fix(model-export): make model TSV download work (#221) - #228
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The model Download menu offered a "TSV" option that called GET /api/models/export?format=tsv, but the ModelSEED API only supports json | sbml | cobrapy (verified against https://modelseed.org/PMS/openapi.json). The option therefore never produced a file. Derive the tabular exports in the browser from the supported `format=json` export instead, and split the single dead entry into two working ones: "Reactions (TSV)" and "Compounds (TSV)". This gives users the cpdtbl/rxntbl style tables requested in the issue. - add lib/utils/modelTsv.ts with pure buildReactionsTsv/buildCompoundsTsv builders reusing the existing RFC-4180 escaper in lib/utils/exportCsv.ts - rewire components/ui/DownloadModelMenu.tsx onto a discriminated 'api' | 'derived-tsv' option union and export EXPORT_OPTIONS - correct the stale exportModelFromApi doc comment that listed 'tsv' - update the model page helper text - add unit tests for the TSV builders plus a contract test asserting no menu entry requests a format outside the backend's supported set Note: the issue also reported that the SBML download is not valid XML. The reporter's own attachment parses as complete, well-formed SBML L3V1-FBCv2 (1100 species, 1127 reactions, fbc objective); the key/value text they saw is the content of legal <notes> blocks. No SBML change was needed.
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Fixes the actionable half of #221.
What was actually wrong
TSV download (real bug). The model Download menu offered a
TSVentry that issuedGET /api/models/export?ref=…&format=tsv. The ModelSEED API only supportsjson,sbmlandcobrapy— verified live against https://modelseed.org/PMS/openapi.json:So that menu entry could never produce a file. Nothing in the repo tested it
(
scripts/api-test.mjsandscripts/comprehensive-api-test.mjsonly cover SBML and JSON).SBML download (not a bug). The reporter's attached
DC1RawModel.xmlwas downloaded andchecked: it is complete, well-formed SBML L3V1 + FBC v2 — 1100
<species>, 1127<reaction>,unit definitions, compartments,
fbc:objective fbc:type="maximize",fbc:listOfGeneProducts,properly closed
</model></sbml>. Thekbase_compartment_data/modelseed_template_id: cpdXXXX_clines they saw are the text of legal
<notes><html><p>…</p></html></notes>blocks, which is what abrowser shows if it renders the file as HTML. No SBML change was made or needed — that file
should load in COBRA Toolbox / cobrapy as-is.
The fix
Build the tabular exports client-side from the supported
format=jsonexport, and split the onedead entry into two working ones:
format=sbml<model>.xml(unchanged)format=json<model>.json(unchanged)format=json<model>.reactions.tsvformat=json<model>.compounds.tsvColumns follow the legacy
rxntbl/cpdtblshape the issue asks for:id,direction,compartment,gpr,name,equation,pathwaysid,name,formula,charge,compartmentcompartmentis derived from the id suffix (cpd00443_c0→c0).Changes
lib/utils/modelTsv.ts— purebuildReactionsTsv/buildCompoundsTsv/compartmentFromId, reusing the existing RFC-4180 escaper inlib/utils/exportCsv.ts(no new escaping code, no new dependency).
components/ui/DownloadModelMenu.tsx— options moved to an exported, typed'api' | 'derived-tsv'discriminated union;downloadingFormat→downloadingKey.Props interface unchanged, so both call sites (model viewer and My Models) are unaffected.
lib/api/modelseed.ts— doc comment corrected; it still advertised a'tsv'format. Nobehaviour change.
app/model/[...path]/page.tsx— helper text updated (one line).Tests
tests/unit/utils/modelTsv.test.ts— header rows, compartment derivation,charge: 0renderingas
0, commas in reaction names staying unquoted under a tab delimiter, missing optional fieldskeeping the full column count, pathway joining, and the empty-model error paths.
tests/unit/components/downloadModelMenuOptions.test.ts— the regression test that would havecaught this: asserts every API-backed menu entry requests a format inside the backend's
documented set
['json','sbml','cobrapy'], and that nothing requeststsvfrom the API.Fixture shapes were taken from the reporter's own
DC1RawModel.json, i.e. real productionformat=jsonoutput.Verification
All green locally, mirroring
.github/workflows/ci.yml:npm run lint— 0 errors (16 pre-existing warnings, none in changed files)npx tsc --noEmit— cleannpm run test:run— 18 files, 145 tests passed (+18 new)npm run build— compiled successfully, 31/31 static pagesnpm audit --omit=dev --audit-level=high— 0 vulnerabilitiesNotes for review
stagingis promoted tomaster.format=cobrapyis documented by the API but was not added to the menu, because it could notbe verified end-to-end without an auth token, and shipping an unverified format is exactly the
bug this PR fixes. Easy follow-up once someone confirms it works.
TSV/cpdtbl export) is a backend concern for
modelseed-api, not this repo.staging; kept separate from the still-open feat(feedback): add homepage GitHub Issues link #227 so the two can be reviewedindependently.