auto-triage: no-bio1 condition returns failed dict instead of raising

tests/unit/test_reconstruct_bio1.py

@@ -0,0 +1,83 @@
+"""Unit tests: reconstruct task returns failed dict when model has no bio1 reaction.
+
+The root cause of issue #36 (modelseed-api-ops) was: tasks.py raised a RuntimeError for a user-input condition
+(genome too small / wrong template), which triggered a Celery task-failure alert.
+The fix changes that path to return {"status": "failed", ...} like other graceful-failure paths in the same function.
+"""
+from __future__ import annotations
+
+import pytest
+
+from unittest.mock import MagicMock, patch
+
+
+def _make_mock_mdlutl(reaction_ids):
+    """Return a minimal mock mdlutl with the given reaction ids."""
+    mock_reactions = [MagicMock(id=rid) for rid in reaction_ids]
+    mock_model = MagicMock()
+    mock_model.reactions = mock_reactions
+    mock_model.genes = []
+    mock_model.metabolites = []
+    mock_model.compartments = {}
+    mock_model.get_data = MagicMock(return_value={"biomasses": []})
+    mock_mdlutl = MagicMock()
+    mock_mdlutl.model = mock_model
+    return mock_mdlutl
+
+
+class TestReconstructBio1Check:
+    """Bio1 check in reconstruct should return a failed-status dict
+    (not raise RuntimeError) when the reconstructed model has no bio1 bo1
+    reaction -- this is a user-input condition, not a code bug."""
+
+    def _run_reconstruct_to_bio1_check(self, mdlutl):
+        """Common harness: patch all heavy deps and run reconstruct with output_path."""
+        from modelseed_api.jobs.tasks import reconstruct
+
+        mock_task = MagicMock()
+        mock_task.update_state = MagicMock()
+
+        mock_recon = MagicMock()
+        mock_recon.get_msgenome_from_dict.return_value = MagicMock()
+        mock_recon.build_metabolic_model.return_value = (
+            {"Reactions": 0, "Model genes": 0, "Class": "Gram Negative"},
+            mdlutl,
+        )
+        mock_bvbrc = MagicMock()
+        mock_ws = MagicMock()
+
+        with (patch("modelseed_api.jobs.tasks._init_kwargs", return_value={}),
+             patch("modelseed_api.jobs.tasks._load_template", return_value=MagicMock()),
+             patch("modelseed_api.jobs.tasks._classify_genome", return_value=("Gram Negative", "gn")),
+             patch("modelseed_api.jobs.tasks._fetch_bvbrc_genome", return_value={"scientific_name": "E. coli", "taxonomy": "", "domain": ""}),
+             patch("kbutillib.BVBRCUtils", return_value=mock_bvbrc),
+             patch("kbutillib.MSReconstructionUtils", return_value=mock_recon),
+             patch("modelseed_api.services.storage_factory.get_storage_service", return_value=mock_ws)):
+            return reconstruct(
+                mock_task,
+                token="un=testuser|tokenid=tok123|expiry=9999999999|sig=test",
+                genome="83332.12",
+                template_type="ar",
+                output_path="/testuser/modelseed/83332.12",
+            )
+
+    def test_missing_bio1_returns_failed_dict(self):
+        """When reconstruction produces a model without a bio1 reaction,
+        the task should return {'status': 'failed'} instead of raising.
+
+        Regression test for modelseed-api-ops issue #36:
+        no-bio1 used to raise RuntimeError, triggering a Celery
+        task-failure alert for a user-input problem.
+        """
+        mdlutl = _make_mock_mdlutl([])  # no reactions at all -- no bio1
+        result = self._run_reconstruct_to_bio1_check(mdlutl)
+        assert result["status"] == "failed"
+        assert "bio1" in result["error"]
+
+    def test_missing_bio1_does_not_raise(self):
+        """Ensure RuntimeError is not raised for the no-bio1 case."""
+        mdlutl = _make_mock_mdlutl(["rxn001", "rxn002"])  # no bio1
+        # Should return a dict, not raise
+        result = self._run_reconstruct_to_bio1_check(mdlutl)
+        assert isinstance(result, dict)
+        assert result["status"] == "failed"