Skip: Update all non-major dependencies (merge commit)

Merge branch 'renovate/all-minor-patch' into 'main'
* revert mypy in pre-commit and fix typing

* reference python 3.11

* remove duplicate mypy from pre-commit

* add typing-extensions module

* don't generate code docs for now

* fix sort  problematic word submitter's

* fix mypy ci

* update pre-commit

* switch to idpyoidc

* Skip: Update all non-major dependencies

See merge request https://gitlab.ci.csc.fi/sds-dev/sd-submit/metadata-submitter/-/merge_requests/831

Approved-by: Joonatan Mäkinen <[email protected]>
Co-authored-by: Stefan Negru <[email protected]>
Co-authored-by: Teemu Kataja <[email protected]>
Merged by Joonatan Mäkinen <[email protected]>

.gitignore

@@ -121,7 +121,7 @@ venv.bak/
 metadata_backend/frontend/*
 config/*
 
-# oidcrp generated directories that store JWKs
+# idpyoidc generated directories that store JWKs
 private
 static
 # ignore pyspelling dictionary

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
     - id: check-useless-excludes
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: no-commit-to-branch
       args: [--branch, develop, --branch, master]
@@ -29,27 +29,27 @@ repos:
       exclude: tests/test_files/study/SRP000539_invalid[0-9]?.xml
 
   - repo: https://github.com/psf/black
-    rev: 23.10.0
+    rev: 24.1.1
     hooks:
     - id: black
       args: [-l, "120"]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     - id: isort
       args: [--profile, black, --filter-files]
 
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
     - id: flake8
       additional_dependencies:
         - flake8-docstrings
         - flake8-annotations
 
   - repo:  https://github.com/PyCQA/bandit
-    rev: 1.7.5
+    rev: 1.7.7
     hooks:
     - id: bandit
       files: ^metadata_backend
@@ -62,7 +62,7 @@ repos:
       files: docs/openapi.yml
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.27.0
+    rev: 0.28.0
     hooks:
       - id: check-metaschema
         name: Validate schemas
@@ -104,13 +104,6 @@ repos:
           -sn, # Don't display the score
         ]
 
-    - id: mypy
-      name: mypy
-      entry: mypy
-      language: system
-      types: [python]
-      files: ^metadata_backend
-
     - id: pyspelling-docs
       name: pyspelling-docs
       entry: ./scripts/dictionary/pyspelling.sh
@@ -119,6 +112,13 @@ repos:
       types_or: [markdown, rst]
       require_serial: true
 
+    - id: mypy
+      name: mypy
+      entry: mypy
+      language: system
+      types: [python]
+      files: ^metadata_backend
+
     - id: pyspelling-schemas
       name: pyspelling-schemas
       entry: ./scripts/dictionary/pyspelling.sh

README.md

@@ -14,7 +14,7 @@ Service also validates submitted metadata objects against EGA XSD metadata model
 ## Install and run
 
 ### Requirements:
-- Python 3.8+
+- Python 3.11+
 - MongoDB
 - Docker + docker-compose
 

docs/dictionary/wordlist.txt

@@ -314,6 +314,7 @@ identifiertype
 identitypython
 ido
 idp
+idpyoidc
 ietf
 igbo
 igsn

docs/submitter.rst

@@ -160,6 +160,3 @@ The REST API is protected and can be accessed in two ways:
 .. important:: A logged in user can only perform operations on the data it has associated.
                The information for the current user can be retrieved at ``/v1/users/current`` (the user ID is ``current``), and
                any additional operations on other users are rejected.
-
-
-.. include:: code.rst

examples/create_token.py

@@ -9,6 +9,7 @@
 3. Generate a token with the instructions in this script
 4. Use the token as a Bearer token, with `valid=timestamp` and `userId=user_id` query parameters
 """
+
 import hmac
 import time
 

metadata_backend/api/auth.py

@@ -7,8 +7,8 @@
 from aiohttp import web
 from aiohttp.client_exceptions import ClientConnectorError, InvalidURL
 from aiohttp.web import Request, Response
-from oidcrp.exception import OidcServiceError  # type: ignore[import, unused-ignore]
-from oidcrp.rp_handler import RPHandler  # type: ignore[import, unused-ignore]
+from idpyoidc.client.rp_handler import RPHandler  # type: ignore[import, unused-ignore]
+from idpyoidc.exception import OidcMsgError  # type: ignore[import, unused-ignore]
 from yarl import URL
 
 from ..conf.conf import aai_config
@@ -55,7 +55,7 @@ def __init__(self, aai: dict[str, Any]) -> None:
                 "add_ons": {
                     # Re-activate this once we have implemented support on AAI side
                     # "dpop": {
-                    #     "function": "oidcrp.oauth2.add_on.dpop.add_support",
+                    #     "function": "idpyoidc.client.oauth2.add_on.dpop.add_support",
                     #     "kwargs": {
                     #         "signing_algorithms": [
                     #             "ES256",
@@ -64,7 +64,7 @@ def __init__(self, aai: dict[str, Any]) -> None:
                     #     },
                     # },
                     "pkce": {
-                        "function": "oidcrp.oauth2.add_on.pkce.add_support",
+                        "function": "idpyoidc.client.oauth2.add_on.pkce.add_support",
                         "kwargs": {
                             "code_challenge_length": 64,
                             "code_challenge_method": "S256",
@@ -88,7 +88,7 @@ async def login(self, _: Request) -> web.HTTPSeeOther:
             session = self.rph.begin("aai")
         except Exception as e:
             # This can be caused if config is improperly configured, and
-            # oidcrp is unable to fetch oidc configuration from the given URL
+            # idpyoidc is unable to fetch oidc configuration from the given URL
             LOG.exception("OIDC authorization request failed with: %r", e)
             raise web.HTTPInternalServerError(reason="OIDC authorization request failed.")
 
