From f46d69eddd7a8a0f4defcea0939dc096b04aafdf Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 12 Dec 2023 18:53:19 -0500
Subject: [PATCH 01/71] Upgrade SQLAlchemy to 2.0

This conflicts with dependency requirements for sqlalchemy-graphene
(used only in toolshed, new WIP client)
---
 lib/galaxy/dependencies/pinned-requirements.txt | 2 +-
 packages/app/setup.cfg                          | 2 +-
 packages/data/setup.cfg                         | 2 +-
 packages/job_execution/setup.cfg                | 2 +-
 packages/web_apps/setup.cfg                     | 2 +-
 packages/web_framework/setup.cfg                | 2 +-
 packages/web_stack/setup.cfg                    | 2 +-
 pyproject.toml                                  | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 9b51bb5490a2..bf5d947867a4 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -186,7 +186,7 @@ sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
-sqlalchemy==1.4.51 ; python_version >= "3.8" and python_version < "3.13"
+sqlalchemy==2.0.25 ; python_version >= "3.8" and python_version < "3.13"
 sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
 starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
index 4360d7181811..1879c3437ee9 100644
--- a/packages/app/setup.cfg
+++ b/packages/app/setup.cfg
@@ -68,7 +68,7 @@ install_requires =
     refgenconf>=0.12.0
     regex
     requests
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
     sqlitedict
     starlette
     svgwrite
diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
index 157324e102a8..3e3e0e085e5c 100644
--- a/packages/data/setup.cfg
+++ b/packages/data/setup.cfg
@@ -58,7 +58,7 @@ install_requires =
     pysam>=0.21
     rocrate
     social-auth-core[openidconnect]==4.0.3
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
     tifffile
     typing-extensions
     WebOb
diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg
index 40c3be56f524..05394dca8e27 100644
--- a/packages/job_execution/setup.cfg
+++ b/packages/job_execution/setup.cfg
@@ -38,7 +38,7 @@ install_requires =
     galaxy-tool-util
     galaxy-util
     MarkupSafe
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
 packages = find:
 python_requires = >=3.8
 
diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
index 20ac5878220b..53ef00625581 100644
--- a/packages/web_apps/setup.cfg
+++ b/packages/web_apps/setup.cfg
@@ -58,7 +58,7 @@ install_requires =
     PyYAML
     requests
     Routes
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
     sqlalchemy-migrate
     starlette
     starlette-context
diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg
index e04d3f101f32..55d3421dade9 100644
--- a/packages/web_framework/setup.cfg
+++ b/packages/web_framework/setup.cfg
@@ -40,7 +40,7 @@ install_requires =
     pydantic>=2,!=2.6.0,!=2.6.1
     requests
     Routes
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
     WebOb
 
 packages = find:
diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg
index f7bc6adc5d54..16e6d08f1c15 100644
--- a/packages/web_stack/setup.cfg
+++ b/packages/web_stack/setup.cfg
@@ -34,7 +34,7 @@ include_package_data = True
 install_requires =
     galaxy-data
     galaxy-util
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
 packages = find:
 python_requires = >=3.8
 
diff --git a/pyproject.toml b/pyproject.toml
index a1b0be2fda3d..86a696525145 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -108,7 +108,7 @@ Routes = "*"
 schema-salad = "!=8.3.20220721194857"  # https://github.com/common-workflow-language/schema_salad/issues/575
 social-auth-core = {version = "==4.0.3", extras = ["openidconnect"]}
 sortedcontainers = "*"
-SQLAlchemy = ">=1.4.25,<2"
+SQLAlchemy = "^2.0"
 sqlitedict = "*"
 sqlparse = "*"
 starlette = "*"

From 5dc6e0731c911314b94cf55679cb7e4851c9da03 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 19 Dec 2023 13:00:19 -0500
Subject: [PATCH 02/71] Remove RemovedIn20Warning from config

This does not exist in SQLAlchemy 2.0
---
 lib/galaxy/config/__init__.py | 31 -------------------------------
 1 file changed, 31 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index ff3ea85a5ae1..a68c692f1cff 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -743,7 +743,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
         self._override_tempdir(kwargs)
-        self._configure_sqlalchemy20_warnings(kwargs)
         self._process_config(kwargs)
         self._set_dependent_defaults()
 
@@ -760,36 +759,6 @@ def _set_dependent_defaults(self):
                     f"{dependent_config_param}, {config_param}"
                 )
 
-    def _configure_sqlalchemy20_warnings(self, kwargs):
-        """
-        This method should be deleted after migration to SQLAlchemy 2.0 is complete.
-        To enable warnings, set `GALAXY_CONFIG_SQLALCHEMY_WARN_20=1`,
-        """
-        warn = string_as_bool(kwargs.get("sqlalchemy_warn_20", False))
-        if warn:
-            import sqlalchemy
-
-            sqlalchemy.util.deprecations.SQLALCHEMY_WARN_20 = True
-            self._setup_sqlalchemy20_warnings_filters()
-
-    def _setup_sqlalchemy20_warnings_filters(self):
-        import warnings
-
-        from sqlalchemy.exc import RemovedIn20Warning
-
-        # Always display RemovedIn20Warning warnings.
-        warnings.filterwarnings("always", category=RemovedIn20Warning)
-        # Optionally, enable filters for specific warnings (raise error, or log, etc.)
-        # messages = [
-        #     r"replace with warning text to match",
-        # ]
-        # for msg in messages:
-        #     warnings.filterwarnings('error', message=msg, category=RemovedIn20Warning)
-        #
-        # See documentation:
-        # https://docs.python.org/3.7/library/warnings.html#the-warnings-filter
-        # https://docs.sqlalchemy.org/en/14/changelog/migration_20.html#migration-to-2-0-step-three-resolve-all-removedin20warnings
-
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 

From 0b75e555ab637a1228d7ffabb87b995b8808112f Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 9 Jan 2024 16:17:09 -0500
Subject: [PATCH 03/71] Update import path for DeclarativeMeta

---
 lib/galaxy/model/__init__.py                   | 4 ++--
 lib/galaxy/model/tool_shed_install/__init__.py | 4 ++--
 lib/tool_shed/webapp/model/__init__.py         | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 97c41e7ee2e1..0a79864fe0a0 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -216,7 +216,7 @@
 
 if TYPE_CHECKING:
     # Workaround for https://github.com/python/mypy/issues/14182
-    from sqlalchemy.orm.decl_api import DeclarativeMeta as _DeclarativeMeta
+    from sqlalchemy.orm import DeclarativeMeta as _DeclarativeMeta
 
     class DeclarativeMeta(_DeclarativeMeta, type):
         pass
@@ -230,7 +230,7 @@ class _HasTable:
         __table__: Table
 
 else:
-    from sqlalchemy.orm.decl_api import DeclarativeMeta
+    from sqlalchemy.orm import DeclarativeMeta
 
     _HasTable = object
 
diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index ab5a7d9a41b8..edec5b1f5c82 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -44,13 +44,13 @@
 
 if TYPE_CHECKING:
     # Workaround for https://github.com/python/mypy/issues/14182
-    from sqlalchemy.orm.decl_api import DeclarativeMeta as _DeclarativeMeta
+    from sqlalchemy.orm import DeclarativeMeta as _DeclarativeMeta
 
     class DeclarativeMeta(_DeclarativeMeta, type):
         pass
 
 else:
-    from sqlalchemy.orm.decl_api import DeclarativeMeta
+    from sqlalchemy.orm import DeclarativeMeta
 
 
 class HasToolBox(common_util.HasToolShedRegistry, Protocol):
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 2f2be9dccfbe..3b2003d3e1be 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -62,13 +62,13 @@
 
 if TYPE_CHECKING:
     # Workaround for https://github.com/python/mypy/issues/14182
-    from sqlalchemy.orm.decl_api import DeclarativeMeta as _DeclarativeMeta
+    from sqlalchemy.orm import DeclarativeMeta as _DeclarativeMeta
 
     class DeclarativeMeta(_DeclarativeMeta, type):
         pass
 
 else:
-    from sqlalchemy.orm.decl_api import DeclarativeMeta
+    from sqlalchemy.orm import DeclarativeMeta
 
 mapper_registry = registry()
 

From 54578a0425c21a72cbc93a161aac8945bc1304f5 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 12 Dec 2023 18:40:19 -0500
Subject: [PATCH 04/71] Move declaration of injected attrs into constructor
 Remove unused import

For context: https://github.com/galaxyproject/galaxy/pull/14717/files#r1486979280

Also, remove model attr type hints that conflict with SA2.0
---
 lib/galaxy/model/__init__.py | 52 +++++++++++++++++-------------------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 0a79864fe0a0..a4bec20b9c47 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -140,7 +140,6 @@
 )
 from galaxy.model.orm.now import now
 from galaxy.model.orm.util import add_object_to_object_session
-from galaxy.objectstore import ObjectStore
 from galaxy.schema.invocation import (
     InvocationCancellationUserRequest,
     InvocationState,
@@ -737,7 +736,7 @@ class User(Base, Dictifiable, RepresentById):
         "FormValues", primaryjoin=(lambda: User.form_values_id == FormValues.id)  # type: ignore[has-type]
     )
     # Add type hint (will this work w/SA?)
-    api_keys: "List[APIKeys]" = relationship(
+    api_keys = relationship(
         "APIKeys",
         back_populates="user",
         order_by=lambda: desc(APIKeys.create_time),
@@ -767,7 +766,7 @@ class User(Base, Dictifiable, RepresentById):
         ),
     )
 
-    preferences: association_proxy  # defined at the end of this module
+    preferences = None
 
     # attributes that will be accessed and returned when calling to_dict( view='collection' )
     dict_collection_visible_keys = ["id", "email", "username", "deleted", "active", "last_password_change"]
@@ -1386,8 +1385,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
         "WorkflowInvocationStep", back_populates="job", uselist=False, cascade_backrefs=False
     )
 
-    any_output_dataset_collection_instances_deleted: column_property  # defined at the end of this module
-    any_output_dataset_deleted: column_property  # defined at the end of this module
+    any_output_dataset_collection_instances_deleted = None
+    any_output_dataset_deleted = None
 
     dict_collection_visible_keys = ["id", "state", "exit_code", "update_time", "create_time", "galaxy_version"]
     dict_element_visible_keys = [
@@ -3032,8 +3031,8 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     update_time = column_property(
         select(func.max(HistoryAudit.update_time)).where(HistoryAudit.history_id == id).scalar_subquery(),
     )
-    users_shared_with_count: column_property  # defined at the end of this module
-    average_rating: column_property  # defined at the end of this module
+    users_shared_with_count = None
+    average_rating = None
 
     # Set up proxy so that
     #   History.users_shared_with
@@ -3972,7 +3971,7 @@ class conversion_messages(str, Enum):
 
     permitted_actions = get_permitted_actions(filter="DATASET")
     file_path = "/tmp/"
-    object_store: Optional[ObjectStore] = None  # This get initialized in mapping.py (method init) by app.py
+    object_store = None  # This get initialized in mapping.py (method init) by app.py
     engine = None
 
     def __init__(
@@ -7427,7 +7426,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
     )
     users_shared_with = relationship("StoredWorkflowUserShareAssociation", back_populates="stored_workflow")
 
-    average_rating: column_property
+    average_rating = None
 
     # Set up proxy so that
     #   StoredWorkflow.users_shared_with
@@ -7555,7 +7554,7 @@ class Workflow(Base, Dictifiable, RepresentById):
     source_metadata = Column(JSONType)
     uuid = Column(UUIDType, nullable=True)
 
-    steps: List["WorkflowStep"] = relationship(
+    steps = relationship(
         "WorkflowStep",
         back_populates="workflow",
         primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id),  # type: ignore[has-type]
@@ -7563,7 +7562,7 @@ class Workflow(Base, Dictifiable, RepresentById):
         cascade="all, delete-orphan",
         lazy=False,
     )
-    comments: List["WorkflowComment"] = relationship(
+    comments = relationship(
         "WorkflowComment",
         back_populates="workflow",
         primaryjoin=(lambda: Workflow.id == WorkflowComment.workflow_id),  # type: ignore[has-type]
@@ -7582,7 +7581,7 @@ class Workflow(Base, Dictifiable, RepresentById):
         back_populates="workflows",
     )
 
-    step_count: column_property
+    step_count = None
 
     dict_collection_visible_keys = ["name", "has_cycles", "has_errors"]
     dict_element_visible_keys = ["name", "has_cycles", "has_errors"]
@@ -7740,7 +7739,7 @@ class WorkflowStep(Base, RepresentById):
     when_expression = Column(JSONType)
     uuid = Column(UUIDType)
     label = Column(Unicode(255))
-    temp_input_connections: Optional[InputConnDictType]
+    temp_input_connections = None
     parent_comment_id = Column(Integer, ForeignKey("workflow_comment.id"), nullable=True)
 
     parent_comment = relationship(
@@ -7749,7 +7748,7 @@ class WorkflowStep(Base, RepresentById):
         back_populates="child_steps",
     )
 
-    subworkflow: Optional[Workflow] = relationship(
+    subworkflow = relationship(
         "Workflow",
         primaryjoin=(lambda: Workflow.id == WorkflowStep.subworkflow_id),
         back_populates="parent_workflow_steps",
@@ -7776,12 +7775,6 @@ class WorkflowStep(Base, RepresentById):
         cascade_backrefs=False,
     )
 
-    # Injected attributes
-    # TODO: code using these should be refactored to not depend on these non-persistent fields
-    module: Optional["WorkflowModule"]
-    state: Optional["DefaultToolState"]
-    upgrade_messages: Optional[Dict]
-
     STEP_TYPE_TO_INPUT_TYPE = {
         "data_input": "dataset",
         "data_collection_input": "dataset_collection",
@@ -7793,6 +7786,11 @@ def __init__(self):
         self.uuid = uuid4()
         self._input_connections_by_name = None
         self._inputs_by_name = None
+        # Injected attributes
+        # TODO: code using these should be refactored to not depend on these non-persistent fields
+        self.module: Optional["WorkflowModule"]
+        self.state: Optional["DefaultToolState"]
+        self.upgrade_messages: Optional[Dict]
 
