File Structure

The files in this repository follow the basic structure:

• cvf_app: The main Quart application folder, as a Python package.

  • auth: Folder containing authentication related code, including KeyCloak and Vault drivers, as well as some decorators and security related function

  • beacon: Beacon related functions, including the class definition, the code to query beacon endpoints, and to process beacon queries. Also containing the management functions to handle beacon sources

  • cv: The Cafe Variome management related code. Almost all endpoints used by frontend are here.

  • federation: The federated network related code. Federated query uses a different authentication model, so it has a different codebase from the regular query

  • legacy: Legacy functions, including the legacy query and views for frontend to manage the legacy code

  • log: The code to handle logging, log reporting, and receiving log from the front end.

  • meta: ON HOLD NOW The code for meta sources and meta-query

  • models: All class definition for data models used in cv and management functions. Specific models, like the query model, are inside the corresponding folder.

  • nexus: The code for nexus mode. The views in this folder do not follow naming conventions of this project, because it needs to be compatible with the V2 API endpoints.

  • query: The code related to querying, including both the query and response model, data searching and sanitization, etc.

  • util: Utility functions, not used by any other part of the code. It's a standalone implementation of a CLI to interact with the system.

• docs: The documentation folder, containing the OpenAPI specification.

• resources: The resource folder, containing the necessary files for backend to run

• static: Static file folder, containing web pages and js scripts that are served directly

• tests: Testing root folder

• utility: The folder containing helper script, etc.