Data Curator App for CSBC

Introduction

The Data Curator App is an R Shiny app that serves as the frontend to the schematic Python package. It allows data contributors to easily annotate, validate and submit their metadata.

---

Get Started and Installation

Follow the steps below to make sure the Data Curator App is fully setup to work with the schematic:

Data Curator App Setup

1. Clone this repo (front-end) with one single branch (i.e., main):

   git clone --single-branch --branch main https://github.com/Sage-Bionetworks/data_curator.git
   

2. Create and modify the configuration file (How to obtain OAuth Credential):

   cp example_oauth_config.yml oauth_config.yml
   chmod 400 oauth_config.yml
   

3. Create and activate a virtual environment within which you can install the package:

   python -m venv .venv
   source .venv/bin/activate
   

4. Install required R pacakges dependencies:

   R -f install-pkgs.R
   

Schematic Setup

1. Clone the schematic (backend) as a folder schematic inside the data_curator folder:

   git clone --single-branch --branch develop https://github.com/Sage-Bionetworks/schematic.git
   

2. Install the latest release of the schematic via pip. IF NOT USING CONDA, install the devel version below:

   python -m pip install schematicpy
   

   For development and test with the latest update from schematic, install the schematic via poetry:

   cd schematic
   poetry build
   pip install dist/schematicpy-1.0.0-py3-none-any.whl
   

3. Modify the schematic_config.yml to set up schematic configuration. To do so, follow the instructions on the schematic's documentation

Data Model Configuration

The app configuration file www/config.json will be used to adapt the schema dropdown menu in the app. The config.json file will be automatically created in the deployment workflow.

For local testing, run below snippet to generate www/config.json and check the docs how to modify it:

1. Create a repo for your data model using this template

2. Clone your data model repo, i.e:

   git clone https://github.com/Sage-Bionetworks/data-models
   

3. Create config.json and placed it in the www folder

   python3 .github/generate_config_json.py \
     -jd data-models/example.model.jsonld \
     -schema 'Sage-Bionetworks/data-models' \
     -service Sage-Bionetworks/schematic'
   

---

Authentication

This utilizes a Synapse Authentication (OAuth) client (code motivated by ShinyOAuthExample and app.R. Each application is required to have its own OAuth client as these clients cannot be shared between one another. View instructions here to learn how to request a client. Once you obtain the client, make sure to add it to the configuration yaml file:

• CLIENT_ID and CLIENT_SECRET
• APP_URL: the redirection url to your app

---

Deployment

To deploy the app to shinyapps.io, please follow the instructions in the shinyapps_deploy.md.

Contributors

Main contributors and developers:

• Rongrong Chai
• Anthony Williams
• Milen Nikolov
• Lauren Wolfe
• Robert Allaway
• Bruno Grande
• Xengie Doan
• Sujay Patil