Merge pull request #454 from sanger/dependabot/pip/flask-3.0.2

Bump flask from 2.2.2 to 3.0.2

Pipfile

@@ -17,7 +17,7 @@ types-flask = "*"
 alembic = "~=1.10"
 autoenv = "~=1.0"
 colorlog = "~=6.8"
-flask = "~=2.2"
+flask = "~=3.0"
 flask-cors = "~=3.0"
 flask-sqlalchemy = "~=3.0"
 gunicorn = "~=20.0"

baracoda/operations.py

@@ -162,8 +162,8 @@ def __validate_prefix(self) -> bool:
         Returns:
             bool -- whether the prefix passed validation
         """
-        if type(self.prefix) != str:
-            return False
+        if not isinstance(self.prefix, str):
+            return False  # type: ignore
 
         pattern = re.compile(r"^[A-Z0-9]{1,10}$")
 

tests/test_barcodes.py

@@ -13,50 +13,50 @@ def test_param_empty_prefix_value(client):
 
 
 def test_invalid_prefix_is_rejected(client):
-    response = client.post("/barcodes/TEST123412_edu/new")
+    response = client.post("/barcodes/TEST123412_edu/new", headers={"Content-Type": "application/json"})
     assert response.status_code == HTTPStatus.BAD_REQUEST
 
 
 def test_get_new_barcode(client):
-    response = client.post("/barcodes/SANG/new")
+    response = client.post("/barcodes/SANG/new", headers={"Content-Type": "application/json"})
     assert response.json == {"barcode": "SANG-30D404"}
     assert response.status_code == HTTPStatus.CREATED
 
 
 def test_get_new_barcode_for_ht(client):
-    response = client.post("/barcodes/HT/new")
+    response = client.post("/barcodes/HT/new", headers={"Content-Type": "application/json"})
     assert response.json == {"barcode": "HT-111111"}
     assert response.status_code == HTTPStatus.CREATED
 
 
 def test_get_new_barcode_for_sqp(client):
-    response = client.post("/barcodes/SQPD/new")
+    response = client.post("/barcodes/SQPD/new", headers={"Content-Type": "application/json"})
     assert response.json == {"barcode": "SQPD-1-C"}
     assert response.status_code == HTTPStatus.CREATED
 
 
 def test_get_new_barcode_with_text(client):
-    response = client.post("/barcodes/SQPD/new?text=T12")
+    response = client.post("/barcodes/SQPD/new?text=T12", headers={"Content-Type": "application/json"})
     assert response.json == {"barcode": "SQPD-T12-1-J"}
     assert response.status_code == HTTPStatus.CREATED
 
 
 def test_get_new_barcode_with_wrong_text(client):
-    response = client.post("/barcodes/SQPD/new?text=T120")
+    response = client.post("/barcodes/SQPD/new?text=T120", headers={"Content-Type": "application/json"})
     assert response.json == {"errors": ["InvalidTextError"]}
     assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR
 
 
 def test_get_new_barcodes_group_as_url_param(client):
-    response = client.post("/barcodes_group/SANG/new?count=3")
+    response = client.post("/barcodes_group/SANG/new?count=3", headers={"Content-Type": "application/json"})
     resp = response.json
     resp["barcodes_group"]["barcodes"].sort()
     assert resp == {"barcodes_group": {"barcodes": ["SANG-30D404", "SANG-30D413", "SANG-30D422"], "id": 1}}
     assert response.status_code == HTTPStatus.CREATED
 
 
 def test_get_new_barcodes_group_without_count(client):
-    response = client.post("/barcodes_group/SANG/new")
+    response = client.post("/barcodes_group/SANG/new", headers={"Content-Type": "application/json"})
     assert response.status_code == HTTPStatus.BAD_REQUEST
 
 
@@ -66,7 +66,7 @@ def test_get_new_barcodes_group_with_wrong_value_count(client):
 
 
 def test_get_new_barcodes_group_with_wrong_value_negative(client):
-    response = client.post("/barcodes_group/SANG/new?count=-124")
+    response = client.post("/barcodes_group/SANG/new?count=-124", headers={"Content-Type": "application/json"})
     assert response.status_code == HTTPStatus.UNPROCESSABLE_ENTITY
 
 
@@ -95,7 +95,7 @@ def test_get_last_barcode(client):
     assert response.status_code == HTTPStatus.NOT_FOUND
 
     # when creating barcodes
-    response = client.post("/barcodes/SANG/new")
+    response = client.post("/barcodes/SANG/new", headers={"Content-Type": "application/json"})
     response = client.get("/barcodes/SANG/last")
     assert response.json == {"barcode": "SANG-30D404"}
     assert response.status_code == HTTPStatus.OK