[ WebAPI | Atlas | Achilles ]

OHDSI Dockerfiles

The respository contains Dockerfiles to set up various OHDSI tools.

WebAPI

The OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications.

Quickstart

Use the following command to spin up the WebAPI. Make sure to change the values of the environment variables as needed.

docker run \
  --name ohdsi-webapi \
  -p 8080:8080 \
  -e "DBHOST=docker.for.mac.host.internal" \
  -e "DBNAME=cdm" \
  -e "DBUSER=postgres" \
  -e "DBPASS=s3cret" \
  -e "DBADMINUSER=postgres" \
  -e "DBADMINPASS=s3cret" \
  -e "DBCDMSCHEMA=public" \
  -e "DBWEBAPISCHEMA=webapi" \
  uwcarg/ohdsi-webapi:2.3.0-postgres

💡 docker.for.mac.host.internal is a magic constant in Docker for macOS that points to the IP address of the host machine.

Test

Navigate to the following URLS to test:

• http://localhost:8080/WebAPI/source/sources
• http://localhost:8080/WebAPI/vocabulary/search/cardiomyopathy

README ≫

Atlas

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data.

Quickstart

Use the following command to spin up Atlas. Make sure to change the values of the environment variables as needed. Atlas depends on the OHDSI WebAPI, so you will need to have that up and running.

docker run \
  --name ohdsi-atlas \
  -p 8081:80 \
  -e "WEBAPIURL=http://localhost:8080/WebAPI/" \
  -e "ORGNAME=Momcorp" \
  uwcarg/ohdsi-atlas:2.3.0

Test

Navigate to the following URL:

• http://localhost:8081/

README ≫

Achilles

Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM database.

Quickstart

Use the following command to spin up Atlas. Make sure to change the values of the environment variables as needed. In the example below the database username and password are represented by postgres:s3cret. Data will be read from ACHILLES_CDM_SCHEMA and ACHILLES_VOCAB_SCHEMA, and the results will be written to ACHILLES_RES_SCHEMA.

docker run \
  --rm \
  --net=host \
  -v "$(pwd)"/output:/opt/app/output \
  -e "ACHILLES_SOURCE=Docker Default" \
  -e "ACHILLES_DB_URI=postgresql://postgres:s3cret@localhost:5432/cdm" \
  -e "ACHILLES_CDM_SCHEMA=public" \
  -e "ACHILLES_VOCAB_SCHEMA=public" \
  -e "ACHILLES_RES_SCHEMA=webapi" \
  -e "ACHILLES_CDM_VERSION=5" \
  uwcarg/ohdsi-achilles:1.5.0

README ≫

License