Feature/update typing

docs/conf.py

@@ -1,7 +1,8 @@
 """Configuration file for the Sphinx documentation builder."""
 
 import datetime
-from typing import Callable
+
+from sphinx.application import Sphinx
 
 # -- Project information -----------------------------------------------------
 
@@ -62,7 +63,7 @@
 html_static_path = ["_static"]
 
 
-def setup(app: Callable) -> None:
+def setup(app: Sphinx) -> None:
     """Add custom stylesheet."""
     app.add_css_file("style.css")
 

metadata_backend/api/auth.py

@@ -1,14 +1,14 @@
 """Handle Access for request and OIDC workflow."""
 
 import time
-from typing import Dict, List, Union
+from typing import Any
 
 import aiohttp_session
 from aiohttp import web
 from aiohttp.client_exceptions import ClientConnectorError, InvalidURL
 from aiohttp.web import Request, Response
-from oidcrp.exception import OidcServiceError
-from oidcrp.rp_handler import RPHandler
+from oidcrp.exception import OidcServiceError  # type: ignore[import, unused-ignore]
+from oidcrp.rp_handler import RPHandler  # type: ignore[import, unused-ignore]
 from yarl import URL
 
 from ..conf.conf import aai_config
@@ -19,15 +19,15 @@
 
 # Type aliases
 # ProjectList is a list of projects and their origins
-ProjectList = List[Dict[str, str]]
+ProjectList = list[dict[str, str]]
 # UserData contains user profile from AAI userinfo, such as name, username and projects
-UserData = Dict[str, Union[ProjectList, str]]
+UserData = dict[str, ProjectList | str]
 
 
 class AccessHandler:
     """Handler for user access methods."""
 
-    def __init__(self, aai: Dict) -> None:
+    def __init__(self, aai: dict[str, Any]) -> None:
         """Define AAI variables and paths.
 
         :param aai: dictionary with AAI specific config
@@ -249,7 +249,7 @@ async def _set_user(
         browser_session["user_info"] = user_id
         return user_id
 
-    async def _create_user_data(self, userinfo: Dict) -> UserData:
+    async def _create_user_data(self, userinfo: dict[str, Any]) -> UserData:
         """Parse user profile data from userinfo endpoint response.
 
         :param userinfo: dict from userinfo containing user profile
@@ -277,7 +277,7 @@ async def _create_user_data(self, userinfo: Dict) -> UserData:
 
         return user_data
 
-    async def _get_projects_from_userinfo(self, userinfo: Dict) -> ProjectList:
+    async def _get_projects_from_userinfo(self, userinfo: dict[str, Any]) -> ProjectList:
         """Parse projects and groups from userinfo endpoint response.
 
         :param userinfo: dict from userinfo containing user profile
@@ -322,7 +322,7 @@ def __init__(self) -> None:
         """Get AAI credentials from config."""
         super().__init__(base_url=URL(aai_config["oidc_url"].rstrip("/")))
 
-    async def _healtcheck(self) -> Dict:
+    async def _healtcheck(self) -> dict[str, str]:
         """Check AAI service hearthbeat.
 
         This will return a JSON with well-known OIDC endpoints.

metadata_backend/api/handlers/common.py

@@ -1,11 +1,11 @@
 """Functions shared between handlers."""
 import csv
 import string
-from typing import Any, Dict, List, Tuple
+from typing import Any
 
 from aiohttp import BodyPartReader, MultipartReader, hdrs, web
 from aiohttp.web import Request
-from defusedxml.ElementTree import ParseError
+from defusedxml.ElementTree import ParseError  # type: ignore[import, unused-ignore]
 from xmlschema import XMLResource
 
 from ...conf.conf import schema_types
@@ -15,7 +15,7 @@
 
 async def multipart_content(
     req: Request, extract_one: bool = False, expect_xml: bool = False
-) -> Tuple[List[Tuple[Any, str, str]], str]:
+) -> tuple[list[tuple[Any, str, str]], str]:
     """Get content(s) and schema type(s) of a multipart request (from either csv or xml format).
 
