[pre-commit.ci] auto fixes from pre-commit.com hooks

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pydatalab/pydatalab/routes/v0_1/collections.py

@@ -109,8 +109,7 @@ def create_collection():
         )
 
     if copy_from_id:
-        raise NotImplementedError(
-            "Copying collections is not yet implemented.")
+        raise NotImplementedError("Copying collections is not yet implemented.")
 
     if CONFIG.TESTING:
         data["creator_ids"] = [24 * "0"]
@@ -135,8 +134,7 @@ def create_collection():
             409,  # 409: Conflict
         )
 
-    data["last_modified"] = data.get(
-        "last_modified", datetime.datetime.now().isoformat())
+    data["last_modified"] = data.get("last_modified", datetime.datetime.now().isoformat())
 
     try:
         data_model = Collection(**data)
@@ -179,8 +177,7 @@ def create_collection():
                 "item_id": {"$in": list(item_ids)},
                 **get_default_permissions(user_only=True),
             },
-            {"$push": {"relationships": {
-                "type": "collections", "immutable_id": immutable_id}}},
+            {"$push": {"relationships": {"type": "collections", "immutable_id": immutable_id}}},
         )
 
         data_model.num_items = results.modified_count
@@ -234,8 +231,7 @@ def save_collection(collection_id):
     updated_data["last_modified"] = datetime.datetime.now().isoformat()
 
     collection = flask_mongo.db.collections.find_one(
-        {"collection_id": collection_id, **
-            get_default_permissions(user_only=True)}
+        {"collection_id": collection_id, **get_default_permissions(user_only=True)}
     )
 
     if not collection:
@@ -282,8 +278,7 @@ def save_collection(collection_id):
 @COLLECTIONS.route("/collections/<collection_id>", methods=["DELETE"])
 def delete_collection(collection_id: str):
     result = flask_mongo.db.collections.delete_one(
-        {"collection_id": collection_id, **
-            get_default_permissions(user_only=True)}
+        {"collection_id": collection_id, **get_default_permissions(user_only=True)}
     )
 
     if result.deleted_count != 1:
@@ -311,8 +306,7 @@ def search_collections():
     query = request.args.get("query", type=str)
     nresults = request.args.get("nresults", default=100, type=int)
 
-    match_obj = {"$text": {"$search": query}, **
-                 get_default_permissions(user_only=True)}
+    match_obj = {"$text": {"$search": query}, **get_default_permissions(user_only=True)}
 
     cursor = [
         json.loads(Collection(**doc).json(exclude_unset=True))
@@ -339,17 +333,15 @@ def add_items_to_collection(collection_id):
     data = request.get_json()
     refcodes = data.get("data", {}).get("refcodes", [])
 
-    collection = flask_mongo.db.collections.find_one(
-        {"collection_id": collection_id})
+    collection = flask_mongo.db.collections.find_one({"collection_id": collection_id})
 
     if not collection:
         return jsonify({"error": "Collection not found"}), 404
 
     if not refcodes:
         return jsonify({"error": "No item provided"}), 400
 
-    item_count = flask_mongo.db.items.count_documents(
-        {"refcode": {"$in": refcodes}})
+    item_count = flask_mongo.db.items.count_documents({"refcode": {"$in": refcodes}})
 
     if item_count == 0:
         return jsonify({"error": "No matching items found"}), 404

pydatalab/tests/server/test_samples.py

@@ -1,4 +1,3 @@
-from bson import ObjectId
 import copy
 import datetime
 import json
@@ -80,8 +79,7 @@ def test_new_sample_with_automatically_generated_id(client, user_id):
     response = client.get(f"/get-item-data/{created_item_id}")
     assert response.status_code == 200
     assert response.json["status"] == "success"
-    assert response.json["item_data"]["refcode"].split(":")[
-        1] == created_item_id
+    assert response.json["item_data"]["refcode"].split(":")[1] == created_item_id
 
     for key in new_sample_data.keys():
         if isinstance(v := new_sample_data[key], datetime.datetime):
@@ -97,8 +95,7 @@ def test_save_good_sample(client, default_sample_dict):
     updated_sample.update({"description": "This is a newer test sample."})
     response = client.post(
         "/save-item/",
-        json={
-            "item_id": default_sample_dict["item_id"], "data": updated_sample},
+        json={"item_id": default_sample_dict["item_id"], "data": updated_sample},
     )
     assert response.status_code == 200, response.json
     assert response.json["status"] == "success"
@@ -117,8 +114,7 @@ def test_save_bad_sample(client, default_sample_dict):
     updated_sample.update({"unknown_key": "This should not be allowed in."})
     response = client.post(
         "/save-item/",
-        json={
-            "item_id": default_sample_dict["item_id"], "data": updated_sample},
+        json={"item_id": default_sample_dict["item_id"], "data": updated_sample},
     )
     assert response.status_code == 200
     response = client.get(f"/get-item-data/{default_sample_dict['item_id']}")
@@ -150,8 +146,7 @@ def test_create_indices(real_mongo_client):
 
