refactor: move UserData class to types module and update imports across the codebase

bencap · bencap · commit 7f3ee78097c6 · 2025-12-24T09:48:11.000-08:00
This change makes circular imports stemming from the import of this dataclass more unlikely.
diff --git a/src/mavedb/lib/authentication.py b/src/mavedb/lib/authentication.py
@@ -1,6 +1,5 @@
 import logging
 import os
-from dataclasses import dataclass
 from datetime import datetime
 from enum import Enum
 from typing import Optional
@@ -19,6 +18,7 @@
 from mavedb import deps
 from mavedb.lib.logging.context import format_raised_exception_info_as_dict, logging_context, save_to_logging_context
 from mavedb.lib.orcid import fetch_orcid_user_email
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.access_key import AccessKey
 from mavedb.models.enums.user_role import UserRole
 from mavedb.models.user import User
@@ -45,12 +45,6 @@ class AuthenticationMethod(str, Enum):
     jwt = "jwt"
 
 
-@dataclass
-class UserData:
-    user: User
-    active_roles: list[UserRole]
-
-
 ####################################################################################################
 # JWT authentication
 ####################################################################################################
diff --git a/src/mavedb/lib/authorization.py b/src/mavedb/lib/authorization.py
@@ -3,8 +3,9 @@
 
 from fastapi import Depends, HTTPException
 
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.enums.user_role import UserRole
 
 logger = logging.getLogger(__name__)
diff --git a/src/mavedb/lib/experiments.py b/src/mavedb/lib/experiments.py
@@ -1,13 +1,13 @@
 import logging
 from typing import Optional
 
-from sqlalchemy import func, or_, not_
+from sqlalchemy import func, not_, or_
 from sqlalchemy.orm import Session
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions import Action
 from mavedb.lib.score_sets import find_superseded_score_set_tail
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.contributor import Contributor
 from mavedb.models.controlled_keyword import ControlledKeyword
 from mavedb.models.experiment import Experiment
diff --git a/src/mavedb/lib/permissions/collection.py b/src/mavedb/lib/permissions/collection.py
@@ -1,10 +1,10 @@
 from typing import Optional
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import save_to_logging_context
 from mavedb.lib.permissions.actions import Action
 from mavedb.lib.permissions.models import PermissionResponse
 from mavedb.lib.permissions.utils import deny_action_for_entity, roles_permitted
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.collection import Collection
 from mavedb.models.enums.contribution_role import ContributionRole
 from mavedb.models.enums.user_role import UserRole
diff --git a/src/mavedb/lib/permissions/core.py b/src/mavedb/lib/permissions/core.py
@@ -1,10 +1,10 @@
 from typing import Any, Callable, Optional
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import save_to_logging_context
 from mavedb.lib.permissions.actions import Action
 from mavedb.lib.permissions.exceptions import PermissionException
 from mavedb.lib.permissions.models import PermissionResponse
+from mavedb.lib.types.authentication import UserData
 from mavedb.lib.types.permissions import EntityType
 from mavedb.models.collection import Collection
 from mavedb.models.experiment import Experiment
diff --git a/src/mavedb/lib/permissions/experiment.py b/src/mavedb/lib/permissions/experiment.py
@@ -1,10 +1,10 @@
 from typing import Optional
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import save_to_logging_context
 from mavedb.lib.permissions.actions import Action
 from mavedb.lib.permissions.models import PermissionResponse
 from mavedb.lib.permissions.utils import deny_action_for_entity, roles_permitted
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.enums.user_role import UserRole
 from mavedb.models.experiment import Experiment
 
diff --git a/src/mavedb/lib/permissions/experiment_set.py b/src/mavedb/lib/permissions/experiment_set.py
@@ -1,10 +1,10 @@
 from typing import Optional
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import save_to_logging_context
 from mavedb.lib.permissions.actions import Action
 from mavedb.lib.permissions.models import PermissionResponse
 from mavedb.lib.permissions.utils import deny_action_for_entity, roles_permitted
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.enums.user_role import UserRole
 from mavedb.models.experiment_set import ExperimentSet
 
diff --git a/src/mavedb/lib/permissions/score_calibration.py b/src/mavedb/lib/permissions/score_calibration.py
@@ -1,10 +1,10 @@
 from typing import Optional
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import save_to_logging_context
 from mavedb.lib.permissions.actions import Action
 from mavedb.lib.permissions.models import PermissionResponse
 from mavedb.lib.permissions.utils import deny_action_for_entity, roles_permitted
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.enums.user_role import UserRole
 from mavedb.models.score_calibration import ScoreCalibration
 
diff --git a/src/mavedb/lib/permissions/score_set.py b/src/mavedb/lib/permissions/score_set.py
@@ -1,10 +1,10 @@
 from typing import Optional
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import save_to_logging_context
 from mavedb.lib.permissions.actions import Action
 from mavedb.lib.permissions.models import PermissionResponse
 from mavedb.lib.permissions.utils import deny_action_for_entity, roles_permitted
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.enums.user_role import UserRole
 from mavedb.models.score_set import ScoreSet
 
diff --git a/src/mavedb/lib/permissions/user.py b/src/mavedb/lib/permissions/user.py
@@ -1,10 +1,10 @@
 from typing import Optional
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import save_to_logging_context
 from mavedb.lib.permissions.actions import Action
 from mavedb.lib.permissions.models import PermissionResponse
 from mavedb.lib.permissions.utils import deny_action_for_entity, roles_permitted
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.enums.user_role import UserRole
 from mavedb.models.user import User
 
diff --git a/src/mavedb/lib/permissions/utils.py b/src/mavedb/lib/permissions/utils.py
@@ -1,9 +1,9 @@
 import logging
 from typing import Optional, Union, overload
 
-from mavedb.lib.authentication import UserData
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions.models import PermissionResponse
+from mavedb.lib.types.authentication import UserData
 from mavedb.lib.types.permissions import EntityType
 from mavedb.models.enums.contribution_role import ContributionRole
 from mavedb.models.enums.user_role import UserRole
diff --git a/src/mavedb/lib/score_sets.py b/src/mavedb/lib/score_sets.py
@@ -23,6 +23,8 @@
     VARIANT_SCORE_DATA,
 )
 from mavedb.lib.mave.utils import is_csv_null
+from mavedb.lib.permissions import has_permission
+from mavedb.lib.types.authentication import UserData
 from mavedb.lib.validation.constants.general import null_values_list
 from mavedb.lib.validation.utilities import is_null as validate_is_null
 from mavedb.lib.variants import get_digest_from_post_mapped, get_hgvs_from_post_mapped, is_hgvs_g, is_hgvs_p
@@ -55,7 +57,6 @@
 from mavedb.view_models.search import ScoreSetsSearch
 
 if TYPE_CHECKING:
-    from mavedb.lib.authentication import UserData
     from mavedb.lib.permissions import Action
 
 VariantData = dict[str, Optional[dict[str, dict]]]
@@ -443,8 +444,6 @@ def find_meta_analyses_for_experiment_sets(db: Session, urns: list[str]) -> list
 def find_superseded_score_set_tail(
     score_set: ScoreSet, action: Optional["Action"] = None, user_data: Optional["UserData"] = None
 ) -> Optional[ScoreSet]:
-    from mavedb.lib.permissions import has_permission
-
     while score_set.superseding_score_set is not None:
         next_score_set_in_chain = score_set.superseding_score_set
 
diff --git a/src/mavedb/lib/types/authentication.py b/src/mavedb/lib/types/authentication.py
@@ -0,0 +1,12 @@
+from dataclasses import dataclass
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from mavedb.models.enums.user_role import UserRole
+    from mavedb.models.user import User
+
+
+@dataclass
+class UserData:
+    user: "User"
+    active_roles: list["UserRole"]
diff --git a/src/mavedb/routers/access_keys.py b/src/mavedb/routers/access_keys.py
@@ -12,10 +12,10 @@
 from sqlalchemy.orm import Session
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData
 from mavedb.lib.authorization import require_current_user
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.access_key import AccessKey
 from mavedb.models.enums.user_role import UserRole
 from mavedb.routers.shared import ACCESS_CONTROL_ERROR_RESPONSES, PUBLIC_ERROR_RESPONSES, ROUTER_BASE_PREFIX
diff --git a/src/mavedb/routers/collections.py b/src/mavedb/routers/collections.py
@@ -9,7 +9,7 @@
 from sqlalchemy.orm.exc import MultipleResultsFound, NoResultFound
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.authorization import require_current_user, require_current_user_with_email
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import (
@@ -18,6 +18,7 @@
     save_to_logging_context,
 )
 from mavedb.lib.permissions import Action, assert_permission, has_permission
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.collection import Collection
 from mavedb.models.collection_user_association import CollectionUserAssociation
 from mavedb.models.enums.contribution_role import ContributionRole
diff --git a/src/mavedb/routers/experiment_sets.py b/src/mavedb/routers/experiment_sets.py
@@ -6,11 +6,12 @@
 from sqlalchemy.orm import Session
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.experiments import enrich_experiment_with_num_score_sets
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions import Action, assert_permission, has_permission
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.experiment_set import ExperimentSet
 from mavedb.routers.shared import ACCESS_CONTROL_ERROR_RESPONSES, PUBLIC_ERROR_RESPONSES, ROUTER_BASE_PREFIX
 from mavedb.view_models import experiment_set
diff --git a/src/mavedb/routers/experiments.py b/src/mavedb/routers/experiments.py
@@ -9,7 +9,7 @@
 from sqlalchemy.orm import Session
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.authorization import require_current_user, require_current_user_with_email
 from mavedb.lib.contributors import find_or_create_contributor
 from mavedb.lib.exceptions import NonexistentOrcidUserError
@@ -25,6 +25,7 @@
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions import Action, assert_permission, has_permission
 from mavedb.lib.score_sets import find_superseded_score_set_tail
+from mavedb.lib.types.authentication import UserData
 from mavedb.lib.validation.exceptions import ValidationError
 from mavedb.lib.validation.keywords import validate_keyword_list
 from mavedb.models.contributor import Contributor
diff --git a/src/mavedb/routers/mapped_variant.py b/src/mavedb/routers/mapped_variant.py
@@ -17,14 +17,14 @@
     variant_study_result,
 )
 from mavedb.lib.annotation.exceptions import MappingDataDoesntExistException
-from mavedb.lib.authentication import UserData
 from mavedb.lib.authorization import get_current_user
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import (
     logging_context,
     save_to_logging_context,
 )
 from mavedb.lib.permissions import Action, assert_permission, has_permission
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.mapped_variant import MappedVariant
 from mavedb.models.variant import Variant
 from mavedb.routers.shared import ACCESS_CONTROL_ERROR_RESPONSES, PUBLIC_ERROR_RESPONSES, ROUTER_BASE_PREFIX
diff --git a/src/mavedb/routers/permissions.py b/src/mavedb/routers/permissions.py
@@ -6,10 +6,11 @@
 from sqlalchemy.orm import Session
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions import Action, has_permission
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.collection import Collection
 from mavedb.models.experiment import Experiment
 from mavedb.models.experiment_set import ExperimentSet
diff --git a/src/mavedb/routers/score_calibrations.py b/src/mavedb/routers/score_calibrations.py
@@ -5,7 +5,7 @@
 from sqlalchemy.orm import Session, selectinload
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.authorization import require_current_user
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import (
@@ -21,6 +21,7 @@
     promote_score_calibration_to_primary,
     publish_score_calibration,
 )
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.score_calibration import ScoreCalibration
 from mavedb.models.score_set import ScoreSet
 from mavedb.view_models import score_calibration
diff --git a/src/mavedb/routers/score_sets.py b/src/mavedb/routers/score_sets.py
@@ -26,7 +26,6 @@
     variant_study_result,
 )
 from mavedb.lib.annotation.exceptions import MappingDataDoesntExistException
-from mavedb.lib.authentication import UserData
 from mavedb.lib.authorization import (
     get_current_user,
     require_current_user,
@@ -61,6 +60,7 @@
 )
 from mavedb.lib.target_genes import find_or_create_target_gene_by_accession, find_or_create_target_gene_by_sequence
 from mavedb.lib.taxonomies import find_or_create_taxonomy
+from mavedb.lib.types.authentication import UserData
 from mavedb.lib.urns import (
     generate_experiment_set_urn,
     generate_experiment_urn,
diff --git a/src/mavedb/routers/target_genes.py b/src/mavedb/routers/target_genes.py
@@ -4,13 +4,14 @@
 from sqlalchemy.orm import Session, selectinload
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.authorization import require_current_user
 from mavedb.lib.permissions import Action, has_permission
 from mavedb.lib.score_sets import find_superseded_score_set_tail
 from mavedb.lib.target_genes import (
     search_target_genes as _search_target_genes,
 )
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.score_set import ScoreSet
 from mavedb.models.target_gene import TargetGene
 from mavedb.routers.shared import ACCESS_CONTROL_ERROR_RESPONSES, PUBLIC_ERROR_RESPONSES, ROUTER_BASE_PREFIX
diff --git a/src/mavedb/routers/users.py b/src/mavedb/routers/users.py
@@ -5,11 +5,11 @@
 from starlette.convertors import Convertor, register_url_convertor
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData
 from mavedb.lib.authorization import RoleRequirer, require_current_user
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions import Action, assert_permission
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.enums.user_role import UserRole
 from mavedb.models.user import User
 from mavedb.routers.shared import ACCESS_CONTROL_ERROR_RESPONSES, PUBLIC_ERROR_RESPONSES, ROUTER_BASE_PREFIX
diff --git a/src/mavedb/routers/variants.py b/src/mavedb/routers/variants.py
@@ -10,10 +10,11 @@
 from sqlalchemy.sql import or_
 
 from mavedb import deps
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.logging import LoggedRoute
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions import Action, assert_permission, has_permission
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.mapped_variant import MappedVariant
 from mavedb.models.score_set import ScoreSet
 from mavedb.models.variant import Variant
diff --git a/tests/conftest_optional.py b/tests/conftest_optional.py
@@ -1,9 +1,10 @@
 import os
+import shutil
+import tempfile
 from concurrent import futures
 from inspect import getsourcefile
 from posixpath import abspath
-import shutil
-import tempfile
+from unittest.mock import patch
 
 import cdot.hgvs.dataproviders
 import pytest
@@ -12,15 +13,14 @@
 from biocommons.seqrepo import SeqRepo
 from fastapi.testclient import TestClient
 from httpx import AsyncClient
-from unittest.mock import patch
 
-from mavedb.lib.authentication import UserData, get_current_user
+from mavedb.deps import get_db, get_seqrepo, get_worker, hgvs_data_provider
+from mavedb.lib.authentication import get_current_user
 from mavedb.lib.authorization import require_current_user
+from mavedb.lib.types.authentication import UserData
 from mavedb.models.user import User
 from mavedb.server_main import app
-from mavedb.deps import get_db, get_worker, hgvs_data_provider, get_seqrepo
-from mavedb.worker.settings import BACKGROUND_FUNCTIONS, BACKGROUND_CRONJOBS
-
+from mavedb.worker.settings import BACKGROUND_CRONJOBS, BACKGROUND_FUNCTIONS
 from tests.helpers.constants import ADMIN_USER, EXTRA_USER, TEST_SEQREPO_INITIAL_STATE, TEST_USER
 
 ####################################################################################################
