Unified repository for Beacon v2 Code & Documentation

Description

This repository is a unified repository representing the different parts of the Beacon API:

framework
models
Beacon v2 Documentation
- authoritive source already in this repository /docs
- rendered version through here (alternative address is docs.genomebeacons.org)

As with other schema projects, here we separate between the schema source files (in src; JSON-Schema written in YAML) and the generated versions for referencing. The current setup allows already the direct referencing of the generated JSON schemas. Examples:

ontologyTerm:
- YAML (source):
  - edit: https://github.com/ga4gh-beacon/beacon-v2/blob/main/framework/src/common/ontologyTerm.yaml
  - raw: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/src/common/ontologyTerm.yaml
- JSON: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json
biosamples/defaultSchema
- YAML (source):
  - edit: https://github.com/ga4gh-beacon/beacon-v2/blob/main/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml
  - raw: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml
- JSON: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/biosamples/defaultSchema.yaml
beaconRequestBody:
- YAML (source): https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/src/requests/beaconRequestBody.yaml
- JSON: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json

There is a set of tools in /bin to facilitate the conversion. ATM, after editing ...yaml schema files somewhere in the /src tree, a (local) run of bin/yamlerRunner.sh - which re-generates the ....json files in the /json tree) has to be performed before pushing changes.

Changelog

2.1.0

Released, July, 19, 2024

Relocated TypedQuantity required to proper level of the schema for complexValue
Added end and start entities for ageRange and iso8601duration for age
Filtering terms scopes changed from string to array of strings

2.0.1

Released July, 16, 2024

Replaced ENSGLOSSARY for SO ontology family in documentation examples
Moved CURIE to beaconCommonComponents
Created filtering terms entity
Removed validation directories
Several fixes to entity types, typos and other non-breaking changes

2.0.0

Released June, 21, 2022

change notes with respect to the repository & documentation are now in docs.genomebeacons.org
NOTE: on 2022-06-20 the previous development repositories have been archived:
- ARCHIVE - beacon-framework-v2
- ARCHIVE - beacon-v2-Models

Directory structure

|-docs          Contain the source (Markdown) for the mkdocs generated documentation
|
|- framework
|   |
|   |- src      schema source in YAML format; for editing
|   |
|   |- json     JSON versions of the schema files generated from src, authorative/referenceable version
|
|- models
|   |
|   |- src      schema source in YAML format; for editing
|   |
|   |- json     JSON versions of the schema files generated from src, authorative/referenceable version
|
|- bin          scripts and configurations for creating the unified structure
    |
    |- yamlerRunner.sh    runs the conversions for the different repos and format options
    |
    |- beaconYamler.py    conversion app
    |
    |- config.yaml        text replacements and options

ga4gh-beacon / beacon-v2

readme