Welcome to the
bycon project documentation¶
Bycon - a Python-based environment for the Beacon v2 genomics API¶
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 is maintained in the
progenetix/bycon repository. Utility scripts & functions reside in the
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¶
- web applications for data access
- Python modules for Beacon query and response functions in
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
- top-level, general configurations
services... specific configuration files for the individual endpoints
- these specify e.g. which configurations are loaded or response content
- YAML ...
- documentation, in Markdown, as source for documentation builded with
- Python libraries
- various resources beyond configuration data
- mapping input table(s)
- external schema dumps
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 ...