YDA-7031

browse.py

@@ -1,11 +1,10 @@
 """Functions for listing collection information."""
 
-__copyright__ = 'Copyright (c) 2019-2025, Utrecht University'
+__copyright__ = 'Copyright (c) 2019-2026, Utrecht University'
 __license__   = 'GPLv3, see LICENSE'
 
 import re
 from collections import OrderedDict
-from typing import Dict
 
 import magic
 from genquery import AS_DICT, Query
@@ -38,7 +37,7 @@ def api_browse_folder(ctx: rule.Context,
 
     :returns: Dict with paginated collection contents
     """
-    def transform(row: Dict) -> Dict:
+    def transform(row: dict) -> dict:
         # Remove ORDER_BY etc. wrappers from column names.
         x = {re.sub(r'.*\((.*)\)', '\\1', k): v for k, v in row.items()}
         if 'DATA_NAME' in x and 'META_DATA_ATTR_VALUE' in x:
@@ -128,7 +127,7 @@ def api_browse_collections(ctx: rule.Context,
 
     :returns: Dict with paginated collection contents
     """
-    def transform(row: Dict) -> Dict:
+    def transform(row: dict) -> dict:
         # Remove ORDER_BY etc. wrappers from column names.
         x = {re.sub(r'.*\((.*)\)', '\\1', k): v for k, v in row.items()}
 
@@ -206,7 +205,7 @@ def api_search(ctx: rule.Context,
 
     :returns: Dict with paginated search results
     """
-    def transform(row: Dict) -> Dict:
+    def transform(row: dict) -> dict:
         # Remove ORDER_BY etc. wrappers from column names.
         x = {re.sub(r'.*\((.*)\)', '\\1', k): v for k, v in row.items()}
 
@@ -295,7 +294,7 @@ def transform(row: Dict) -> Dict:
                         ('items', datas)])
 
 
-def _filter_vault_deposit_index(row: Dict) -> bool:
+def _filter_vault_deposit_index(row: dict) -> bool:
     """This internal function filters out index collections in deposit vault collections.
        These collections are used internally by Yoda for indexing data package metadata, and
        should not be displayed.

datacite.py

@@ -1,18 +1,17 @@
 """Functions for communicating with DataCite and some utilities."""
 
-__copyright__ = 'Copyright (c) 2019-2024, Utrecht University'
+__copyright__ = 'Copyright (c) 2019-2026, Utrecht University'
 __license__ = 'GPLv3, see LICENSE'
 
 import random
 import string
-from typing import Dict
 
 import requests
 
 from util import *
 
 
-def metadata_post(payload: Dict) -> requests.Response:
+def metadata_post(payload: dict) -> requests.Response:
     """Register DOI metadata with DataCite."""
     url = "{}/dois".format(config.datacite_rest_api_url)
     auth = (config.datacite_username, config.datacite_password)

datarequest.py

@@ -11,7 +11,7 @@
 from collections import OrderedDict
 from datetime import datetime
 from enum import Enum
-from typing import Dict, List, Optional
+from typing import Optional
 
 import jsonschema
 from genquery import AS_DICT, AS_LIST, Query, row_iterator
@@ -283,7 +283,7 @@ def type_get(ctx: rule.Context, request_id: str) -> type:
     return datarequest_type
 
 
-def available_documents_get(ctx: rule.Context, request_id: str, datarequest_type: str, datarequest_status: str) -> List:
+def available_documents_get(ctx: rule.Context, request_id: str, datarequest_type: str, datarequest_status: str) -> list:
     # Construct list of existing documents
     available_documents = []
     if datarequest_type == type.REGULAR.value:
@@ -362,7 +362,7 @@ def generate_request_id(ctx: rule.Context) -> int:
 
 
 @api.make()
-def api_datarequest_action_permitted(ctx: rule.Context, request_id: str, roles: List, statuses: List) -> api.Result:
+def api_datarequest_action_permitted(ctx: rule.Context, request_id: str, roles: list, statuses: Optional[list]) -> api.Result:
     """Wrapper around datarequest_action_permitted.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -382,7 +382,7 @@ def get_status(stat: str) -> status:
     return datarequest_action_permitted(ctx, request_id, roles, statuses)
 
