Clean install, CPT processing fails

[jtheobaldhp]

docker-compose --profile omop-vocab-pg-load --env-file .env up

UMLS api key in secrets file.

omop-vocab-load  | fetch https://dl-cdn.alpinelinux.org/alpine/v3.18/community/x86_64/APKINDEX.tar.gz
omop-vocab-load  | v3.18.6-197-gcea87010f56 [https://dl-cdn.alpinelinux.org/alpine/v3.18/main]
omop-vocab-load  | v3.18.6-197-gcea87010f56 [https://dl-cdn.alpinelinux.org/alpine/v3.18/community]
omop-vocab-load  | OK: 20079 distinct packages available
omop-vocab-load  | OK: 267 MiB in 55 packages
omop-vocab-load  | Running CPT4 process
omop-vocab-load  | OK: 267 MiB in 55 packages
omop-vocab-load  | chmod: ./cpt.sh: No such file or directory
omop-vocab-load exited with code 1

Fresh install with the the vocab load profile. UMLS api key provided. Looks like bash script not located where expected.

[ajb5d]

I had this same issue and it was because I misread part of the documentation:

To load a new OMOP Vocabulary into a Postgres schema, review and fill out Section 9 of the .env file. Please note: this service will attempt to run the CPT4 import process for the CONCEPT table, so you will need a UMLS API Key from https://uts.nlm.nih.gov/uts/profile; store this in a file and set the path to the file as UMLS_API_KEY_FILE.

The Broadsea atlasdb Postgres instance is listed by default, but you can use an external Postgres instance. You need to copy your Athena downloaded files into ./omop_vocab/files.

The last line is the important part. I found these instructions from the Athena Github Wiki about how to download the vocabulary. I copied the files and then my load was successful.