BRP Toolkit Demo Data
A CLI to manage data for The Biorepository Toolkit Demonstration
# Build Docker image docker build -t brp-demo-data . # Start postgres instance docker run -d --name upntb_pg -p :5432 postgres:9.4 # Create brp_demodatabase on postgres instance docker run --rm --link upntb_pg:db postgres:9.4 createdb -h db -U postgres demo_data # Run ETL docker run --rm --link upntb_pg:db brptoolkit-demo-data etl container
Run in Docker with custom config
docker run --rm --link brp_demo_pg:db -v $(pwd)/config.yaml:/go/src/app/config.yaml brp-demo-data etl container
Run all ETL
brptoolkit-demo-data etl <target>
Run staging ETL only
brptoolkit-demo-data <source> <target>
brptoolkit-demo-data redcap local
** Note: Transforms are dependent on the staging data so you will want to run transformations just once, only after staging has been performed. **
brptoolkit-demo-data transform <target>
Targets are defined in the
config.yaml file which exists in the same directory as the
For example, the target
local could be configured as such:
targets: local: host: localhost port: 5432 user: user password: db: brp_demo_data
brptoolkit-demo-data uses REDCap as a means of capturing clinical data regarding subjects on study.
In order to pull data users must configure the REDCap portion of
config.yaml. brptoolkit-demo-data uses go-cap to pull REDCap data.
REDCap: url: "https://redcap.chop.edu/api/" projects: upntb: "your API key"
brptoolkit-demo-data will pull all forms for the API key given and persist them. brptoolkit-demo-data will ignore legacy forms with "old" in the name.
brptoolkit-demo-data uses the eHB to manage identities across systems. Groups of subjects are defined in the Biorepository Portal as Protocols. brptoolkit-demo-data the API provided by the BRP to pull external samples associated with groups of patients to build a link table -- linking a Subject in the portal to its associated REDCap records
BRP: url: "https://<brp_host>/api/" token: "<your_token>" protocols: - 1 - 2 - 3 - 4