Gen3-data-dictionary-dev

This repository contains dev notes and instructions for how to create and manage a Gen3 data dictionary using the Australian BioCommons Gen3 Schema Dev tools and UMCCR-dictionary for USyd use cases.

Set up and tooling

Run notebooks provided here with PyCharm community edition or VScode.

Generate the schema DAG

See USyd gen3 data dictionary repo.

1. Get a copy of the code

git submodule add https://github.com/Sydney-Informatics-Hub/usyd-gen3-data-dictionary usyd-gen3-data-dictionary
git submodule add https://github.com/AustralianBioCommons/gen3schemadev.git gen3schemadev 

2. Launch containers. Need to have Docker desktop installed to run the following commands:

cd ./usyd-gen3-data-dictionary && git pull
make pull # pull updates/dependencies for project
make up # spin up containers 
make ps # display status of containers

3. Refactor the yamls into json

cp -r ../dictionary/thyroid dictionary/.
make compile program=thyroid # write schema to json 
make validate program=thyroid # do validation checks

4. Generate and visualise the DAG

open http://localhost:8080/#schema/thyroid.json