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
...