TODO, Bugs & Changes

TODO

Documentation

  • [x] re-structuring of Framework page
    • [ ] add part about necessary files, dependening on installation type (e.g. if not needing to support OpenAPI)
  • [ ] fix https (probably @mbaudis has to do some registrar configuration...)
  • [ ] add more Implementations
  • [ ] extend Query documentation
    • [x] expand the table comparing different "variant types"
    • [ ] use more content from the variant scouts document

Changes

2022-06-20: Retiring of beacon-framework-v2 and beacon-v2-Models repos

  • all issues and PRs were either resolved or transferred to this repository
  • [x] repos were clearly labeled as archived w/ pointers to this one here and archived (i.e. set to read only)
  • also archiving of the implementations-v2 repository (part of documentation)

2022-05-11: Retiring ReadTheDocs configuration & more

  • removed ReadTheDocs configuration files
  • added some "how to implement" instructions

2022-04-21: GA4GH approval notice

2022-04-18: Documentation updates

  • Shuffled small fragments to facilitate comprehension.

2022-04-17: Documentation updates

  • Updated default schemas tables according to the newest changes.
  • Moved filters.md from section Beacon Components to Implement....
  • Dismissed pages w/o content (_rest-api.md and _tips-for-implementers.md).
  • Dismissed link to RTD version (deprecated).

2022-04-01: Documentation updates

  • Partial update of Default schemas Tables (still work in progress)
  • Updated bin files that parse JSON schemas

2022-03-30: Documentation updates

  • Updated diagram in Models page.
  • Removal of some outdated text, e.g. reference to TEMPLATE model (for now)
  • continuous updates from upstream

2022-03-28: Documentation updates

  • added content to the Standards page (VRS, Phenopackets, coordinates)
  • Queries page now with comparison table for (some) variant type terms

2022-03-25: Miscellanea changes in docs/*.md

  • Changes in multiple Markdown pages.
  • Moved from mermaid to mermaid2 plugin.

2022-03-24: Retiring Separate Implementations Repository

2022-03-23: Name Change to beacon-v2

  • The repository name and file paths have been changed from beacon-v2-unity-testing to beacon-v2.
  • Added miscellanea suggestions from Jorge (not all of them).

2022-03-22: More Reorganization of Navigation

  • Moved content from implementations-and-networks to other-implementations and left only the "Networks" Part.
  • Added mkdocs-mermaid2-plugin both to mkdocs.yaml and to github workflows.
  • Moved Schemas (Markdown Tables) and Terms List from main navigation to Beacon Compoments/Models
  • Reorganization of navigation
  • Added pages: Tips for Implementers

2022-03-21: Reorganization of navigation

2022-03-18: Macros and Variables for Documentation pages

The mkdocs-macros-plugin has been activated, allowing the use of site-wide variables:

  • repo_model_url: https://github.com/ga4gh-beacon/beacon-v2/tree/main/models/src
  • this can be used inline as {{config.repo_model_url}}

2022-03-16: Documentation Content and Formats Updates

  • [x] addition of more variant query examples
  • [x] new landing pages for Implementations and Networks and Standards Integration
  • [x] many adjustments to documentation structure, appearance and representation (e.g. content tabs for query examples)

2022-03-14: Documentation in Repository

As of today the new/emerging Beacon v2 documentation is meintained in this repository. We're testing rendered versions (same text/code base) through Github actions (here) and ReadTheDocs.

  • [x] testing of ReadTheDocs version vs. a material themed build
  • [x] created and linked docs.genomebeacons.org sub-domain to the Github hosted version of the rendered documentation
  • [x] merging of previous separate documentation repository content from beacon-v2-schema-documentation in the "unity" repository and archiving of the old one

2022-03-11: Removing yaml export version

Since moving to source in YAML the existence of a separate yaml export seems unnecessary & maybe confusing. Removed.

2022-03-09: Nesting models

The structure of the models directory has now be changed to have the default model as one of possibly multiple options as per the discussions in #1. The current structure (below) might not be final (e.g. placing of the beaconConfiguration.yaml, beaconMap.yaml, endpoints.yaml files?).

beacon
  |
  |-- framework ...
  |-- models
  |    |-- src
  |    |    |-- beacon-v2-default-model
  |    |         |-- analyses ...
  |    |         |-- biosamples ...
  |    |         |-- genomicVariations ...
  |    |         |-- ...
  |    |         |-- endpoints.yaml
  |    |     
  |    |-- json
  |         |-- beacon-v2-default-model
  |              |-- analyses ...
  |              |-- biosamples ...
  |              |-- genomicVariations ...
  |              |-- ...
  |              |-- endpoints.yaml
  |
  |-- bin ...
  |-- docs ...               
...

2022-03-08: Automated pulling from current origin repos

  • added simple pull commands to the conversion for automatic update to the donor repos
git -C $BEACONMODELPATH pull
git -C $BEACONFRAMEWORKPATH pull
  • updated to current crop of PRs

2022-02-24: Path fixes

2022-02-23: Re-tool

  • [x] replacement of the previopus general yamler.py with a dedicated beaconYamler.py
  • [x] moving replacements to bin/config.yaml
  • [x] requirement for complete arguments (in and out paths, in- and out formats) - see bin/yamlerRunner.sh

2022-02-22: Creation of repository

  • [x] design of directory structure
  • [x] test tooling & population with auto-converted files