     @reconstructor
     def init_on_load(self):
@@ -8196,20 +8194,20 @@ class WorkflowComment(Base, RepresentById):
         back_populates="comments",
     )
 
-    child_steps: List["WorkflowStep"] = relationship(
+    child_steps = relationship(
         "WorkflowStep",
         primaryjoin=(lambda: WorkflowStep.parent_comment_id == WorkflowComment.id),
         back_populates="parent_comment",
     )
 
-    parent_comment: "WorkflowComment" = relationship(
+    parent_comment = relationship(
         "WorkflowComment",
         primaryjoin=(lambda: WorkflowComment.id == WorkflowComment.parent_comment_id),
         back_populates="child_comments",
         remote_side=[id],
     )
 
-    child_comments: List["WorkflowComment"] = relationship(
+    child_comments = relationship(
         "WorkflowComment",
         primaryjoin=(lambda: WorkflowComment.parent_comment_id == WorkflowComment.id),
         back_populates="parent_comment",
@@ -8321,7 +8319,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         order_by=lambda: WorkflowInvocationStep.order_index,
         cascade_backrefs=False,
     )
-    workflow: Workflow = relationship("Workflow")
+    workflow = relationship("Workflow")
     output_dataset_collections = relationship(
         "WorkflowInvocationOutputDatasetCollectionAssociation",
         back_populates="workflow_invocation",
@@ -8968,7 +8966,7 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
         select(WorkflowStep.order_index).where(WorkflowStep.id == workflow_step_id).scalar_subquery()
     )
 
-    subworkflow_invocation_id: column_property
+    subworkflow_invocation_id = None
 
     dict_collection_visible_keys = [
         "id",
@@ -10054,7 +10052,7 @@ class Page(Base, HasTags, Dictifiable, RepresentById):
     )
     users_shared_with = relationship("PageUserShareAssociation", back_populates="page")
 
-    average_rating: column_property  # defined at the end of this module
+    average_rating = None
 
     # Set up proxy so that
     #   Page.users_shared_with
@@ -10181,7 +10179,7 @@ class Visualization(Base, HasTags, Dictifiable, RepresentById):
     )
     users_shared_with = relationship("VisualizationUserShareAssociation", back_populates="visualization")
 
-    average_rating: column_property  # defined at the end of this module
+    average_rating = None
 
     # Set up proxy so that
     #   Visualization.users_shared_with

From 1f207ece9f594723c6c27a038e41fd5ab4126674 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 20 Dec 2023 16:58:01 -0500
Subject: [PATCH 05/71] Apply Mapped/mapped_column to model definitions

Included models: galaxy, tool shed, tool shed install
Column types:
DateTime
Integer
Boolan
Unicode
String (Text/TEXT/TrimmedString/VARCHAR)
UUID
Numeric

NOTE on typing of nullability: db schema != python app

- Mapped[datetime] specifies correct type for the python app;
- nullable=True specifies correct mapping to the db schema (that's what
  the CREATE TABLE sql statement will reflect).

mapped_column.nullable takes precedence over typing annotation of
Mapped. So, if we have:

foo: Mapped[str] = mapped_column(String, nullable=True)

- that means that the foo db field will allow NULL, but the python app
  will not allow foo = None. And vice-versa:

bar: Mapped[Optional[str]] = mapped_column(String, nullable=False)

- the bar db field is NOT NULL, but bar = None is OK.

This might need to be applied to other column definitions, but for now
this addresses specific mypy errors.

Ref: https://docs.sqlalchemy.org/en/20/orm/declarative_tables.html#mapped-column-derives-the-datatype-and-nullability-from-the-mapped-annotation
---
 lib/galaxy/model/__init__.py                  | 2124 +++++++++--------
 .../model/tool_shed_install/__init__.py       |   93 +-
 lib/tool_shed/webapp/model/__init__.py        |  193 +-
 3 files changed, 1294 insertions(+), 1116 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index a4bec20b9c47..25dcb625cf9f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -18,7 +18,11 @@
 import string
 from collections import defaultdict
 from collections.abc import Callable
-from datetime import timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
+from decimal import Decimal
 from enum import Enum
 from secrets import token_hex
 from string import Template
@@ -100,6 +104,8 @@
     column_property,
     deferred,
     joinedload,
+    Mapped,
+    mapped_column,
     object_session,
     Query,
     reconstructor,
@@ -434,11 +440,11 @@ class WorkerProcess(Base, UsesCreateAndUpdateTime):
     __tablename__ = "worker_process"
     __table_args__ = (UniqueConstraint("server_name", "hostname"),)
 
-    id = Column(Integer, primary_key=True)
-    server_name = Column(String(255), index=True)
-    hostname = Column(String(255))
-    pid = Column(Integer)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    server_name: Mapped[Optional[str]] = mapped_column(String(255), index=True)
+    hostname: Mapped[Optional[str]] = mapped_column(String(255))
+    pid: Mapped[Optional[int]] = mapped_column(Integer)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
 
 
 def cached_id(galaxy_model_object):
@@ -681,22 +687,22 @@ class User(Base, Dictifiable, RepresentById):
 
     __tablename__ = "galaxy_user"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    email = Column(TrimmedString(255), index=True, nullable=False)
-    username = Column(TrimmedString(255), index=True, unique=True)
-    password = Column(TrimmedString(255), nullable=False)
-    last_password_change = Column(DateTime, default=now)
-    external = Column(Boolean, default=False)
-    form_values_id = Column(Integer, ForeignKey("form_values.id"), index=True)
-    preferred_object_store_id = Column(String(255), nullable=True)
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
-    disk_usage = Column(Numeric(15, 0), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    email: Mapped[str] = mapped_column(TrimmedString(255), index=True, nullable=False)
+    username: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True, unique=True)
+    password: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    last_password_change: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    external: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    form_values_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_values.id"), index=True)
+    preferred_object_store_id: Mapped[str] = mapped_column(String(255), nullable=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    disk_usage: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0), index=True)
     # Column("person_metadata", JSONType),  # TODO: add persistent, configurable metadata rep for workflow creator
-    active = Column(Boolean, index=True, default=True, nullable=False)
-    activation_token = Column(TrimmedString(64), nullable=True, index=True)
+    active: Mapped[bool] = mapped_column(Boolean, index=True, default=True, nullable=False)
+    activation_token: Mapped[Optional[str]] = mapped_column(TrimmedString(64), nullable=True, index=True)
 
     addresses = relationship(
         "UserAddress", back_populates="user", order_by=lambda: desc(UserAddress.update_time), cascade_backrefs=False
@@ -1210,10 +1216,10 @@ def count_stored_workflow_user_assocs(self, stored_workflow) -> int:
 class PasswordResetToken(Base):
     __tablename__ = "password_reset_token"
 
-    token = Column(String(32), primary_key=True, unique=True, index=True)
-    expiration_time = Column(DateTime)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user = relationship("User")
+    token: Mapped[str] = mapped_column(String(32), primary_key=True, unique=True, index=True)
+    expiration_time: Mapped[Optional[datetime]] = mapped_column(DateTime)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user: Mapped["User"] = relationship("User")
 
     def __init__(self, user, token=None):
         if token:
@@ -1227,17 +1233,17 @@ def __init__(self, user, token=None):
 class DynamicTool(Base, Dictifiable, RepresentById):
     __tablename__ = "dynamic_tool"
 
-    id = Column(Integer, primary_key=True)
-    uuid = Column(UUIDType())
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, index=True, default=now, onupdate=now)
-    tool_id = Column(Unicode(255))
-    tool_version = Column(Unicode(255))
-    tool_format = Column(Unicode(255))
-    tool_path = Column(Unicode(255))
-    tool_directory = Column(Unicode(255))
-    hidden = Column(Boolean, default=True)
-    active = Column(Boolean, default=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    uuid: Mapped[Optional[str]] = mapped_column(UUIDType())
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, index=True, default=now, onupdate=now, nullable=True)
+    tool_id: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    tool_version: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    tool_format: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    tool_path: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    tool_directory: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    hidden: Mapped[Optional[bool]] = mapped_column(Boolean, default=True)
+    active: Mapped[Optional[bool]] = mapped_column(Boolean, default=True)
     value = Column(MutableJSONType)
 
     dict_collection_visible_keys = ("id", "tool_id", "tool_format", "tool_version", "uuid", "active", "hidden")
@@ -1264,41 +1270,41 @@ def __init__(self, plugin, metric_name, metric_value):
 class JobMetricText(BaseJobMetric, RepresentById):
     __tablename__ = "job_metric_text"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    plugin = Column(Unicode(255))
-    metric_name = Column(Unicode(255))
-    metric_value = Column(Unicode(JOB_METRIC_MAX_LENGTH))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    plugin: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    metric_name: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    metric_value: Mapped[Optional[str]] = mapped_column(Unicode(JOB_METRIC_MAX_LENGTH))
 
 
 class JobMetricNumeric(BaseJobMetric, RepresentById):
     __tablename__ = "job_metric_numeric"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    plugin = Column(Unicode(255))
-    metric_name = Column(Unicode(255))
-    metric_value = Column(Numeric(JOB_METRIC_PRECISION, JOB_METRIC_SCALE))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    plugin: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    metric_name: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    metric_value: Mapped[Optional[Decimal]] = mapped_column(Numeric(JOB_METRIC_PRECISION, JOB_METRIC_SCALE))
 
 
 class TaskMetricText(BaseJobMetric, RepresentById):
     __tablename__ = "task_metric_text"
 
-    id = Column(Integer, primary_key=True)
-    task_id = Column(Integer, ForeignKey("task.id"), index=True)
-    plugin = Column(Unicode(255))
-    metric_name = Column(Unicode(255))
-    metric_value = Column(Unicode(JOB_METRIC_MAX_LENGTH))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    task_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("task.id"), index=True)
+    plugin: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    metric_name: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    metric_value: Mapped[Optional[str]] = mapped_column(Unicode(JOB_METRIC_MAX_LENGTH))
 
 
 class TaskMetricNumeric(BaseJobMetric, RepresentById):
     __tablename__ = "task_metric_numeric"
 
-    id = Column(Integer, primary_key=True)
-    task_id = Column(Integer, ForeignKey("task.id"), index=True)
-    plugin = Column(Unicode(255))
-    metric_name = Column(Unicode(255))
-    metric_value = Column(Numeric(JOB_METRIC_PRECISION, JOB_METRIC_SCALE))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    task_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("task.id"), index=True)
+    plugin: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    metric_name: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    metric_value: Mapped[Optional[Decimal]] = mapped_column(Numeric(JOB_METRIC_PRECISION, JOB_METRIC_SCALE))
 
 
 class IoDicts(NamedTuple):
@@ -1315,40 +1321,44 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
 
     __tablename__ = "job"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now, index=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    library_folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
-    tool_id = Column(String(255))
-    tool_version = Column(TEXT, default="1.0.0")
-    galaxy_version = Column(String(64), default=None)
-    dynamic_tool_id = Column(Integer, ForeignKey("dynamic_tool.id"), index=True, nullable=True)
-    state = Column(String(64), index=True)
-    info = Column(TrimmedString(255))
-    copied_from_job_id = Column(Integer, nullable=True)
-    command_line = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, index=True, nullable=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    library_folder_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library_folder.id"), index=True)
+    tool_id: Mapped[Optional[str]] = mapped_column(String(255))
+    tool_version: Mapped[Optional[str]] = mapped_column(TEXT, default="1.0.0")
+    galaxy_version: Mapped[Optional[str]] = mapped_column(String(64), default=None)
+    dynamic_tool_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("dynamic_tool.id"), index=True, nullable=True
+    )
+    state: Mapped[Optional[str]] = mapped_column(String(64), index=True)
+    info: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    copied_from_job_id: Mapped[Optional[int]] = mapped_column(Integer, nullable=True)
+    command_line: Mapped[Optional[str]] = mapped_column(TEXT)
     dependencies = Column(MutableJSONType, nullable=True)
     job_messages = Column(MutableJSONType, nullable=True)
-    param_filename = Column(String(1024))
-    runner_name = Column(String(255))
-    job_stdout = Column(TEXT)
-    job_stderr = Column(TEXT)
-    tool_stdout = Column(TEXT)
-    tool_stderr = Column(TEXT)
-    exit_code = Column(Integer, nullable=True)
-    traceback = Column(TEXT)
-    session_id = Column(Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
-    job_runner_name = Column(String(255))
-    job_runner_external_id = Column(String(255), index=True)
-    destination_id = Column(String(255), nullable=True)
+    param_filename: Mapped[Optional[str]] = mapped_column(String(1024))
+    runner_name: Mapped[Optional[str]] = mapped_column(String(255))
+    job_stdout: Mapped[Optional[str]] = mapped_column(TEXT)
+    job_stderr: Mapped[Optional[str]] = mapped_column(TEXT)
+    tool_stdout: Mapped[Optional[str]] = mapped_column(TEXT)
+    tool_stderr: Mapped[Optional[str]] = mapped_column(TEXT)
+    exit_code: Mapped[Optional[int]] = mapped_column(Integer, nullable=True)
+    traceback: Mapped[Optional[str]] = mapped_column(TEXT)
+    session_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
+    job_runner_name: Mapped[Optional[str]] = mapped_column(String(255))
+    job_runner_external_id: Mapped[Optional[str]] = mapped_column(String(255), index=True)
+    destination_id: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
     destination_params = Column(MutableJSONType, nullable=True)
-    object_store_id = Column(TrimmedString(255), index=True)
-    imported = Column(Boolean, default=False, index=True)
-    params = Column(TrimmedString(255), index=True)
-    handler = Column(TrimmedString(255), index=True)
-    preferred_object_store_id = Column(String(255), nullable=True)
+    object_store_id: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    imported: Mapped[Optional[bool]] = mapped_column(Boolean, default=False, index=True)
+    params: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    handler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    preferred_object_store_id: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
     object_store_id_overrides = Column(JSONType)
 
     user = relationship("User")
@@ -2083,27 +2093,29 @@ class Task(Base, JobLike, RepresentById):
 
