The Biomedical Research Integrated Domain Group (BRIDG) Model ¹

Implemented in Python with support for persistence using SQLAlchemy. Also a web interface for electronic data capture (EDC).

OpenAPI

Schemas of models in the api/models have same names as the models. The rest of schemas are named the way Pydantic will do it.

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Below is the old README:

Configuration and Profiles

The web app has notion of profiles. The profile can be set using BRIDG_ENV environment variable, which is development by default.

Depending on the profile the app loads environment variables from .env file and profile specific .env.xxx file. Though the profile specific file doesn't override variables set in .env file. This is done for compatibility with flask cli command.

By default the repository contains .env.development and .env.testing files for corresponding profiles. And the file for the production profile .env.production is added to .gitignore, so it won't be present in repository ever, because it may contain secrets.

Build

Bulding web assets.

flask --app web.app assets build
flask --app web.app assets-extra webfonts

Bulding localizations.

pybabel compile -d web/translations

Development

Copy .env.example to .env and modify as needed.

Install Python and NPM dependencies.

poetry install
npm install

The rest commands are run in virtualenv. Start shell using poetry shell or prefix commands with poetry run.

Reset database from scratch.

./dev/db-reset.sh

Run web app.

./dev/run.sh

You may want to build web assets, at least copy fonts, see Build chapter.

Footnotes

1. BRIDG: An international standard for biomedical research concepts designed to support computable semantic interoperability ↩