Issue using CodeListGenerator locally
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 35/100
Research direction
Start by following the linked Getting OMOP CDM Vocabularies vignette with the Athena vocabulary dated 27/08/2025, using the local vocabulary database setup. Inspect the warning about drug_strength and the resulting cdm_reference object; done means drug_strength is available there and code searches complete without the reported error.
Written by the indexing model from the issue text.
Description
Describe the bug
I'm following this vignette to use CodelistGenerator locally: https://darwin-eu.github.io/CodelistGenerator/articles/a01_GettingOmopCdmVocabularies.html#create-a-local-vocabulary-database
It creates a cdm reference effectively but I get a warning message related to drug_strength. When searching for codes, I get an error saying that drug_strength does not exist in the cdm_reference object.
To Reproduce
Follow the same vignette using the Vocabulary downloaded from Athena (version 27/08/2025)
Screenshots
Additional context
I'm using macOS; CodelistGenerator version 3.5; Omopgenerics version 1.3.2.
- Dominant language
- R
- Stars
- 18
- Forks
- 9
- PR merge metrics
- No merged PRs in 30d
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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