     __tablename__ = "task"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    execution_time = Column(DateTime)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    state = Column(String(64), index=True)
-    command_line = Column(TEXT)
-    param_filename = Column(String(1024))
-    runner_name = Column(String(255))
-    job_stdout = Column(TEXT)  # job_stdout makes sense here because it is short for job script standard out
-    job_stderr = Column(TEXT)
-    tool_stdout = Column(TEXT)
-    tool_stderr = Column(TEXT)
-    exit_code = Column(Integer, nullable=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    execution_time: Mapped[Optional[datetime]] = mapped_column(DateTime)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    state: Mapped[Optional[str]] = mapped_column(String(64), index=True)
+    command_line: Mapped[Optional[str]] = mapped_column(TEXT)
+    param_filename: Mapped[Optional[str]] = mapped_column(String(1024))
+    runner_name: Mapped[Optional[str]] = mapped_column(String(255))
+    job_stdout: Mapped[Optional[str]] = mapped_column(
+        TEXT
+    )  # job_stdout makes sense here because it is short for job script standard out
+    job_stderr: Mapped[Optional[str]] = mapped_column(TEXT)
+    tool_stdout: Mapped[Optional[str]] = mapped_column(TEXT)
+    tool_stderr: Mapped[Optional[str]] = mapped_column(TEXT)
+    exit_code: Mapped[Optional[int]] = mapped_column(Integer, nullable=True)
     job_messages = Column(MutableJSONType, nullable=True)
-    info = Column(TrimmedString(255))
-    traceback = Column(TEXT)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True, nullable=False)
-    working_directory = Column(String(1024))
-    task_runner_name = Column(String(255))
-    task_runner_external_id = Column(String(255))
-    prepare_input_files_cmd = Column(TEXT)
+    info: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    traceback: Mapped[Optional[str]] = mapped_column(TEXT)
+    job_id: Mapped[int] = mapped_column(Integer, ForeignKey("job.id"), index=True, nullable=False)
+    working_directory: Mapped[Optional[str]] = mapped_column(String(1024))
+    task_runner_name: Mapped[Optional[str]] = mapped_column(String(255))
+    task_runner_external_id: Mapped[Optional[str]] = mapped_column(String(255))
+    prepare_input_files_cmd: Mapped[Optional[str]] = mapped_column(TEXT)
     job = relationship("Job", back_populates="tasks")
     text_metrics = relationship("TaskMetricText")
     numeric_metrics = relationship("TaskMetricNumeric")
@@ -2253,10 +2265,10 @@ def set_prepare_input_files_cmd(self, prepare_input_files_cmd):
 class JobParameter(Base, RepresentById):
     __tablename__ = "job_parameter"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    name = Column(String(255))
-    value = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255))
+    value: Mapped[Optional[str]] = mapped_column(TEXT)
 
     def __init__(self, name, value):
         self.name = name
@@ -2269,11 +2281,11 @@ def copy(self):
 class JobToInputDatasetAssociation(Base, RepresentById):
     __tablename__ = "job_to_input_dataset"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    dataset_version = Column(Integer)
-    name = Column(String(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    dataset_version: Mapped[Optional[int]] = mapped_column(Integer)
+    name: Mapped[Optional[str]] = mapped_column(String(255))
     dataset = relationship("HistoryDatasetAssociation", lazy="joined", back_populates="dependent_jobs")
     job = relationship("Job", back_populates="input_datasets")
 
@@ -2287,10 +2299,10 @@ def __init__(self, name, dataset):
 class JobToOutputDatasetAssociation(Base, RepresentById):
     __tablename__ = "job_to_output_dataset"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    name = Column(String(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255))
     dataset = relationship("HistoryDatasetAssociation", lazy="joined", back_populates="creating_job_associations")
     job = relationship("Job", back_populates="output_datasets")
 
@@ -2307,10 +2319,12 @@ def item(self):
 class JobToInputDatasetCollectionAssociation(Base, RepresentById):
     __tablename__ = "job_to_input_dataset_collection"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
-    name = Column(String(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    )
+    name: Mapped[Optional[str]] = mapped_column(String(255))
     dataset_collection = relationship("HistoryDatasetCollectionAssociation", lazy="joined")
     job = relationship("Job", back_populates="input_dataset_collections")
 
@@ -2322,10 +2336,12 @@ def __init__(self, name, dataset_collection):
 class JobToInputDatasetCollectionElementAssociation(Base, RepresentById):
     __tablename__ = "job_to_input_dataset_collection_element"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    dataset_collection_element_id = Column(Integer, ForeignKey("dataset_collection_element.id"), index=True)
-    name = Column(Unicode(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    dataset_collection_element_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("dataset_collection_element.id"), index=True
+    )
+    name: Mapped[Optional[str]] = mapped_column(Unicode(255))
     dataset_collection_element = relationship("DatasetCollectionElement", lazy="joined")
     job = relationship("Job", back_populates="input_dataset_collection_elements")
 
@@ -2339,10 +2355,12 @@ def __init__(self, name, dataset_collection_element):
 class JobToOutputDatasetCollectionAssociation(Base, RepresentById):
     __tablename__ = "job_to_output_dataset_collection"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
-    name = Column(Unicode(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    )
+    name: Mapped[Optional[str]] = mapped_column(Unicode(255))
     dataset_collection_instance = relationship("HistoryDatasetCollectionAssociation", lazy="joined")
     job = relationship("Job", back_populates="output_dataset_collection_instances")
 
@@ -2361,10 +2379,12 @@ def item(self):
 class JobToImplicitOutputDatasetCollectionAssociation(Base, RepresentById):
     __tablename__ = "job_to_implicit_output_dataset_collection"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    dataset_collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True)
-    name = Column(Unicode(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("dataset_collection.id"), index=True
+    )
+    name: Mapped[Optional[str]] = mapped_column(Unicode(255))
     dataset_collection = relationship("DatasetCollection")
     job = relationship("Job", back_populates="output_dataset_collections")
 
@@ -2376,10 +2396,12 @@ def __init__(self, name, dataset_collection):
 class JobToInputLibraryDatasetAssociation(Base, RepresentById):
     __tablename__ = "job_to_input_library_dataset"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True)
-    name = Column(Unicode(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    ldda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True
+    )
+    name: Mapped[Optional[str]] = mapped_column(Unicode(255))
     job = relationship("Job", back_populates="input_library_datasets")
     dataset = relationship("LibraryDatasetDatasetAssociation", lazy="joined", back_populates="dependent_jobs")
 
@@ -2392,10 +2414,12 @@ def __init__(self, name, dataset):
 class JobToOutputLibraryDatasetAssociation(Base, RepresentById):
     __tablename__ = "job_to_output_library_dataset"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True)
-    name = Column(Unicode(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    ldda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True
+    )
+    name: Mapped[Optional[str]] = mapped_column(Unicode(255))
     job = relationship("Job", back_populates="output_library_datasets")
     dataset = relationship(
         "LibraryDatasetDatasetAssociation", lazy="joined", back_populates="creating_job_associations"
@@ -2410,11 +2434,11 @@ def __init__(self, name, dataset):
 class JobStateHistory(Base, RepresentById):
     __tablename__ = "job_state_history"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    state = Column(String(64), index=True)
-    info = Column(TrimmedString(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    state: Mapped[Optional[str]] = mapped_column(String(64), index=True)
+    info: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
 
     def __init__(self, job):
         self.job_id = job.id
@@ -2425,10 +2449,14 @@ def __init__(self, job):
 class ImplicitlyCreatedDatasetCollectionInput(Base, RepresentById):
     __tablename__ = "implicitly_created_dataset_collection_inputs"
 
-    id = Column(Integer, primary_key=True)
-    dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
-    input_dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
-    name = Column(Unicode(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    )
+    input_dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    )
+    name: Mapped[Optional[str]] = mapped_column(Unicode(255))
 
     input_dataset_collection = relationship(
         "HistoryDatasetCollectionAssociation",
@@ -2446,8 +2474,8 @@ def __init__(self, name, input_dataset_collection):
 class ImplicitCollectionJobs(Base, Serializable):
     __tablename__ = "implicit_collection_jobs"
 
-    id = Column(Integer, primary_key=True)
-    populated_state = Column(TrimmedString(64), default="new", nullable=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    populated_state: Mapped[str] = mapped_column(TrimmedString(64), default="new", nullable=False)
     jobs = relationship(
         "ImplicitCollectionJobsJobAssociation", back_populates="implicit_collection_jobs", cascade_backrefs=False
     )
@@ -2477,10 +2505,14 @@ def _serialize(self, id_encoder, serialization_options):
 class ImplicitCollectionJobsJobAssociation(Base, RepresentById):
     __tablename__ = "implicit_collection_jobs_job_association"
 
-    id = Column(Integer, primary_key=True)
-    implicit_collection_jobs_id = Column(Integer, ForeignKey("implicit_collection_jobs.id"), index=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)  # Consider making this nullable...
-    order_index = Column(Integer, nullable=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    implicit_collection_jobs_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("implicit_collection_jobs.id"), index=True
+    )
+    job_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("job.id"), index=True
+    )  # Consider making this nullable...
+    order_index: Mapped[int] = mapped_column(Integer, nullable=False)
     implicit_collection_jobs = relationship("ImplicitCollectionJobs", back_populates="jobs")
     job = relationship("Job", back_populates="implicit_collection_jobs_association")
 
@@ -2488,10 +2520,12 @@ class ImplicitCollectionJobsJobAssociation(Base, RepresentById):
 class PostJobAction(Base, RepresentById):
     __tablename__ = "post_job_action"
 
-    id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True, nullable=True)
-    action_type = Column(String(255), nullable=False)
-    output_name = Column(String(255), nullable=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_step.id"), index=True, nullable=True
+    )
+    action_type: Mapped[str] = mapped_column(String(255), nullable=False)
+    output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
     action_arguments = Column(MutableJSONType, nullable=True)
     workflow_step = relationship(
         "WorkflowStep",
@@ -2510,9 +2544,11 @@ def __init__(self, action_type, workflow_step=None, output_name=None, action_arg
 class PostJobActionAssociation(Base, RepresentById):
     __tablename__ = "post_job_action_association"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True, nullable=False)
-    post_job_action_id = Column(Integer, ForeignKey("post_job_action.id"), index=True, nullable=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[int] = mapped_column(Integer, ForeignKey("job.id"), index=True, nullable=False)
+    post_job_action_id: Mapped[int] = mapped_column(
+        Integer, ForeignKey("post_job_action.id"), index=True, nullable=False
+    )
     post_job_action = relationship("PostJobAction")
     job = relationship("Job", back_populates="post_job_actions")
 
@@ -2530,21 +2566,21 @@ def __init__(self, pja, job=None, job_id=None):
 class JobExternalOutputMetadata(Base, RepresentById):
     __tablename__ = "job_external_output_metadata"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    history_dataset_association_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    history_dataset_association_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True
     )
-    library_dataset_dataset_association_id = Column(
+    library_dataset_dataset_association_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True
     )
-    is_valid = Column(Boolean, default=True)
-    filename_in = Column(String(255))
-    filename_out = Column(String(255))
-    filename_results_code = Column(String(255))
-    filename_kwds = Column(String(255))
-    filename_override_metadata = Column(String(255))
-    job_runner_external_pid = Column(String(255))
+    is_valid: Mapped[Optional[bool]] = mapped_column(Boolean, default=True)
+    filename_in: Mapped[Optional[str]] = mapped_column(String(255))
+    filename_out: Mapped[Optional[str]] = mapped_column(String(255))
+    filename_results_code: Mapped[Optional[str]] = mapped_column(String(255))
+    filename_kwds: Mapped[Optional[str]] = mapped_column(String(255))
+    filename_override_metadata: Mapped[Optional[str]] = mapped_column(String(255))
+    job_runner_external_pid: Mapped[Optional[str]] = mapped_column(String(255))
     history_dataset_association = relationship("HistoryDatasetAssociation", lazy="joined")
     library_dataset_dataset_association = relationship("LibraryDatasetDatasetAssociation", lazy="joined")
     job = relationship("Job", back_populates="external_output_metadata")
@@ -2587,12 +2623,12 @@ def __eq__(self, other):
 class JobExportHistoryArchive(Base, RepresentById):
     __tablename__ = "job_export_history_archive"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
-    compressed = Column(Boolean, index=True, default=False)
-    history_attrs_filename = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset.id"), index=True)
+    compressed: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    history_attrs_filename: Mapped[Optional[str]] = mapped_column(TEXT)
     job = relationship("Job")
     dataset = relationship("Dataset")
     history = relationship("History", back_populates="exports")
@@ -2675,10 +2711,10 @@ def to_dict(self):
 class JobImportHistoryArchive(Base, RepresentById):
     __tablename__ = "job_import_history_archive"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    archive_dir = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    archive_dir: Mapped[Optional[str]] = mapped_column(TEXT)
     job = relationship("Job")
     history = relationship("History")
 
@@ -2687,24 +2723,24 @@ class StoreExportAssociation(Base, RepresentById):
     __tablename__ = "store_export_association"
     __table_args__ = (Index("ix_store_export_object", "object_id", "object_type"),)
 