 
-def datarequest_action_permitted(ctx: rule.Context, request_id: str, roles: List, statuses: List | None) -> bool:
+def datarequest_action_permitted(ctx: rule.Context, request_id: str, roles: list, statuses: Optional[list]) -> bool:
     """Check if current user and data request status meet specified restrictions.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -425,7 +425,7 @@ def datarequest_action_permitted(ctx: rule.Context, request_id: str, roles: List
 
 
 @api.make()
-def api_datarequest_roles_get(ctx: rule.Context, request_id: str | None = None) -> api.Result:
+def api_datarequest_roles_get(ctx: rule.Context, request_id: Optional[str] = None) -> api.Result:
     """Get roles of invoking user.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -437,7 +437,7 @@ def api_datarequest_roles_get(ctx: rule.Context, request_id: str | None = None)
     return datarequest_roles_get(ctx, request_id)
 
 
-def datarequest_roles_get(ctx: rule.Context, request_id: str | None = None) -> List:
+def datarequest_roles_get(ctx: rule.Context, request_id: Optional[str] = None) -> list:
     """Get roles of invoking user.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -517,7 +517,7 @@ def datarequest_is_reviewer(ctx: rule.Context, request_id: str, pending: bool =
     return is_reviewer
 
 
-def datarequest_reviewers_get(ctx: rule.Context, request_id: str, pending: bool = False) -> List[str]:
+def datarequest_reviewers_get(ctx: rule.Context, request_id: str, pending: bool = False) -> list[str]:
     """Return a list of users assigned as reviewers to a data request.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -636,7 +636,7 @@ def datarequest_provenance_write(ctx: rule.Context, request_id: str, request_sta
         return api.Error("write_error", "Could not write timestamp to provenance log: {}.".format(e))
 
 
-def datarequest_data_valid(ctx: rule.Context, data: Dict, schema_name: str | None = None, schema: str | None = None) -> bool:
+def datarequest_data_valid(ctx: rule.Context, data: dict, schema_name: str | None = None, schema: str | None = None) -> bool:
     """Check if form data contains no errors
 
     Default mode of operation is to provide schema data and the schema name of the schema against
@@ -677,7 +677,7 @@ def datarequest_data_valid(ctx: rule.Context, data: Dict, schema_name: str | Non
         return False
 
 
-def cc_email_addresses_get(contact_object: Dict) -> str | None:
+def cc_email_addresses_get(contact_object: dict) -> str | None:
     try:
         cc = contact_object['cc_email_addresses']
         return cc.replace(' ', '')
@@ -765,7 +765,7 @@ def api_datarequest_browse(ctx: rule.Context,
     dac_member = user.is_member_of(ctx, GROUP_DAC)
     coll       = "/{}/{}".format(user.zone(ctx), DRCOLLECTION)
 
-    def transform(row: Dict) -> Dict:
+    def transform(row: dict) -> dict:
         # Remove ORDER_BY etc. wrappers from column names.
         x = {re.sub(r'.*\((.*)\)', '\\1', k): v for k, v in row.items()}
 
@@ -774,14 +774,14 @@ def transform(row: Dict) -> Dict:
                 'create_time': int(x['COLL_CREATE_TIME']),
                 'status':      x['META_DATA_ATTR_VALUE']}
 
-    def transform_title(row: Dict) -> Dict:
+    def transform_title(row: dict) -> dict:
         # Remove ORDER_BY etc. wrappers from column names.
         x = {re.sub(r'.*\((.*)\)', '\\1', k): v for k, v in row.items()}
 
         return {'id':          x['COLL_NAME'].split('/')[-1],
                 'title':       x['META_DATA_ATTR_VALUE']}
 
-    def transform_status(row: Dict) -> Dict:
+    def transform_status(row: dict) -> dict:
         # Remove ORDER_BY etc. wrappers from column names.
         x = {re.sub(r'.*\((.*)\)', '\\1', k): v for k, v in row.items()}
 
@@ -853,7 +853,7 @@ def transform_status(row: Dict) -> Dict:
     return OrderedDict([('total', qcoll.total_rows()), ('items', colls)])
 
 
-def datarequest_process_expired_review_periods(ctx: rule.Context, request_ids: List) -> None:
+def datarequest_process_expired_review_periods(ctx: rule.Context, request_ids: list) -> None:
     """Process expired review periods by setting their status to REVIEWED.
 
     :param ctx:         Combined type of a callback and rei struct
@@ -863,7 +863,7 @@ def datarequest_process_expired_review_periods(ctx: rule.Context, request_ids: L
         status_set(ctx, request_id, status.REVIEWED)
 
 
-def file_write(ctx: rule.Context, coll_path: str, filename: str, data: Dict, readers: List[str]) -> None:
+def file_write(ctx: rule.Context, coll_path: str, filename: str, data: dict, readers: list[str]) -> None:
     """Grant temporary write permission and write file to disk.
 
     :param ctx:       Combined type of a callback and rei struct
@@ -897,7 +897,7 @@ def file_write(ctx: rule.Context, coll_path: str, filename: str, data: Dict, rea
     msi.set_acl(ctx, "default", "own", "rods", file_path)
 
 
-def file_lock(ctx: rule.Context, coll_path: str, filename: str, readers: List[str]) -> None:
+def file_lock(ctx: rule.Context, coll_path: str, filename: str, readers: list[str]) -> None:
     """Revoke temporary write permission.
 
     :param ctx:       Combined type of a callback and rei struct
@@ -922,7 +922,7 @@ def file_lock(ctx: rule.Context, coll_path: str, filename: str, readers: List[st
 
 
 @api.make()
-def api_datarequest_submit(ctx: rule.Context, data: Dict, draft: bool, draft_request_id: str | None = None) -> api.Result:
+def api_datarequest_submit(ctx: rule.Context, data: dict, draft: bool, draft_request_id: Optional[str] = None) -> api.Result:
     """Persist a data request to disk.
 
     :param ctx:              Combined type of a callback and rei struct
@@ -1056,7 +1056,7 @@ def api_datarequest_submit(ctx: rule.Context, data: Dict, draft: bool, draft_req
 
 
 @api.make()
-def api_datarequest_get(ctx: rule.Context, request_id: int) -> api.Result:
+def api_datarequest_get(ctx: rule.Context, request_id: str) -> api.Result:
     """Retrieve a data request.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -1195,7 +1195,7 @@ def api_datarequest_attachments_get(ctx: rule.Context, request_id: str) -> api.R
     return attachments
 
 
-def datarequest_attachments_get(ctx: rule.Context, request_id: str) -> Optional[List[str]]:
+def datarequest_attachments_get(ctx: rule.Context, request_id: str) -> Optional[list[str]]:
     """Get all attachments of a given data request.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -1245,7 +1245,7 @@ def api_datarequest_attachments_submit(ctx: rule.Context, request_id: str) -> ap
 
 
 @api.make()
-def api_datarequest_preliminary_review_submit(ctx: rule.Context, data: Dict, request_id: str) -> api.Result:
+def api_datarequest_preliminary_review_submit(ctx: rule.Context, data: dict, request_id: str) -> api.Result:
     """Persist a preliminary review to disk.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -1328,7 +1328,7 @@ def datarequest_preliminary_review_get(ctx: rule.Context, request_id: str) -> st
 
 
 @api.make()
-def api_datarequest_datamanager_review_submit(ctx: rule.Context, data: Dict, request_id: str) -> api.Result:
+def api_datarequest_datamanager_review_submit(ctx: rule.Context, data: dict, request_id: str) -> api.Result:
     """Persist a datamanager review to disk.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -1417,7 +1417,7 @@ def api_datarequest_dac_members_get(ctx: rule.Context, request_id: str) -> api.R
     return datarequest_dac_members_get(ctx, request_id)
 
 
-def datarequest_dac_members_get(ctx: rule.Context, request_id: str) -> List:
+def datarequest_dac_members_get(ctx: rule.Context, request_id: str) -> list:
     """Get list of DAC members
 
