check values in set instead of list

checking a set should be faster than checking a list

metadata_backend/api/handlers/folder.py

@@ -41,11 +41,11 @@ def _check_patch_folder(self, patch_ops: Any) -> None:
         for op in patch_ops:
             if _tags.match(op["path"]):
                 LOG.info(f"{op['op']} on tags in folder")
-                if "submissionType" in op["value"].keys() and op["value"]["submissionType"] not in [
+                if "submissionType" in op["value"].keys() and op["value"]["submissionType"] not in {
                     "XML",
                     "CSV",
                     "Form",
-                ]:
+                }:
                     reason = "submissionType is restricted to either 'CSV', 'XML' or 'Form' values."
                     LOG.error(reason)
                     raise web.HTTPBadRequest(reason=reason)
@@ -55,7 +55,7 @@ def _check_patch_folder(self, patch_ops: Any) -> None:
                     reason = f"Request contains '{op['path']}' key that cannot be updated to folders."
                     LOG.error(reason)
                     raise web.HTTPBadRequest(reason=reason)
-                if op["op"] in ["remove", "copy", "test", "move"]:
+                if op["op"] in {"remove", "copy", "test", "move"}:
                     reason = f"{op['op']} on {op['path']} is not allowed."
                     LOG.error(reason)
                     raise web.HTTPUnauthorized(reason=reason)
@@ -73,7 +73,7 @@ def _check_patch_folder(self, patch_ops: Any) -> None:
                         if (
                             "tags" in item
                             and "submissionType" in item["tags"]
-                            and item["tags"]["submissionType"] not in ["XML", "Form"]
+                            and item["tags"]["submissionType"] not in {"XML", "CSV", "Form"}
                         ):
                             reason = "submissionType is restricted to either 'XML' or 'Form' values."
                             LOG.error(reason)
@@ -98,7 +98,7 @@ async def get_folders(self, req: Request) -> Response:
         # Check if only published or draft folders are requestsed
         if "published" in req.query:
             pub_param = req.query.get("published", "").title()
-            if pub_param in ["True", "False"]:
+            if pub_param in {"True", "False"}:
                 folder_query["published"] = {"$eq": bool(strtobool(pub_param))}
             else:
                 reason = "'published' parameter must be either 'true' or 'false'"

metadata_backend/api/handlers/user.py

@@ -36,7 +36,11 @@ def _check_patch_user(self, patch_ops: Any) -> None:
         for op in patch_ops:
             if _tags.match(op["path"]):
                 LOG.info(f"{op['op']} on tags in folder")
-                if "submissionType" in op["value"].keys() and op["value"]["submissionType"] not in ["XML", "Form"]:
+                if "submissionType" in op["value"].keys() and op["value"]["submissionType"] not in {
+                    "XML",
+                    "CSV",
+                    "Form",
+                }:
                     reason = "submissionType is restricted to either 'XML' or 'Form' values."
                     LOG.error(reason)
                     raise web.HTTPBadRequest(reason=reason)
@@ -46,7 +50,7 @@ def _check_patch_user(self, patch_ops: Any) -> None:
                     reason = f"Request contains '{op['path']}' key that cannot be updated to user object"
                     LOG.error(reason)
                     raise web.HTTPBadRequest(reason=reason)
-                if op["op"] in ["remove", "copy", "test", "move", "replace"]:
+                if op["op"] in {"remove", "copy", "test", "move", "replace"}:
                     reason = f"{op['op']} on {op['path']} is not allowed."
                     LOG.error(reason)
                     raise web.HTTPUnauthorized(reason=reason)
@@ -65,7 +69,7 @@ def _check_patch_user(self, patch_ops: Any) -> None:
                         if (
                             "tags" in item
                             and "submissionType" in item["tags"]
-                            and item["tags"]["submissionType"] not in ["XML", "Form"]
+                            and item["tags"]["submissionType"] not in {"XML", "CSV", "Form"}
                         ):
                             reason = "submissionType is restricted to either 'XML' or 'Form' values."
                             LOG.error(reason)
@@ -187,7 +191,7 @@ async def _get_user_items(self, req: Request, user: Dict, item_type: str) -> Tup
         :returns: Paginated list of user draft templates and link header
         """
         # Check item_type parameter is not faulty
-        if item_type not in ["templates", "folders"]:
+        if item_type not in {"templates", "folders"}:
             reason = f"{item_type} is a faulty item parameter. Should be either folders or templates"
             LOG.error(reason)
             raise web.HTTPBadRequest(reason=reason)