-    id = Column(Integer, primary_key=True)
-    task_uuid = Column(UUIDType(), index=True, unique=True)
-    create_time = Column(DateTime, default=now)
-    object_type = Column(TrimmedString(32))
-    object_id = Column(Integer)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    task_uuid: Mapped[Optional[str]] = mapped_column(UUIDType(), index=True, unique=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    object_type: Mapped[Optional[str]] = mapped_column(TrimmedString(32))
+    object_id: Mapped[Optional[int]] = mapped_column(Integer)
     export_metadata = Column(JSONType)
 
 
 class JobContainerAssociation(Base, RepresentById):
     __tablename__ = "job_container_association"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    container_type = Column(TEXT)
-    container_name = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    container_type: Mapped[Optional[str]] = mapped_column(TEXT)
+    container_name: Mapped[Optional[str]] = mapped_column(TEXT)
     container_info = Column(MutableJSONType, nullable=True)
-    created_time = Column(DateTime, default=now)
-    modified_time = Column(DateTime, default=now, onupdate=now)
+    created_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    modified_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
     job = relationship("Job", back_populates="container")
 
     def __init__(self, **kwd):
@@ -2717,24 +2753,24 @@ def __init__(self, **kwd):
 class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById):
     __tablename__ = "interactivetool_entry_point"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    name = Column(TEXT)
-    token = Column(TEXT)
-    tool_port = Column(Integer)
-    host = Column(TEXT)
-    port = Column(Integer)
-    protocol = Column(TEXT)
-    entry_url = Column(TEXT)
-    requires_domain = Column(Boolean, default=True)
-    requires_path_in_url = Column(Boolean, default=False)
-    requires_path_in_header_named = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    name: Mapped[Optional[str]] = mapped_column(TEXT)
+    token: Mapped[Optional[str]] = mapped_column(TEXT)
+    tool_port: Mapped[Optional[int]] = mapped_column(Integer)
+    host: Mapped[Optional[str]] = mapped_column(TEXT)
+    port: Mapped[Optional[int]] = mapped_column(Integer)
+    protocol: Mapped[Optional[str]] = mapped_column(TEXT)
+    entry_url: Mapped[Optional[str]] = mapped_column(TEXT)
+    requires_domain: Mapped[Optional[bool]] = mapped_column(Boolean, default=True)
+    requires_path_in_url: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    requires_path_in_header_named: Mapped[Optional[str]] = mapped_column(TEXT)
     info = Column(MutableJSONType, nullable=True)
-    configured = Column(Boolean, default=False)
-    deleted = Column(Boolean, default=False)
-    created_time = Column(DateTime, default=now)
-    modified_time = Column(DateTime, default=now, onupdate=now)
-    label = Column(TEXT)
+    configured: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    created_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    modified_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    label: Mapped[Optional[str]] = mapped_column(TEXT)
     job = relationship("Job", back_populates="interactivetool_entry_points", uselist=False)
 
     dict_collection_visible_keys = [
@@ -2793,14 +2829,14 @@ def output_datasets_ids(self):
 class GenomeIndexToolData(Base, RepresentById):  # TODO: params arg is lost
     __tablename__ = "genome_index_tool_data"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
-    fasta_path = Column(String(255))
-    created_time = Column(DateTime, default=now)
-    modified_time = Column(DateTime, default=now, onupdate=now)
-    indexer = Column(String(64))
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset.id"), index=True)
+    fasta_path: Mapped[Optional[str]] = mapped_column(String(255))
+    created_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    modified_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    indexer: Mapped[Optional[str]] = mapped_column(String(64))
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
     job = relationship("Job")
     dataset = relationship("Dataset")
     user = relationship("User")
@@ -2809,11 +2845,11 @@ class GenomeIndexToolData(Base, RepresentById):  # TODO: params arg is lost
 class Group(Base, Dictifiable, RepresentById):
     __tablename__ = "galaxy_group"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(String(255), index=True, unique=True)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255), index=True, unique=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     quotas = relationship("GroupQuotaAssociation", back_populates="group")
     roles = relationship("GroupRoleAssociation", back_populates="group", cascade_backrefs=False)
     users = relationship("UserGroupAssociation", back_populates="group")
@@ -2829,11 +2865,11 @@ def __init__(self, name=None):
 class UserGroupAssociation(Base, RepresentById):
     __tablename__ = "user_group_association"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    group_id = Column(Integer, ForeignKey("galaxy_group.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    group_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_group.id"), index=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
     user = relationship("User", back_populates="groups")
     group = relationship("Group", back_populates="users")
 
@@ -2846,20 +2882,20 @@ def __init__(self, user, group):
 class Notification(Base, Dictifiable, RepresentById):
     __tablename__ = "notification"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    publication_time = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    publication_time: Mapped[Optional[datetime]] = mapped_column(
         DateTime, default=now
     )  # The date of publication, can be a future date to allow scheduling
-    expiration_time = Column(
+    expiration_time: Mapped[Optional[datetime]] = mapped_column(
         DateTime, default=now() + timedelta(days=30 * 6)
     )  # The expiration date, expired notifications will be permanently removed from DB regularly
-    source = Column(String(32), index=True)  # Who (or what) generated the notification
-    category = Column(
+    source: Mapped[Optional[str]] = mapped_column(String(32), index=True)  # Who (or what) generated the notification
+    category: Mapped[Optional[str]] = mapped_column(
         String(64), index=True
     )  # Category of the notification, defines its contents. Used for filtering, un/subscribing, etc
-    variant = Column(
+    variant: Mapped[Optional[str]] = mapped_column(
         String(16), index=True
     )  # Defines the 'importance' of the notification ('info', 'warning', 'urgent', etc.). Used for filtering, highlight rendering, etc
     # A bug in early 23.1 led to values being stored as json string, so we use this special type to process the result value twice.
@@ -2878,12 +2914,12 @@ def __init__(self, source: str, category: str, variant: str, content):
 class UserNotificationAssociation(Base, RepresentById):
     __tablename__ = "user_notification_association"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    notification_id = Column(Integer, ForeignKey("notification.id"), index=True)
-    seen_time = Column(DateTime, nullable=True)
-    deleted = Column(Boolean, index=True, default=False)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    notification_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("notification.id"), index=True)
+    seen_time: Mapped[Optional[datetime]] = mapped_column(DateTime, nullable=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
 
     user = relationship("User", back_populates="all_notifications")
     notification = relationship("Notification", back_populates="user_notification_associations")
@@ -2902,8 +2938,8 @@ class HistoryAudit(Base, RepresentById):
     __tablename__ = "history_audit"
     __table_args__ = (PrimaryKeyConstraint(sqlite_on_conflict="IGNORE"),)
 
-    history_id = Column(Integer, ForeignKey("history.id"), primary_key=True, nullable=False)
-    update_time = Column(DateTime, default=now, primary_key=True, nullable=False)
+    history_id = mapped_column(Integer, ForeignKey("history.id"), primary_key=True, nullable=False)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, primary_key=True, nullable=False)
 
     # This class should never be instantiated.
     # See https://github.com/galaxyproject/galaxy/pull/11914 for details.
@@ -2937,22 +2973,26 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     __tablename__ = "history"
     __table_args__ = (Index("ix_history_slug", "slug", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    _update_time = Column("update_time", DateTime, index=True, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    name = Column(TrimmedString(255))
-    hid_counter = Column(Integer, default=1)
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
-    importing = Column(Boolean, index=True, default=False)
-    genome_build = Column(TrimmedString(40))
-    importable = Column(Boolean, default=False)
-    slug = Column(TEXT)
-    published = Column(Boolean, index=True, default=False)
-    preferred_object_store_id = Column(String(255), nullable=True)
-    archived = Column(Boolean, index=True, default=False, server_default=false())
-    archive_export_id = Column(Integer, ForeignKey("store_export_association.id"), nullable=True, default=None)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    _update_time: Mapped[datetime] = mapped_column(
+        "update_time", DateTime, index=True, default=now, onupdate=now, nullable=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    hid_counter: Mapped[Optional[int]] = mapped_column(Integer, default=1)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    importing: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    genome_build: Mapped[Optional[str]] = mapped_column(TrimmedString(40))
+    importable: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    slug: Mapped[Optional[str]] = mapped_column(TEXT)
+    published: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    preferred_object_store_id: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    archived: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False, server_default=false())
+    archive_export_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("store_export_association.id"), nullable=True, default=None
+    )
 
     datasets = relationship(
         "HistoryDatasetAssociation", back_populates="history", cascade_backrefs=False, order_by=lambda: asc(HistoryDatasetAssociation.hid)  # type: ignore[has-type]
@@ -3516,9 +3556,9 @@ class UserShareAssociation(RepresentById):
 class HistoryUserShareAssociation(Base, UserShareAssociation):
     __tablename__ = "history_user_share_association"
 
-    id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user = relationship("User")
     history = relationship("History", back_populates="users_shared_with")
 
@@ -3526,11 +3566,11 @@ class HistoryUserShareAssociation(Base, UserShareAssociation):
 class UserRoleAssociation(Base, RepresentById):
     __tablename__ = "user_role_association"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
 
     user = relationship("User", back_populates="roles")
     role = relationship("Role", back_populates="users")
@@ -3544,11 +3584,11 @@ def __init__(self, user, role):
 class GroupRoleAssociation(Base, RepresentById):
     __tablename__ = "group_role_association"
 
-    id = Column(Integer, primary_key=True)
-    group_id = Column(Integer, ForeignKey("galaxy_group.id"), index=True)
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    group_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_group.id"), index=True)
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
     group = relationship("Group", back_populates="roles")
     role = relationship("Role", back_populates="groups")
 
@@ -3561,13 +3601,13 @@ def __init__(self, group, role):
 class Role(Base, Dictifiable, RepresentById):
     __tablename__ = "role"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(String(255), index=True, unique=True)
-    description = Column(TEXT)
-    type = Column(String(40), index=True)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255), index=True, unique=True)
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    type: Mapped[Optional[str]] = mapped_column(String(40), index=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     dataset_actions = relationship("DatasetPermissions", back_populates="role")
     groups = relationship("GroupRoleAssociation", back_populates="role")
     users = relationship("UserRoleAssociation", back_populates="role")
@@ -3596,22 +3636,22 @@ class UserQuotaSourceUsage(Base, Dictifiable, RepresentById):
 
     dict_element_visible_keys = ["disk_usage", "quota_source_label"]
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    quota_source_label = Column(String(32), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    quota_source_label: Mapped[Optional[str]] = mapped_column(String(32), index=True)
     # user had an index on disk_usage - does that make any sense? -John
-    disk_usage = Column(Numeric(15, 0), default=0, nullable=False)
+    disk_usage: Mapped[Decimal] = mapped_column(Numeric(15, 0), default=0, nullable=False)
     user = relationship("User", back_populates="quota_source_usages")
 
 
 class UserQuotaAssociation(Base, Dictifiable, RepresentById):
     __tablename__ = "user_quota_association"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    quota_id = Column(Integer, ForeignKey("quota.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    quota_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("quota.id"), index=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
     user = relationship("User", back_populates="quotas")
     quota = relationship("Quota", back_populates="users")
 
@@ -3626,11 +3666,11 @@ def __init__(self, user, quota):
 class GroupQuotaAssociation(Base, Dictifiable, RepresentById):
     __tablename__ = "group_quota_association"
 
-    id = Column(Integer, primary_key=True)
-    group_id = Column(Integer, ForeignKey("galaxy_group.id"), index=True)
-    quota_id = Column(Integer, ForeignKey("quota.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    group_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_group.id"), index=True)
+    quota_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("quota.id"), index=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
     group = relationship("Group", back_populates="quotas")
     quota = relationship("Quota", back_populates="groups")
 
@@ -3646,15 +3686,15 @@ class Quota(Base, Dictifiable, RepresentById):
     __tablename__ = "quota"
     __table_args__ = (Index("ix_quota_quota_source_label", "quota_source_label"),)
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(String(255), index=True, unique=True)
-    description = Column(TEXT)
-    bytes = Column(BigInteger)
-    operation = Column(String(8))
-    deleted = Column(Boolean, index=True, default=False)
-    quota_source_label = Column(String(32), default=None)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255), index=True, unique=True)
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    bytes: Mapped[Optional[int]] = mapped_column(BigInteger)
+    operation: Mapped[Optional[str]] = mapped_column(String(8))
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    quota_source_label: Mapped[Optional[str]] = mapped_column(String(32), default=None)
     default = relationship("DefaultQuotaAssociation", back_populates="quota", cascade_backrefs=False)
     groups = relationship("GroupQuotaAssociation", back_populates="quota")
     users = relationship("UserQuotaAssociation", back_populates="quota")
@@ -3708,11 +3748,11 @@ def display_amount(self):
 class DefaultQuotaAssociation(Base, Dictifiable, RepresentById):
     __tablename__ = "default_quota_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    type = Column(String(32))
-    quota_id = Column(Integer, ForeignKey("quota.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    type: Mapped[Optional[str]] = mapped_column(String(32))
+    quota_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("quota.id"), index=True)
     quota = relationship("Quota", back_populates="default")
 
     dict_element_visible_keys = ["type"]
@@ -3731,12 +3771,12 @@ def __init__(self, type, quota):
 class DatasetPermissions(Base, RepresentById):
     __tablename__ = "dataset_permissions"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    action = Column(TEXT)
-    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    action: Mapped[Optional[str]] = mapped_column(TEXT)
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset.id"), index=True)
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
     dataset = relationship("Dataset", back_populates="actions")
     role = relationship("Role", back_populates="dataset_actions")
 
@@ -3753,12 +3793,12 @@ def __init__(self, action, dataset, role=None, role_id=None):
 class LibraryPermissions(Base, RepresentById):
     __tablename__ = "library_permissions"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    action = Column(TEXT)
-    library_id = Column(Integer, ForeignKey("library.id"), nullable=True, index=True)
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    action: Mapped[Optional[str]] = mapped_column(TEXT)
+    library_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library.id"), nullable=True, index=True)
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
     library = relationship("Library", back_populates="actions")
     role = relationship("Role")
 
