diff --git a/swh/indexer/storage/model.py b/swh/indexer/storage/model.py
--- a/swh/indexer/storage/model.py
+++ b/swh/indexer/storage/model.py
@@ -55,12 +55,15 @@
         return cls(**d)  # type: ignore
 
     def unique_key(self) -> Dict:
-        if self.indexer_configuration_id is None:
-            raise ValueError(
-                "Can only call unique_key() on objects without "
-                "indexer_configuration_id."
-            )
-        return {key: getattr(self, key) for key in self.UNIQUE_KEY_FIELDS}
+        obj = self
+
+        # tool["id"] and obj.indexer_configuration_id are the same value, but
+        # only one of them is set for any given object
+        if obj.indexer_configuration_id is None:
+            assert obj.tool  # constructors ensures tool XOR indexer_configuration_id
+            obj = attr.evolve(obj, indexer_configuration_id=obj.tool["id"], tool=None)
+
+        return {key: getattr(obj, key) for key in self.UNIQUE_KEY_FIELDS}
 
 
 @attr.s
diff --git a/swh/indexer/tests/storage/test_model.py b/swh/indexer/tests/storage/test_model.py
new file mode 100644
--- /dev/null
+++ b/swh/indexer/tests/storage/test_model.py
@@ -0,0 +1,26 @@
+# Copyright (C) 2020  The Software Heritage developers
+# See the AUTHORS file at the top-level directory of this distribution
+# License: GNU General Public License version 3, or any later version
+# See top-level LICENSE file for more information
+
+from swh.indexer.storage.model import BaseRow, ContentLicenseRow
+
+
+def test_unique_key():
+    assert BaseRow(id=12, indexer_configuration_id=34).unique_key() == {
+        "id": 12,
+        "indexer_configuration_id": 34,
+    }
+
+    assert BaseRow(id=12, tool={"id": 34, "name": "foo"}).unique_key() == {
+        "id": 12,
+        "indexer_configuration_id": 34,
+    }
+
+    assert ContentLicenseRow(
+        id=12, indexer_configuration_id=34, license="BSD"
+    ).unique_key() == {"id": 12, "indexer_configuration_id": 34, "license": "BSD"}
+
+    assert ContentLicenseRow(
+        id=12, tool={"id": 34, "name": "foo"}, license="BSD"
+    ).unique_key() == {"id": 12, "indexer_configuration_id": 34, "license": "BSD"}