Fix drain_list loading: create DM_ demand reactions during model build#25
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cshenry merged 1 commit intocshenry:mainfrom Apr 14, 2026
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MSTemplateBuilder.from_dict() was silently dropping the drain_list from template JSON files, so template.drains stayed empty. This meant MSBuilder.build_drains() fell back to DEFAULT_SINKS and only created SK_ (sink) reactions, never DM_ (demand) reactions. Without DM_cpd11416_c0, cobrapy FBA returns 0 growth because the biomass compound (cpd11416) produced by bio1 has no outlet. Two fixes: 1. mstemplate.py: from_dict() now reads drain_list into builder.drains 2. msbuilder.py: build_demands() creates DM_ reactions for all drain compounds (previously required lower_bound < 0, but template drain_list entries use [0, 1000]) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
MSTemplateBuilder.from_dict()was silently dropping thedrain_listfrom template JSON files, sotemplate.drainsstayed emptyMSBuilder.build_drains()fell back toDEFAULT_SINKSand only created SK_ (sink) reactions, never DM_ (demand) reactionsDM_cpd11416_c0, cobrapy FBA returns 0 growth becausecpd11416(Biomass) produced bybio1has no outletChanges
mstemplate.py:from_dict()now readsdrain_listintobuilder.drainsmsbuilder.py:build_demands()creates DM_ reactions for all drain compounds (previously requiredlower_bound < 0, but template drain_list entries use[0, 1000])Context
Found while building the modelseed-api REST backend. When loading templates from local JSON files via
MSTemplateBuilder.from_dict()(instead of KBase workspace), models built withMSBuilder.build()had SK_ reactions but no DM_ reactions. The gapfiller adds DM_ to its internal clone, but they don't persist to the final model unless the LP solver includes them in the solution.In KBase, templates loaded via the workspace object factory (
kbase_api.get_from_ws()) may handle drain_list differently, which is why this wasn't caught before.🤖 Generated with Claude Code