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Welcome to the bycon project documentation

Bycon - a Python-based environment for the Beacon v2 genomics API

The bycon project - at least at its current stage - is a mix of Progenetix (i.e. GA4GH object model derived, MongoDB implemented) - data management, and the implementation of middleware & server for the Beacon API.

Bycon Code

The bycon code is maintained in the progenetix/bycon repository. Utility scripts & functions reside in the byconaut and (this one is really "scripty") byconeer repositories but are so far not (well) documented & may contain deprecated or "internal use" code.

More information about the original use Progenetix case can be found on the project's documentation site.

bycon Directory Structure

beaconServer

  • web applications for data access
  • Python modules for Beacon query and response functions in lib

config

  • top-level, general configurations
  • in beaconServer, services ... specific configuration files for the individual endpoints
  • these specify e.g. which configurations are loaded or response content
  • YAML ...

docs

  • documentation, in Markdown, as source for documentation builded with mkdocs

lib

  • Python libraries

rsrc

  • various resources beyond configuration data
    • mapping input table(s)
    • external schema dumps
    • ...

Overview

bycon
  |
  |- bycon
  |   |
  |   |- beaconServer
  |   |   |
  |   |   |- beacon.py
  |   |   |- datasets.py
  |   |   |- configuration.py
  |   |   |- entryTypes.py
  |   |   |- filteringTerms.py
  |   |   `- ... .py
  |   |
  |   |- config
  |   |   |
  |   |   |- beacon_mappings.yaml
  |   |   |- config.yaml
  |   |   |- dataset_definitions.yaml
  |   |   |- filter_definitions.yaml
  |   |   `- ..._definitions.yaml
  |   |
  |   |- lib
  |   |   |
  |   |   |- cgi_parsing.py
  |   |   |- read_specs.py
  |   |   |- filter_parsing.py
  |   |   |- query_generation.py
  |   |   |- query_execution.py
  |   |    `- ...
  |   |
  |   |- rsrc
  |   |   `- ...
  |   |
  |   `- schemas
  |       `- ...
  |
  |- docs
  |    `- ... documentation website source files ...
  |
  |- local
  |   |
  |   |- beacon_defaults.yaml
  |   |- dataset_definitions.yaml
  |   `- local_paths.yaml
  |
  |- install.py
  |- install.yaml
  `- `requirements.txt` and other Python packaging files
...

External services

The bycon environment - together with the Progenetix resource - provide a growing numer of data services in (cancer) genomics and disease ontologies. Since bycon 1.0.55 (2023-06-22) /services resides in the byconaut repository.