KGX problem while transforming to tsv due to Unknown CURIE prefix: file

Knowledge-Graph-Hub / kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub

https://knowledge-graph-hub.github.io/kg-obo/getting_started.html

GNU General Public License v3.0

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KGX problem while transforming to tsv due to Unknown CURIE prefix: file #183

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

Describe the bug

Transforms with classes involving the prefix file: fail when converting json to tsv.

To Reproduce

python run.py --bucket kg-hub-public-data --include_only gaz

This should yield:

[KGX][cli_utils.py][    transform_source] INFO: Processing source 'gaz.json'
KGX problem while transforming ['data/gaz/no_version/gaz.json'] to tsv due to Unknown CURIE prefix: file

Expected behavior

Node normalization should handle these - these nodes probably aren't resolvable