Fix a bunch of type checking issues

isic/core/api/collection.py

@@ -279,7 +279,7 @@ def collection_populate_from_search(request, id: int, payload: SearchQueryIn):
     if collection.locked:
         return 409, {"error": "Collection is locked"}
 
-    if collection.public and payload.to_queryset(request.user).private().exists():  # type: ignore[attr-defined]
+    if collection.public and payload.to_queryset(request.user).private().exists():
         return 409, {"error": "Collection is public and cannot contain private images."}
 
     # Pass data instead of validated_data because the celery task is going to revalidate.

isic/core/dsl.py

@@ -183,7 +183,7 @@ def es_query(s, loc, toks):
 
 
 def es_query_and(s, loc, toks):
-    ret = {"bool": {"filter": []}}
+    ret: dict[str, Any] = {"bool": {"filter": []}}
     if isinstance(toks, ParseResults):
         # Explicit ANDs come in as parse results
         q_objects = toks.asList()
@@ -204,7 +204,7 @@ def es_query_and(s, loc, toks):
 
 
 def es_query_or(s, loc, toks):
-    ret = {"bool": {"should": []}}
+    ret: dict[str, Any] = {"bool": {"should": []}}
     for tok in toks[0]:
         ret["bool"]["should"].append(tok)
     toks[0] = ret

isic/core/management/commands/anonymize_database.py

@@ -5,6 +5,7 @@
 metadata. All users are given the password "password".
 """
 
+from collections.abc import Callable
 import hashlib
 import logging
 import random
@@ -16,6 +17,7 @@
 from django.contrib.auth.models import User
 from django.contrib.sessions.models import Session
 from django.db import connection, transaction
+from django.db.models import Model, QuerySet
 import djclick as click
 from faker import Faker
 from oauth2_provider.models import AccessToken, RefreshToken
@@ -124,17 +126,27 @@ def anonymize_hash_id(salt: str, hash_id: str, *, seen: set) -> str:
     raise RuntimeError(f"Failed to generate unique hash_id after 100 attempts: {hash_id}")
 
 
-def _batch_anonymize(queryset, fields, transform, *, label, dry_run, batch_size):  # noqa: PLR0913
+def _batch_anonymize[M: Model](  # noqa: PLR0913
+    queryset: QuerySet[M],
+    fields: list[str],
+    transform: Callable[[M], None],
+    *,
+    label: str,
+    dry_run: bool,
+    batch_size: int,
+) -> int:
     model_class = queryset.model
     total = queryset.count()
-    objects_to_update = []
+    objects_to_update: list[M] = []
 
     if dry_run:
         label = f"[DRY RUN] {label}"
 
     def _flush():
         if objects_to_update and not dry_run:
-            model_class.objects.bulk_update(objects_to_update, fields, batch_size=batch_size)
+            model_class._default_manager.bulk_update(
+                objects_to_update, fields, batch_size=batch_size
+            )
 
     with click.progressbar(
         queryset.iterator(), length=total, label=label, show_eta=True, show_percent=True
@@ -154,8 +166,8 @@ def _flush():
 
 def _anonymize_users(faker, salt, *, dry_run, batch_size):
     password_hash = make_password("password")
-    names_cache = {}
-    emails_cache = {}
+    names_cache: dict[str, str] = {}
+    emails_cache: dict[str, str] = {}
 
     def transform(user):
         user.username = anonymize_username(salt, user.username)
@@ -244,7 +256,7 @@ def _anonymize_private_ids(salt, *, dry_run, batch_size):
 
     counts = {}
     for model_class, field_name, id_type in models_to_process:
-        cache = {}
+        cache: dict[str, str] = {}
 
         def transform(obj, _field=field_name, _type=id_type, _cache=cache):
             current_value = getattr(obj, _field)

isic/core/management/commands/set_isic_permissions.py

@@ -53,7 +53,7 @@ def add_staff_group():
         User,
         ZipUpload,
     ]:
-        content_type = ContentType.objects.get_for_model(model)  # type: ignore[arg-type]
+        content_type = ContentType.objects.get_for_model(model)
         for permission in ["view", "change"]:
             group.permissions.add(
                 Permission.objects.get(

isic/core/models/collection.py

@@ -1,17 +1,23 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
 from django.contrib.auth.models import User
 from django.contrib.postgres.indexes import GinIndex, OpClass
 from django.core.exceptions import ValidationError
 from django.db import models
 from django.db.models.constraints import CheckConstraint, UniqueConstraint
 from django.db.models.expressions import F
 from django.db.models.functions import Upper
-from django.db.models.query import QuerySet
 from django.db.models.query_utils import Q
 from django.urls import reverse
 from django_extensions.db.models import TimeStampedModel
 
 from .image import Image
 
+if TYPE_CHECKING:
+    from django.db.models.query import QuerySet
+
 
 class CollectionQuerySet(models.QuerySet["Collection"]):
     def pinned(self):
@@ -62,7 +68,9 @@ class Meta(TimeStampedModel.Meta):
 
     creator = models.ForeignKey(User, on_delete=models.PROTECT, related_name="collections")
 
-    images = models.ManyToManyField(Image, related_name="collections", through="CollectionImage")
+    images: models.ManyToManyField[Image, CollectionImage] = models.ManyToManyField(
+        Image, related_name="collections", through="CollectionImage"
+    )
 
     # unique per user. names of pinned collections can't be used.
     name = models.CharField(max_length=200)
@@ -73,7 +81,7 @@ class Meta(TimeStampedModel.Meta):
 
     public = models.BooleanField(default=False)
 
-    shares = models.ManyToManyField(
+    shares: models.ManyToManyField[User, CollectionShare] = models.ManyToManyField(
         User,
         through="CollectionShare",
         through_fields=("collection", "grantee"),
@@ -135,11 +143,11 @@ def counts(self):
             }
         return self.cached_counts
 
-    def full_clean(self, exclude=None, validate_unique=True):  # noqa: FBT002
-        if self.pk and self.public and self.images.private().exists():  # type: ignore[attr-defined]
+    def full_clean(self, *args, **kwargs):
+        if self.pk and self.public and self.images.private().exists():
             raise ValidationError("Can't make collection public, it contains private images.")
 
-        return super().full_clean(exclude=exclude, validate_unique=validate_unique)
+        return super().full_clean(*args, **kwargs)
 
 
 class CollectionImage(models.Model):

isic/core/models/image.py

@@ -96,7 +96,9 @@ class Meta(CreationSortedTimeStampedModel.Meta):
     # index is used because public is filtered in every permissions check
     public = models.BooleanField(default=False, db_index=True)
 
-    shares = models.ManyToManyField(User, through="ImageShare", through_fields=("image", "grantee"))
+    shares: models.ManyToManyField[User, ImageShare] = models.ManyToManyField(
+        User, through="ImageShare", through_fields=("image", "grantee")
+    )
 
     objects = ImageManager()
 

isic/core/pagination.py

@@ -41,7 +41,7 @@ def _clamp(val: int, min_: int, max_: int) -> int:
     return max(min_, min(val, max_))
 
 
-def _reverse_order(order: tuple):
+def _reverse_order(order: Sequence[str]):
     """
     Reverse the ordering specification for a Django ORM query.
 
@@ -83,8 +83,8 @@ def decode_cursor(cls, encoded_cursor: str | None) -> Cursor:
                 offset = int(tokens.get("o", ["0"])[0])
                 offset = _clamp(offset, 0, CursorPagination._offset_cutoff)
 
-                reverse = tokens.get("r", ["0"])[0]
-                reverse = bool(int(reverse))
+                reverse_str = tokens.get("r", ["0"])[0]
+                reverse = bool(int(reverse_str))
 
                 position = tokens.get("p", [None])[0]
             except (TypeError, ValueError) as e:
@@ -117,7 +117,7 @@ def paginate_queryset(
         if not queryset.query.order_by:
             queryset = queryset.order_by(*self.ordering)
 
-        order = queryset.query.order_by
+        order: tuple[str, ...] = queryset.query.order_by
 
         total_count = (
             # let the queryset define a custom_count attribute in the event that computing
@@ -227,11 +227,11 @@ def next_link(  # noqa: PLR0913
         base_url: str,
         page: list,
         cursor: Cursor,
-        order: tuple,
+        order: Sequence[str],
         has_previous: bool,
         limit: int,
-        next_position: str,
-        previous_position: str,
+        next_position: str | None,
+        previous_position: str | None,
     ) -> str:
         if page and cursor.reverse and cursor.offset:
             # If we're reversing direction and we have an offset cursor
@@ -287,12 +287,12 @@ def previous_link(  # noqa: PLR0913
         base_url: str,
         page: list,
         cursor: Cursor,
-        order: tuple,
+        order: Sequence[str],
         has_next: bool,
         limit: int,
-        next_position: str,
-        previous_position: str,
-    ):
+        next_position: str | None,
+        previous_position: str | None,
+    ) -> str:
         if page and not cursor.reverse and cursor.offset:
             # If we're reversing direction and we have an offset cursor
             # then we cannot use the first position we find as a marker.

isic/core/permissions.py

@@ -1,4 +1,5 @@
 from functools import wraps
+from typing import Any
 from urllib.parse import urlparse
 
 import django.apps
@@ -27,7 +28,7 @@ def authenticate(self, request: HttpRequest, key: str | None) -> User | None:
 class UserPermissions:
     model = User
     perms = ["view_staff"]
-    filters = {}
+    filters: dict[str, Any] = {}
 
     @staticmethod
     def view_staff(user_obj, _=None):

isic/core/search.py

@@ -24,7 +24,7 @@
 
 logger = logging.getLogger(__name__)
 
-IMAGE_INDEX_MAPPINGS = {"properties": {}}
+IMAGE_INDEX_MAPPINGS: dict[str, Any] = {"properties": {}}
 DEFAULT_SEARCH_AGGREGATES = {}
 COUNTS_AGGREGATES = {}
 
@@ -170,7 +170,7 @@ def add_to_search_index(image: Image) -> None:
     image = Image.objects.with_elasticsearch_properties().get(pk=image.pk)
     get_elasticsearch_client().index(
         index=settings.ISIC_ELASTICSEARCH_IMAGES_INDEX,
-        id=image.pk,
+        id=str(image.pk),
         document=image.to_elasticsearch_document(source_only=True),
     )
 

isic/core/serializers.py

@@ -80,7 +80,7 @@ def to_queryset(
             qs = qs.from_search_query(self.query)  # type: ignore[attr-defined]
 
         if self.collections:
-            qs = qs.filter(  # type: ignore[union-attr]
+            qs = qs.filter(
                 collections__in=get_visible_objects(
                     user,
                     "core.view_collection",

isic/core/services/__init__.py

@@ -55,7 +55,7 @@ def staff_image_metadata_csv(*, qs: QuerySet[Image]) -> Generator[list[str] | di
         .distinct()
     )
 
-    remapped_keys = reduce(
+    remapped_keys: list[str] = reduce(
         operator.iadd,
         [
             [field.internal_id_name, field.csv_field_name]

isic/core/services/collection/doi.py

@@ -35,7 +35,7 @@
 from isic.ingest.services.publish import unembargo_image
 
 if TYPE_CHECKING:
-    from collections.abc import Iterable
+    from collections.abc import Sequence
     from urllib.parse import ParseResult
 
     from django.contrib.auth.models import User
@@ -120,8 +120,8 @@ def check_create_draft_doi_allowed(
     *,
     user: User,
     collection: Collection,
-    supplemental_files: Iterable[dict[str, str]] | None = None,
-    related_identifiers: Iterable[RelatedIdentifierIn] | None = None,
+    supplemental_files: Sequence[dict[str, str]] | None = None,
+    related_identifiers: Sequence[RelatedIdentifierIn] | None = None,
 ) -> None:
     if not user.has_perm("core.create_doi", collection):
         raise ValidationError("You don't have permissions to do that.")
@@ -190,8 +190,8 @@ def create_collection_draft_doi(
     user: User,
     collection: Collection,
     description: str,
-    supplemental_files: Iterable[dict[str, str]] | None = None,
-    related_identifiers: Iterable[RelatedIdentifierIn] | None = None,
+    supplemental_files: Sequence[dict[str, str]] | None = None,
+    related_identifiers: Sequence[RelatedIdentifierIn] | None = None,
 ) -> DraftDoi:
     check_create_draft_doi_allowed(
         user=user,

isic/core/services/collection/image.py

@@ -64,7 +64,7 @@ def move_collection_images(
     if not ignore_lock and (src_collection.locked or dest_collection.locked):
         raise ValidationError("Can't move images to/from a locked collection.")
 
-    if dest_collection.public and src_collection.images.private().exists():  # type: ignore[attr-defined]
+    if dest_collection.public and src_collection.images.private().exists():
         raise ValidationError("Can't move private images to a public collection.")
 
     with transaction.atomic():

isic/core/tests/test_doi.py

@@ -261,9 +261,11 @@ def test_doi_files(
     doi.refresh_from_db()
 
     assert doi.bundle is not None
+    assert doi.bundle_size is not None
     assert doi.bundle_size > 0
 
     assert doi.metadata is not None
+    assert doi.metadata_size is not None
     assert doi.metadata_size > 0
 
     with tempfile.TemporaryDirectory() as temp_dir, zipfile.ZipFile(doi.bundle) as zf:
@@ -322,7 +324,7 @@ def test_api_doi_creation(
 
     draft_doi = DraftDoi.objects.get(collection=public_collection_with_public_images)
     assert draft_doi.supplemental_files.count() == 1
-    assert draft_doi.supplemental_files.first().description == "test supplemental file"
+    assert draft_doi.supplemental_files.get().description == "test supplemental file"
 
     assert draft_doi.related_identifiers.count() == 2
 
@@ -368,7 +370,7 @@ def test_doi_bundle_includes_supplemental_files(
 
     assert doi.bundle is not None
     assert doi.supplemental_files.count() == 1
-    supplemental_file = doi.supplemental_files.first()
+    supplemental_file = doi.supplemental_files.get()
 
     with tempfile.TemporaryDirectory() as temp_dir, zipfile.ZipFile(doi.bundle) as zf:
         zf.extractall(temp_dir)
@@ -553,7 +555,7 @@ def test_draft_doi_complete_lifecycle(  # noqa: PLR0915
     assert draft_doi.collection == collection
 
     assert draft_doi.supplemental_files.count() == 1
-    supplemental_file = draft_doi.supplemental_files.first()
+    supplemental_file = draft_doi.supplemental_files.get()
     assert supplemental_file.description == "Test supplemental file"
     assert storages["default"].exists(supplemental_file.blob.name)
 
@@ -611,7 +613,7 @@ def test_draft_doi_complete_lifecycle(  # noqa: PLR0915
     }
 
     assert final_doi.supplemental_files.count() == 1
-    final_supplemental_file = final_doi.supplemental_files.first()
+    final_supplemental_file = final_doi.supplemental_files.get()
     assert final_supplemental_file.description == "Test supplemental file"
 
     assert storages["sponsored"].exists(final_supplemental_file.blob.name)
@@ -627,8 +629,10 @@ def test_draft_doi_complete_lifecycle(  # noqa: PLR0915
     assert mock_datacite_promote_draft_doi_to_findable.call_count == 1
 
     assert final_doi.bundle is not None
+    assert final_doi.bundle_size is not None
     assert final_doi.bundle_size > 0
     assert final_doi.metadata is not None
+    assert final_doi.metadata_size is not None
     assert final_doi.metadata_size > 0