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Babel v1.10.0 #424

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Babel v1.10.0 #424

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@gaurav gaurav commented Mar 13, 2025

This is Babel v1.10.0.

Changes:

  • Updated RxNorm from 01062025 to 03032025.

gaurav and others added 25 commits March 13, 2025 01:28
@gaurav
Updated RxNorm version.
be6151a
@gaurav
Python 3.13 doesn't appear to work with bmt.
9486570 
So let's try Python 3.12.
@gaurav
Added on:push trigger for testing.
97ef387
@gaurav
Updated Babel k8s version for testing.
5b9427f
@gaurav
First stab at a PubMed verifier.
d2d9fd7
@gaurav
Fixed reference to output file.
3668f1a
@gaurav
Fixed dir reference.
907896c
@gaurav
Added trailing '/' to PubMed base.
d8284e4
@gaurav
Added a further check.
f81f549
@gaurav
Added even more checks.
5830130
@gaurav
Left out done file from PubMed download, oops.
378bde8
@gaurav
Actually, don't remove them -- truncate them.
eab1015 
If we remove them, we lose track that they were ever here -- so
if we can't download them properly, the next time we run this
code the file will be skipped entirely. Let's not do that.
@gaurav
Added length to truncate, improved documentation.
17be3ef
@gaurav
Slightly improved logging on util.gzip_files().
9bd58b9
@gaurav
Updated synonyms check to look for .gz files.
ac9e1a0
@gaurav
Explicitly compressed and temp()ed DrugChemicalConflated.txt.
e63503f
@gaurav
Compressed CellLine.
521cd42
@gaurav
Modified DuckDB synonyms load to use gzipped file.
862108c
@gaurav
Put umls_done in the right place.
0bd266a
@gaurav
Removed done file from leftover UMLS.
338101a
@gaurav
Removed variable left over after delete.
8b026b6
@gaurav
generate_sapbert_training_data() now uses .gz files.
193d675
@gaurav
Modified drugchemical_conflated_synonyms to use gzipped files.
7e25141
@gaurav
Removed DrugChemical re-gzipping Chemical outputs.
172507f
@gaurav
This is just crazy enough to work.
7a3eeea
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@gaurav