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. This gives an ETL a file-level validation step before loading data 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 status for automation, reports for review.

The same run can return a compact command-line result and optional TSV or XLSX reports for row-level inspection.

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.