Skip to content

fix(connectors): name all BioSimulators model formats - #911

Merged
Aayam Bansal (aayambansal) merged 1 commit into
synthetic-sciences:mainfrom
randsu:fix/biosimulators-format-names
Oct 2, 2026
Merged

Aayam Bansal (aayambansal) merged 1 commit into
synthetic-sciences:mainfrom
randsu:fix/biosimulators-format-names

Conversation

@randsu

Copy link
Copy Markdown
Contributor

What does this PR do, and why?

The registry uses 15 model formats. The connector names four of them (SBML, CellML, NeuroML, BNGL), so the other eleven can only be found by EDAM id and show up as ids in results.

On main today:

  • science_search for Kappa returns nothing, although KaSim and PySB read Kappa.
  • A NEURON hit lists its formats as format_9004, NeuroML, format_9005.

14 of the 54 simulators list at least one unnamed format, and four list only unnamed ones (kasim, rbapy, smoldyn, xpp).

This adds the eleven missing names, taken as written from the registry's /ontologies/EDAM/<id> endpoint, the same source the existing four come from.

Linked issue

Small fix, no issue. Follow-up to #907.

How did you verify it?

One new test in test/science/biosimulators.test.ts. It fails on main and passes with the change.

cd backend/cli
bun test --timeout 15000 ./test/science/biosimulators.test.ts   # 7 pass
bun test --timeout 15000 ./test/science ./test/settings         # 964 pass

Against the live registry, before and after:

Search Before After
Kappa 0 hits kasim, pysb
Virtual Cell Markup Language 0 hits vcell
Low Entropy Model Specification 0 hits brian2, jneuroml, netpyne, neuron, pyneuroml
SBML 32 hits 32 hits

Format check and typecheck pass. A full bun run check on Linux gave 4,984 backend tests passed and one failed: test/project/authority-signal.test.ts ("a watcher that polled past its own process's settled burst does not resync"). It fails now and then in the full run on main as well and passes alone, so I left the first box open. The ui, sdk, docs and workspace suites pass.

Checklist

  • bun run check is green (format, typecheck, backend + frontend/ui + SDK tests)
  • bun run --cwd frontend/workspace build succeeds if I touched frontend/workspace or frontend/ui
  • ./tooling/repo/generate.ts was run and the tooling/sdk output committed if I changed backend/cli/src/server
  • CHANGELOG.md has an Unreleased entry if the change is user-visible
  • The matching docs page under frontend/docs/src/content/openscience/ is updated if behavior changed
  • Screenshots or a short video are attached for UI changes
  • No version bumps (package.json versions and tags are written by the release workflow)
  • install and frontend/landing/public/install are still byte-identical if I touched either

The registry uses 15 formats; only four had names, so Kappa and others
could not be searched and showed as raw EDAM ids.
@vercel

vercel Bot commented Oct 2, 2026

Copy link
Copy Markdown

Richard Sundby Anderssen (@randsu) is attempting to deploy a commit to the InkVell Team on Vercel.

A member of the Team first needs to authorize it.

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Reviewed the complete diff. No blocking findings.

  • All 15 format labels match the registry's live EDAM endpoints.
  • 52 focused BioSimulators/fetch tests passed (119 assertions).
  • Live searches returned KaSim/PySB for Kappa, VCell for Virtual Cell Markup Language, the five expected LEMS simulators, and 32 SBML simulators.
  • All required checks passed. The Vercel preview requests contributor authorization; it is not a required check and this PR changes no frontend code.

One initial live catalog response was truncated; a fresh request and the complete repeat passed. That source-response behavior is independent of this static mapping change.

Including this fix in the next release, with a fresh full rehearsal on the merged main commit.

@aayambansal
Aayam Bansal (aayambansal) merged commit 4c48372 into synthetic-sciences:main Oct 2, 2026
8 of 9 checks passed
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.

2 participants