Skip to content

apps, docs, fixtures, README: read the fhir leaves and render them - #13

Draft
s23b wants to merge 1 commit into
dark-bio:mainfrom
s23b:fhir-leaves
Draft

s23b wants to merge 1 commit into
dark-bio:mainfrom
s23b:fhir-leaves

Conversation

@s23b

@s23b s23b commented Oct 23, 2026

Copy link
Copy Markdown

The examples gain an app for the genome tree's FHIR R4 output, the fhir leaf beside every place, change and copy.

  • 12-fhir-view reads one of each kind of FHIR endpoint: the site Bundle at rs671, TAS2R38's gene Bundle and its change entries, UGT2B17's copy segment, and the haploid site at chrM 263. For each one it renders the Observations as tables of LOINC codes and values, and below them the leaf's own JSON, re-indented with its content and key order unchanged.
  • Only rs671 is required. The two genes and the chrM site are optional grants, so the app also runs on the smaller fixture roots, and it reports anything ungranted or unanswered as absent. The public datasets grant tells a missing copy number upload apart from an empty answer.
  • The report counts what it read and stays within the output cap, cutting long JSON with a count of what it left out.
  • docs/03-data-paths.md adds fhir to the tree and a FHIR section: the profiles each endpoint follows, when a leaf is absent, why it carries no dates, how its IDs are derived, and its size limits.
  • The fixtures gain the fhir leaves the app reads, byte for byte what an Ark serves for the same calls, plus the chrM 263 site.

The app ran on Ark Emulator against 1000 Genomes sample HG02953 with every slot filled. rs671 and chrM 263 read absent, since that sample has no genotype at either, and the TAS2R38 and UGT2B17 endpoints rendered with their real calls.

The fhir leaves need an ArkOS release that serves them. On earlier firmware every endpoint reads absent.

Co-authored-by: Astra <noreply@openai.com>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant