Restrict importModel to SBML L3V1 FBCv2 and drop legacy format handling#633
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importModel now supports only SBML Level 3 Version 1 with the FBC v2 package, which is what RAVEN itself writes. An early check rejects other formats with a message to convert the file or use an older RAVEN version. With that guarantee, the legacy/non-FBC code paths are removed: - genes and complexes stored as species (E_/Cx_ prefixes), including the complex-forming-reaction skip and the gene-as-species collectors - the Yeast 7.6 systematic-gene-name resolution workaround - non-FBC reaction bounds (kineticLaw parameters) - gene associations from notes (GENE_ASSOCIATION) and from modifiers - reaction compartment, metabolite charge and formula read from notes - EC codes and MIRIAM/taxonomy in urn:miriam: and http://identifiers.org/ form (https://identifiers.org/ is retained) Genes are now taken solely from fbc_geneProduct (or grRules). Behaviour on valid L3V1 FBCv2 models is unchanged, verified by identical imports of empty.xml, iAL1006 and a round-tripped model. importModel.m drops from 1157 to 891 lines.
Restricting MIRIAM, EC-code and taxonomy parsing to https://identifiers.org/ made importModel fragile: a model annotated with the equally-valid http://identifiers.org/ scheme would silently lose all its cross-references. Restore detection of both http and https (still dropping the long-obsolete urn:miriam: form). Verified that an http-converted copy of iAL1006 yields identical metMiriams, rxnMiriams, geneMiriams and eccodes to the https original.
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Summary
importModelnow supports only SBML Level 3 Version 1 with the FBC v2 package — the format RAVEN itself writes. An early check rejects anything else with a clear message (convert the file elsewhere, or use an older RAVEN version). With that guarantee, the legacy/non-FBC branches that made the function a 1157-line monolith are removed.Removed (all legacy / non-FBCv2)
E_/Cx_prefixes), the complex-forming-reaction skip, and the gene-as-species collector variableskineticLawparameters)GENE_ASSOCIATION) and from modifiersurn:miriam:andhttp://identifiers.org/form (https://identifiers.org/retained)Genes now come solely from
fbc_geneProduct(orgrRules). RAVEN conventions that are not legacy — reaction notes for SUBSYSTEM/Confidence Level/AUTHORS/NOTES,groups_groupsubsystems, SBO handling, InChI/fbc_charge/fbc_chemicalFormula, ID unescaping, prefix removal — are kept.Verification
Behaviour on valid L3V1 FBCv2 models is unchanged, checked with
isequalnagainst pre-refactor imports ofempty.xml,iAL1006 v1.00.xml(1632 reactions) and a round-tripped model — all identical. The format check correctly rejects a non-FBCv2 file.tIO(18/19, 1 filtered for missing pyyaml) andimportExportTests(7/7) pass with no failures.io/importModel.m: 1157 → 891 lines (−266).