auto-triage: guard bio1 objective assignment in reconstruct (issue #23)#4
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auto-triage: guard bio1 objective assignment in reconstruct (issue #23)#4jplfaria wants to merge 1 commit into
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Models built from non-standard templates may not have a 'bio1' reaction, causing ValueError: invalid objective at save time. Use _set_biomass_objective() which falls back to the first biomass-like reaction and silently skips if none is found. Fixes ModelSEED/modelseed-api-ops#23 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
model.objective = "bio1"in thereconstructtask with_set_biomass_objective()helper that falls back gracefully whenbio1is absent.job_scripts/reconstruct.py.try/exceptat line 1266 oftasks.pyin favour of the shared helper.Root cause
build_metabolic_modeldoes not guarantee the biomass reaction is always namedbio1. For models built from non-standard templates or sparse genomes the biomass reaction may be named differently (bio2,BIOMASS_*, etc.), causingcobrato raiseValueError: invalid objective.Fixes ModelSEED/modelseed-api-ops#23
Test plan
tests/unit/test_set_biomass_objective.pycover: bio1 present, bio1 absent with fallback, no biomass reactions (silent skip), empty model.pytest tests/unit/locally.