README.md

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