@@ -3775,12 +3815,14 @@ def __init__(self, action, library_item, role):
 class LibraryFolderPermissions(Base, RepresentById):
     __tablename__ = "library_folder_permissions"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    action = Column(TEXT)
-    library_folder_id = Column(Integer, ForeignKey("library_folder.id"), nullable=True, index=True)
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    action: Mapped[Optional[str]] = mapped_column(TEXT)
+    library_folder_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_folder.id"), nullable=True, index=True
+    )
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
     folder = relationship("LibraryFolder", back_populates="actions")
     role = relationship("Role")
 
@@ -3797,12 +3839,14 @@ def __init__(self, action, library_item, role):
 class LibraryDatasetPermissions(Base, RepresentById):
     __tablename__ = "library_dataset_permissions"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    action = Column(TEXT)
-    library_dataset_id = Column(Integer, ForeignKey("library_dataset.id"), nullable=True, index=True)
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    action: Mapped[Optional[str]] = mapped_column(TEXT)
+    library_dataset_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset.id"), nullable=True, index=True
+    )
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
     library_dataset = relationship("LibraryDataset", back_populates="actions")
     role = relationship("Role")
 
@@ -3819,14 +3863,14 @@ def __init__(self, action, library_item, role):
 class LibraryDatasetDatasetAssociationPermissions(Base, RepresentById):
     __tablename__ = "library_dataset_dataset_association_permissions"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    action = Column(TEXT)
-    library_dataset_dataset_association_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    action: Mapped[Optional[str]] = mapped_column(TEXT)
+    library_dataset_dataset_association_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True, index=True
     )
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
     library_dataset_dataset_association = relationship("LibraryDatasetDatasetAssociation", back_populates="actions")
     role = relationship("Role")
 
@@ -3843,10 +3887,10 @@ def __init__(self, action, library_item, role):
 class DefaultUserPermissions(Base, RepresentById):
     __tablename__ = "default_user_permissions"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    action = Column(TEXT)
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    action: Mapped[Optional[str]] = mapped_column(TEXT)
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
     user = relationship("User", back_populates="default_permissions")
     role = relationship("Role")
 
@@ -3860,10 +3904,10 @@ def __init__(self, user, action, role):
 class DefaultHistoryPermissions(Base, RepresentById):
     __tablename__ = "default_history_permissions"
 
-    id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    action = Column(TEXT)
-    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    action: Mapped[Optional[str]] = mapped_column(TEXT)
+    role_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("role.id"), index=True)
     history = relationship("History", back_populates="default_permissions")
     role = relationship("Role")
 
@@ -3884,21 +3928,21 @@ def flush(self):
 class Dataset(Base, StorableObject, Serializable):
     __tablename__ = "dataset"
 
-    id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True, nullable=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, index=True, default=now, onupdate=now)
-    state = Column(TrimmedString(64), index=True)
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
-    purgable = Column(Boolean, default=True)
-    object_store_id = Column(TrimmedString(255), index=True)
-    external_filename = Column(TEXT)
-    _extra_files_path = Column(TEXT)
-    created_from_basename = Column(TEXT)
-    file_size = Column(Numeric(15, 0))
-    total_size = Column(Numeric(15, 0))
-    uuid = Column(UUIDType())
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True, nullable=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, index=True, default=now, onupdate=now, nullable=True)
+    state: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purgable: Mapped[Optional[bool]] = mapped_column(Boolean, default=True)
+    object_store_id: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    external_filename: Mapped[Optional[str]] = mapped_column(TEXT)
+    _extra_files_path: Mapped[Optional[str]] = mapped_column(TEXT)
+    created_from_basename: Mapped[Optional[str]] = mapped_column(TEXT)
+    file_size: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0))
+    total_size: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0))
+    uuid: Mapped[Optional[str]] = mapped_column(UUIDType())
 
     actions = relationship("DatasetPermissions", back_populates="dataset")
     job = relationship(Job, primaryjoin=(lambda: Dataset.job_id == Job.id))
@@ -4264,10 +4308,10 @@ def to_int(n) -> Optional[int]:
 class DatasetSource(Base, Dictifiable, Serializable):
     __tablename__ = "dataset_source"
 
-    id = Column(Integer, primary_key=True)
-    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
-    source_uri = Column(TEXT)
-    extra_files_path = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset.id"), index=True)
+    source_uri: Mapped[Optional[str]] = mapped_column(TEXT)
+    extra_files_path: Mapped[Optional[str]] = mapped_column(TEXT)
     transform = Column(MutableJSONType)
     dataset = relationship("Dataset", back_populates="sources")
     hashes = relationship("DatasetSourceHash", back_populates="source")
@@ -4302,10 +4346,10 @@ def copy(self) -> "DatasetSource":
 class DatasetSourceHash(Base, Serializable):
     __tablename__ = "dataset_source_hash"
 
-    id = Column(Integer, primary_key=True)
-    dataset_source_id = Column(Integer, ForeignKey("dataset_source.id"), index=True)
-    hash_function = Column(TEXT)
-    hash_value = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    dataset_source_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset_source.id"), index=True)
+    hash_function: Mapped[Optional[str]] = mapped_column(TEXT)
+    hash_value: Mapped[Optional[str]] = mapped_column(TEXT)
     source = relationship("DatasetSource", back_populates="hashes")
 
     def _serialize(self, id_encoder, serialization_options):
@@ -4327,11 +4371,11 @@ def copy(self) -> "DatasetSourceHash":
 class DatasetHash(Base, Dictifiable, Serializable):
     __tablename__ = "dataset_hash"
 
-    id = Column(Integer, primary_key=True)
-    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
-    hash_function = Column(TEXT)
-    hash_value = Column(TEXT)
-    extra_files_path = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset.id"), index=True)
+    hash_function: Mapped[Optional[str]] = mapped_column(TEXT)
+    hash_value: Mapped[Optional[str]] = mapped_column(TEXT)
+    extra_files_path: Mapped[Optional[str]] = mapped_column(TEXT)
     dataset = relationship("Dataset", back_populates="hashes")
     dict_collection_visible_keys = ["id", "hash_function", "hash_value", "extra_files_path"]
     dict_element_visible_keys = ["id", "hash_function", "hash_value", "extra_files_path"]
@@ -5357,14 +5401,16 @@ def type_id(cls):
 class HistoryDatasetAssociationHistory(Base, Serializable):
     __tablename__ = "history_dataset_association_history"
 
-    id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    update_time = Column(DateTime, default=now)
-    version = Column(Integer)
-    name = Column(TrimmedString(255))
-    extension = Column(TrimmedString(64))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_dataset_association_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True
+    )
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    version: Mapped[Optional[int]] = mapped_column(Integer)
+    name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    extension: Mapped[Optional[str]] = mapped_column(TrimmedString(64))
     _metadata = Column("metadata", MetadataType)
-    extended_metadata_id = Column(Integer, ForeignKey("extended_metadata.id"), index=True)
+    extended_metadata_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("extended_metadata.id"), index=True)
 
     def __init__(
         self,
@@ -5391,12 +5437,14 @@ def __init__(
 class HistoryDatasetAssociationDisplayAtAuthorization(Base, RepresentById):
     __tablename__ = "history_dataset_association_display_at_authorization"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, index=True, default=now, onupdate=now)
-    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    site = Column(TrimmedString(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, index=True, default=now, onupdate=now, nullable=True)
+    history_dataset_association_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    site: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
     history_dataset_association = relationship("HistoryDatasetAssociation")
     user = relationship("User")
 
@@ -5409,10 +5457,14 @@ def __init__(self, hda=None, user=None, site=None):
 class HistoryDatasetAssociationSubset(Base, RepresentById):
     __tablename__ = "history_dataset_association_subset"
 
-    id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    history_dataset_association_subset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    location = Column(Unicode(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_dataset_association_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True
+    )
+    history_dataset_association_subset_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True
+    )
+    location: Mapped[Optional[str]] = mapped_column(Unicode(255), index=True)
 
     hda = relationship(
         "HistoryDatasetAssociation",
@@ -5437,15 +5489,15 @@ def __init__(self, hda, subset, location):
 class Library(Base, Dictifiable, HasName, Serializable):
     __tablename__ = "library"
 
-    id = Column(Integer, primary_key=True)
-    root_folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(String(255), index=True)
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
-    description = Column(TEXT)
-    synopsis = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    root_folder_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library_folder.id"), index=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255), index=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    synopsis: Mapped[Optional[str]] = mapped_column(TEXT)
     root_folder = relationship("LibraryFolder", back_populates="library_root")
     actions = relationship("LibraryPermissions", back_populates="library", cascade_backrefs=False)
 
@@ -5515,17 +5567,19 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
     __tablename__ = "library_folder"
     __table_args__ = (Index("ix_library_folder_name", "name", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    parent_id = Column(Integer, ForeignKey("library_folder.id"), nullable=True, index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(TEXT)
-    description = Column(TEXT)
-    order_id = Column(Integer)  # not currently being used, but for possible future use
-    item_count = Column(Integer)
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
-    genome_build = Column(TrimmedString(40))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    parent_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_folder.id"), nullable=True, index=True
+    )
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    name: Mapped[Optional[str]] = mapped_column(TEXT)
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    order_id: Mapped[Optional[int]] = mapped_column(Integer)  # not currently being used, but for possible future use
+    item_count: Mapped[Optional[int]] = mapped_column(Integer)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    genome_build: Mapped[Optional[str]] = mapped_column(TrimmedString(40))
 
     folders = relationship(
         "LibraryFolder",
@@ -5656,9 +5710,9 @@ def parent_library(self):
 class LibraryDataset(Base, Serializable):
     __tablename__ = "library_dataset"
 
-    id = Column(Integer, primary_key=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
     # current version of dataset, if null, there is not a current version selected
-    library_dataset_dataset_association_id = Column(
+    library_dataset_dataset_association_id: Mapped[Optional[int]] = mapped_column(
         Integer,
         ForeignKey(
             "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk"
@@ -5666,17 +5720,17 @@ class LibraryDataset(Base, Serializable):
         nullable=True,
         index=True,
     )
-    folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
+    folder_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library_folder.id"), index=True)
     # not currently being used, but for possible future use
-    order_id = Column(Integer)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    order_id: Mapped[Optional[int]] = mapped_column(Integer)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
     # when not None/null this will supercede display in library (but not when imported into user's history?)
-    _name = Column("name", TrimmedString(255), index=True)
+    _name: Mapped[Optional[str]] = mapped_column("name", TrimmedString(255), index=True)
     # when not None/null this will supercede display in library (but not when imported into user's history?)
-    _info = Column("info", TrimmedString(255))
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
+    _info: Mapped[Optional[str]] = mapped_column("info", TrimmedString(255))
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     folder = relationship("LibraryFolder")
     library_dataset_dataset_association = relationship(
         "LibraryDatasetDatasetAssociation", foreign_keys=library_dataset_dataset_association_id, post_update=True
@@ -5962,7 +6016,7 @@ def update_parent_folder_update_times(self):
 class ExtendedMetadata(Base, RepresentById):
     __tablename__ = "extended_metadata"
 
-    id = Column(Integer, primary_key=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
     data = Column(MutableJSONType)
     children = relationship("ExtendedMetadataIndex", back_populates="extended_metadata")
 
@@ -5973,12 +6027,12 @@ def __init__(self, data):
 class ExtendedMetadataIndex(Base, RepresentById):
     __tablename__ = "extended_metadata_index"
 
-    id = Column(Integer, primary_key=True)
-    extended_metadata_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    extended_metadata_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("extended_metadata.id", onupdate="CASCADE", ondelete="CASCADE"), index=True
     )
-    path = Column(String(255))
-    value = Column(TEXT)
+    path: Mapped[Optional[str]] = mapped_column(String(255))
+    value: Mapped[Optional[str]] = mapped_column(TEXT)
     extended_metadata = relationship("ExtendedMetadata", back_populates="children")
 
     def __init__(self, extended_metadata, path, value):
@@ -5990,12 +6044,12 @@ def __init__(self, extended_metadata, path, value):
 class LibraryInfoAssociation(Base, RepresentById):
     __tablename__ = "library_info_association"
 
-    id = Column(Integer, primary_key=True)
-    library_id = Column(Integer, ForeignKey("library.id"), index=True)
-    form_definition_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
-    form_values_id = Column(Integer, ForeignKey("form_values.id"), index=True)
-    inheritable = Column(Boolean, index=True, default=False)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    library_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library.id"), index=True)
+    form_definition_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_definition.id"), index=True)
+    form_values_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_values.id"), index=True)
+    inheritable: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
 
     library = relationship(
         "Library",
@@ -6020,12 +6074,14 @@ def __init__(self, library, form_definition, info, inheritable=False):
 class LibraryFolderInfoAssociation(Base, RepresentById):
     __tablename__ = "library_folder_info_association"
 
-    id = Column(Integer, primary_key=True)
-    library_folder_id = Column(Integer, ForeignKey("library_folder.id"), nullable=True, index=True)
-    form_definition_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
-    form_values_id = Column(Integer, ForeignKey("form_values.id"), index=True)
-    inheritable = Column(Boolean, index=True, default=False)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    library_folder_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_folder.id"), nullable=True, index=True
+    )
+    form_definition_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_definition.id"), index=True)
+    form_values_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_values.id"), index=True)
+    inheritable: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
 
     folder = relationship(
         "LibraryFolder",
@@ -6051,13 +6107,13 @@ def __init__(self, folder, form_definition, info, inheritable=False):
 class LibraryDatasetDatasetInfoAssociation(Base, RepresentById):
     __tablename__ = "library_dataset_dataset_info_association"
 
-    id = Column(Integer, primary_key=True)
-    library_dataset_dataset_association_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    library_dataset_dataset_association_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True, index=True
     )
-    form_definition_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
-    form_values_id = Column(Integer, ForeignKey("form_values.id"), index=True)
-    deleted = Column(Boolean, index=True, default=False)
+    form_definition_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_definition.id"), index=True)
+    form_values_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_values.id"), index=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
 
     library_dataset_dataset_association = relationship(
         "LibraryDatasetDatasetAssociation",
@@ -6091,16 +6147,24 @@ def inheritable(self):
 class ImplicitlyConvertedDatasetAssociation(Base, Serializable):
     __tablename__ = "implicitly_converted_dataset_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True)
-    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True)
-    hda_parent_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    ldda_parent_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True)
-    deleted = Column(Boolean, index=True, default=False)
-    metadata_safe = Column(Boolean, index=True, default=True)
-    type = Column(TrimmedString(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    hda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True
+    )
+    ldda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True
+    )
+    hda_parent_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True
+    )
+    ldda_parent_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True
+    )
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    metadata_safe: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=True)
+    type: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
 
     parent_hda = relationship(
         "HistoryDatasetAssociation",
@@ -6201,13 +6265,13 @@ def produce_filter(self, table):
 class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
     __tablename__ = "dataset_collection"
 
-    id = Column(Integer, primary_key=True)
-    collection_type = Column(Unicode(255), nullable=False)
-    populated_state = Column(TrimmedString(64), default="ok", nullable=False)
-    populated_state_message = Column(TEXT)
-    element_count = Column(Integer, nullable=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    collection_type: Mapped[str] = mapped_column(Unicode(255), nullable=False)
+    populated_state: Mapped[str] = mapped_column(TrimmedString(64), default="ok", nullable=False)
+    populated_state_message: Mapped[Optional[str]] = mapped_column(TEXT)
+    element_count: Mapped[Optional[int]] = mapped_column(Integer, nullable=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
 
     elements = relationship(
         "DatasetCollectionElement",
@@ -6659,21 +6723,23 @@ class HistoryDatasetCollectionAssociation(
 
     __tablename__ = "history_dataset_collection_association"
 
-    id = Column(Integer, primary_key=True)
-    collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    name = Column(TrimmedString(255))
-    hid = Column(Integer)
-    visible = Column(Boolean)
-    deleted = Column(Boolean, default=False)
-    copied_from_history_dataset_collection_association_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    collection_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset_collection.id"), index=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    hid: Mapped[Optional[int]] = mapped_column(Integer)
+    visible: Mapped[Optional[bool]] = mapped_column(Boolean)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    copied_from_history_dataset_collection_association_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("history_dataset_collection_association.id"), nullable=True
     )
-    implicit_output_name = Column(Unicode(255), nullable=True)
-    job_id = Column(ForeignKey("job.id"), index=True, nullable=True)
-    implicit_collection_jobs_id = Column(ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now, index=True)
+    implicit_output_name: Mapped[Optional[str]] = mapped_column(Unicode(255), nullable=True)
+    job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True, nullable=True)
+    implicit_collection_jobs_id: Mapped[Optional[int]] = mapped_column(
+        ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True
+    )
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, index=True, nullable=True)
 
     collection = relationship("DatasetCollection")
     history = relationship("History", back_populates="dataset_collections")
@@ -7039,11 +7105,11 @@ class LibraryDatasetCollectionAssociation(Base, DatasetCollectionInstance, Repre
 
     __tablename__ = "library_dataset_collection_association"
 
-    id = Column(Integer, primary_key=True)
-    collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True)
-    folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
-    name = Column(TrimmedString(255))
-    deleted = Column(Boolean, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    collection_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset_collection.id"), index=True)
+    folder_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library_folder.id"), index=True)
+    name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
 
     collection = relationship("DatasetCollection")
     folder = relationship("LibraryFolder")
@@ -7083,16 +7149,24 @@ class DatasetCollectionElement(Base, Dictifiable, Serializable):
 
     __tablename__ = "dataset_collection_element"
 
-    id = Column(Integer, primary_key=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
     # Parent collection id describing what collection this element belongs to.
-    dataset_collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True, nullable=False)
+    dataset_collection_id: Mapped[int] = mapped_column(
+        Integer, ForeignKey("dataset_collection.id"), index=True, nullable=False
+    )
     # Child defined by this association - HDA, LDDA, or another dataset association...
-    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True)
-    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True)
-    child_collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True, nullable=True)
+    hda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True
+    )
+    ldda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True
+    )
+    child_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("dataset_collection.id"), index=True, nullable=True
+    )
     # Element index and identifier to define this parent-child relationship.
-    element_index = Column(Integer)
-    element_identifier = Column(Unicode(255))
+    element_index: Mapped[Optional[int]] = mapped_column(Integer)
+    element_identifier: Mapped[Optional[str]] = mapped_column(Unicode(255))
 
     hda = relationship(
         "HistoryDatasetAssociation",
@@ -7271,14 +7345,16 @@ def _serialize(self, id_encoder, serialization_options):
 class Event(Base, RepresentById):
     __tablename__ = "event"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True, nullable=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
-    message = Column(TrimmedString(1024))
-    session_id = Column(Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True)
-    tool_id = Column(String(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True, nullable=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
+    message: Mapped[Optional[str]] = mapped_column(TrimmedString(1024))
+    session_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True
+    )
+    tool_id: Mapped[Optional[str]] = mapped_column(String(255))
 
     history = relationship("History")
     user = relationship("User")
@@ -7288,21 +7364,21 @@ class Event(Base, RepresentById):
 class GalaxySession(Base, RepresentById):
     __tablename__ = "galaxy_session"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
-    remote_host = Column(String(255))
-    remote_addr = Column(String(255))
-    referer = Column(TEXT)
-    current_history_id = Column(Integer, ForeignKey("history.id"), nullable=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
+    remote_host: Mapped[Optional[str]] = mapped_column(String(255))
+    remote_addr: Mapped[Optional[str]] = mapped_column(String(255))
+    referer: Mapped[Optional[str]] = mapped_column(TEXT)
+    current_history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), nullable=True)
     # unique 128 bit random number coerced to a string
-    session_key = Column(TrimmedString(255), index=True, unique=True)
-    is_valid = Column(Boolean, default=False)
+    session_key: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True, unique=True)
+    is_valid: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     # saves a reference to the previous session so we have a way to chain them together
-    prev_session_id = Column(Integer)
-    disk_usage = Column(Numeric(15, 0), index=True)
-    last_action = Column(DateTime)
+    prev_session_id: Mapped[Optional[int]] = mapped_column(Integer)
+    disk_usage: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0), index=True)
+    last_action: Mapped[Optional[datetime]] = mapped_column(DateTime)
     current_history = relationship("History")
     histories = relationship(
         "GalaxySessionToHistoryAssociation", back_populates="galaxy_session", cascade_backrefs=False
@@ -7334,10 +7410,10 @@ def set_disk_usage(self, bytes):
 class GalaxySessionToHistoryAssociation(Base, RepresentById):
     __tablename__ = "galaxy_session_to_history"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    session_id = Column(Integer, ForeignKey("galaxy_session.id"), index=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    session_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_session.id"), index=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
     galaxy_session = relationship("GalaxySession", back_populates="histories")
     history = relationship("History", back_populates="galaxy_sessions")
 
@@ -7366,20 +7442,20 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
     __tablename__ = "stored_workflow"
     __table_args__ = (Index("ix_stored_workflow_slug", "slug", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now, index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
-    latest_workflow_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, index=True, nullable=True)
+    user_id: Mapped[int] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
+    latest_workflow_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("workflow.id", use_alter=True, name="stored_workflow_latest_workflow_id_fk"), index=True
     )
-    name = Column(TEXT)
-    deleted = Column(Boolean, default=False)
-    hidden = Column(Boolean, default=False)
-    importable = Column(Boolean, default=False)
-    slug = Column(TEXT)
-    from_path = Column(TEXT)
-    published = Column(Boolean, index=True, default=False)
+    name: Mapped[Optional[str]] = mapped_column(TEXT)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    hidden: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    importable: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    slug: Mapped[Optional[str]] = mapped_column(TEXT)
+    from_path: Mapped[Optional[str]] = mapped_column(TEXT)
+    published: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
 
     user = relationship(
         "User", primaryjoin=(lambda: User.id == StoredWorkflow.user_id), back_populates="stored_workflows"
@@ -7539,20 +7615,24 @@ class Workflow(Base, Dictifiable, RepresentById):
 
     __tablename__ = "workflow"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
     # workflows will belong to either a stored workflow or a parent/nesting workflow.
-    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True, nullable=True)
-    parent_workflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=True)
-    name = Column(TEXT)
-    has_cycles = Column(Boolean)
-    has_errors = Column(Boolean)
+    stored_workflow_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("stored_workflow.id"), index=True, nullable=True
+    )
+    parent_workflow_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow.id"), index=True, nullable=True
+    )
+    name: Mapped[Optional[str]] = mapped_column(TEXT)
+    has_cycles: Mapped[Optional[bool]] = mapped_column(Boolean)
+    has_errors: Mapped[Optional[bool]] = mapped_column(Boolean)
     reports_config = Column(JSONType)
     creator_metadata = Column(JSONType)
-    license = Column(TEXT)
+    license: Mapped[Optional[str]] = mapped_column(TEXT)
     source_metadata = Column(JSONType)
-    uuid = Column(UUIDType, nullable=True)
+    uuid: Mapped[Optional[str]] = mapped_column(UUIDType, nullable=True)
 
     steps = relationship(
         "WorkflowStep",
@@ -7722,25 +7802,27 @@ class WorkflowStep(Base, RepresentById):
 
     __tablename__ = "workflow_step"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    workflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
-    subworkflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=True)
-    dynamic_tool_id = Column(Integer, ForeignKey("dynamic_tool.id"), index=True, nullable=True)
-    type: str = Column(String(64))
-    tool_id = Column(TEXT)
-    tool_version = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    workflow_id: Mapped[int] = mapped_column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
+    subworkflow_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow.id"), index=True, nullable=True)
+    dynamic_tool_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("dynamic_tool.id"), index=True, nullable=True
+    )
+    type: Mapped[Optional[str]] = mapped_column(String(64))
+    tool_id: Mapped[Optional[str]] = mapped_column(TEXT)
+    tool_version: Mapped[Optional[str]] = mapped_column(TEXT)
     tool_inputs = Column(JSONType)
     tool_errors = Column(JSONType)
     position = Column(MutableJSONType)
     config = Column(JSONType)
-    order_index: int = Column(Integer)
+    order_index: Mapped[Optional[int]] = mapped_column(Integer)
     when_expression = Column(JSONType)
-    uuid = Column(UUIDType)
-    label = Column(Unicode(255))
+    uuid: Mapped[Optional[str]] = mapped_column(UUIDType)
+    label: Mapped[Optional[str]] = mapped_column(Unicode(255))
     temp_input_connections = None
-    parent_comment_id = Column(Integer, ForeignKey("workflow_comment.id"), nullable=True)
+    parent_comment_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_comment.id"), nullable=True)
 
     parent_comment = relationship(
         "WorkflowComment",
@@ -8037,16 +8119,16 @@ class WorkflowStepInput(Base, RepresentById):
         ),
     )
 
-    id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
-    name = Column(TEXT)
-    merge_type = Column(TEXT)
-    scatter_type = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"), index=True)
+    name: Mapped[Optional[str]] = mapped_column(TEXT)
+    merge_type: Mapped[Optional[str]] = mapped_column(TEXT)
+    scatter_type: Mapped[Optional[str]] = mapped_column(TEXT)
     value_from = Column(MutableJSONType)
-    value_from_type = Column(TEXT)
+    value_from_type: Mapped[Optional[str]] = mapped_column(TEXT)
     default_value = Column(MutableJSONType)
-    default_value_set = Column(Boolean, default=False)
-    runtime_value = Column(Boolean, default=False)
+    default_value_set: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    runtime_value: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
 
     workflow_step = relationship(
         "WorkflowStep",
@@ -8081,11 +8163,15 @@ def copy(self, copied_step):
 class WorkflowStepConnection(Base, RepresentById):
     __tablename__ = "workflow_step_connection"
 
-    id = Column(Integer, primary_key=True)
-    output_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
-    input_step_input_id = Column(Integer, ForeignKey("workflow_step_input.id"), index=True)
-    output_name = Column(TEXT)
-    input_subworkflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    output_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"), index=True)
+    input_step_input_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_step_input.id"), index=True
+    )
+    output_name: Mapped[Optional[str]] = mapped_column(TEXT)
+    input_subworkflow_step_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_step.id"), index=True
+    )
 
     input_step_input = relationship(
         "WorkflowStepInput",
@@ -8137,11 +8223,11 @@ def copy(self):
 class WorkflowOutput(Base, Serializable):
     __tablename__ = "workflow_output"
 
-    id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True, nullable=False)
-    output_name = Column(String(255), nullable=True)
-    label = Column(Unicode(255))
-    uuid = Column(UUIDType)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_step_id: Mapped[int] = mapped_column(Integer, ForeignKey("workflow_step.id"), index=True, nullable=False)
+    output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    label: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    uuid: Mapped[Optional[str]] = mapped_column(UUIDType)
     workflow_step = relationship(
         "WorkflowStep",
         back_populates="workflow_outputs",
@@ -8178,15 +8264,15 @@ class WorkflowComment(Base, RepresentById):
 
     __tablename__ = "workflow_comment"
 
-    id = Column(Integer, primary_key=True)
-    order_index: int = Column(Integer)
-    workflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    order_index: Mapped[Optional[int]] = mapped_column(Integer)
+    workflow_id: Mapped[int] = mapped_column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
     position = Column(MutableJSONType)
     size = Column(JSONType)
-    type = Column(String(16))
-    color = Column(String(16))
+    type: Mapped[Optional[str]] = mapped_column(String(16))
+    color: Mapped[Optional[str]] = mapped_column(String(16))
     data = Column(JSONType)
-    parent_comment_id = Column(Integer, ForeignKey("workflow_comment.id"), nullable=True)
+    parent_comment_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_comment.id"), nullable=True)
 
     workflow = relationship(
         "Workflow",
@@ -8249,9 +8335,9 @@ def from_dict(dict):
 class StoredWorkflowUserShareAssociation(Base, UserShareAssociation):
     __tablename__ = "stored_workflow_user_share_connection"
 
