Format Conversion Test Suite

This repository provides a reproducible build test for model format conversion using the SBML Semantic Test Suite.

SBML → Heta → canonical JSON + DynMS

Each selected SBML case is built with heta-compiler. The suite records whether the build produced its canonical JSON and DynMS artifacts; it does not compare generated files with stored baselines and does not validate numerical simulations.

Report viewer

The dependency-free Report viewer loads a local report.json or a public report URL. Its files are in viewer/; see viewer/README.md for usage.

Configuration

config/options.json is the source of truth for the SBML Semantic Test Suite version, archive URL, checksum, and extraction target.

Check that this configuration is valid and that the archive URL is reachable:

npm run verify:config

Prepare cases

Download and verify the configured SBML archive:

npm run fetch:sbml

Create cases/index.json from the downloaded suite:

npm run index:sbml

The index contains available SBML paths, source metadata, and the pinned test-suite identity. Both cases/ and results/ are generated and ignored by Git.

Build a report

npx fcts sbml-report --source=cases/index --input-field=sbmlL3V2Path \
  --target=results/candidate --concurrency=1 --skip=0 --limit=10

The target directory is recreated for each run. report.json records the conversion description, generator and run metadata, command parameters, build status for every selected case, and relative paths to artifacts from successful builds. After a successful compiler build, canonical JSON and DynMS artifacts are validated against the heta-compiler/heta-json-schema and heta-compiler/dynms-schema exports. A schema violation marks the case as failed while preserving buildStatus: "success" and validation errors. The target also receives badge.json, which is compatible with the Shields endpoint badge. It contains successful assessed cases over all assessed cases; not-evaluated cases are excluded.

--input-field accepts sbmlL3V2Path (default) or sbmlL2V5Path. To build cases while excluding selected tags from assessment, use --skip-component-tags and --skip-test-tags; matching cases keep their build result but receive status not-evaluated. Excluded cases do not affect the overall report status: a report is success when every assessed case succeeds.

GitHub Actions

The manual Verify heta-compiler conversion workflow downloads and indexes the SBML suite, builds L3V2 and L2V5 reports for the chosen heta-compiler ref, and fails if any selected case has status failed. It uploads the generated build reports for inspection.

License

See LICENSE.