib64/python3.11/site-packages/ghevaluator/__main__.py", line 28, in main
    ghevaluator.ghevaluator(
  File "/home/user/arbeit/galaxy/training-material/.direnv/python-3.11/lib64/python3.11/site-packages/ghevaluator/__init__.py", line 349, in ghevaluator
    ref_wf = get_standard_workflow(wf_url)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/arbeit/galaxy/training-material/.direnv/python-3.11/lib64/python3.11/site-packages/ghevaluator/__init__.py", line 70, in get_standard_workflow
    return r.json()
           ^^^^^^^^
  File "/home/user/arbeit/galaxy/training-material/.direnv/python-3.11/lib64/python3.11/site-packages/requests/models.py", line 975, in json
    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 5 column 1 (char 4)

I considered that maybe it is not trying to interpret the Galaxy URL, and tried with https://usegalaxy.eu/u/helena-rasche/w/genome-annotation-with-prokka-feb-2020-imported-from-uploaded-file/json but that also did not seem to work.

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