-    id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    stored_workflow_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user = relationship("User")
     stored_workflow = relationship("StoredWorkflow", back_populates="users_shared_with")
 
@@ -8259,10 +8345,10 @@ class StoredWorkflowUserShareAssociation(Base, UserShareAssociation):
 class StoredWorkflowMenuEntry(Base, RepresentById):
     __tablename__ = "stored_workflow_menu_entry"
 
-    id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    order_index = Column(Integer)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    stored_workflow_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    order_index: Mapped[Optional[int]] = mapped_column(Integer)
 
     stored_workflow = relationship("StoredWorkflow")
     user = relationship(
@@ -8279,15 +8365,15 @@ class StoredWorkflowMenuEntry(Base, RepresentById):
 class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     __tablename__ = "workflow_invocation"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now, index=True)
-    workflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
-    state = Column(TrimmedString(64), index=True)
-    scheduler = Column(TrimmedString(255), index=True)
-    handler = Column(TrimmedString(255), index=True)
-    uuid = Column(UUIDType())
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, index=True, nullable=True)
+    workflow_id: Mapped[int] = mapped_column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
+    state: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True)
+    scheduler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    handler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    uuid: Mapped[Optional[str]] = mapped_column(UUIDType())
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
 
     history = relationship("History", back_populates="workflow_invocations")
     input_parameters = relationship(
@@ -8825,10 +8911,16 @@ def log_str(self):
 class WorkflowInvocationToSubworkflowInvocationAssociation(Base, Dictifiable, RepresentById):
     __tablename__ = "workflow_invocation_to_subworkflow_invocation_association"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id", name="fk_wfi_swi_wfi"), index=True)
-    subworkflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id", name="fk_wfi_swi_swi"), index=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id", name="fk_wfi_swi_ws"))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id", name="fk_wfi_swi_wfi"), index=True
+    )
+    subworkflow_invocation_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id", name="fk_wfi_swi_swi"), index=True
+    )
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_step.id", name="fk_wfi_swi_ws")
+    )
 
     subworkflow_invocation = relationship(
         "WorkflowInvocation",
@@ -8853,16 +8945,22 @@ class WorkflowInvocationToSubworkflowInvocationAssociation(Base, Dictifiable, Re
 
 class WorkflowInvocationMessage(Base, Dictifiable, Serializable):
     __tablename__ = "workflow_invocation_message"
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False)
-    reason = Column(String(32))
-    details = Column(TrimmedString(255), nullable=True)
-    output_name = Column(String(255), nullable=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), nullable=True)
-    dependent_workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), nullable=True)
-    job_id = Column(Integer, ForeignKey("job.id"), nullable=True)
-    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), nullable=True)
-    hdca_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), nullable=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_id: Mapped[int] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False
+    )
+    reason: Mapped[Optional[str]] = mapped_column(String(32))
+    details: Mapped[Optional[str]] = mapped_column(TrimmedString(255), nullable=True)
+    output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"), nullable=True)
+    dependent_workflow_step_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_step.id"), nullable=True
+    )
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), nullable=True)
+    hda_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history_dataset_association.id"), nullable=True)
+    hdca_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), nullable=True
+    )
 
     workflow_invocation = relationship("WorkflowInvocation", back_populates="messages", lazy=True)
     workflow_step = relationship("WorkflowStep", foreign_keys=workflow_step_id, lazy=True)
@@ -8926,14 +9024,18 @@ def is_split_configuration(self):
 class WorkflowInvocationStep(Base, Dictifiable, Serializable):
     __tablename__ = "workflow_invocation_step"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True, nullable=False)
-    state = Column(TrimmedString(64), index=True)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True, nullable=True)
-    implicit_collection_jobs_id = Column(Integer, ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    workflow_invocation_id: Mapped[int] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False
+    )
+    workflow_step_id: Mapped[int] = mapped_column(Integer, ForeignKey("workflow_step.id"), index=True, nullable=False)
+    state: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True, nullable=True)
+    implicit_collection_jobs_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True
+    )
     action = Column(MutableJSONType, nullable=True)
 
     workflow_step = relationship("WorkflowStep")
@@ -9134,13 +9236,13 @@ class WorkflowRequestInputParameter(Base, Dictifiable, Serializable):
 
     __tablename__ = "workflow_request_input_parameters"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE"), index=True
     )
-    name = Column(Unicode(255))
-    value = Column(TEXT)
-    type = Column(Unicode(255))
+    name: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    value: Mapped[Optional[str]] = mapped_column(TEXT)
+    type: Mapped[Optional[str]] = mapped_column(Unicode(255))
     workflow_invocation = relationship("WorkflowInvocation", back_populates="input_parameters")
 
     dict_collection_visible_keys = ["id", "name", "value", "type"]
@@ -9164,11 +9266,11 @@ class WorkflowRequestStepState(Base, Dictifiable, Serializable):
 
     __tablename__ = "workflow_request_step_states"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE"), index=True
     )
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"))
     value = Column(MutableJSONType)
     workflow_step = relationship("WorkflowStep")
     workflow_invocation = relationship("WorkflowInvocation", back_populates="step_states")
@@ -9187,11 +9289,13 @@ class WorkflowRequestToInputDatasetAssociation(Base, Dictifiable, Serializable):
 
     __tablename__ = "workflow_request_to_input_dataset"
 
-    id = Column(Integer, primary_key=True)
-    name = Column(String(255))
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
-    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255))
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id"), index=True
+    )
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"))
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history_dataset_association.id"), index=True)
 
     workflow_step = relationship("WorkflowStep")
     dataset = relationship("HistoryDatasetAssociation")
@@ -9215,11 +9319,15 @@ class WorkflowRequestToInputDatasetCollectionAssociation(Base, Dictifiable, Seri
 
     __tablename__ = "workflow_request_to_input_collection_dataset"
 
-    id = Column(Integer, primary_key=True)
-    name = Column(String(255))
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
-    dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255))
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id"), index=True
+    )
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"))
+    dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    )
     workflow_step = relationship("WorkflowStep")
     dataset_collection = relationship("HistoryDatasetCollectionAssociation")
     workflow_invocation = relationship("WorkflowInvocation", back_populates="input_dataset_collections")
@@ -9242,9 +9350,11 @@ class WorkflowRequestInputStepParameter(Base, Dictifiable, Serializable):
 
     __tablename__ = "workflow_request_input_step_parameter"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id"), index=True
+    )
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"))
     parameter_value = Column(MutableJSONType)
 
     workflow_step = relationship("WorkflowStep")
@@ -9264,11 +9374,13 @@ class WorkflowInvocationOutputDatasetAssociation(Base, Dictifiable, Serializable
 
     __tablename__ = "workflow_invocation_output_dataset_association"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
-    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    workflow_output_id = Column(Integer, ForeignKey("workflow_output.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id"), index=True
+    )
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"), index=True)
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    workflow_output_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_output.id"), index=True)
 
     workflow_invocation = relationship("WorkflowInvocation", back_populates="output_datasets")
     workflow_step = relationship("WorkflowStep")
@@ -9291,13 +9403,17 @@ class WorkflowInvocationOutputDatasetCollectionAssociation(Base, Dictifiable, Se
 
     __tablename__ = "workflow_invocation_output_dataset_collection_association"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id", name="fk_wiodca_wii"), index=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id", name="fk_wiodca_wsi"), index=True)
-    dataset_collection_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id", name="fk_wiodca_wii"), index=True
+    )
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_step.id", name="fk_wiodca_wsi"), index=True
+    )
+    dataset_collection_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("history_dataset_collection_association.id", name="fk_wiodca_dci"), index=True
     )
-    workflow_output_id = Column(Integer, ForeignKey("workflow_output.id", name="fk_wiodca_woi"), index=True)
+    workflow_output_id = mapped_column(Integer, ForeignKey("workflow_output.id", name="fk_wiodca_woi"), index=True)
 
     workflow_invocation = relationship("WorkflowInvocation", back_populates="output_dataset_collections")
     workflow_step = relationship("WorkflowStep")
@@ -9322,10 +9438,12 @@ class WorkflowInvocationOutputValue(Base, Dictifiable, Serializable):
 
     __tablename__ = "workflow_invocation_output_value"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
-    workflow_output_id = Column(Integer, ForeignKey("workflow_output.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation.id"), index=True
+    )
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"))
+    workflow_output_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_output.id"), index=True)
     value = Column(MutableJSONType)
 
     workflow_invocation = relationship("WorkflowInvocation", back_populates="output_values")
@@ -9361,10 +9479,12 @@ class WorkflowInvocationStepOutputDatasetAssociation(Base, Dictifiable, Represen
 
     __tablename__ = "workflow_invocation_step_output_dataset_association"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_step_id = Column(Integer, ForeignKey("workflow_invocation_step.id"), index=True)
-    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    output_name = Column(String(255), nullable=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_step_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_invocation_step.id"), index=True
+    )
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
     workflow_invocation_step = relationship("WorkflowInvocationStep", back_populates="output_datasets")
     dataset = relationship("HistoryDatasetAssociation")
 
@@ -9376,15 +9496,17 @@ class WorkflowInvocationStepOutputDatasetCollectionAssociation(Base, Dictifiable
 
     __tablename__ = "workflow_invocation_step_output_dataset_collection_association"
 
-    id = Column(Integer, primary_key=True)
-    workflow_invocation_step_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_invocation_step_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("workflow_invocation_step.id", name="fk_wisodca_wisi"), index=True
     )
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id", name="fk_wisodca_wsi"), index=True)
-    dataset_collection_id = Column(
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("workflow_step.id", name="fk_wisodca_wsi"), index=True
+    )
+    dataset_collection_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("history_dataset_collection_association.id", name="fk_wisodca_dci"), index=True
     )
-    output_name = Column(String(255), nullable=True)
+    output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
 
     workflow_invocation_step = relationship("WorkflowInvocationStep", back_populates="output_dataset_collections")
     dataset_collection = relationship("HistoryDatasetCollectionAssociation")
@@ -9395,16 +9517,20 @@ class WorkflowInvocationStepOutputDatasetCollectionAssociation(Base, Dictifiable
 class MetadataFile(Base, StorableObject, Serializable):
     __tablename__ = "metadata_file"
 
-    id = Column(Integer, primary_key=True)
-    name = Column(TEXT)
-    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True)
-    lda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, index=True, default=now, onupdate=now)
-    object_store_id = Column(TrimmedString(255), index=True)
-    uuid = Column(UUIDType(), index=True)
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    name: Mapped[Optional[str]] = mapped_column(TEXT)
+    hda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True
+    )
+    lda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True
+    )
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, index=True, default=now, onupdate=now, nullable=True)
+    object_store_id: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    uuid: Mapped[Optional[str]] = mapped_column(UUIDType(), index=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
 
     history_dataset = relationship("HistoryDatasetAssociation")
     library_dataset = relationship("LibraryDatasetDatasetAssociation")
@@ -9477,16 +9603,16 @@ def _serialize(self, id_encoder, serialization_options):
 class FormDefinition(Base, Dictifiable, RepresentById):
     __tablename__ = "form_definition"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(TrimmedString(255), nullable=False)
-    desc = Column(TEXT)
-    form_definition_current_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    name: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    desc: Mapped[Optional[str]] = mapped_column(TEXT)
+    form_definition_current_id: Mapped[int] = mapped_column(
         Integer, ForeignKey("form_definition_current.id", use_alter=True), index=True, nullable=False
     )
     fields = Column(MutableJSONType)
-    type = Column(TrimmedString(255), index=True)
+    type: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     layout = Column(MutableJSONType)
     form_definition_current = relationship(
         "FormDefinitionCurrent",
@@ -9549,11 +9675,11 @@ def grid_fields(self, grid_index):
 class FormDefinitionCurrent(Base, RepresentById):
     __tablename__ = "form_definition_current"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    latest_form_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    latest_form_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_definition.id"), index=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     forms = relationship(
         "FormDefinition",
         back_populates="form_definition_current",
@@ -9573,10 +9699,10 @@ def __init__(self, form_definition=None):
 class FormValues(Base, RepresentById):
     __tablename__ = "form_values"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    form_definition_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    form_definition_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_definition.id"), index=True)
     content = Column(MutableJSONType)
     form_definition = relationship(
         "FormDefinition", primaryjoin=(lambda: FormValues.form_definition_id == FormDefinition.id)
@@ -9590,21 +9716,21 @@ def __init__(self, form_def=None, content=None):
 class UserAddress(Base, RepresentById):
     __tablename__ = "user_address"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    desc = Column(TrimmedString(255))
-    name = Column(TrimmedString(255), nullable=False)
-    institution = Column(TrimmedString(255))
-    address = Column(TrimmedString(255), nullable=False)
-    city = Column(TrimmedString(255), nullable=False)
-    state = Column(TrimmedString(255), nullable=False)
-    postal_code = Column(TrimmedString(255), nullable=False)
-    country = Column(TrimmedString(255), nullable=False)
-    phone = Column(TrimmedString(255))
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    desc: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    name: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    institution: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    address: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    city: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    state: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    postal_code: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    country: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    phone: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     # `desc` needs to be fully qualified because it is shadowed by `desc` Column defined above
     # TODO: db migration to rename column, then use `desc`
     user = relationship("User", back_populates="addresses", order_by=sqlalchemy.desc("update_time"))
@@ -9627,13 +9753,13 @@ def to_dict(self, trans):
 class PSAAssociation(Base, AssociationMixin, RepresentById):
     __tablename__ = "psa_association"
 
-    id = Column(Integer, primary_key=True)
-    server_url = Column(VARCHAR(255))
-    handle = Column(VARCHAR(255))
-    secret = Column(VARCHAR(255))
-    issued = Column(Integer)
-    lifetime = Column(Integer)
-    assoc_type = Column(VARCHAR(64))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
+    handle: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
+    secret: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
+    issued: Mapped[Optional[int]] = mapped_column(Integer)
+    lifetime: Mapped[Optional[int]] = mapped_column(Integer)
+    assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -9691,9 +9817,9 @@ class PSACode(Base, CodeMixin, RepresentById):
     __tablename__ = "psa_code"
     __table_args__ = (UniqueConstraint("code", "email"),)
 
