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Fix bug in report.py when dealing with empty list #803

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y9c
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@y9c y9c commented Aug 28, 2024

cutseq report this error when eranges is None.

  File ".micromamba/lib/python3.12/site-packages/cutadapt/report.py", line 246, in as_json
    self._adapter_statistics_as_json(
  File ".micromamba/lib/python3.12/site-packages/cutadapt/report.py", line 302, in _adapter_statistics_as_json
    "error_lengths": make_line(eranges),
                     ^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable

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y9c commented Aug 28, 2024

close #804

@marcelm
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marcelm commented Sep 13, 2024

How did you trigger this? Would be good to have a test as well.

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marcelm commented Sep 13, 2024

Oh, you’re calling _adapter_statistics_as_json with one_line=False.

Your suggested fix is not correct because error_lengths needs to be null when not available as documented.

I think the correct fix is to change:

        make_line = OneLine if one_line else list

to

        make_line = OneLine if one_line else lambda x: x

@marcelm marcelm closed this in bddd1aa Nov 14, 2024
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2 participants