I assume it’s no longer relevant to you since this is a post from three years ago, but in case someone stumbles on this thread after encountering this error, like I did -
what solved it to me, was downloading ALL relevant vocabularies from https://athena.ohdsi.org/.
Originally, I followed the instructions here:
https://github.com/OHDSI/ETL-CMS/tree/master/python_etl
which state:
“Download vocabulary files from http://www.ohdsi.org/web/athena/, ensuring that you select at minimum, the following vocabularies: SNOMED, ICD9CM, ICD9Proc, CPT4, HCPCS, LOINC, RxNorm, and NDC.”
My mistake was only downloading these vocabularies that they state as a MINIMUM.
This caused these errors, since not all required concepts were downloaded.
I suggest instead to download ALL vocabularies that are selected by default.