This page only lists changes w/ regard to the documentation and general organization of the Beacon project site(s) as well as with overarching repository organization.
- new separation of navigation areas into "Introducing Beacon", "Using Beacons", "Creating Beacons" and "Beacon Development", with subtopics such as "Data Discovery", "Data Delivery" ...
- combined "what-is-beacon-v2" into rewritten index page
- new pages for "Data Delivery": Biosamples, Variants... and Data Handovers - so far limited content
@mbaudis
- extended & clarified "filters" documentation
- filter types in line with specification
- example for pseudo-numerical value queries in
GETcontext
- fixed
HTTPSissue (by brute-forcing all links on site tohttps://)
@mbaudis
To protect the code branches we are using now a separate website-docs branch in beacon-v2 for documentation
website updates. Please make sure all documentation edits happen there!
@mbaudis
- all issues and PRs were either resolved or transferred to this repository
- repos were clearly labeled as
archivedw/ pointers to this one here and archived (i.e. set to read only) - also archiving of the
implementations-v2repository (part of documentation)
- removed ReadTheDocs configuration files
- added some "how to implement" instructions
- Shuffled small fragments to facilitate comprehension.
- Updated default schemas tables according to the newest changes.
- Moved
filters.mdfrom section Beacon Components to Implement.... - Dismissed pages w/o content (
_rest-api.mdand_tips-for-implementers.md). - Dismissed link to RTD version (deprecated).
- Partial update of Default schemas Tables (still work in progress)
- Updated
binfiles that parse JSON schemas
- Updated diagram in Models page.
- Removal of some outdated text, e.g. reference to TEMPLATE model (for now)
- continuous updates from upstream
- added content to the Standards page (VRS, Phenopackets, coordinates)
- Queries page now with comparison table for (some) variant type terms
- Changes in multiple Markdown pages.
- Moved from
mermaidtomermaid2plugin.
- Started adding content to pages such as
networks.md androles.md` - Moved pages to different locations in navigation. Created
security.mdunder Beacon Types. - Example implementations have been moved from the
implementations-v2repository to the Beacon v2 Documentation - web access here.
- The repository name and file paths have been changed from
beacon-v2-unity-testingtobeacon-v2. - Added miscellanea suggestions from Jorge (not all of them).
- Moved content from
implementations-and-networkstoother-implementationsand left only the "Networks" Part. - Added
mkdocs-mermaid2-pluginboth tomkdocs.yamland 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
- Reorganization of navigation
- Deleted page
implement-and-deploy.md - Added pages: What is Beacon v2 and Implementation options
- Filters Page Updated
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}}
- addition of more variant query examples
- new landing pages for
Implementations and Networksand Standards Integration - many adjustments to documentation structure, appearance and representation (e.g. content tabs for query examples)
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.
- testing of ReadTheDocs version vs. a
materialthemed build - created and linked docs.genomebeacons.org sub-domain to the Github hosted version of the rendered documentation
- merging of previous separate documentation repository content from beacon-v2-schema-documentation in the "unity" repository and archiving of the old one
Since moving to source in YAML the existence of a separate yaml export seems unnecessary & maybe confusing. Removed.
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 ...
...
- 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
- changed the path replacements to the current repo, resulting in e.g. https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconInformationalResponseMeta.json
- replacement of the previopus general
yamler.pywith a dedicatedbeaconYamler.py - moving replacements to bin/config.yaml
- requirement for complete arguments (in and out paths, in- and out formats) - see bin/yamlerRunner.sh
- design of directory structure
- test tooling & population with auto-converted files
- re-structuring of Framework page
- add part about necessary files, dependening on installation type (e.g. if not needing to support OpenAPI)
- add more Implementations
- extend Query documentation
- expand the table comparing different "variant types"
- use more content from the variant scouts document