Add API tests for collections/<collection_id> POST route

Update test_samples.py to test add_items_to_collection route

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Update test_graph.py to test add_items_to_collection route

Remove unused thing and add default_permissions

Add default_permissions

Co-authored-by: Matthew Evans <[email protected]>

default_permissions

Co-authored-by: Matthew Evans <[email protected]>

Add default_permissions

Co-authored-by: Matthew Evans <[email protected]>

pre-commit run --all-files

Update test_samples.py to check presence of refcodes in the collection

pydatalab/pydatalab/routes/v0_1/collections.py

@@ -333,27 +333,32 @@ def add_items_to_collection(collection_id):
     data = request.get_json()
     refcodes = data.get("data", {}).get("refcodes", [])
 
-    collection = flask_mongo.db.collections.find_one({"_id": ObjectId(collection_id)})
+    collection = flask_mongo.db.collections.find_one(
+        {"collection_id": collection_id, **get_default_permissions()}
+    )
+
     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}, **get_default_permissions()}
+    )
 
     if item_count == 0:
         return jsonify({"error": "No matching items found"}), 404
 
     update_result = flask_mongo.db.items.update_many(
-        {"refcode": {"$in": refcodes}},
+        {"refcode": {"$in": refcodes}, **get_default_permissions()},
         {
             "$addToSet": {
                 "relationships": {
                     "description": "Is a member of",
                     "relation": None,
                     "type": "collections",
-                    "immutable_id": ObjectId(collection_id),
+                    "immutable_id": ObjectId(collection["_id"]),
                 }
             }
         },

pydatalab/tests/server/test_graph.py

@@ -22,6 +22,21 @@ def test_simple_graph(admin_client):
 
     child_2 = Sample(
         item_id="child_2",
+        refcode="test:TEST02",
+        synthesis_constituents=[
+            Constituent(item={"type": "samples", "item_id": "parent"}, quantity=None),
+        ],
+    )
+
+    child_3 = Sample(
+        item_id="child_3",
+        synthesis_constituents=[
+            Constituent(item={"type": "samples", "item_id": "parent"}, quantity=None),
+        ],
+    )
+
+    child_4 = Sample(
+        item_id="child_4",
         synthesis_constituents=[
             Constituent(item={"type": "samples", "item_id": "parent"}, quantity=None),
         ],
@@ -45,25 +60,30 @@ def test_simple_graph(admin_client):
         cell_format="swagelok",
     )
 
-    new_samples = [json.loads(d.json()) for d in [parent, child_1, child_2, missing_child, cell]]
+    new_samples = [
+        json.loads(d.json())
+        for d in [parent, child_1, child_2, child_3, child_4, missing_child, cell]
+    ]
 
-    response = admin_client.post(
+    sample_list = admin_client.post(
         "/new-samples/",
         json={"new_sample_datas": new_samples},
     )
 
-    assert response.status_code == 207
-    assert all(d == 201 for d in response.json["http_codes"])
+    assert sample_list.status_code == 207
+    assert all(d == 201 for d in sample_list.json["http_codes"])
 
     graph = admin_client.get("/item-graph").json
     assert {n["data"]["id"] for n in graph["nodes"]} == {
         "parent",
         "child_1",
         "child_2",
+        "child_3",
+        "child_4",
         "missing_child",
         "abcd-1-2-3",
     }
-    assert len(graph["edges"]) == 4
+    assert len(graph["edges"]) == 6
 
     response = admin_client.post("/delete-sample/", json={"item_id": "missing_child"})
     assert response
@@ -73,18 +93,20 @@ def test_simple_graph(admin_client):
         "parent",
         "child_1",
         "child_2",
+        "child_3",
+        "child_4",
         "abcd-1-2-3",
     }
 
