auto-triage: reconstruct returns structured failure when bio1 absent

src/job_scripts/reconstruct.py

@@ -347,7 +347,13 @@ def now():
             ws = get_storage_service(args.token)
 
             import cobra.io
-            mdlutl.model.objective = "bio1"
+            reaction_ids = {r.id for r in mdlutl.model.reactions}
+            if "bio1" in reaction_ids:
+                mdlutl.model.objective = "bio1"
+            else:
+                bio_rxns = [r for r in mdlutl.model.reactions if r.id.startswith("bio")]
+                if bio_rxns:
+                    mdlutl.model.objective = bio_rxns[0].id
             cobra_json = json.dumps(cobra.io.model_to_dict(mdlutl.model))
 
             if not hasattr(mdlutl.model, 'get_data'):

src/modelseed_api/jobs/tasks.py

@@ -744,13 +744,19 @@ def reconstruct(
         if "bio1" in {r.id for r in mdlutl.model.reactions}:
             mdlutl.model.objective = "bio1"
         else:
-            raise RuntimeError(
-                "Model has no 'bio1' biomass reaction; reconstruction "
-                "produced an incomplete model. Common causes: input "
-                "genome too small for the classifier, or the selected "
-                "template lacks a biomass definition. Try template_type "
-                "explicitly (gn/gp/ar) or provide a larger input genome."
+            logger.error(
+                "Reconstruction produced no bio1 for genome %s", genome_id,
             )
+            return {
+                "status": "failed",
+                "error": (
+                    "Model has no bio1 biomass reaction; reconstruction"
+                    " produced an incomplete model. Common causes: input genome"
+                    " too small for the classifier, or the selected template"
+                    " lacks a biomass definition. Try template_type explicitly"
+                    " (gn/gp/ar) or provide a larger input genome."
+                ),
+            }
         cobra_json = json.dumps(cobra.io.model_to_dict(mdlutl.model))
 
         if not hasattr(mdlutl.model, 'get_data'):

tests/unit/test_reconstruct_bio1_guard.py

@@ -0,0 +1,33 @@
+"""Unit tests for bio1 objective guard logic."""
+import pytest
+
+pytestmark = pytest.mark.unit
+
+
+def _make_reactions(ids):
+    """Create mock reactions from a list of IDs."""
+    return [type("R", (), {"id": i})() for i in ids]
+
+
+class TestBio1Check:
+    def test_bio1_present_passes_guard(self):
+        reactions = _make_reactions(["rxn00001", "bio1"])
+        assert "bio1" in {r.id for r in reactions}
+
+    def test_bio1_absent_triggers_failure_path(self):
+        reactions = _make_reactions(["rxn00001", "rxn00002"])
+        assert "bio1" not in {r.id for r in reactions}
+
+    def test_bio_fallback_finds_bio2(self):
+        reactions = _make_reactions(["rxn00001", "bio2"])
+        fallback = next(
+            (r.id for r in reactions if r.id.startswith("bio")), None
+        )
+        assert fallback == "bio2"
+
+    def test_no_biomass_reaction_returns_none(self):
+        reactions = _make_reactions(["rxn00001", "rxn00002"])
+        fallback = next(
+            (r.id for r in reactions if r.id.startswith("bio")), None
+        )
+        assert fallback is None