Closed kevinschaper closed 10 months ago
sssupport.
🐍
Is this about rewiring at ingest time?
@matentzn yeah, I wasn't sure if it should happen in koza, kgx, or a standalone tool and I got excited about koza support because we don't need to iterate over all the rows a second time.
(Plus also that ideally koza and kgx should probably both be able to rewire based on a sssom file/df)
OK cool. So the rewire code will leave in a single module that is shared by both tools, or will this be duplicated? I would be interested to review that code once it is there, just so you know if you would like another pair of eyes on it!
KGX has a SSSOM source written by @hrshdhgd https://github.com/biolink/kgx/blob/master/kgx/source/sssom_source.py
Is that for applying mappings to rewire edges or transforming the SSSOM itself into other formats?
I don't recall writing this code.
see #109
Let's do our mapping with Koza.
We need to leave the original mapping support code available, since it's
Config changes:
SSSOM reader:
SSSOM utils:
kgx writer:
Note: I had been thinking of writing both un-mapped output and separately write the mapped files, but that feels like kind of a waste of space, since you can (fairly) easily rewind the mapping logic