     create_default_indices(real_mongo_client)
     indexes = list(real_mongo_client.get_database().items.list_indexes())
-    expected_index_names = (
-        "_id_", "items full-text search", "item type", "unique item ID")
+    expected_index_names = ("_id_", "items full-text search", "item type", "unique item ID")
     names = [index["name"] for index in indexes]
 
     assert all(name in names for name in expected_index_names)
@@ -349,8 +344,7 @@ def test_copy_from_sample(client, complicated_sample):
 
     # Now try to directly make a copy that has the same data with a new ID
     copy_doc = {"item_id": "copy_of_complicated_sample"}
-    copy_request = {"new_sample_data": copy_doc,
-                    "copy_from_item_id": complicated_sample.item_id}
+    copy_request = {"new_sample_data": copy_doc, "copy_from_item_id": complicated_sample.item_id}
     response = client.post("/new-sample/", json=copy_request)
 
     assert response.status_code == 201, response.json
@@ -412,8 +406,7 @@ def test_create_multiple_samples(client, complicated_sample):
 
 @pytest.mark.dependency(depends=["test_create_multiple_samples"])
 def test_create_cell(client, default_cell):
-    response = client.post(
-        "/new-sample/", json=json.loads(default_cell.json()))
+    response = client.post("/new-sample/", json=json.loads(default_cell.json()))
     assert response.status_code == 201, response.json
     assert response.json["status"] == "success"
 
@@ -423,12 +416,10 @@ def test_create_cell(client, default_cell):
         "item_id": test_id,
         "type": "cells",
         "electrolyte": [
-            {"item": {"name": "salt", "chemform": "NaCl"},
-                "quantity": 100, "unit": "ml"}
+            {"item": {"name": "salt", "chemform": "NaCl"}, "quantity": 100, "unit": "ml"}
         ],
     }
-    copy_request = {"new_sample_data": copy_doc,
-                    "copy_from_item_id": default_cell.item_id}
+    copy_request = {"new_sample_data": copy_doc, "copy_from_item_id": default_cell.item_id}
     response = client.post("/new-sample/", json=copy_request)
     # Check that the copy retains the old components and the new
     assert response.status_code == 201, response.json
@@ -470,8 +461,7 @@ def test_cell_from_scratch(client):
     )
     response = client.post(
         "/new-sample/",
-        json={"new_sample_data": cell,
-              "copy_from_item_id": "test_cell_from_scratch"},
+        json={"new_sample_data": cell, "copy_from_item_id": "test_cell_from_scratch"},
     )
     assert response.status_code == 201
 
@@ -489,8 +479,7 @@ def test_create_collections(client, default_collection):
     assert response.status_code == 200
 
     # Create an empty collection
-    response = client.put(
-        "/collections", json={"data": json.loads(default_collection.json())})
+    response = client.put("/collections", json={"data": json.loads(default_collection.json())})
     assert response.status_code == 201, response.json
     assert response.json["status"] == "success"
     assert response.json["data"]["collection_id"] == "test_collection"
@@ -565,8 +554,7 @@ def test_items_added_to_existing_collection(client, default_collection, default_
     # Create a new item that is inside the default collection by passing collection_id
     new_id = "testing_collection_insert_by_id"
     default_sample_dict["item_id"] = new_id
-    default_sample_dict["collections"] = [
-        {"collection_id": default_collection.collection_id}]
+    default_sample_dict["collections"] = [{"collection_id": default_collection.collection_id}]
     response = client.post("/new-sample/", json=default_sample_dict)
     assert response.status_code == 201, response.json
     response = client.get(f"/collections/{default_collection.collection_id}")
@@ -586,8 +574,7 @@ def test_items_added_to_existing_collection(client, default_collection, default_
     # Create a new item that is inside the default collection by passing immutable id
     new_id2 = "testing_collection_insert_by_immutable"
     default_sample_dict["item_id"] = new_id2
-    default_sample_dict["collections"] = [
-        {"immutable_id": collection_immutable_id}]
+    default_sample_dict["collections"] = [{"immutable_id": collection_immutable_id}]
     response = client.post("/new-sample/", json=default_sample_dict)
     assert response.status_code == 201, response.json
     response = client.get(f"/collections/{default_collection.collection_id}")
@@ -600,8 +587,7 @@ def test_items_added_to_existing_collection(client, default_collection, default_
         {"immutable_id": collection_immutable_id},
         {"collection_id": "test_collection_2"},
     ]
-    response = client.post(
-        "/save-item/", json={"data": default_sample_dict, "item_id": new_id2})
+    response = client.post("/save-item/", json={"data": default_sample_dict, "item_id": new_id2})
     assert response.status_code == 200, response.json
 
