Validate OMOP CDM CSV exports before database ingestion

OMOP CSV Validator

OMOP CSV Validator checks the columns, nulls, and scalar values in an OMOP CDM CSV export before the file is loaded into a database. It derives the validation rules from PostgreSQL OMOP DDL, so ETL development can use the same table definitions as the target database.

📘 Documentation: https://cnag-biomedical-informatics.github.io/omop-csv-validator/

📦 CPAN Distribution: https://metacpan.org/pod/OMOP::CSV::Validator

🐳 Docker Hub Image: https://hub.docker.com/r/manuelrueda/omop-csv-validator/tags

Quick start

Install the release from CPAN:

cpan OMOP::CSV::Validator

omop-csv-validator \
  --ddl path/to/OMOPCDM_postgresql_5.4_ddl.sql \
  --input path/to/DRUG_EXPOSURE.csv

✅ CSV file 'path/to/DRUG_EXPOSURE.csv' is valid against the 'DRUG_EXPOSURE' schema.

Each invocation validates one CSV file against one OMOP table. See Installation for the recommended user-local setup and the Docker or Apptainer alternative; see the Quick Start for runnable valid and invalid examples.

Scope

This project validates CSV structure and scalar values against DDL-derived rules. It complements database-level OMOP data-quality tools; it does not replace terminology, clinical, or post-load quality review.

Development

Use the development installation and run prove -l t/.

Citation and license

Citation metadata is available in CITATION.cff. The project is released under the Artistic License 2.0.