Merge pull request #22463 from mvdbeek/warnings/pydantic-v2-mechanical

Warnings/pydantic v2 cleanup

client/src/api/schema/schema.ts

@@ -8459,8 +8459,8 @@ export interface components {
         /** CollectionElementCollectionRequestUri */
         CollectionElementCollectionRequestUri: {
             /**
-             * Class
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
             class: "Collection";
             /** Collection Type */
@@ -8479,8 +8479,8 @@ export interface components {
         /** CollectionElementDataRequestUri */
         CollectionElementDataRequestUri: {
             /**
-             * Class
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
             class: "File";
             /** Created From Basename */
@@ -20712,7 +20712,7 @@ export interface components {
             /** Dry Run */
             dry_run: boolean;
             /** Workflow */
-            workflow: string;
+            workflow: unknown;
         };
         /** RegexJobMessage */
         RegexJobMessage: {

lib/galaxy/dependencies/dev-requirements.txt

@@ -203,7 +203,7 @@ text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
 tomli==2.4.1 ; python_full_version <= '3.11'
-total-perspective-vortex==3.2.0
+total-perspective-vortex==3.2.1
 trio==0.33.0
 trio-websocket==0.12.2
 tuspy==1.1.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -95,7 +95,7 @@ google-auth==2.49.2
 google-cloud-batch==0.21.0
 google-genai==1.72.0
 googleapis-common-protos==1.74.0
-gravity==1.2.0
+gravity==1.2.1
 greenlet==3.4.0 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
 griffelib==2.0.2
 groq==1.1.2
@@ -206,7 +206,7 @@ pydantic-evals==1.80.0
 pydantic-graph==1.80.0
 pydantic-handlebars==0.1.0
 pydantic-settings==2.13.1
-pydantic-tes==0.3.0
+pydantic-tes==0.4.0
 pydicom==3.0.2
 pydot==4.0.1
 pyeventsystem==0.1.0

lib/galaxy/dependencies/pinned-test-requirements.txt

@@ -155,7 +155,7 @@ text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
 tomli==2.4.1 ; python_full_version <= '3.11'
-total-perspective-vortex==3.2.0
+total-perspective-vortex==3.2.1
 trio==0.33.0
 trio-websocket==0.12.2
 tuspy==1.1.0

lib/galaxy/managers/datasets.py

@@ -33,7 +33,10 @@ from galaxy.model import (
     DatasetPermissions,
     HistoryDatasetAssociation,
 )
-from galaxy.model.db.role import get_private_role_user_emails_dict
+from galaxy.model.db.role import (
+    get_private_role_user_emails_dict,
+    role_name_id_pairs,
+)
 from galaxy.schema.tasks import (
     ComputeDatasetHashTaskRequest,
     PurgeDatasetsTaskRequest,
@@ -472,23 +475,14 @@ class DatasetAssociationManager(
             )
         all_role_ids = {r.id for r in access_roles | manage_roles | modify_roles}
         private_role_emails = get_private_role_user_emails_dict(self.session(), role_ids=all_role_ids)
+        encode_id = self.app.security.encode_id
 
-        def make_tuples(roles: set):
-            tuples = []
-            for role in roles:
-                # use role name for non-private roles, and user.email from private rules
-                displayed_name = private_role_emails.get(role.id, role.name)
-                role_tuple = (displayed_name, self.app.security.encode_id(role.id))
-                tuples.append(role_tuple)
-            return tuples
-
-        access_dataset_role_list = make_tuples(access_roles)
-        manage_dataset_role_list = make_tuples(manage_roles)
-
-        rval = dict(access_dataset_roles=access_dataset_role_list, manage_dataset_roles=manage_dataset_role_list)
+        rval = dict(
+            access_dataset_roles=role_name_id_pairs(access_roles, private_role_emails, encode_id),
+            manage_dataset_roles=role_name_id_pairs(manage_roles, private_role_emails, encode_id),
+        )
         if library_dataset is not None:
-            modify_item_role_list = make_tuples(modify_roles)
-            rval["modify_item_roles"] = modify_item_role_list
+            rval["modify_item_roles"] = role_name_id_pairs(modify_roles, private_role_emails, encode_id)
         return rval
 
     def ensure_dataset_on_disk(self, trans, dataset: U):

lib/galaxy/managers/datatypes.py

@@ -3,7 +3,7 @@ from typing import (
     Union,
 )
 
-from pydantic.tools import parse_obj_as
+from pydantic import TypeAdapter
 
 from galaxy.datatypes._schema import (
     DatatypeConverterList,
@@ -87,7 +87,7 @@ def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
                     "tool_id": targets[target_type].id,
                 }
             )
-    return parse_obj_as(DatatypeConverterList, converters)
+    return TypeAdapter(DatatypeConverterList).validate_python(converters)
 
 
 def _get_edam_details(datatypes_registry: Registry, edam_ids: dict[str, str]) -> dict[str, dict]:
@@ -158,7 +158,7 @@ def view_visualization_mappings(
                 }
             )
 
-    return parse_obj_as(DatatypeVisualizationMappingsList, mappings)
+    return TypeAdapter(DatatypeVisualizationMappingsList).validate_python(mappings)
 
 
 def get_preferred_visualization(datatypes_registry: Registry, datatype_extension: str) -> Optional[dict[str, str]]:

lib/galaxy/managers/folders.py

@@ -47,7 +47,10 @@ from galaxy.model import (
     LibraryFolder,
     LibraryFolderPermissions,
 )
-from galaxy.model.db.role import get_private_role_user_emails_dict
+from galaxy.model.db.role import (
+    get_private_role_user_emails_dict,
+    role_name_id_pairs,
+)
 from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.schema import LibraryFolderContentsIndexQueryPayload
 from galaxy.security import RBACAgent
@@ -324,20 +327,11 @@ class FolderManager:
         )
         all_role_ids = {r.id for r in modify_roles | manage_roles | add_roles}
         private_role_emails = get_private_role_user_emails_dict(trans.sa_session, role_ids=all_role_ids)
-
-        def make_tuples(roles: set):
-            tuples = []
-            for role in roles:
-                # use role name for non-private roles, and user.email from private rules
-                displayed_name = private_role_emails.get(role.id, role.name)
-                role_tuple = (displayed_name, trans.security.encode_id(role.id))
-                tuples.append(role_tuple)
-            return tuples
-
+        encode_id = trans.security.encode_id
         return dict(
-            modify_folder_role_list=make_tuples(modify_roles),
-            manage_folder_role_list=make_tuples(manage_roles),
-            add_library_item_role_list=make_tuples(add_roles),
+            modify_folder_role_list=role_name_id_pairs(modify_roles, private_role_emails, encode_id),
+            manage_folder_role_list=role_name_id_pairs(manage_roles, private_role_emails, encode_id),
+            add_library_item_role_list=role_name_id_pairs(add_roles, private_role_emails, encode_id),
         )
 
     def can_add_item(self, trans, folder):

lib/galaxy/managers/histories.py

@@ -15,6 +15,7 @@ from typing import (
     TYPE_CHECKING,
     Union,
 )
+from uuid import UUID
 
 from sqlalchemy import (
     asc,
@@ -718,6 +719,11 @@ class HistoryExportManager:
         if "target_uri" in payload_raw:
             payload = WriteStoreToPayload.model_construct(**payload_raw)
         else:
+            # UUID field bypasses validation under model_construct, so coerce the
+            # stored string to UUID so Pydantic's serializer emits it cleanly.
+            request_id = payload_raw.get("short_term_storage_request_id")
+            if isinstance(request_id, str):
+                payload_raw["short_term_storage_request_id"] = UUID(request_id)
             payload = ShortTermStoreExportPayload.model_construct(**payload_raw)
         request_data = ExportObjectRequestMetadata.model_construct(
             object_id=request_data_raw.get("object_id"),

lib/galaxy/managers/libraries.py

@@ -27,7 +27,10 @@ from galaxy.model.db.library import (
     get_library_ids,
     get_library_permissions_by_role,
 )
-from galaxy.model.db.role import get_private_role_user_emails_dict
+from galaxy.model.db.role import (
+    get_private_role_user_emails_dict,
+    role_name_id_pairs,
+)
 from galaxy.util import (
     pretty_print_time_interval,
     unicodify,
@@ -278,21 +281,12 @@ class LibraryManager:
         add_roles = self.get_add_roles(trans, library)
         all_role_ids = {r.id for r in access_roles | modify_roles | manage_roles | add_roles}
         private_role_emails = get_private_role_user_emails_dict(trans.sa_session, role_ids=all_role_ids)
-
-        def make_tuples(roles: set):
-            tuples = []
-            for role in roles:
-                # use role name for non-private roles, and user.email from private rules
-                displayed_name = private_role_emails.get(role.id, role.name)
-                role_tuple = (displayed_name, trans.security.encode_id(role.id))
-                tuples.append(role_tuple)
-            return tuples
-
+        encode_id = trans.security.encode_id
         return dict(
-            access_library_role_list=make_tuples(access_roles),
-            modify_library_role_list=make_tuples(modify_roles),
-            manage_library_role_list=make_tuples(manage_roles),
-            add_library_item_role_list=make_tuples(add_roles),
+            access_library_role_list=role_name_id_pairs(access_roles, private_role_emails, encode_id),
+            modify_library_role_list=role_name_id_pairs(modify_roles, private_role_emails, encode_id),
+            manage_library_role_list=role_name_id_pairs(manage_roles, private_role_emails, encode_id),
+            add_library_item_role_list=role_name_id_pairs(add_roles, private_role_emails, encode_id),
         )
 
     def get_access_roles(self, trans, library: Library) -> set[Role]:

lib/galaxy/managers/notification.py

@@ -395,7 +395,7 @@ class NotificationManager:
         if request.expiration_time is not None:
             stmt = stmt.values(expiration_time=request.expiration_time)
         if request.content is not None:
-            stmt = stmt.values(content=request.content.json())
+            stmt = stmt.values(content=request.content.model_dump_json())
         result = cast(CursorResult, self.sa_session.execute(stmt))
         updated_row_count = result.rowcount
         self.sa_session.commit()

lib/galaxy/managers/quotas.py

@@ -53,7 +53,7 @@ class QuotaManager:
         return cast(DatabaseQuotaAgent, self.app.quota_agent)
 
     def create_quota(self, payload: dict, decode_id=None) -> tuple[model.Quota, str]:
-        params = CreateQuotaParams.parse_obj(payload)
+        params = CreateQuotaParams.model_validate(payload)
         create_amount = self._parse_amount(params.amount)
         stmt = select(Quota).where(Quota.name == params.name).limit(1)
         if self.sa_session.scalars(stmt).first():

lib/galaxy/managers/workflows.py

@@ -2394,7 +2394,7 @@ class WorkflowContentsManager(UsesAnnotations):
         return sa_session.execute(stmnt.order_by(model.StoredWorkflow.id.desc()).limit(1)).scalar()
 
 
-def safe_wraps(v: Any, nxt: SerializerFunctionWrapHandler) -> str:
+def safe_wraps(v: Any, nxt: SerializerFunctionWrapHandler) -> Any:
     try:
         return nxt(v)
     except Exception:

lib/galaxy/model/__init__.py

@@ -10230,7 +10230,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
 
     def add_message(self, message: "InvocationMessageUnion"):
 
-        message_dict = message.dict(
+        message_dict = message.model_dump(
             exclude_unset=True,
             exclude={"history_id"},  # history_id comes in through workflow_invocation and isn't persisted in database
         )

lib/galaxy/model/db/role.py

@@ -1,3 +1,8 @@
+from collections.abc import (
+    Callable,
+    Iterable,
+)
+
 from sqlalchemy import (
     and_,
     false,
@@ -99,3 +104,18 @@ def get_private_role_user_emails_dict(session, role_ids: set[int] | None = None)
         stmt = stmt.where(UserRoleAssociation.role_id.in_(role_ids))
     roleid_email_tuples = session.execute(stmt).all()
     return dict(roleid_email_tuples)
+
+
+def role_name_id_pairs(
+    roles: Iterable[Role],
+    private_role_emails: dict[int, str],
+    encode_id: Callable[[int], str],
+) -> list[list[str]]:
+    """Build [displayed_name, encoded_id] pairs for a set of roles.
+
+    Private roles render as the owning user's email (looked up via
+    ``private_role_emails``); other roles render as their role name.
+    The return shape matches RoleNameIdTuple in the API schema, which
+    is declared as list[str] (a 2-element array on the wire).
+    """
+    return [[private_role_emails.get(role.id, role.name), encode_id(role.id)] for role in roles]

lib/galaxy/schema/notifications.py

@@ -348,7 +348,7 @@ class NotificationCreatedResponse(Model):
 class NotificationUpdateRequest(Model):
     def has_changes(self) -> bool:
         """Whether the notification update request contains at least one change."""
-        return any(getattr(self, field) is not None for field in self.__fields__.keys())
+        return any(getattr(self, field) is not None for field in type(self).model_fields)
 
 
 class UserNotificationUpdateRequest(NotificationUpdateRequest):

lib/galaxy/schema/schema.py

@@ -22,11 +22,13 @@ from pydantic import (
     BaseModel,
     BeforeValidator,
     ConfigDict,
+    Discriminator,
     Field,
     HttpUrl,
     Json,
     model_validator,
     RootModel,
+    Tag,
     UUID4,
 )
 from pydantic_core import core_schema
@@ -1979,11 +1981,25 @@ class ExportObjectType(str, Enum):
     INVOCATION = "invocation"
 
 
+def _store_export_payload_discriminator(value: Any) -> str:
+    # Route untagged persisted/constructed payloads to the right union branch
+    # without requiring a tag field on the payload classes themselves.
+    if isinstance(value, dict):
+        return "short_term" if "short_term_storage_request_id" in value else "write"
+    return "short_term" if isinstance(value, ShortTermStoreExportPayload) else "write"
+
+
 class ExportObjectRequestMetadata(Model):
     object_id: EncodedDatabaseIdField
     object_type: ExportObjectType
     user_id: Optional[EncodedDatabaseIdField] = None
-    payload: Union[WriteStoreToPayload, ShortTermStoreExportPayload]
+    payload: Annotated[
+        Union[
+            Annotated[WriteStoreToPayload, Tag("write")],
+            Annotated[ShortTermStoreExportPayload, Tag("short_term")],
+        ],
+        Discriminator(_store_export_payload_discriminator),
+    ]
 
 
 class ExportObjectResultMetadata(Model):

lib/galaxy/tool_util/data/__init__.py

@@ -871,7 +871,7 @@ class TabularToolDataField(Dictifiable):
         rval = super().to_dict(view, value_mapper)
         rval["name"] = self.data["value"]
         rval["fields"] = self.data
-        rval["base_dir"] = (self.get_base_dir(),)
+        rval["base_dir"] = [self.get_base_dir()]
         rval["files"] = self.get_filesize_map(True)
         rval["fingerprint"] = self.get_fingerprint()
         return rval

lib/galaxy/tool_util/parser/output_objects.py

@@ -472,7 +472,7 @@ class ToolOutputCollectionStructure:
         return collection_prototype
 
     def to_dict(self):
-        return self.to_model().dict()
+        return self.to_model().model_dump()
 
     def to_model(self) -> ToolOutputCollectionStructureModel:
         discover_datasets = []

lib/galaxy/tool_util/verify/parse.py

@@ -145,7 +145,7 @@ def _description_from_tool_source(
     request_schema: Optional[Dict[str, Any]] = None
     if request_and_schema:
         request = request_and_schema.request.input_state
-        request_schema = request_and_schema.request_schema.dict()
+        request_schema = request_and_schema.request_schema.model_dump()
 
     value_state_representation = raw_test_dict.get("value_state_representation", "test_case_xml")
     tool_id, tool_version = _tool_id_and_version(tool_source, tool_guid)

lib/galaxy/tool_util_models/parameters.py

@@ -609,12 +609,7 @@ class CollectionElementCollectionRequestUri(StrictModel):
         validation_alias=AliasChoices("identifier", "name"),
     )
     collection_type: StrictStr
-    elements: List[
-        Annotated[
-            Union["CollectionElementCollectionRequestUri", CollectionElementDataRequestUri],
-            Field(discriminator="class_"),
-        ]
-    ]
+    elements: List["CollectionRequestUriElement"]
 
     @model_validator(mode="before")
     @classmethod
@@ -628,14 +623,39 @@ class CollectionElementCollectionRequestUri(StrictModel):
         return data
 
 
+def _collection_element_discriminator(value: Any) -> Optional[str]:
+    if isinstance(value, dict):
+        return value.get("class") or value.get("class_")
+    return getattr(value, "class_", None)
+
+
+# A callable Discriminator avoids the PydanticJsonSchemaWarning emitted for
+# the recursive Field(discriminator="class_") on this self-referential union;
+# json_schema_extra restores the OpenAPI discriminator metadata.
+CollectionRequestUriElement = Annotated[
+    Union[
+        Annotated[CollectionElementCollectionRequestUri, Tag("Collection")],
+        Annotated[CollectionElementDataRequestUri, Tag("File")],
+    ],
+    Discriminator(_collection_element_discriminator),
+    Field(
+        json_schema_extra={
+            "discriminator": {
+                "propertyName": "class",
+                "mapping": {
+                    "Collection": "#/components/schemas/CollectionElementCollectionRequestUri",
+                    "File": "#/components/schemas/CollectionElementDataRequestUri",
+                },
+            }
+        }
+    ),
+]
+
+
 class DataRequestCollectionUri(StrictModel):
     class_: Literal["Collection"] = Field(..., alias="class")
     collection_type: str
-    elements: List[
-        Annotated[
-            Union[CollectionElementCollectionRequestUri, CollectionElementDataRequestUri], Field(discriminator="class_")
-        ]
-    ]
+    elements: List[CollectionRequestUriElement]
     deferred: StrictBool = False
     name: Optional[StrictStr] = None
     src: None = Field(None, exclude=True)
@@ -658,6 +678,7 @@ DataRequestLdda.model_rebuild()
 DataRequestDce.model_rebuild()
 DataRequestUri.model_rebuild()
 DataRequestHdca.model_rebuild()
+CollectionElementCollectionRequestUri.model_rebuild()
 DataRequestCollectionUri.model_rebuild()
 
 DataOrCollectionRequestAdapter: TypeAdapter[DataOrCollectionRequest] = TypeAdapter(DataOrCollectionRequest)

lib/galaxy/tool_util_models/sample_sheet.py

@@ -12,6 +12,10 @@ from typing import (
     Union,
 )
 
+from pydantic import (
+    ConfigDict,
+    with_config,
+)
 from typing_extensions import (
     Literal,
     NotRequired,
@@ -31,6 +35,7 @@ SampleSheetColumnValueT = Union[int, float, bool, str, NoneType]
 
 
 # type ignore because mypy can't handle closed TypedDicts yet
+@with_config(ConfigDict(extra="forbid"))
 class SampleSheetColumnDefinition(TypedDict, closed=True):  # type: ignore[call-arg]
     name: str
     description: NotRequired[Optional[str]]

lib/galaxy/tool_util_models/tool_source.py

@@ -6,7 +6,9 @@ from typing import (
 )
 
 from pydantic import (
+    ConfigDict,
     Field,
+    with_config,
 )
 from typing_extensions import (
     Annotated,
@@ -173,6 +175,7 @@ FieldType = Union[CwlType, List[CwlType]]
 
 
 # type ignore because mypy can't handle closed TypedDicts yet
+@with_config(ConfigDict(extra="forbid"))
 class FieldDict(TypedDict, closed=True):  # type: ignore[call-arg]
     name: str
     type: FieldType

lib/galaxy/tools/parameters/basic.py

@@ -2052,12 +2052,12 @@ def src_id_to_item(
             for item in adapting:
                 element = TransientCollectionAdapterDatasetInstanceElement(
                     item.name,
-                    cast(HistoryDatasetAssociation, src_id_to_item(sa_session, item.dict(), security)),
+                    cast(HistoryDatasetAssociation, src_id_to_item(sa_session, item.model_dump(), security)),
                 )
                 elements.append(element)
             return recover_adapter(elements, adapter_model)
         else:
-            value = adapting.dict()
+            value = adapting.model_dump()
     src_to_class = {
         "hda": HistoryDatasetAssociation,
         "ldda": LibraryDatasetDatasetAssociation,
@@ -2994,7 +2994,7 @@ def history_item_to_json(value, app, use_security):
     collection_adapter: Optional[CollectionAdapter] = None
     if isinstance(value, CollectionAdapter):
         collection_adapter = value
-        return collection_adapter.to_adapter_model().dict()
+        return collection_adapter.to_adapter_model().model_dump()
     if isinstance(value, MutableMapping) and "src" in value and "id" in value:
         return value
     elif isinstance(value, DatasetCollectionElement):

lib/galaxy/tours/_impl.py

@@ -6,7 +6,7 @@ import logging
 import os
 
 import yaml
-from pydantic import parse_obj_as
+from pydantic import TypeAdapter
 
 from galaxy.exceptions import ObjectNotFound
 from galaxy.navigation.data import load_root_component
@@ -106,7 +106,7 @@ class ToursRegistryImpl:
                 "requirements": self.tours[k].get("requirements"),
             }
             tours.append(tourdata)
-        return parse_obj_as(TourList, tours)
+        return TypeAdapter(TourList).validate_python(tours)
 
     def tour_contents(self, tour_id):
         """Return tour contents."""

lib/galaxy/webapps/galaxy/api/configuration.py

@@ -138,7 +138,15 @@ class FastAPIConfiguration:
 def _user_to_model(user):
     if user:
         return UserModel.model_construct(
-            **user.to_dict(view="element", value_mapper={"id": Security.security.encode_id})
+            **user.to_dict(
+                view="element",
+                value_mapper={
+                    "id": Security.security.encode_id,
+                    # Dictifiable otherwise stringifies datetimes via isoformat(); keep the
+                    # datetime object so UserModel.last_password_change serializes correctly.
+                    "last_password_change": lambda v: v,
+                },
+            )
         )
     return None
 

lib/galaxy/webapps/galaxy/api/exports.py

@@ -9,6 +9,7 @@ from typing import (
     Optional,
     Union,
 )
+from uuid import UUID
 
 from fastapi import Query
 
@@ -20,6 +21,8 @@ from galaxy.schema.schema import (
     ExportObjectResultMetadata,
     ExportTaskListResponse,
     ObjectExportTaskResponse,
+    ShortTermStoreExportPayload,
+    WriteStoreToPayload,
 )
 from galaxy.webapps.galaxy.api import (
     depends,
@@ -105,11 +108,26 @@ class FastAPIExports:
         request_data_raw = metadata.get("request_data", {})
         result_data_raw = metadata.get("result_data")
 
+        payload_raw = request_data_raw.get("payload") or {}
+        # Pick the right payload flavour by presence of target_uri
+        # (WriteStoreToPayload has it, ShortTermStoreExportPayload does not).
+        if "target_uri" in payload_raw:
+            payload: Union[WriteStoreToPayload, ShortTermStoreExportPayload] = WriteStoreToPayload.model_construct(
+                **payload_raw
+            )
+        else:
+            # UUID field bypasses validation under model_construct, so coerce the
+            # stored string to UUID so Pydantic's serializer emits it cleanly.
+            request_id = payload_raw.get("short_term_storage_request_id")
+            if isinstance(request_id, str):
+                payload_raw["short_term_storage_request_id"] = UUID(request_id)
+            payload = ShortTermStoreExportPayload.model_construct(**payload_raw)
+
         request_data = ExportObjectRequestMetadata.model_construct(
             object_id=request_data_raw.get("object_id"),
             object_type=request_data_raw.get("object_type"),
             user_id=request_data_raw.get("user_id"),
-            payload=request_data_raw.get("payload"),
+            payload=payload,
         )
 
         result_data = None

lib/galaxy/webapps/galaxy/api/histories.py

@@ -22,6 +22,10 @@ from fastapi import (
     Response,
     status,
 )
+from pydantic import (
+    Discriminator,
+    Tag,
+)
 from pydantic.fields import Field
 from pydantic.main import BaseModel
 
@@ -186,6 +190,19 @@ IndexExportsAcceptHeader = Annotated[
 ]
 
 
+def _index_exports_response_discriminator(value: Any) -> str:
+    return "tasks" if isinstance(value, ExportTaskListResponse) else "jobs"
+
+
+IndexExportsResponse = Annotated[
+    Union[
+        Annotated[JobExportHistoryArchiveListResponse, Tag("jobs")],
+        Annotated[ExportTaskListResponse, Tag("tasks")],
+    ],
+    Discriminator(_index_exports_response_discriminator),
+]
+
+
 @router.cbv
 class FastAPIHistories:
     service: HistoriesService = depends(HistoriesService)
@@ -551,7 +568,7 @@ class FastAPIHistories:
         limit: Optional[int] = LimitQueryParam,
         offset: Optional[int] = OffsetQueryParam,
         accept: IndexExportsAcceptHeader = "application/json",
-    ) -> Union[JobExportHistoryArchiveListResponse, ExportTaskListResponse]:
+    ) -> IndexExportsResponse:
         """
         By default the legacy job-based history exports (jeha) are returned.
 

lib/galaxy/webapps/galaxy/services/dataset_collections.py

@@ -182,7 +182,7 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
         :returns:   element view of new dataset collection
         """
         # TODO: Error handling...
-        create_params = api_payload_to_create_params(payload.dict(exclude_unset=True, by_alias=True))
+        create_params = api_payload_to_create_params(payload.model_dump(exclude_unset=True, by_alias=True))
         if payload.instance_type == "history":
             if payload.history_id is None:
                 raise exceptions.RequestParameterInvalidException("Parameter history_id is required.")

lib/galaxy/webapps/galaxy/services/histories.py

@@ -395,7 +395,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
             duration=short_term_storage_target.duration,
             user=trans.async_request_user,
             export_association_id=export_association.id,
-            **payload.dict(),
+            **payload.model_dump(),
         )
         result = prepare_history_download.delay(request=request, task_user_id=getattr(trans.user, "id", None))
         task_summary = async_task_summary(result)
@@ -412,7 +412,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
             user=trans.async_request_user,
             history_id=history.id,
             export_association_id=export_association.id,
-            **payload.dict(),
+            **payload.model_dump(),
         )
         result = write_history_to.delay(request=request, task_user_id=getattr(trans.user, "id", None))
         task_summary = async_task_summary(result)

lib/galaxy/webapps/galaxy/services/sharable.py

@@ -31,6 +31,7 @@ from galaxy.schema.schema import (
     ShareWithStatus,
     SharingOptions,
     SharingStatus,
+    UserEmail,
     UserIdentifier,
 )
 from galaxy.webapps.galaxy.services.notifications import NotificationService
@@ -108,7 +109,10 @@ class ShareableService:
         users, errors = self._get_users(trans, payload.user_ids)
         extra, users_to_notify = self._share_with_options(trans, item, users, errors, payload.share_option)
         base_status = self._get_sharing_status(trans, item)
-        status = self.share_with_status_cls.model_construct(**base_status.model_dump(), extra=extra)
+        # Use dict() for a shallow field copy so nested UserEmail instances in
+        # users_shared_with survive; model_dump() would deep-serialize them to
+        # dicts that model_construct won't re-validate back to UserEmail.
+        status = self.share_with_status_cls.model_construct(**dict(base_status), extra=extra)
         status.errors.extend(errors)
         galaxy_url = str(trans.url_builder("/", qualified=True)).rstrip("/") if trans.url_builder else None
         self._send_notification_to_users(users_to_notify, item, status, galaxy_url)
@@ -138,7 +142,7 @@ class ShareableService:
         status = self.serializer.serialize_to_view(
             item, user=trans.user, trans=trans, default_view="sharing", encode_id=False
         )
-        status["users_shared_with"] = [{"id": a.user.id, "email": a.user.email} for a in item.users_shared_with]
+        status["users_shared_with"] = [UserEmail(id=a.user.id, email=a.user.email) for a in item.users_shared_with]
         return SharingStatus(**status)
 
     def _get_users(self, trans, emails_or_ids: list[UserIdentifier]) -> tuple[set[User], set[str]]:

lib/tool_shed/managers/model_cache.py

@@ -59,4 +59,4 @@ class ModelCache:
         if not os.path.exists(parent_directory):
             os.makedirs(parent_directory)
         with open(cache_target, "w") as f:
-            json.dump(model_object.dict(), f)
+            json.dump(model_object.model_dump(), f)

lib/tool_shed/test/base/testcase.py

@@ -559,7 +559,7 @@ class StandaloneToolShedInstallationClient(ToolShedInstallationClient):
             installed_repository.id,
         )
         response = CheckForUpdatesResponse(message=message, status=status)
-        response_dict = response.dict()
+        response_dict = response.model_dump()
         if verify_no_updates:
             assert "message" in response_dict
             message = response_dict["message"]

pytest.ini

@@ -4,6 +4,7 @@ asyncio_mode = auto
 log_level = DEBUG
 consider_namespace_packages = true
 filterwarnings =
+    error::pydantic.warnings.PydanticDeprecatedSince20
     ignore::DeprecationWarning:pkg_resources
     ignore::DeprecationWarning:refgenconf
     ignore::UserWarning:refgenconf