     response = client.get(f"/get-item-data/{new_id2}")
@@ -618,8 +604,7 @@ def test_items_added_to_existing_collection(client, default_collection, default_
     default_sample_dict["collections"] = [
         {"collection_id": "test_collection_2"},
     ]
-    response = client.post(
-        "/save-item/", json={"data": default_sample_dict, "item_id": new_id2})
+    response = client.post("/save-item/", json={"data": default_sample_dict, "item_id": new_id2})
     assert response.status_code == 200, response.json
 
     response = client.get(f"/get-item-data/{new_id2}")
@@ -636,17 +621,15 @@ def test_items_added_to_existing_collection(client, default_collection, default_
     default_sample_dict["collections"] = [
         {"collection_id": "test_collection_3"},
     ]
-    response = client.post(
-        "/save-item/", json={"data": default_sample_dict, "item_id": new_id2})
+    response = client.post("/save-item/", json={"data": default_sample_dict, "item_id": new_id2})
     assert response.status_code == 401, response.json
 
     # Check that sending same collection multiple times doesn't lead to duplicates
     default_sample_dict["item_id"] = new_id2
     default_sample_dict["collections"] = [
         {"collection_id": "test_collection_2"},
     ]
-    response = client.post(
-        "/save-item/", json={"data": default_sample_dict, "item_id": new_id2})
+    response = client.post("/save-item/", json={"data": default_sample_dict, "item_id": new_id2})
     assert response.status_code == 200, response.json
 
     response = client.get(f"/get-item-data/{new_id2}")
@@ -656,31 +639,28 @@ def test_items_added_to_existing_collection(client, default_collection, default_
     ]
     assert len(response.json["item_data"]["collections"]) == 1
     assert (
-        len([d for d in response.json["item_data"]
-            ["relationships"] if d["type"] == "collections"])
+        len([d for d in response.json["item_data"]["relationships"] if d["type"] == "collections"])
         == 1
     )
 
 
 ##!
 
+
 @pytest.mark.dependency()
 def test_add_items_to_collection_not_found(client):
     collection_id = "invalid_collection_id"
 
-    response = client.post(f"/collections/{collection_id}", json={
-        "data": {"refcodes": []}
-    })
+    response = client.post(f"/collections/{collection_id}", json={"data": {"refcodes": []}})
     assert response.status_code == 404
     assert response.json["error"] == "Collection not found"
 
 
 @pytest.mark.dependency(depends=["test_add_items_to_collection_not_found"])
 def test_add_items_to_collection_no_items(client, default_collection):
-
-    response = client.post(f"/collections/{default_collection.collection_id}", json={
-        "data": {"refcodes": []}
-    })
+    response = client.post(
+        f"/collections/{default_collection.collection_id}", json={"data": {"refcodes": []}}
+    )
 
     assert response.status_code == 400
     assert response.json["error"] == "No item provided"
@@ -690,18 +670,20 @@ def test_add_items_to_collection_no_items(client, default_collection):
 def test_add_items_to_collection_no_matching_items(client, default_collection):
     refcodes = ["item123", "item456"]
 
-    response = client.post(f"/collections/{default_collection.collection_id}", json={
-        "data": {"refcodes": refcodes}
-    })
+    response = client.post(
+        f"/collections/{default_collection.collection_id}", json={"data": {"refcodes": refcodes}}
+    )
     assert response.status_code == 404
     assert response.json["error"] == "No matching items found"
 
 
 @pytest.mark.dependency(depends=["test_add_items_to_collection_no_matching_items"])
-def test_add_items_to_collection_success(client, default_collection, default_sample, complicated_sample):
-
-    response = client.post(f"/collections/{default_collection.collection_id}", json={
-        "data": {"refcodes": [default_sample.refcode, complicated_sample.refcode]}
-    })
+def test_add_items_to_collection_success(
+    client, default_collection, default_sample, complicated_sample
+):
+    response = client.post(
+        f"/collections/{default_collection.collection_id}",
+        json={"data": {"refcodes": [default_sample.refcode, complicated_sample.refcode]}},
+    )
     assert response.status_code == 200
     assert response.json["status"] == "success"