     Note: for multiple files support check: https://docs.aiohttp.org/en/stable/multipart.html#hacking-multipart
@@ -26,8 +26,8 @@ async def multipart_content(
     :raises: HTTPBadRequest for multiple different reasons
     :returns: content and schema type for each uploaded file and file type of the upload
     """
-    xml_files: List[Tuple[str, str, str]] = []
-    csv_files: List[Tuple[Dict, str, str]] = []
+    xml_files: list[tuple[str, str, str]] = []
+    csv_files: list[tuple[dict[str, Any], str, str]] = []
     try:
         reader = await req.multipart()
     except AssertionError as exc:
@@ -75,7 +75,7 @@ async def multipart_content(
     return _get_content_with_type(xml_files, csv_files)
 
 
-async def _extract_upload(part: BodyPartReader) -> Tuple[str, str]:
+async def _extract_upload(part: BodyPartReader) -> tuple[str, str]:
     """Extract a submitted file from upload.
 
     :param part: Multipart reader for single body part
@@ -137,8 +137,8 @@ def _check_xml(content: str) -> bool:
 
 
 def _get_content_with_type(
-    xml_files: List[Tuple[str, str, str]], csv_files: List[Tuple[Dict, str, str]]
-) -> Tuple[List[Tuple[Any, str, str]], str]:
+    xml_files: list[tuple[str, str, str]], csv_files: list[tuple[dict[str, Any], str, str]]
+) -> tuple[list[tuple[Any, str, str]], str]:
     """Return either list of XML or CSV files with the file type info.
 
     :param xml_files: List of xml contents with schema types

metadata_backend/api/handlers/object.py

@@ -1,7 +1,7 @@
 """Handle HTTP methods for server."""
 from datetime import datetime
 from math import ceil
-from typing import Any, Dict, List, Tuple, Union
+from typing import Any
 
 import ujson
 from aiohttp import web
@@ -37,7 +37,7 @@ async def _handle_query(self, req: Request) -> Response:
         per_page = self._get_page_param(req, "per_page", 10)
         db_client = req.app["db_client"]
 
-        filter_list: List = []  # DEPRECATED, users don't own submissions anymore
+        filter_list: list[Any] = []  # DEPRECATED, users don't own submissions anymore
         data, page_num, page_size, total_objects = await ObjectOperator(db_client).query_metadata_database(
             collection, req.query, page, per_page, filter_list
         )
@@ -135,8 +135,8 @@ async def post_object(self, req: Request) -> Response:
             LOG.info(reason)
             raise web.HTTPBadRequest(reason=reason)
 
-        content: Union[Dict[str, Any], str, List[Tuple[Any, str, str]]]
-        operator: Union[ObjectOperator, XMLObjectOperator]
+        content: dict[str, Any] | str | list[tuple[Any, str, str]]
+        operator: ObjectOperator | XMLObjectOperator
         if req.content_type == "multipart/form-data":
             _only_xml = schema_type not in _allowed_csv
             files, cont_type = await multipart_content(req, extract_one=True, expect_xml=_only_xml)
@@ -174,9 +174,9 @@ async def post_object(self, req: Request) -> Response:
 
         # Add a new metadata object or multiple objects if multiple were extracted
         url = f"{req.scheme}://{req.host}{req.path}"
-        data: Union[List[Dict[str, str]], Dict[str, str]]
-        objects: List[Tuple[Dict[str, Any], str]] = []
-        if isinstance(content, List):
+        data: list[dict[str, str]] | dict[str, str]
+        objects: list[tuple[dict[str, Any], str]] = []
+        if isinstance(content, list):
             LOG.debug("Inserting multiple objects for collection: %r.", schema_type)
             if is_single_instance and len(content) > 1:
                 reason = f"Submission of type {workflow.name} can only have one '{schema_type}'. Cannot add multiple."
@@ -296,8 +296,8 @@ async def put_object(self, req: Request) -> Response:
         collection = f"draft-{schema_type}" if req.path.startswith(f"{API_PREFIX}/drafts") else schema_type
 
