Skip to main content

OMOP CSV Validator

OMOP CSV Validator is a small Perl project for validating OMOP CDM CSV extracts against rules derived from PostgreSQL DDL.

It validates files row by row, so it can be used on large OMOP exports without first loading the full CSV into memory.

What it is for​

  • checking whether a CSV file matches the expected OMOP table structure
  • validating column types without hand-writing table-specific validators
  • using the same validation logic from a CLI or from Perl code

Core workflow​

The validator works in three steps:

  1. read PostgreSQL DDL containing CREATE TABLE statements
  2. derive a schema for each table
  3. stream through the CSV and validate each row against the selected table schema

Project surfaces​

  • bin/omop-csv-validator
    • main command-line interface
  • lib/OMOP/CSV/Validator.pm
    • reusable Perl module
  • utils/reorder-csv.pl
    • helper script for reordering CSV columns to match DDL order

What these docs optimize for​

This documentation is intentionally narrower than the docs in larger application repositories.

It focuses on:

  • installation and local use
  • the main validation workflow
  • command reference
  • real caveats you are likely to hit with OMOP exports

It does not attempt to present this project as a larger platform than it is.

Current boundaries​

These docs assume:

  • PostgreSQL-style OMOP DDL files
  • CSV files whose table name can be inferred from the filename, unless overridden
  • local execution by analysts or developers working with OMOP extracts

Known limitations are described in Troubleshooting.