Fix pytest

Author: BenjaminCharmes

pydatalab/src/pydatalab/routes/v0_1/info.py

@@ -109,22 +109,14 @@ def get_info():
     versions, features and so on.
 
     """
-    attributes_data = {
-        "identifier_prefix": CONFIG.IDENTIFIER_PREFIX,
-        "features": FEATURE_FLAGS.model_dump()
-        if hasattr(FEATURE_FLAGS, "model_dump")
-        else FEATURE_FLAGS.__dict__,
-    }
-
-    if CONFIG.DEPLOYMENT_METADATA:
-        deployment_meta = CONFIG.DEPLOYMENT_METADATA.model_dump(exclude_none=True)
-        attributes_data.update(deployment_meta)
+    metadata = _get_deployment_metadata_once().copy()
+    info = Info(**metadata)
 
     return (
         jsonify(
             json.loads(
                 JSONAPIResponse(
-                    data=Data(id="/", type="info", attributes=Attributes(**attributes_data)),
+                    data=Data(id="/", type="info", attributes=info),
                     meta=Meta(query=request.query_string.decode() if request.query_string else ""),
                     links=Links(self=request.url),
                 ).model_dump_json()

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

@@ -904,7 +904,6 @@ def get_item_data(
             doc = None
 
         if not doc:
-            LOGGER.error(f"No document found for {match}")
             return (
                 jsonify(
                     {
@@ -1040,6 +1039,7 @@ def save_item():
         "creators",
         "creator_ids",
         "item_id",
+        "relationships",
     ):
         if k in updated_data:
             del updated_data[k]
@@ -1084,46 +1084,54 @@ def save_item():
             404,
         )
 
-    if "collections" in updated_data:
-        if updated_data.get("collections", []):
-            try:
-                updated_data["collections"] = _check_collections(updated_data)
-            except ValueError as exc:
-                return (
-                    dict(
-                        status="error",
-                        message=f"Cannot update {item_id!r} with missing collections {updated_data['collections']!r}: {exc}",
-                        item_id=item_id,
-                    ),
-                    401,
-                )
+    if updated_data.get("collections", []):
+        try:
+            updated_data["collections"] = _check_collections(updated_data)
+        except ValueError as exc:
+            return (
+                dict(
+                    status="error",
+                    message=f"Cannot update {item_id!r} with missing collections {updated_data['collections']!r}: {exc}",
+                    item_id=item_id,
+                ),
+                401,
+            )
 
-        existing_item = flask_mongo.db.items.find_one({"item_id": item_id})
-        if existing_item:
-            existing_relationships = existing_item.get("relationships", [])
-            non_collection_relationships = [
-                rel for rel in existing_relationships if rel.get("type") != "collections"
-            ]
+    existing_item = flask_mongo.db.items.find_one({"item_id": item_id})
+    if existing_item:
+        existing_relationships = existing_item.get("relationships", [])
+        non_collection_relationships = [
+            rel for rel in existing_relationships if rel.get("type") != "collections"
+        ]
 
-            collection_relationships = []
-            for coll in updated_data.get("collections", []):
-                immutable_id = coll.get("immutable_id")
-                if immutable_id:
-                    if isinstance(immutable_id, str):
-                        from bson import ObjectId
+        collection_relationships = []
+        for coll in updated_data.get("collections", []):
+            immutable_id = coll.get("immutable_id")
+            collection_id = coll.get("collection_id")
 
-                        immutable_id = ObjectId(immutable_id)
+            if immutable_id:
+                if isinstance(immutable_id, str):
+                    from bson import ObjectId
 
-                    collection_relationships.append(
-                        {
-                            "relation": None,
-                            "immutable_id": immutable_id,
-                            "type": "collections",
-                            "description": "Is a member of",
-                        }
-                    )
+                    immutable_id = ObjectId(immutable_id)
+            elif collection_id:
+                collection_doc = flask_mongo.db.collections.find_one(
+                    {"collection_id": collection_id}
+                )
+                if collection_doc:
+                    immutable_id = collection_doc["_id"]
 
-            updated_data["relationships"] = non_collection_relationships + collection_relationships
+            if immutable_id:
+                collection_relationships.append(
+                    {
+                        "relation": None,
+                        "immutable_id": immutable_id,
+                        "type": "collections",
+                        "description": "Is a member of",
+                    }
+                )
+
+        updated_data["relationships"] = non_collection_relationships + collection_relationships
 
     item_type = item["type"]
     item.update(updated_data)
@@ -1136,7 +1144,6 @@ def save_item():
             by_alias=True,
             exclude={"collections", "creators"},
         )
-
     except ValidationError as exc:
         return (
             jsonify(

pydatalab/tests/server/test_samples.py

@@ -341,13 +341,13 @@ def test_saved_sample_has_new_relationships(client, default_sample_dict, complic
     """
 
     default_sample_dict["item_id"] = "debug"
+
     response = client.post("/new-sample/", json=default_sample_dict)
 
     assert response.json
 
-    response = client.get(
-        f"/get-item-data/{default_sample_dict['item_id']}",
-    )
+    response = client.get(f"/get-item-data/{default_sample_dict['item_id']}")
+
     new_refcode = response.json["item_data"]["refcode"]
     assert new_refcode.startswith("test:")
 
@@ -356,7 +356,11 @@ def test_saved_sample_has_new_relationships(client, default_sample_dict, complic
     sample_dict = response.json["item_data"]
     sample_dict["synthesis_constituents"] = [
         {
-            "item": {"item_id": complicated_sample.item_id, "type": "samples"},
+            "item": {
+                "item_id": complicated_sample.item_id,
+                "type": "samples",
+                "name": complicated_sample.name,
+            },
             "quantity": 25.2,
             "unit": "g",
         }
@@ -366,15 +370,22 @@ def test_saved_sample_has_new_relationships(client, default_sample_dict, complic
         "/save-item/", json={"item_id": sample_dict["item_id"], "data": sample_dict}
     )
 
-    # Saving this link *should* add a searchable relationship in the database on both the new and old sample
+    print(response.status_code)
+    print(response.data)
+
     response = client.get(
         f"/get-item-data/{default_sample_dict['item_id']}",
     )
+
+    print(response.status_code)
+    print(response.data)
+
     assert complicated_sample.item_id in response.json["parent_items"]
 
     response = client.get(
         f"/get-item-data/{complicated_sample.item_id}",
     )
+
     assert sample_dict["item_id"] in response.json["child_items"]
 
 
@@ -692,6 +703,7 @@ def test_items_added_to_existing_collection(client, default_collection, default_
     assert response.status_code == 200, response.json
 
     response = client.get(f"/get-item-data/{new_id2}")
+
     assert response.status_code == 200, response.json
     assert "test_collection_2" in [
         d["collection_id"] for d in response.json["item_data"]["collections"]