fix: unblock bulk-reconstruct code path (biochem_db parens + dead print_json_debug_file) - #46
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fix: unblock bulk-reconstruct code path (biochem_db parens + dead print_json_debug_file)#46jplfaria wants to merge 1 commit into
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…nt_json_debug_file) Two latent bugs along the compute_ontology_model_changes -> build_metabolic_model -> _add_reactions_from_gene_mapping path. Neither has an active call site in the existing KBase-wrapped flows (kb_build_metabolic_models guards them out in practice), but they are hard-blocking the modelseed-api bulk-reconstruct endpoint which calls these primitives directly per Chris's guidance. Bug 1: ms_reconstruction_utils.py:111 modelseeddb = self.biochem_db() biochem_db is a @Property (MSBiochemUtils, line 85), not a method. The parens call the returned ModelSEEDDatabase instance as a function and raise TypeError on the first reaction added via this path. Bug 2: ms_reconstruction_utils.py:379 + kb_model_utils.py:425, 600 self.print_json_debug_file(...) print_json_debug_file is referenced 3 times but defined nowhere in the active code (only in kb_model_utils.py.bak, which isn't loaded). Any call path through compute_ontology_model_changes or save-without-workspace AttributeErrors immediately. The debug hook was leftover from a refactor; drop the calls. Re-add via the proper debug interface if needed later. Verified end-to-end against poplar bulk_reconstruct (KO-annotated test genomes) once both fixes were applied: model build succeeds, reactions.csv + genes.csv populated, COBRA JSON written to workspace. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Two latent bugs along the
compute_ontology_model_changes->build_metabolic_model->_add_reactions_from_gene_mappingpath. Neither has an active call site in the existing KBase-wrapped flows (kb_build_metabolic_modelsguards them out in practice), but they are hard-blocking the modelseed-api bulk-reconstruct endpoint which calls these primitives directly per the Phase 3 PRD path you'd suggested.Bug 1:
biochem_dbcalled as a functionsrc/kbutillib/ms_reconstruction_utils.py:111biochem_dbis a@property(MSBiochemUtils:85), not a method. The parens call the returnedModelSEEDDatabaseinstance as a function and raiseTypeError: 'ModelSEEDDatabase' object is not callableon the first reaction added via this path. Fix: drop the parens.Bug 2:
print_json_debug_filereferences with no definitionsrc/kbutillib/ms_reconstruction_utils.py:379,src/kbutillib/kb_model_utils.py:425, 600print_json_debug_fileis referenced 3 times but defined nowhere in the active code (only inkb_model_utils.py.bak, which isn't loaded). Any call path throughcompute_ontology_model_changesor save-without-workspaceAttributeErrors immediately. The debug hook was leftover from a refactor; this PR drops the three calls. Re-add via the proper debug interface if needed later.Verification
Verified end-to-end against poplar
/api/jobs/bulk_reconstruct(KO-annotated test genomes) once both fixes were applied locally: model build succeeds,reactions.csv+genes.csvpopulated, COBRA JSON written to workspace.🤖 Generated with Claude Code