         db_client = req.app["db_client"]
-        content: Union[Dict, str]
-        operator: Union[ObjectOperator, XMLObjectOperator]
+        content: dict[str, Any] | str
+        operator: ObjectOperator | XMLObjectOperator
         filename = ""
         if req.content_type == "multipart/form-data":
             files, _ = await multipart_content(req, extract_one=True, expect_xml=True)
@@ -347,7 +347,7 @@ async def patch_object(self, req: Request) -> Response:
         collection = f"draft-{schema_type}" if req.path.startswith(f"{API_PREFIX}/drafts") else schema_type
 
         db_client = req.app["db_client"]
-        operator: Union[ObjectOperator, XMLObjectOperator]
+        operator: ObjectOperator | XMLObjectOperator
         if req.content_type == "multipart/form-data":
             reason = "XML patching is not possible."
             raise web.HTTPUnsupportedMediaType(reason=reason)
@@ -380,7 +380,9 @@ async def patch_object(self, req: Request) -> Response:
         LOG.info("PATCH object with accession ID: %r in collection: %r was successful.", accession_id, collection)
         return web.Response(body=body, status=200, content_type="application/json")
 
-    def _prepare_submission_patch_new_object(self, schema: str, objects: List, cont_type: str) -> List:
+    def _prepare_submission_patch_new_object(
+        self, schema: str, objects: list[Any], cont_type: str
+    ) -> list[dict[str, Any]]:
         """Prepare patch operations list for adding an object or objects to a submission.
 
         :param schema: schema of objects to be added to the submission
@@ -400,7 +402,7 @@ def _prepare_submission_patch_new_object(self, schema: str, objects: List, cont_
             path = "/metadataObjects/-"
 
         patch = []
-        patch_ops: Dict[str, Any] = {}
+        patch_ops: dict[str, Any] = {}
         for obj, filename in objects:
             try:
                 title = obj["descriptor"]["studyTitle"] if schema in ["study", "draft-study"] else obj["title"]
@@ -429,7 +431,9 @@ def _prepare_submission_patch_new_object(self, schema: str, objects: List, cont_
 
         return patch
 
-    def _prepare_submission_patch_update_object(self, schema: str, data: Dict, filename: str = "") -> List:
+    def _prepare_submission_patch_update_object(
+        self, schema: str, data: dict[str, Any], filename: str = ""
+    ) -> list[dict[str, Any]]:
         """Prepare patch operation for updating object's title in a submission.
 
         :param schema: schema of object to be updated

metadata_backend/api/handlers/publish.py

@@ -1,6 +1,6 @@
 """Handle HTTP methods for server."""
 from datetime import date, datetime
-from typing import Dict, List, Tuple
+from typing import Any
 
 import ujson
 from aiohttp import web
@@ -20,7 +20,7 @@ class PublishSubmissionAPIHandler(RESTAPIIntegrationHandler):
     """API Handler for publishing submissions."""
 
     @staticmethod
-    def _make_discovery_url(obj_data: Dict) -> str:
+    def _make_discovery_url(obj_data: dict[str, Any]) -> str:
         """Make an url that points to a discovery service."""
         if "metaxIdentifier" in obj_data:
             url = f"{doi_config['discovery_url']}{obj_data['metaxIdentifier']}"
@@ -29,7 +29,9 @@ def _make_discovery_url(obj_data: Dict) -> str:
         return url
 
     @staticmethod
-    def _prepare_datacite_study(study_data: Dict, general_info: Dict, discovery_url: str) -> Dict:
+    def _prepare_datacite_study(
+        study_data: dict[str, Any], general_info: dict[str, Any], discovery_url: str
+    ) -> dict[str, Any]:
         """Prepare Study object for publishing.
 
         :param study_data: Study Object read from the database
@@ -99,7 +101,9 @@ def _prepare_datacite_study(study_data: Dict, general_info: Dict, discovery_url:
 
         return study
 
-    def _prepare_datacite_dataset(self, study_doi: str, dataset_data: Dict, general_info: Dict) -> Dict:
+    def _prepare_datacite_dataset(
+        self, study_doi: str, dataset_data: dict[str, Any], general_info: dict[str, Any]
+    ) -> dict[str, Any]:
         """Prepare Dataset object for publishing.
 