@@ -135,7 +135,7 @@ async def callback(self, req: Request) -> Response:
         except KeyError as e:
             LOG.exception("Issuer: %s not found, failed with: %r.", session["iss"], e)
             raise web.HTTPBadRequest(reason="Token issuer not found.")
-        except OidcServiceError as e:
+        except OidcMsgError as e:
             # This exception is raised if RPHandler encounters an error due to:
             # 1. "code" is wrong, so token request failed
             # 2. token validation failed

metadata_backend/api/handlers/common.py

@@ -1,4 +1,5 @@
 """Functions shared between handlers."""
+
 import csv
 import string
 from typing import Any

metadata_backend/api/handlers/files.py

@@ -1,4 +1,5 @@
 """Handle HTTP methods for server."""
+
 import aiohttp_session
 from aiohttp import web
 

metadata_backend/api/handlers/object.py

@@ -1,4 +1,5 @@
 """Handle HTTP methods for server."""
+
 from datetime import datetime
 from math import ceil
 from typing import Any
@@ -39,7 +40,7 @@ async def _handle_query(self, req: Request) -> Response:
 
         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  # type: ignore
+            collection, req.query, page, per_page, filter_list
         )
 
         result = ujson.dumps(

metadata_backend/api/handlers/publish.py

@@ -1,4 +1,5 @@
 """Handle HTTP methods for server."""
+
 from datetime import date, datetime
 from typing import Any
 

metadata_backend/api/handlers/rems_proxy.py

@@ -1,4 +1,5 @@
 """Get and process REMS data for the frontend."""
+
 from typing import Any, TypedDict
 
 from aiohttp import web

metadata_backend/api/handlers/restapi.py

@@ -1,4 +1,5 @@
 """Handle HTTP methods for server."""
+
 import json
 from collections.abc import AsyncIterator, Iterator
 from math import ceil

metadata_backend/api/handlers/static.py

@@ -1,4 +1,5 @@
 """Handle HTTP methods for server."""
+
 import mimetypes
 from pathlib import Path
 

metadata_backend/api/handlers/submission.py

@@ -1,4 +1,5 @@
 """Handle HTTP methods for server."""
+
 from datetime import datetime
 from math import ceil
 from typing import Any

metadata_backend/api/handlers/xml_submission.py

@@ -1,4 +1,5 @@
 """Handle HTTP methods for server."""
+
 from collections import Counter
 from typing import Any
 

metadata_backend/api/health.py

@@ -1,4 +1,5 @@
 """Handle health check endpoint."""
+
 import time
 
 import ujson
@@ -81,24 +82,24 @@ async def get_health_status(self, _: Request) -> Response:
             body=ujson.dumps(full_status, escape_forward_slashes=False), status=200, content_type="application/json"
         )
 
-    async def create_test_db_client(self) -> AsyncIOMotorClient:
+    async def create_test_db_client(self) -> AsyncIOMotorClient:  # type: ignore
         """Initialize a new database client to test Mongo connection.
 
         :returns: Coroutine-based Motor client for Mongo operations
         """
-        new_client = AsyncIOMotorClient(url, connectTimeoutMS=4000, serverSelectionTimeoutMS=4000)
+        new_client = AsyncIOMotorClient(url, connectTimeoutMS=4000, serverSelectionTimeoutMS=4000)  # type: ignore
         LOG.debug("Initialised a new DB client as a test")
         return new_client
 
-    async def try_db_connection(self, db_client: AsyncIOMotorClient) -> None | float:
+    async def try_db_connection(self, db_client: AsyncIOMotorClient) -> None | float:  # type: ignore
         """Check the connection to database.
 
         :param db_client: Motor client used for database connections
         :returns: Connection time or None if connection fails
         """
         try:
             start = time.time()
-            await db_client.server_info()
+            await db_client.server_info()  # type: ignore
             LOG.debug("Connection to db succeeded.")
             perf_time = time.time() - start
             return perf_time

metadata_backend/api/middlewares.py

@@ -1,4 +1,5 @@
 """Middleware methods for server."""
+
 import time
 from hmac import new
 from http import HTTPStatus

metadata_backend/api/operators/base.py

@@ -1,4 +1,5 @@
 """Base operator class shared by operators."""
+
 from abc import ABC
 from uuid import uuid4
 
@@ -16,7 +17,7 @@ class BaseOperator(ABC):
     :param ABC: The abstract base class
     """
 
-    def __init__(self, db_client: AsyncIOMotorClient) -> None:
+    def __init__(self, db_client: AsyncIOMotorClient) -> None:  # type: ignore
         """Init db_service.
 
         :param db_client: Motor client used for database connections. Should be

metadata_backend/api/operators/file.py

@@ -1,4 +1,5 @@
 """File operator class."""
+
 from dataclasses import dataclass
 from datetime import datetime
 from typing import Any, Optional