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fix(connectors): name all BioSimulators model formats - #911
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Aayam Bansal (aayambansal) merged 1 commit intoOct 2, 2026
Merged
Aayam Bansal (aayambansal) merged 1 commit into
Aayam Bansal (aayambansal) merged 1 commit into
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The registry uses 15 formats; only four had names, so Kappa and others could not be searched and showed as raw EDAM ids.
Richard Sundby Anderssen (randsu)
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Aayam Bansal (aayambansal) and
Ishaan Gangwani (ishaan1124)
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October 2, 2026 14:36
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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. |
Aayam Bansal (aayambansal)
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Oct 2, 2026
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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.
Aayam Bansal (aayambansal)
merged commit Oct 2, 2026
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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
maintoday:science_searchforKappareturns nothing, although KaSim and PySB read Kappa.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 onmainand passes with the change.Against the live registry, before and after:
KappaVirtual Cell Markup LanguageLow Entropy Model SpecificationSBMLFormat check and typecheck pass. A full
bun run checkon 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 onmainas well and passes alone, so I left the first box open. The ui, sdk, docs and workspace suites pass.Checklist
bun run checkis green (format, typecheck, backend + frontend/ui + SDK tests)bun run --cwd frontend/workspace buildsucceeds if I touchedfrontend/workspaceorfrontend/ui./tooling/repo/generate.tswas run and thetooling/sdkoutput committed if I changedbackend/cli/src/serverfrontend/docs/src/content/openscience/is updated if behavior changedpackage.jsonversions and tags are written by the release workflow)installandfrontend/landing/public/installare still byte-identical if I touched either