     :param ctx:        Combined type of a callback and rei struct
@@ -1436,7 +1436,7 @@ def datarequest_dac_members_get(ctx: rule.Context, request_id: str) -> List:
 
 
 @api.make()
-def api_datarequest_assignment_submit(ctx: rule.Context, data: Dict, request_id: str) -> api.Result:
+def api_datarequest_assignment_submit(ctx: rule.Context, data: dict, request_id: str) -> api.Result:
     """Persist an assignment to disk.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -1578,7 +1578,7 @@ def datarequest_assignment_get(ctx: rule.Context, request_id: str) -> api.Result
 
 
 @api.make()
-def api_datarequest_review_submit(ctx: rule.Context, data: Dict, request_id: str) -> api.Result:
+def api_datarequest_review_submit(ctx: rule.Context, data: dict, request_id: str) -> api.Result:
     """Persist a data request review to disk.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -1676,7 +1676,7 @@ def api_datarequest_reviews_get(ctx: rule.Context, request_id: str) -> api.Resul
 
 
 @api.make()
-def api_datarequest_evaluation_submit(ctx: rule.Context, data: Dict, request_id: str) -> api.Result:
+def api_datarequest_evaluation_submit(ctx: rule.Context, data: dict, request_id: str) -> api.Result:
     """Persist an evaluation to disk.
 
     :param ctx:        Combined type of a callback and rei struct
@@ -1868,7 +1868,7 @@ def api_datarequest_feedback_get(ctx: rule.Context, request_id: str) -> api.Resu
 
 
 @api.make()
-def api_datarequest_preregistration_submit(ctx: rule.Context, data: Dict, request_id: str) -> api.Result:
+def api_datarequest_preregistration_submit(ctx: rule.Context, data: dict, request_id: str) -> api.Result:
     """Persist a preregistration to disk.
 
     :param ctx:        Combined type of a callback and rei struct

deposit.py

@@ -1,12 +1,11 @@
 """Functions for deposit module."""
 from __future__ import annotations
 
-__copyright__ = 'Copyright (c) 2021-2025, Utrecht University'
+__copyright__ = 'Copyright (c) 2021-2026, Utrecht University'
 __license__   = 'GPLv3, see LICENSE'
 
 import re
 from collections import OrderedDict
-from typing import Dict
 
 import genquery
 from genquery import AS_DICT, Query
@@ -100,7 +99,7 @@ def api_deposit_create(ctx: rule.Context, deposit_group: str) -> api.Result:
     return {"deposit_path": result["deposit_path"]}
 
 
-def deposit_create(ctx: rule.Context, deposit_group: str | None) -> Dict:
+def deposit_create(ctx: rule.Context, deposit_group: str | None) -> dict:
     """Create deposit collection.
 
     :param ctx:           Combined type of a callback and rei struct
@@ -217,7 +216,7 @@ def api_deposit_overview(ctx: rule.Context,
 
     :returns: Dict with paginated collection contents
     """
-    def transform(row: Dict) -> Dict:
+    def transform(row: dict) -> dict:
         # Remove ORDER_BY etc. wrappers from column names.
         x = {re.sub(r'.*\((.*)\)', '\\1', k): v for k, v in row.items()}
 

epic.py

@@ -1,10 +1,9 @@
 """Functions for communicating with EPIC and some utilities."""
 
-__copyright__ = 'Copyright (c) 2019-2024, Utrecht University'
+__copyright__ = 'Copyright (c) 2019-2026, Utrecht University'
 __license__   = 'GPLv3, see LICENSE'
 
 import uuid
-from typing import Dict
 
 import publication
 from util import *
@@ -21,7 +20,7 @@ def generate_uuid(ctx: rule.Context) -> str:
 rule_generate_uuid = rule.make(inputs=[], outputs=[0])(generate_uuid)
 
 
-def register_epic_pid(ctx: rule.Context, target: str) -> Dict:
+def register_epic_pid(ctx: rule.Context, target: str) -> dict:
     """Create and try to register an EPIC PID.
 
     :param ctx:    Combined type of a callback and rei struct