Pre-ingestion OMOP checks

OMOP CSV Validator

Validate OMOP CDM CSV files before database ingestion.

Each run checks one CSV file for one OMOP table against OMOP PostgreSQL DDL. Run it during ETL development, before loading the file into PostgreSQL.

Validate a CSV Review reports Read docs

Example validation run

$ omop-csv-validator \
  --ddl OMOPCDM.sql \
  --input PERSON.csv
OK PERSON.csv is valid

$ omop-csv-validator \
  --ddl OMOPCDM.sql \
  --input DRUG_EXPOSURE.csv
ERROR 1 row failed validation

Valid filesexit 0

Invalid filesexit 1

Reportsoptional

Validation output

Terminal, JSON, TSV, and XLSX output

The exit code and terminal output report the result. Optional TSV and XLSX files include one status per row.

OMOP CSV Validator command-line and spreadsheet result preview

First run

Quick start

Run bundled valid and failing examples and inspect the real results.

Batch

Validate a folder

Use a shell loop or workflow job to run the validator once per CSV file.

Review

Spreadsheet reports

Create TSV or XLSX reports that show which rows need attention.

Automation

Use JSON output

Call the same CLI from R, Python, notebooks, or workflow jobs.