https://github.com/sydney-informatics-hub/gen3-data-dictionary-dev
https://github.com/sydney-informatics-hub/gen3-data-dictionary-dev
Last synced: over 1 year ago
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- Host: GitHub
- URL: https://github.com/sydney-informatics-hub/gen3-data-dictionary-dev
- Owner: Sydney-Informatics-Hub
- Created: 2024-04-19T02:50:13.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-08-16T01:35:39.000Z (almost 2 years ago)
- Last Synced: 2025-01-22T11:12:55.346Z (over 1 year ago)
- Language: Python
- Size: 168 KB
- Stars: 1
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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](https://github.com/AustralianBioCommons/gen3schemadev) and [UMCCR-dictionary](https://github.com/AustralianBioCommons/umccr-dictionary) for USyd use cases.
## Set up and tooling
Run notebooks provided here with [PyCharm community edition](https://www.jetbrains.com/pycharm/download) or VScode.
## Generate the schema DAG
See [USyd gen3 data dictionary repo](https://github.com/Sydney-Informatics-Hub/usyd-gen3-data-dictionary).
1. Get a copy of the code
```bash
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:
```bash
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
```bash
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
```bash
open http://localhost:8080/#schema/thyroid.json
```