Validate OMOP CDM CSV files against schemas derived from PostgreSQL DDL

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

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

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OMOP CSV Validator

OMOP CSV Validator is a small Perl CLI and module for validating OMOP CDM CSV files against schemas derived from PostgreSQL DDL.

Documentation

Full project documentation lives in the Docusaurus site under docs-site.

• Docs overview
• Installation
• Validate a CSV
• CLI reference
• Implementation
• Troubleshooting

Installation

Install the packaged release from CPAN:

cpanm -n OMOP::CSV::Validator

If you want the latest repository checkout instead:

git clone https://github.com/CNAG-Biomedical-Informatics/omop-csv-validator.git
cd omop-csv-validator
cpanm -n --installdeps .

Quick start

If you installed from CPAN:

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

If you are running from a repository checkout:

bin/omop-csv-validator \
  --ddl ddl/OMOPCDM_postgresql_5.4_ddl.sql \
  --input example/DRUG_EXPOSURE.csv

Tests

Run the test suite:

prove -l t/

Citation

If you use OMOP CSV Validator in a publication, pipeline, or shared resource, please cite or acknowledge it. Citation metadata is available in CITATION.cff, which GitHub can also expose through the repository citation panel.

License

Released under the Artistic License 2.0.