         :param study_doi: Study DOI to link dataset to study at Datacite
@@ -181,7 +185,9 @@ def _prepare_datacite_dataset(self, study_doi: str, dataset_data: Dict, general_
 
         return dataset
 
-    async def _prepare_datacite_publication(self, obj_op: ObjectOperator, submission: Dict) -> Tuple[dict, list]:
+    async def _prepare_datacite_publication(
+        self, obj_op: ObjectOperator, submission: dict[str, Any]
+    ) -> tuple[dict[str, Any], list[dict[str, Any]]]:
         """Prepare dictionary with values for the Datacite DOI update.
 
         We need to prepare data for Study and Datasets, publish doi for each,
@@ -194,9 +200,9 @@ async def _prepare_datacite_publication(self, obj_op: ObjectOperator, submission
         :param submission: Submission data
         :returns: Tuple with the Study and list of Datasets and list of identifiers for publishing to Metax
         """
-        datacite_study = {}
-        datacite_datasets: List[dict] = []
-        datacite_bpdatasets: List[dict] = []
+        datacite_study: dict[str, Any] = {}
+        datacite_datasets: list[dict[str, Any]] = []
+        datacite_bpdatasets: list[dict[str, Any]] = []
 
         # we need to re-format these for Datacite, as in the JSON schemas
         # we split the words so that front-end will display them nicely
@@ -291,7 +297,9 @@ async def _prepare_datacite_publication(self, obj_op: ObjectOperator, submission
 
         return datacite_study, datacite_datasets
 
-    async def _publish_datacite(self, submission: dict, obj_op: ObjectOperator, operator: SubmissionOperator) -> dict:
+    async def _publish_datacite(
+        self, submission: dict[str, Any], obj_op: ObjectOperator, operator: SubmissionOperator
+    ) -> dict[str, Any]:
         """Prepare dictionary with values to be published to Metax.
 
         :param submission: Submission data
@@ -337,8 +345,8 @@ async def _publish_datacite(self, submission: dict, obj_op: ObjectOperator, oper
         return datacite_study
 
     async def _pre_publish_metax(
-        self, submission: dict, obj_op: ObjectOperator, operator: SubmissionOperator, external_user_id: str
-    ) -> List[dict]:
+        self, submission: dict[str, Any], obj_op: ObjectOperator, operator: SubmissionOperator, external_user_id: str
+    ) -> list[dict[str, Any]]:
         """Prepare dictionary with values to be published to Metax.
 
         :param submission: Submission data
@@ -347,7 +355,7 @@ async def _pre_publish_metax(
         :param external_user_id: user_id
         :returns: Whether publishing to Metax succeeded
         """
-        metax_datasets: List[dict] = []
+        metax_datasets: list[dict[str, Any]] = []
         async for _, schema, object_data in self.iter_submission_objects_data(submission, obj_op):
             if schema in DATACITE_SCHEMAS:
                 doi = object_data["doi"]
@@ -374,14 +382,14 @@ async def _pre_publish_metax(
         )
         return metax_datasets
 
-    async def _publish_rems(self, submission: dict, obj_op: ObjectOperator) -> None:
+    async def _publish_rems(self, submission: dict[str, Any], obj_op: ObjectOperator) -> None:
         """Prepare dictionary with values to be published to REMS.
 
         :param submission: Submission data
         :param obj_op: ObjectOperator for reading objects from database.
         :returns: Whether publishing to REMS succeeded
         """
-        rems_datasets: List[dict] = []
+        rems_datasets: list[dict[str, Any]] = []
 
         async for accession_id, schema, object_data in self.iter_submission_objects_data(submission, obj_op):
             if schema in {"dataset", "bpdataset"}:
@@ -572,7 +580,7 @@ async def publish_submission(self, req: Request) -> Response:
 
         # Patch the submission into a published state
         _now = int(datetime.now().timestamp())
-        patch = [
+        patch: list[dict[str, Any]] = [
             {"op": "replace", "path": "/published", "value": True},
             {"op": "replace", "path": "/drafts", "value": []},
             {"op": "add", "path": "/datePublished", "value": _now},