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loinc / comp-loinc

Computational LOINC in OWL.
MIT License
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Missing input files #27

Closed joeflack4 closed 5 months ago

joeflack4 commented 2 years ago

Summary

@putmantime I was playing with the CLI today, but I noticed some of the files I need are missing. I wrote this up, but then I just realized that something about this was in the README.md.

Details

1. Arg: part_primary_file

Commands used in: parts Path: local_data/LoincPartLink_Primary.csv

2. Arg: part_supplementary_file

Commands used in: parts Path: local_data/LoincPartLink_Supplementary.csv

Causes

It looks like local_data is in the .gitignore. Would you be able to supply these to me?

Additional concerns

1. Some files from local_data are committed:

git ls-files | grep local_data
local_data/CHEM_HIERARCHY_LPL_DATA.xlsx
local_data/CHEM_HIERARCHY_REVISED.TSV
local_data/METHOD_CHEM_HIERARCHY.TSV
local_data/PROPERTY_CHEM_HIERARCHY.TSV
local_data/SYSTEM_CHEM_HIERARCHY.TSV
local_data/TIME_CHEM_HIERARCHY.TSV

There's a note in the README.md that says that local_data/CHEM_HIERARCHY_LPL_DATA.xlsx should be ignored. Is this the only one of these that should indeed be ignored here, or all of them?

If you'd like, I can remove these (or just that 1 file) from the current commit or the entire history if you like (at least I think I can, using a tool called BFG that I've used before).

2. Programmatic download

If you provide me w/ the missing files I can handle the programmatic download part, maybe via GoogleDrive or AWS S3 or git-lfs.

joeflack4 commented 5 months ago

This is no longer relevant, I think, as the codebase structure has change significantly.