Emit curated input/output stoichiometry; fix .env loading and duplicate reaction rows - #49
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…up rows - Curated stoichiometry: _resolve_vr_entities hardcoded every reaction input/output edge to stoichiometry=1, discarding the curated coefficient. Now reads Reactome's coefficient from the input/output relationship (new get_reaction_io_stoichiometry, same rel.stoichiometry property that get_complex_components uses) and attaches it per node — each expanded set member inherits its entity's coefficient; coefficients sum when two annotated entities map to one node; defaults to 1 absent curation. This feeds the stoichiometry_weighted export/pathway-rollup view (previously always 1). - .env loading: create-pathways.py used dotenv_values (a local dict that never populates os.environ), so NEO4J_URL/USER/PASSWORD/OUTPUT_DIR/LOG_LEVEL from .env were silently ignored and the connector fell back to hardcoded defaults. Switched to load_dotenv (non-clobbering) so credentials can be supplied when the Neo4j instance needs them. - get_reaction_connections: added RETURN DISTINCT — the hasEvent* traversal returns the same reaction pair via multiple sub-pathway paths, inflating the cached reaction_connections.csv. Behaviour-preserving (consumers dedupe). Test updated to assert curated coefficients flow through; full non-Neo4j suite passes (922). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Three fixes from a bug sweep. The headline is curated stoichiometry finally reaching the emitted networks.
Changes
logic_network_generator.py,neo4j_connector.py) —_resolve_vr_entitieshardcoded every reaction input/output edge tostoichiometry=1, discarding the curated coefficient. It now reads Reactome's coefficient from theinput/outputrelationship (newget_reaction_io_stoichiometry, samerel.stoichiometrypropertyget_complex_componentsalready uses) and attaches it per node — each expanded EntitySet member inherits its entity's coefficient, coefficients sum when two entities map to one node, and it defaults to 1 absent curation. Regenerated networks carry real coefficients (2/3/4/6/12/14 on assembly subunits). Phase-3 emission already consumed these maps, so no downstream change was needed..envloading (create-pathways.py) — useddotenv_values(a local dict that never populatesos.environ), soNEO4J_*/OUTPUT_DIR/LOG_LEVELfrom.envwere silently ignored and the connector fell back to hardcoded defaults. Switched toload_dotenv(non-clobbering) so credentials can be supplied when needed.get_reaction_connectionsDISTINCT (neo4j_connector.py) — thehasEvent*traversal returns the same reaction pair via multiple sub-pathway paths, inflating the cachedreaction_connections.csv. Behavior-preserving (consumers already dedupe).Scope note
The curated stoichiometry currently feeds the
stoichiometry_weightedexport/pathway-rollup view (what the pathway-browser overlay shows). Wiring it into the deltasignal solver was built and A/B-tested separately and A/B'd as a small regression, so it stays off by default — see #48 for the full result. This PR is the generator-side correctness fix, independent of that.Verification
Test updated to assert curated coefficients flow through; full non-Neo4j suite passes (922). The 8 pre-existing failures require a live Reactome Neo4j and are unaffected by this change.
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