metadata_backend/api/middlewares.py

@@ -18,7 +18,7 @@
 def _check_error_page_requested(req: Request, error_code: int) -> web.Response:  # type:ignore
     """Return the correct error page with correct status code."""
     if "Accept" in req.headers and req.headers["Accept"]:
-        if req.headers["Accept"].split(",")[0] in ["text/html", "application/xhtml+xml"]:
+        if req.headers["Accept"].split(",")[0] in {"text/html", "application/xhtml+xml"}:
             raise web.HTTPSeeOther(
                 f"/error{str(error_code)}",
                 headers={
@@ -115,7 +115,7 @@ async def check_login(request: Request, handler: Callable) -> StreamResponse:
     if request.path.startswith(tuple(controlled_paths)) and "OIDC_URL" in os.environ and bool(os.getenv("OIDC_URL")):
         cookie = decrypt_cookie(request)
         session = request.app["Session"].setdefault(cookie["id"], {})
-        if not all(x in ["access_token", "user_info", "oidc_state"] for x in session):
+        if not all(x in {"access_token", "user_info", "oidc_state"} for x in session):
             LOG.debug("checked session parameter")
             response = web.HTTPSeeOther(f"{aai_config['domain']}/aai")
             response.headers["Location"] = "/aai"

metadata_backend/api/operators.py

@@ -145,7 +145,7 @@ async def _insert_formatted_object_to_db(self, schema_type: str, data: Dict) ->
             raise web.HTTPBadRequest(reason=reason)
         if insert_success:
             try:
-                title = data["descriptor"]["studyTitle"] if schema_type in ["study", "draft-study"] else data["title"]
+                title = data["descriptor"]["studyTitle"] if schema_type in {"study", "draft-study"} else data["title"]
             except (TypeError, KeyError):
                 title = ""
             return data["accessionId"], title
@@ -176,7 +176,7 @@ async def _replace_object_from_db(self, schema_type: str, accession_id: str, dat
             raise web.HTTPBadRequest(reason=reason)
         if replace_success:
             try:
-                title = data["descriptor"]["studyTitle"] if schema_type in ["study", "draft-study"] else data["title"]
+                title = data["descriptor"]["studyTitle"] if schema_type in {"study", "draft-study"} else data["title"]
             except (TypeError, KeyError):
                 title = ""
             return accession_id, title

metadata_backend/database/db_service.py

@@ -35,8 +35,8 @@ async def retry(*args: Any, **kwargs: Any) -> Any:
                     message = f"Connection to database failed after {attempt} tries"
                     raise ConnectionFailure(message=message)
                 LOG.error(
-                    "Connection not successful, trying to reconnect."
-                    f"Reconnection attempt number {attempt}, waiting for {default_timeout} seconds."
+                    "Connection not successful, trying to reconnect. "
+                    + f"Reconnection attempt number {attempt}, waiting for {default_timeout} seconds."
                 )
                 continue
 
@@ -84,7 +84,7 @@ async def exists(self, collection: str, accession_id: str) -> bool:
         :param accession_id: ID of the object/folder/user to be searched
         :returns: True if exists and False if it does not
         """
-        id_key = f"{collection}Id" if (collection in ["folder", "user"]) else "accessionId"
+        id_key = f"{collection}Id" if (collection in {"folder", "user"}) else "accessionId"
         projection = {"_id": False, "externalId": False} if collection == "user" else {"_id": False}
         find_by_id = {id_key: accession_id}
         exists = await self.database[collection].find_one(find_by_id, projection)
@@ -124,7 +124,7 @@ async def read(self, collection: str, accession_id: str) -> Dict:
         :param accession_id: ID of the object/folder/user to be searched
         :returns: First document matching the accession_id
         """
-        id_key = f"{collection}Id" if (collection in ["folder", "user"]) else "accessionId"
+        id_key = f"{collection}Id" if (collection in {"folder", "user"}) else "accessionId"
         projection = {"_id": False, "eppn": False} if collection == "user" else {"_id": False}
         find_by_id = {id_key: accession_id}
         LOG.debug(f"DB doc in {collection} read for {accession_id}.")
@@ -160,7 +160,7 @@ async def update(self, collection: str, accession_id: str, data_to_be_updated: D
         updated to object, can replace previous fields and add new ones.
         :returns: True if operation was successful
         """
-        id_key = f"{collection}Id" if (collection in ["folder", "user"]) else "accessionId"
+        id_key = f"{collection}Id" if (collection in {"folder", "user"}) else "accessionId"
         find_by_id = {id_key: accession_id}
         update_op = {"$set": data_to_be_updated}
         result = await self.database[collection].update_one(find_by_id, update_op)
@@ -177,7 +177,7 @@ async def remove(self, collection: str, accession_id: str, data_to_be_removed: A
         updated to removed.
         :returns: True if operation was successful
         """
-        id_key = f"{collection}Id" if (collection in ["folder", "user"]) else "accessionId"
+        id_key = f"{collection}Id" if (collection in {"folder", "user"}) else "accessionId"
         find_by_id = {id_key: accession_id}
         remove_op = {"$pull": data_to_be_removed}
         result = await self.database[collection].find_one_and_update(
@@ -196,7 +196,7 @@ async def append(self, collection: str, accession_id: str, data_to_be_addded: An
         updated to removed.
         :returns: True if operation was successful
         """
-        id_key = f"{collection}Id" if (collection in ["folder", "user"]) else "accessionId"
+        id_key = f"{collection}Id" if (collection in {"folder", "user"}) else "accessionId"
         find_by_id = {id_key: accession_id}
         # push vs addtoSet
         # push allows us to specify the postion but it does not check the items are unique
@@ -241,7 +241,7 @@ async def delete(self, collection: str, accession_id: str) -> bool:
         :param accession_id: ID for object/folder/user to be deleted
         :returns: True if operation was successful
         """
-        id_key = f"{collection}Id" if (collection in ["folder", "user"]) else "accessionId"
+        id_key = f"{collection}Id" if (collection in {"folder", "user"}) else "accessionId"
         find_by_id = {id_key: accession_id}
         result = await self.database[collection].delete_one(find_by_id)
         LOG.debug(f"DB doc in {collection} deleted for {accession_id}.")

