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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 byconeer and byconaut repositories but are so far not documented & may contain deprecated or "internal use" code.

More information about the current status of the package can be found in the inline documentation which is also presented in an accessible format on the Progenetix website.

bycon Directory Structure

beaconServer

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

services

The bycon environment - together with the Progenetix resource - provide a growing numer of data services in (cancer) genomics and disease ontologies. bycon's services are tools to enable the APIs.

  • web applications and libraries extending the bycon environment

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
  |
  |- config
  |    |- beacon_mappings.yaml
  |    |- config.yaml
  |    |- dataset_definitions.yaml
  |    |- filter_definitions.yaml
  |    |- ..._definitions.yaml
  |
  |- docs
  |    `- ... documentation website source files ...
  |
  |- beaconServer
  |    |- datasets.py
  |    |- biosamples.py
  |    |- filteringTerms.py
  |    |- variants.py
  |    |- ... .py
  |    |
  |    |    |- config
  |    |    |- schemas
  |    |    |   |- beacon.yaml
  |    |    |   |- ... .yaml
  |    |    |
  |    |    |- biosamples.yaml
  |    |    |- ... .yaml
  |    |
  |    |- doc
  |    |    |- bycon.md
  |    |    |- handovers.md
  |    |    |- ... .md
  |    |
  |    |- lib
  |    |    |- cgi_parsing.py
  |    |    |- read_specs.py
  |    |    |- filter_parsing.py
  |    |    |- query_generation.py
  |    |    |- query_execution.py
  |    |
  |    |- rsrc
  |         |- ...
  |
  |- services
  |    |- config
...