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Weird behaviour if overlapping uri expansions during sssom parse #269

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matentzn opened this issue Jun 13, 2022 · 0 comments · Fixed by #409
Closed

Weird behaviour if overlapping uri expansions during sssom parse #269

matentzn opened this issue Jun 13, 2022 · 0 comments · Fixed by #409
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sssom parse uberon-base.json --input-format obographs-json --metadata metadata.yml --prefix-map-mode merged --output uberon.sssom.tsv

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@matentzn matentzn self-assigned this Jun 13, 2022
@ehartley ehartley mentioned this issue Aug 8, 2023
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@hrshdhgd hrshdhgd mentioned this issue Aug 10, 2023
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hrshdhgd added a commit that referenced this issue Aug 11, 2023
@hrshdhgd @matentzn
Use curies' Converter in strict=False mode. (#409)
a23c4dd 
- [x] Fixes #408 
- [x] Fixes #269 

This way, when a `prefix_map` has duplicate `uri_prefix` or `prefix`
from the user, `curies` will not throw an error. `sssom-py` already
gives priority to a user-defined prefix map over the default one (which
now is EPM from bioregistry).

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Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
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Use curies' Converter in strict=False mode. mapping-commons/sssom-py
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