Made changes to maje mypy happy.

Author: JPBergsma

optimade/server/entry_collections/mongo.py

@@ -102,21 +102,24 @@ def count(self, **kwargs: Any) -> int:
             kwargs["filter"] = {}
         return len(self.collection.find(**kwargs))
 
-    def insert(self, content: bytes, filename: str, metadata: dict = {}) -> None:
+    def insert(self, data: list) -> None:
         """Add the given entries to the underlying database.
 
         Warning:
             No validation is performed on the incoming data.
 
         Arguments:
-            content: The file content to add to gridfs.
-            filename: The filename of the added content.
-            metadata: extra metadata to add to the gridfs entry.
+            data: a list of dictionaries. Each dictionary contains the data belonging to one file.
+                These dictionaries contain the fields:
+                    data: The file content to add to gridfs.
+                    filename: The filename of the added content.
+                    metadata: extra metadata to add to the gridfs entry.
         """
-        self.collection.put(content, filename=filename, metadata=metadata)
+        for entry in data:  # todo check whether I can insert multiple files in one go.
+            self.collection.put(**entry)
 
     def handle_query_params(
-        self, params: Union[SingleEntryQueryParams, PartialDataQueryParams]
+        self, params: Union[SingleEntryQueryParams, PartialDataQueryParams]  # type: ignore[override]
     ) -> Dict[str, Any]:
         """Parse and interpret the backend-agnostic query parameter models into a dictionary
         that can be used by MongoDB.
@@ -373,7 +376,7 @@ def insert(self, data: List[EntryResource]) -> None:
         self.collection.insert_many(data)
 
     def handle_query_params(
-        self, params: Union[EntryListingQueryParams, SingleEntryQueryParams]
+        self, params: Union[EntryListingQueryParams, SingleEntryQueryParams]  # type: ignore[override]
     ) -> Dict[str, Any]:
         """Parse and interpret the backend-agnostic query parameter models into a dictionary
         that can be used by MongoDB.

optimade/server/exception_handlers.py

@@ -230,7 +230,7 @@ def general_exception_handler(request: Request, exc: Exception) -> JSONAPIRespon
     (OptimadeHTTPException, http_exception_handler),
     (RequestValidationError, request_validation_exception_handler),
     (ValidationError, validation_exception_handler),
-    (VisitError, grammar_not_implemented_handler),
+    (VisitError, grammar_not_implemented_handler),  # type: ignore[list-item] # not entirely sure why this entry triggers mypy
     (NotImplementedError, not_implemented_handler),  # type: ignore[list-item] # not entirely sure why this entry triggers mypy
     (Exception, general_exception_handler),
 ]

optimade/server/main.py

@@ -101,7 +101,7 @@ def read_array_header(fobj):
                             "name": numpy_meta[2].name,
                             "itemsize": numpy_meta[2].itemsize,
                         }
-                partial_data_coll.insert(f, filename=filename, metadata=metadata)
+                partial_data_coll.insert([{"data": f, "filename": filename, "metadata": metadata}])  # type: ignore[list-item] # Todo : Perhaps this can be reduced to a single insert statement.
 
     def load_entries(endpoint_name: str, endpoint_collection: EntryCollection):
         LOGGER.debug("Loading test %s...", endpoint_name)

optimade/server/routers/utils.py

@@ -420,11 +420,13 @@ def get_partial_entry(
         )
 
     array = np.frombuffer(
-        results["attributes"]["data"],
-        dtype=getattr(np, results["attributes"]["dtype"]["name"]),
-    ).reshape(results["attributes"]["shape"])
+        results["attributes"]["data"],  # type: ignore[call-overload]
+        dtype=getattr(np, results["attributes"]["dtype"]["name"]),  # type: ignore[call-overload]
+    ).reshape(
+        results["attributes"]["shape"]
+    )  # type: ignore[call-overload]
     # slice array
-    property_ranges = results["attributes"]["property_ranges"]
+    property_ranges = results["attributes"]["property_ranges"]  # type: ignore[call-overload]
     slice_ind = [
         slice(
             0,
@@ -455,14 +457,14 @@ def get_partial_entry(
         "has_references": False,
     }  # Todo: add support for non_dense data
     if more_data_available:
-        next_link = ["PARTIAL-DATA-NEXT", [results["attributes"].pop("next")]]
+        next_link = ["PARTIAL-DATA-NEXT", [results["attributes"].pop("next")]]  # type: ignore[call-overload]
 
     if params.response_format == "json":
         for key in header:
-            results["attributes"][key] = header[key]
-        results["attributes"]["data"] = array.tolist()
+            results["attributes"][key] = header[key]  # type: ignore[call-overload]
+        results["attributes"]["data"] = array.tolist()  # type: ignore[call-overload]
         if more_data_available:
-            results["attributes"]["next"] = next_link
+            results["attributes"]["next"] = next_link  # type: ignore[call-overload]
         return dict(
             links=links,
             data=[results] if results else None,