-    assert len(graph["edges"]) == 3
+    assert len(graph["edges"]) == 5
 
     graph = admin_client.get("/item-graph/child_1").json
     assert len(graph["nodes"]) == 2
     assert len(graph["edges"]) == 1
 
     graph = admin_client.get("/item-graph/parent").json
-    assert len(graph["nodes"]) == 4
-    assert len(graph["edges"]) == 3
+    assert len(graph["nodes"]) == 6
+    assert len(graph["edges"]) == 5
 
     collection_id = "testcoll"
     collection_json = {
@@ -107,5 +129,32 @@ def test_simple_graph(admin_client):
     assert len(graph["edges"]) == 2
 
     graph = admin_client.get("/item-graph/parent").json
+    assert len(graph["nodes"]) == 7
+    assert len(graph["edges"]) == 10
+
+    samples = sample_list.json["responses"]
+
+    refcode_child_3 = None
+    refcode_child_4 = None
+
+    for item in samples:
+        if item["item_id"] == "child_3":
+            refcode_child_3 = item["sample_list_entry"].get("refcode")
+        elif item["item_id"] == "child_4":
+            refcode_child_4 = item["sample_list_entry"].get("refcode")
+
+    response = admin_client.post(
+        f"/collections/{collection_id}",
+        json={"data": {"refcodes": [refcode_child_3, refcode_child_4]}},
+    )
+
+    assert response.status_code == 200
+    assert response.json["status"] == "success"
+
+    graph = admin_client.get(f"/item-graph?collection_id={collection_id}").json
     assert len(graph["nodes"]) == 5
-    assert len(graph["edges"]) == 8
+    assert len(graph["edges"]) == 4
+
+    graph = admin_client.get("/item-graph/parent").json
+    assert len(graph["nodes"]) == 7
+    assert len(graph["edges"]) == 14

pydatalab/tests/server/test_samples.py

@@ -642,3 +642,56 @@ def test_items_added_to_existing_collection(client, default_collection, default_
         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": []}})
+    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": []}}
+    )
+
+    assert response.status_code == 400
+    assert response.json["error"] == "No item provided"
+
+
+@pytest.mark.dependency(depends=["test_add_items_to_collection_no_items"])
+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}}
+    )
+    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, example_items):
+    refcodes = [
+        item["refcode"] for item in example_items if item["item_id"] in {"12345", "sample_1"}
+    ]
+
+    response = client.post(
+        f"/collections/{default_collection.collection_id}",
+        json={"data": {"refcodes": refcodes}},
+    )
+
+    assert response.status_code == 200
+    assert response.json["status"] == "success"
+
+    response = client.get(f"/collections/{default_collection.collection_id}")
+    assert response.status_code == 200
+
+    collection_data = response.json
+    child_refcodes = [item["refcode"] for item in collection_data["child_items"]]
+
+    assert all(refcode in child_refcodes for refcode in refcodes)

webapp/src/components/AddToCollectionModal.vue

@@ -63,7 +63,7 @@ export default {
   methods: {
     async submitForm() {
       try {
-        const collectionIds = this.startInCollection.map((collection) => collection.immutable_id);
+        const collectionIds = this.startInCollection.map((collection) => collection.collection_id);
         const refcodes = this.itemsSelected.map((item) => item.refcode);
 
         for (const collectionId of collectionIds) {

webapp/src/server_fetch_utils.js

@@ -513,6 +513,8 @@ export function addABlock(item_id, block_type, index = null) {
 export function saveItem(item_id) {
   console.log("saveItem Called!");
   var item_data = store.state.all_item_data[item_id];
+  console.log("Item data before saving:", item_data);
+
   store.commit("setItemSaved", { item_id: item_id, isSaved: false });
   fetch_post(`${API_URL}/save-item/`, {
     item_id: item_id,
@@ -705,8 +707,8 @@ export function getBlocksInfos() {
     });
 }
 
-export function addItemsToCollection(collectionId, refcodes) {
-  return fetch_post(`${API_URL}/collections/${collectionId}`, {
+export function addItemsToCollection(collection_id, refcodes) {
+  return fetch_post(`${API_URL}/collections/${collection_id}`, {
     data: { refcodes },
   })
     .then(function (response_json) {