metadata_backend/helpers/parser.py

@@ -52,7 +52,7 @@ def _flatten(self, data: Any) -> Union[Dict, List, str, None]:
         :param schema_type: XML data
         :returns: XML element flattened.
         """
-        links = [
+        links = {
             "studyLinks",
             "sampleLinks",
             "runLinks",
@@ -64,7 +64,7 @@ def _flatten(self, data: Any) -> Union[Dict, List, str, None]:
             "datasetLinks",
             "assemblyLinks",
             "submissionLinks",
-        ]
+        }
 
         attrs = [
             "studyAttributes",
@@ -82,14 +82,14 @@ def _flatten(self, data: Any) -> Union[Dict, List, str, None]:
             "dataUses",
         ]
 
-        refs = ["analysisRef", "sampleRef", "runRef", "experimentRef"]
+        refs = {"analysisRef", "sampleRef", "runRef", "experimentRef"}
 
         children: Any = self.dict()
 
         for key, value, _ in self.map_content(data.content):
             key = self._to_camel(key.lower())
 
-            if key in attrs and len(value) == 1:
+            if key in set(attrs) and len(value) == 1:
                 attrs = list(value.values())
                 children[key] = attrs[0] if isinstance(attrs[0], list) else attrs
                 continue
@@ -106,7 +106,7 @@ def _flatten(self, data: Any) -> Union[Dict, List, str, None]:
                 continue
 
             if "assembly" in key:
-                if next(iter(value)) in ["standard", "custom"]:
+                if next(iter(value)) in {"standard", "custom"}:
                     children[key] = next(iter(value.values()))
                     if "accessionId" in children[key]:
                         children[key]["accession"] = children[key].pop("accessionId")
@@ -377,7 +377,7 @@ def parse(self, schema_type: str, content: str) -> List:
         """
         csv_reader = csv.DictReader(StringIO(content), delimiter=",", quoting=csv.QUOTE_NONE)
 
-        _sample_list = [
+        _sample_list = {
             "title",
             "alias",
             "description",
@@ -389,7 +389,7 @@ def parse(self, schema_type: str, content: str) -> List:
             "cellLine",
             "region",
             "phenotype",
-        ]
+        }
 
         if (
             csv_reader.fieldnames

metadata_backend/helpers/schema_loader.py

@@ -39,7 +39,7 @@ def _identify_file(self, schema_type: str) -> Path:
         """
         schema_type = schema_type.lower()
         schema_file = None
-        for file in [x for x in self.path.iterdir()]:
+        for file in set([x for x in self.path.iterdir()]):
             if schema_type in file.name and file.name.endswith(self.loader_type):
                 schema_file = file
                 break

tests/integration/mongo_indexes.py

@@ -36,7 +36,7 @@ async def create_indexes(url: str) -> None:
     db = client[DATABASE]
     LOG.debug(f"Current database: {db}")
     LOG.debug("=== Create collections ===")
-    for col in ["folder", "user"]:
+    for col in {"folder", "user"}:
         try:
             await db.create_collection(col)
         except pymongo.errors.CollectionInvalid as e: