brptoolkit-demo-data

README

BRP Toolkit Demo Data

A CLI to manage data for The Biorepository Toolkit Demonstration

Quickstart

# 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>

For example: brptoolkit-demo-data redcap local

Run transforms

** 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

Targets are defined in the config.yaml file which exists in the same directory as the brptoolkit-demo-data binary.

For example, the target local could be configured as such:

targets:
  local:
    host: localhost
    port: 5432
    user: user
    password:
    db: brp_demo_data

Source Data

REDCap

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.

eHB

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