Fixed bug with InChI not being populated by listener

CHANGELOG.md

@@ -5,6 +5,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased]
 
+### Fixed
+
+- **Identity auto-population event listeners** (`add_inchi_identities_before_flush`, `add_smiles_extras_before_flush`, `add_hill_extras_before_flush`): Now correctly handle `StationaryPointRow` objects created with relationship objects (`geometry=geo_row`) in addition to foreign key IDs (`geometry_id=geom.id`). Previously, the listeners only checked `geometry_id` and used `session.get()` to load the geometry, which failed when objects were created with relationships and added together without intermediate flushes (as in batch workflow patterns). The fix tries the relationship first, then falls back to FK-based loading, supporting both creation patterns.
+
 ## [0.0.14] - 2026-09-01
 ### Changed
 -- **Bump** `automol` to v0.0.23 to resolve dependency installations

src/autostorage/events.py

@@ -228,11 +228,11 @@ def add_inchi_identities_before_flush(
         if not isinstance(obj, StationaryPointRow):
             continue
 
-        if obj.geometry_id is None or obj.identities:
-            continue
-
-        # Load the geometry
-        geometry_row = session.get(GeometryRow, obj.geometry_id)
+        # Get geometry - try relationship first (for `geometry=geo_row`),
+        # then load via FK (for `geometry_id=id`)
+        geometry_row = obj.geometry
+        if geometry_row is None and obj.geometry_id is not None:
+            geometry_row = session.get(GeometryRow, obj.geometry_id)
         if geometry_row is None:
             continue
 
@@ -298,11 +298,15 @@ def add_smiles_extras_before_flush(
         if not isinstance(obj, StationaryPointRow):
             continue
 
-        if obj.geometry_id is None or not obj.identities:
+        # Skip if no identities attached yet
+        if not obj.identities:
             continue
 
-        # Load the geometry
-        geometry_row = session.get(GeometryRow, obj.geometry_id)
+        # Get geometry - try relationship first (for `geometry=geo_row`),
+        # then load via FK (for `geometry_id=id`)
+        geometry_row = obj.geometry
+        if geometry_row is None and obj.geometry_id is not None:
+            geometry_row = session.get(GeometryRow, obj.geometry_id)
         if geometry_row is None:
             continue
 
@@ -349,11 +353,15 @@ def add_hill_extras_before_flush(
         if not isinstance(obj, StationaryPointRow):
             continue
 
-        if obj.geometry_id is None or not obj.identities:
+        # Skip if no identities attached yet
+        if not obj.identities:
             continue
 
-        # Load the geometry
-        geometry_row = session.get(GeometryRow, obj.geometry_id)
+        # Get geometry - try relationship first (for `geometry=geo_row`),
+        # then load via FK (for `geometry_id=id`)
+        geometry_row = obj.geometry
+        if geometry_row is None and obj.geometry_id is not None:
+            geometry_row = session.get(GeometryRow, obj.geometry_id)
         if geometry_row is None:
             continue
 

tests/test_events.py

@@ -1216,6 +1216,43 @@ def test_different_geometries_create_different_identities(
             identity_count = session.query(IdentityRow).count()
             assert identity_count == EXPECTED_IDENTITY_COUNT_TWO
 
+    def test_inchi_identity_added_with_relationship_object(
+        self, database: Database, make_model_opt: Callable[[], ModelRow]
+    ) -> None:
+        """InChI identity is added when StationaryPointRow uses relationship object."""
+        with database.session() as session:
+            model = make_model_opt()
+            session.add(model)
+            session.flush()
+
+            calc = CalculationRow(
+                calc_type="opt",
+                model_id=model.id,
+                input_provenance={},
+                output_provenance={},
+            )
+            geom = GeometryRow(
+                symbols=["C", "O"],
+                coordinates=[[0.0, 0.0, 0.0], [1.5, 0.0, 0.0]],
+                charge=0,
+                spin=1,
+            )
+
+            # Create StationaryPointRow with relationship objects (no IDs)
+            # This mimics the pattern used in the demo where objects are created
+            # and added together without intermediate flushes
+            stat_point = StationaryPointRow(calculation=calc, geometry=geom, order=0)
+
+            session.add_all([calc, geom, stat_point])
+            session.flush()
+
+            # Identity should be auto-populated despite using relationship objects
+            assert len(stat_point.identities) == 1
+            identity = stat_point.identities[0]
+            assert identity.kind == "stereoisomer"
+            assert identity.algorithm == "rdkit inchi"
+            assert identity.value.startswith("InChI=")
+
 
 class TestAddSmilesExtras:
     """Tests for add_smiles_extras_before_flush event listener."""