INCATools / INCATools/ontology-access-kit

Chore: Backslash character in test data causes pronto to have error

Open
#853 8 comments 0 reactions 0 assignees View on GitHub
chore
Dominant language
Python
Stars
198
Forks
35
Avg merge
3d 4h
Merged PRs (30d)
1

Description

Currently have to downgrade pronto to <2.6 because of line 3705 below

https://github.com/INCATools/ontology-access-kit/blob/aaede8e497e98fe7677e82730eeb56039241ac3b/tests/input/interneuron.obo#L3704-L3706

It can't handle a backslash in while parsing the file. Interested to know if this is a format error in the obo file or a bug in pronto.

Contributor guide

Open the contributing guide

Research direction

Start with tests/input/interneuron.obo around lines 3704-3706 and reproduce parsing it with pronto 2.6 or later. Check whether the backslash is valid OBO syntax or exposes a pronto parsing bug; done means documenting the cause and resolving the incompatibility with a focused regression test or confirmed format correction.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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