thehyve / ohdsi-etl-prias

Transformation from PRIAS to the OMOP CDM

PRIAS to OMOP v6.x

ETL scripts to convert the Prostate cancer Research International: Active Surveillance (PRIAS) datasets to a PIONEER modification of OMOP CDM v6.x.

• Oncology WG extensions.

Mapping Document

The mapping document can be found here.

Dependencies

• Postgres (9.5+)
  • public schema
• Python 3
  • Package requirements
• OMOP vocabularies:
  • OMOP generated (Gender, Race, Type Concepts)
  • SNOMED
  • LIONC
  • NAACCR (note: NAACCR is not included in the Athena download by default, and should be selected manually)
  • UCUM
  • PIONEER custom vocabulary

Run

main.py -s <path_to_source_data> -h <host> -p <port> -d <target_db> -u <user_name> -w <password>

A log of the run will be written to logs/.log

Docker

cd ohdsi-etl-prias

docker-compose up -d will start the following containers:

• postgresql
• broadsea-webtools
• broadsea-methods-library
• jupyter
• etl

To view the progress of the database setup and etl, view the logs:

• To check the postgres database: docker-compose logs -f postgresql
• To check the ETL: docker-compose logs -f etl

To run ETL again: docker-compose up -d --build etl and check the etl logs.

Target

The resulting OMOP CDM is written to the public schema.

Updating Docker image

To download the newest image run the following commands: docker-compose down -v followed by docker-compose up -d

Note that this will remove and recreate all the OMOP vocabularies and will take a while to complete. Check the postgres with docker-compose logs -f postgresql.

Another command option to download the newest image when down -v is not working properly: docker pull thehyve/ohdsi_postgresql