Fix relationship cleanup on deletion

pydatalab/src/pydatalab/routes/v0_1/items.py

@@ -808,9 +808,30 @@ def update_item_permissions(refcode: str):
 
 @ITEMS.route("/delete-sample/", methods=["POST"])
 def delete_sample():
-    request_json = request.get_json()  # noqa: F821 pylint: disable=undefined-variable
+    request_json = request.get_json()
     item_id = request_json["item_id"]
 
+    item_to_delete = flask_mongo.db.items.find_one(
+        {"item_id": item_id, **get_default_permissions(user_only=True, deleting=True)},
+        projection={"refcode": 1, "_id": 1, "name": 1, "chemform": 1},
+    )
+
+    if not item_to_delete:
+        return (
+            jsonify(
+                {
+                    "status": "error",
+                    "message": f"Authorization required to attempt to delete sample with {item_id=} from the database.",
+                }
+            ),
+            401,
+        )
+
+    refcode = item_to_delete.get("refcode")
+    immutable_id = item_to_delete["_id"]
+    item_name = item_to_delete.get("name") or item_id
+    item_chemform = item_to_delete.get("chemform")
+
     result = flask_mongo.db.items.delete_one(
         {"item_id": item_id, **get_default_permissions(user_only=True, deleting=True)}
     )
@@ -825,6 +846,53 @@ def delete_sample():
             ),
             401,
         )
+
+    flask_mongo.db.items.update_many(
+        {"relationships.item_id": item_id}, {"$pull": {"relationships": {"item_id": item_id}}}
+    )
+
+    if refcode:
+        flask_mongo.db.items.update_many(
+            {"relationships.refcode": refcode}, {"$pull": {"relationships": {"refcode": refcode}}}
+        )
+
+    flask_mongo.db.items.update_many(
+        {"relationships.immutable_id": immutable_id},
+        {"$pull": {"relationships": {"immutable_id": immutable_id}}},
+    )
+
+    inline_item = {"name": item_name}
+    if item_chemform:
+        inline_item["chemform"] = item_chemform
+
+    items_with_constituent = flask_mongo.db.items.find(
+        {
+            "$or": [
+                {"synthesis_constituents.item.item_id": item_id},
+                {"synthesis_constituents.item.refcode": refcode},
+                {"synthesis_constituents.item.immutable_id": immutable_id},
+            ]
+        }
+    )
+
+    for item in items_with_constituent:
+        updated_constituents = []
+        for constituent in item.get("synthesis_constituents", []):
+            constituent_item = constituent.get("item", {})
+
+            if (
+                constituent_item.get("item_id") == item_id
+                or constituent_item.get("refcode") == refcode
+                or constituent_item.get("immutable_id") == immutable_id
+            ):
+                constituent["item"] = inline_item.copy()
+
+            updated_constituents.append(constituent)
+
+        flask_mongo.db.items.update_one(
+            {"_id": item["_id"]}, {"$set": {"synthesis_constituents": updated_constituents}}
+        )
+
     return (
         jsonify(
             {

pydatalab/tests/server/test_graph.py

@@ -158,3 +158,61 @@ def test_simple_graph(admin_client):
     graph = admin_client.get("/item-graph/parent").json
     assert len(graph["nodes"]) == 6
     assert len(graph["edges"]) == 5
+
+
+def test_delete_item_cleans_relationships_and_constituents(admin_client):
+    """Test that deleting an item removes relationships and transforms synthesis_constituents to inline."""
+
+    parent = Sample(item_id="parent_to_delete", name="Test Parent", chemform="NaCl")
+    response = admin_client.post(
+        "/new-sample/",
+        json={"new_sample_data": json.loads(parent.json())},
+    )
+    assert response.status_code == 201
+
+    child = Sample(
+        item_id="child_with_constituent",
+        synthesis_constituents=[
+            Constituent(item={"type": "samples", "item_id": "parent_to_delete"}, quantity=5.0)
+        ],
+    )
+    response = admin_client.post(
+        "/new-sample/",
+        json={"new_sample_data": json.loads(child.json())},
+    )
+    assert response.status_code == 201
+
+    response = admin_client.get("/get-item-data/child_with_constituent")
+    assert response.status_code == 200
+    assert "parent_to_delete" in response.json["parent_items"]
+    relationships = response.json["item_data"]["relationships"]
+    assert any(r.get("item_id") == "parent_to_delete" for r in relationships)
+
+    constituents = response.json["item_data"]["synthesis_constituents"]
+    assert len(constituents) == 1
+    assert constituents[0]["item"]["item_id"] == "parent_to_delete"
+    assert constituents[0]["item"]["type"] == "samples"
+
+    response = admin_client.post("/delete-sample/", json={"item_id": "parent_to_delete"})
+    assert response.status_code == 200
+
+    response = admin_client.get("/get-item-data/child_with_constituent")
+    assert response.status_code == 200
+    assert "parent_to_delete" not in response.json["parent_items"]
+    relationships = response.json["item_data"]["relationships"]
+    assert not any(r.get("item_id") == "parent_to_delete" for r in relationships)
+
+    constituents = response.json["item_data"]["synthesis_constituents"]
+    assert len(constituents) == 1
+    constituent_item = constituents[0]["item"]
+    assert constituent_item["name"] == "Test Parent"
+    assert constituent_item["chemform"] == "NaCl"
+    assert "item_id" not in constituent_item
+    assert "refcode" not in constituent_item
+    assert "type" not in constituent_item
+    assert "immutable_id" not in constituent_item
+
+    graph = admin_client.get("/item-graph/child_with_constituent").json
+    assert graph["status"] == "success"
+    assert len(graph["nodes"]) == 1
+    assert graph["nodes"][0]["data"]["id"] == "child_with_constituent"