auto-triage: guard bio1 objective assignment in reconstruct (issue #23)

src/job_scripts/reconstruct.py

@@ -55,6 +55,16 @@ def merge_ws_metadata(ws, obj_path, new_meta):
     ws.update_metadata({"objects": [[obj_path, merged]]})
 
 
+def _set_biomass_objective(model) -> None:
+    """Set the model objective to bio1 if present, otherwise fall back to the first
+    biomass-like reaction. Silently skips if no biomass reaction is found."""
+    if "bio1" in {r.id for r in model.reactions}:
+        model.objective = "bio1"
+        return
+    biomass_rxns = [r for r in model.reactions if "bio" in r.id.lower()]
+    if biomass_rxns:
+        model.objective = biomass_rxns[0].id
+
 def main():
     parser = argparse.ArgumentParser(description="Model reconstruction job")
     parser.add_argument("--job-id", required=True)
@@ -346,7 +356,7 @@ def main():
             ws = get_storage_service(args.token)
 
             import cobra.io
-            mdlutl.model.objective = "bio1"
+            _set_biomass_objective(mdlutl.model)
             cobra_json = json.dumps(cobra.io.model_to_dict(mdlutl.model))
 
             if not hasattr(mdlutl.model, 'get_data'):

src/modelseed_api/jobs/tasks.py

@@ -450,6 +450,16 @@ def _fix_gapfilling_metadata(ws_data: dict, media_workspace_ref: str | None) ->
                     gd[new_id] = gd.pop(old_id)
 
 
+def _set_biomass_objective(model) -> None:
+    """Set the model objective to bio1 if present, otherwise fall back to the first
+    biomass-like reaction. Silently skips if no biomass reaction is found."""
+    if "bio1" in {r.id for r in model.reactions}:
+        model.objective = "bio1"
+        return
+    biomass_rxns = [r for r in model.reactions if "bio" in r.id.lower()]
+    if biomass_rxns:
+        model.objective = biomass_rxns[0].id
+
 @app.task(bind=True, name="modelseed.reconstruct")
 def reconstruct(
     self,
@@ -731,7 +741,7 @@ def reconstruct(
         # Save cobra JSON BEFORE CobraModelConverter (which loses exchange
         # bounds and breaks FBA). cobra.io roundtrip is lossless.
         import cobra.io
-        mdlutl.model.objective = "bio1"
+        _set_biomass_objective(mdlutl.model)
         cobra_json = json.dumps(cobra.io.model_to_dict(mdlutl.model))
 
         if not hasattr(mdlutl.model, 'get_data'):
@@ -1262,10 +1272,7 @@ def _reconstruct_one_genome(
     if do_fva:
         # Configure model objective for FVA; both runs use the same model
         # but with different media bounds applied (handled by media-pkg).
-        try:
-            mdlutl.model.objective = "bio1"
-        except Exception:
-            pass
+        _set_biomass_objective(mdlutl.model)
         try:
             fva_rich = compute_fva_classes(mdlutl.model, media_or_setup="rich")
             fva_min = compute_fva_classes(mdlutl.model, media_or_setup="minimal")

tests/unit/test_set_biomass_objective.py

@@ -0,0 +1,49 @@
+"""Unit tests for _set_biomass_objective helper."""
+import pytest
+
+pytestmark = pytest.mark.unit
+
+
+def _make_mock_model(reaction_ids):
+    """Build a minimal mock cobra Model with the given reaction IDs."""
+    import unittest.mock as mock
+
+    reactions = []
+    for rid in reaction_ids:
+        r = mock.MagicMock()
+        r.id = rid
+        r.__str__ = lambda self: self.id
+        reactions.append(r)
+
+    model = mock.MagicMock()
+    model.reactions = reactions
+    model.objective = None
+    return model
+
+
+class TestSetBiomassObjective:
+    def test_bio1_present_sets_bio1(self):
+        from modelseed_api.jobs.tasks import _set_biomass_objective
+        model = _make_mock_model(["rxn00001", "bio1", "rxn00002"])
+        _set_biomass_objective(model)
+        assert model.objective == "bio1"
+
+    def test_no_bio1_falls_back_to_biomass_reaction(self):
+        from modelseed_api.jobs.tasks import _set_biomass_objective
+        model = _make_mock_model(["rxn00001", "bio2", "rxn00002"])
+        _set_biomass_objective(model)
+        assert model.objective == "bio2"
+
+    def test_no_biomass_reaction_skips_silently(self):
+        from modelseed_api.jobs.tasks import _set_biomass_objective
+        model = _make_mock_model(["rxn00001", "rxn00002"])
+        original = model.objective
+        _set_biomass_objective(model)
+        assert model.objective == original
+
+    def test_empty_model_skips_silently(self):
+        from modelseed_api.jobs.tasks import _set_biomass_objective
+        model = _make_mock_model([])
+        original = model.objective
+        _set_biomass_objective(model)
+        assert model.objective == original