Broadsea-atlasdb

This container is part of the OHDSI Broadsea set of Docker containers.

A Postgres database in a Docker container pre-configured with OHDSI Atlas/WebAPI application schema tables and loaded with a demo CDM containing synthetic patient data (Eunomia) It also contains a very simple demo concept set & cohort definition. See the OHDSI/Eunomia GitHub repo for information about the OHDSI Eunomia sqlite database.

Optional support for Atlas database based security is included with two pre-configured Atlas users: userid=ohdsi, password=ohdsi and userid=admin, password=admin

This database is intended to be used with the Broadsea-Webtools Atlas/WebAPI Docker container for Atlas application demo/training and for Atlas/WebAPI software unit testing.

See the OHDSI/Broadsea GitHub repo Broadsea documentation for instructions and a docker-compose.yml file to start the Atlas application using Broadsea-Webtools with this database container.

Start this Postgres database container

docker compose up -d

Database userid: postgres Default password (can be changed in the docker-compose.yml file): mypass

Postgres database data management

This container uses a docker volume to manage the Postgres data. It will create a new docker volume called atlasdb-postgres-data if it does not already exist. The Postgres database data will be retained in the docker volume (even if the container is restarted using docker compose down / up -d).

To list the docker volumes on the host server use the below command:

docker volume ls

To reset the postgres database data use the below command. Note this command will permanently delete any data changes made to the demo CDM dataset:

docker volume rm atlasdb-postgres-data

postgresql database JDBC connection string - used to connect to this database from a postgresql client

Use localhost as the database host IP address to connect from the local computer where this database container is running (127.0.0.1 is equivalent), Otherwise use the IP address of the remote server where the container is running

jdbc:postgresql://localhost:5432/postgres?user=postgres&password=mypass

Build the container - only needed to customize the contents of the database

The preferred approach is to just pull the pre-built Docker container image in Docker Hub. Below is the command to build the container:

docker compose build

Vendored SQL for offline, deterministic builds

This repository includes pre-generated SQL artifacts under vendor/ that are used during image build:

• vendor/cdm/omop_cdm_postgres_ddl.sql
• vendor/webapi/results_postgresql.ddl
• vendor/webapi/webapi_baseline_V2.2.5.20180212152023_postgresql.sql

Regenerating vendored SQL (maintainers)

Prerequisites: git, Java (JRE), and either Maven, curl, or wget. Set the default versions to use for the SQL (DDL) regeneration script in the Makefile SQLRENDER_VERSION WEBAPI_VERSION CDM_VERSION

• Run the script to regenerate the vendored SQL (DDL) from the required OHDSI WEBAPI and OMOP CDM GitHub versions:

make regen-webapi-sql

• Clean temp files and vendored outputs (keep Maven cache):

make clean

• Purge SqlRender from Maven cache only (forces re-download on next regen):

make clean-sqlrender

If needed, you can point the regen script at a local SqlRender jar:

SQLRENDER_JAR=/path/to/SqlRender-1.9.2.jar make regen-webapi-sql