-    id = Column(Integer, primary_key=True)
-    email = Column(VARCHAR(200))
-    code = Column(VARCHAR(32))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    email: Mapped[Optional[str]] = mapped_column(VARCHAR(200))
+    code: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -9719,10 +9845,10 @@ def get_code(cls, code):
 class PSANonce(Base, NonceMixin, RepresentById):
     __tablename__ = "psa_nonce"
 
-    id = Column(Integer, primary_key=True)
-    server_url = Column(VARCHAR(255))
-    timestamp = Column(Integer)
-    salt = Column(VARCHAR(40))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
+    timestamp: Mapped[Optional[int]] = mapped_column(Integer)
+    salt: Mapped[Optional[str]] = mapped_column(VARCHAR(40))
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -9757,11 +9883,11 @@ def use(cls, server_url, timestamp, salt):
 class PSAPartial(Base, PartialMixin, RepresentById):
     __tablename__ = "psa_partial"
 
-    id = Column(Integer, primary_key=True)
-    token = Column(VARCHAR(32))
-    data = Column(TEXT)
-    next_step = Column(Integer)
-    backend = Column(VARCHAR(32))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    token: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
+    data: Mapped[Optional[str]] = mapped_column(TEXT)
+    next_step: Mapped[Optional[int]] = mapped_column(Integer)
+    backend: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -9801,13 +9927,13 @@ class UserAuthnzToken(Base, UserMixin, RepresentById):
     __tablename__ = "oidc_user_authnz_tokens"
     __table_args__ = (UniqueConstraint("provider", "uid"),)
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    uid = Column(VARCHAR(255))
-    provider = Column(VARCHAR(32))
-    extra_data = Column(MutableJSONType, nullable=True)
-    lifetime = Column(Integer)
-    assoc_type = Column(VARCHAR(64))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    uid: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
+    provider: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
+    extra_data: Mapped[Optional[str]] = mapped_column(MutableJSONType, nullable=True)
+    lifetime: Mapped[Optional[int]] = mapped_column(Integer)
+    assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))
     user = relationship("User", back_populates="social_auth")
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
@@ -9964,31 +10090,31 @@ class CustosAuthnzToken(Base, RepresentById):
         UniqueConstraint("external_user_id", "provider"),
     )
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"))
-    external_user_id = Column(String(255))
-    provider = Column(String(255))
-    access_token = Column(Text)
-    id_token = Column(Text)
-    refresh_token = Column(Text)
-    expiration_time = Column(DateTime)
-    refresh_expiration_time = Column(DateTime)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"))
+    external_user_id: Mapped[Optional[str]] = mapped_column(String(255))
+    provider: Mapped[Optional[str]] = mapped_column(String(255))
+    access_token: Mapped[Optional[str]] = mapped_column(Text)
+    id_token: Mapped[Optional[str]] = mapped_column(Text)
+    refresh_token: Mapped[Optional[str]] = mapped_column(Text)
+    expiration_time: Mapped[Optional[datetime]] = mapped_column(DateTime)
+    refresh_expiration_time: Mapped[Optional[datetime]] = mapped_column(DateTime)
     user = relationship("User", back_populates="custos_auth")
 
 
 class CloudAuthz(Base):
     __tablename__ = "cloudauthz"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    provider = Column(String(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    provider: Mapped[Optional[str]] = mapped_column(String(255))
     config = Column(MutableJSONType)
-    authn_id = Column(Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True)
+    authn_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True)
     tokens = Column(MutableJSONType)
-    last_update = Column(DateTime)
-    last_activity = Column(DateTime)
-    description = Column(TEXT)
-    create_time = Column(DateTime, default=now)
+    last_update: Mapped[Optional[datetime]] = mapped_column(DateTime)
+    last_activity: Mapped[Optional[datetime]] = mapped_column(DateTime)
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
     user = relationship("User", back_populates="cloudauthz")
     authn = relationship("UserAuthnzToken")
 
@@ -10016,18 +10142,18 @@ class Page(Base, HasTags, Dictifiable, RepresentById):
     __tablename__ = "page"
     __table_args__ = (Index("ix_page_slug", "slug", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
-    latest_revision_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    user_id: Mapped[int] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
+    latest_revision_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("page_revision.id", use_alter=True, name="page_latest_revision_id_fk"), index=True
     )
-    title = Column(TEXT)
-    deleted = Column(Boolean, index=True, default=False)
-    importable = Column(Boolean, index=True, default=False)
-    slug = Column(TEXT)
-    published = Column(Boolean, index=True, default=False)
+    title: Mapped[Optional[str]] = mapped_column(TEXT)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    importable: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    slug: Mapped[Optional[str]] = mapped_column(TEXT)
+    published: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     user = relationship("User")
     revisions = relationship(
         "PageRevision",
@@ -10095,13 +10221,13 @@ def email_hash(self):
 class PageRevision(Base, Dictifiable, RepresentById):
     __tablename__ = "page_revision"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    page_id = Column(Integer, ForeignKey("page.id"), index=True, nullable=False)
-    title = Column(TEXT)
-    content = Column(TEXT)
-    content_format = Column(TrimmedString(32))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    page_id: Mapped[int] = mapped_column(Integer, ForeignKey("page.id"), index=True, nullable=False)
+    title: Mapped[Optional[str]] = mapped_column(TEXT)
+    content: Mapped[Optional[str]] = mapped_column(TEXT)
+    content_format: Mapped[Optional[str]] = mapped_column(TrimmedString(32))
     page = relationship("Page", primaryjoin=(lambda: Page.id == PageRevision.page_id))
     DEFAULT_CONTENT_FORMAT = "html"
     dict_element_visible_keys = ["id", "page_id", "title", "content", "content_format"]
@@ -10119,9 +10245,9 @@ def to_dict(self, view="element"):
 class PageUserShareAssociation(Base, UserShareAssociation):
     __tablename__ = "page_user_share_association"
 
-    id = Column(Integer, primary_key=True)
-    page_id = Column(Integer, ForeignKey("page.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    page_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("page.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user = relationship("User")
     page = relationship("Page", back_populates="users_shared_with")
 
@@ -10133,22 +10259,22 @@ class Visualization(Base, HasTags, Dictifiable, RepresentById):
         Index("ix_visualization_slug", "slug", mysql_length=200),
     )
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
-    latest_revision_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    user_id: Mapped[int] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
+    latest_revision_id: Mapped[Optional[int]] = mapped_column(
         Integer,
         ForeignKey("visualization_revision.id", use_alter=True, name="visualization_latest_revision_id_fk"),
         index=True,
     )
-    title = Column(TEXT)
-    type = Column(TEXT)
-    dbkey = Column(TEXT)
-    deleted = Column(Boolean, default=False, index=True)
-    importable = Column(Boolean, default=False, index=True)
-    slug = Column(TEXT)
-    published = Column(Boolean, default=False, index=True)
+    title: Mapped[Optional[str]] = mapped_column(TEXT)
+    type: Mapped[Optional[str]] = mapped_column(TEXT)
+    dbkey: Mapped[Optional[str]] = mapped_column(TEXT)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, default=False, index=True)
+    importable: Mapped[Optional[bool]] = mapped_column(Boolean, default=False, index=True)
+    slug: Mapped[Optional[str]] = mapped_column(TEXT)
+    published: Mapped[Optional[bool]] = mapped_column(Boolean, default=False, index=True)
 
     user = relationship("User")
     revisions = relationship(
@@ -10247,12 +10373,12 @@ class VisualizationRevision(Base, RepresentById):
     __tablename__ = "visualization_revision"
     __table_args__ = (Index("ix_visualization_revision_dbkey", "dbkey", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True, nullable=False)
-    title = Column(TEXT)
-    dbkey = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    visualization_id: Mapped[int] = mapped_column(Integer, ForeignKey("visualization.id"), index=True, nullable=False)
+    title: Mapped[Optional[str]] = mapped_column(TEXT)
+    dbkey: Mapped[Optional[str]] = mapped_column(TEXT)
     config = Column(MutableJSONType)
     visualization = relationship(
         "Visualization",
@@ -10275,9 +10401,9 @@ def copy(self, visualization=None):
 class VisualizationUserShareAssociation(Base, UserShareAssociation):
     __tablename__ = "visualization_user_share_association"
 
-    id = Column(Integer, primary_key=True)
-    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    visualization_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("visualization.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user = relationship("User")
     visualization = relationship("Visualization", back_populates="users_shared_with")
 
@@ -10286,10 +10412,10 @@ class Tag(Base, RepresentById):
     __tablename__ = "tag"
     __table_args__ = (UniqueConstraint("name"),)
 
-    id = Column(Integer, primary_key=True)
-    type = Column(Integer)
-    parent_id = Column(Integer, ForeignKey("tag.id"))
-    name = Column(TrimmedString(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    type: Mapped[Optional[int]] = mapped_column(Integer)
+    parent_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"))
+    name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
     children = relationship("Tag", back_populates="parent")
     parent = relationship("Tag", back_populates="children", remote_side=[id])
 
@@ -10300,8 +10426,8 @@ def __str__(self):
 class ItemTagAssociation(Dictifiable):
     dict_collection_visible_keys = ["id", "user_tname", "user_value"]
     dict_element_visible_keys = dict_collection_visible_keys
-    user_tname: Column
-    user_value = Column(TrimmedString(255), index=True)
+    user_tname: Mapped[Optional[str]]
+    user_value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
 
     def __init_subclass__(cls, **kwargs):
         super().__init_subclass__(**kwargs)
@@ -10321,12 +10447,12 @@ def copy(self, cls=None):
 class HistoryTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "history_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     history = relationship("History", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10335,12 +10461,14 @@ class HistoryTagAssociation(Base, ItemTagAssociation, RepresentById):
 class HistoryDatasetAssociationTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "history_dataset_association_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_dataset_association_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True
+    )
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     history_dataset_association = relationship("HistoryDatasetAssociation", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10349,14 +10477,14 @@ class HistoryDatasetAssociationTagAssociation(Base, ItemTagAssociation, Represen
 class LibraryDatasetDatasetAssociationTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "library_dataset_dataset_association_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    library_dataset_dataset_association_id = Column(
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    library_dataset_dataset_association_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("library_dataset_dataset_association.id"), index=True
     )
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     library_dataset_dataset_association = relationship("LibraryDatasetDatasetAssociation", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10365,12 +10493,12 @@ class LibraryDatasetDatasetAssociationTagAssociation(Base, ItemTagAssociation, R
 class PageTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "page_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    page_id = Column(Integer, ForeignKey("page.id"), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    page_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("page.id"), index=True)
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     page = relationship("Page", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10379,12 +10507,12 @@ class PageTagAssociation(Base, ItemTagAssociation, RepresentById):
 class WorkflowStepTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "workflow_step_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"), index=True)
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     workflow_step = relationship("WorkflowStep", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10393,12 +10521,12 @@ class WorkflowStepTagAssociation(Base, ItemTagAssociation, RepresentById):
 class StoredWorkflowTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "stored_workflow_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    stored_workflow_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     stored_workflow = relationship("StoredWorkflow", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10407,12 +10535,12 @@ class StoredWorkflowTagAssociation(Base, ItemTagAssociation, RepresentById):
 class VisualizationTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "visualization_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    visualization_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("visualization.id"), index=True)
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     visualization = relationship("Visualization", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10421,12 +10549,14 @@ class VisualizationTagAssociation(Base, ItemTagAssociation, RepresentById):
 class HistoryDatasetCollectionTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "history_dataset_collection_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    history_dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    )
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     dataset_collection = relationship("HistoryDatasetCollectionAssociation", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10435,12 +10565,14 @@ class HistoryDatasetCollectionTagAssociation(Base, ItemTagAssociation, Represent
 class LibraryDatasetCollectionTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "library_dataset_collection_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    library_dataset_collection_id = Column(Integer, ForeignKey("library_dataset_collection_association.id"), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    library_dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_collection_association.id"), index=True
+    )
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     dataset_collection = relationship("LibraryDatasetCollectionAssociation", back_populates="tags")
     tag = relationship("Tag")
     user = relationship("User")
@@ -10449,12 +10581,12 @@ class LibraryDatasetCollectionTagAssociation(Base, ItemTagAssociation, Represent
 class ToolTagAssociation(Base, ItemTagAssociation, RepresentById):
     __tablename__ = "tool_tag_association"
 
-    id = Column(Integer, primary_key=True)
-    tool_id = Column(TrimmedString(255), index=True)
-    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user_tname = Column(TrimmedString(255), index=True)
-    value = Column(TrimmedString(255), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    tool_id: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    tag_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("tag.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user_tname: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     tag = relationship("Tag")
     user = relationship("User")
 
@@ -10464,10 +10596,10 @@ class HistoryAnnotationAssociation(Base, RepresentById):
     __tablename__ = "history_annotation_association"
     __table_args__ = (Index("ix_history_anno_assoc_annotation", "annotation", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    annotation = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    annotation: Mapped[Optional[str]] = mapped_column(TEXT)
     history = relationship("History", back_populates="annotations")
     user = relationship("User")
 
@@ -10476,10 +10608,12 @@ class HistoryDatasetAssociationAnnotationAssociation(Base, RepresentById):
     __tablename__ = "history_dataset_association_annotation_association"
     __table_args__ = (Index("ix_history_dataset_anno_assoc_annotation", "annotation", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    annotation = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_dataset_association_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    annotation: Mapped[Optional[str]] = mapped_column(TEXT)
     hda = relationship("HistoryDatasetAssociation", back_populates="annotations")
     user = relationship("User")
 
@@ -10488,10 +10622,10 @@ class StoredWorkflowAnnotationAssociation(Base, RepresentById):
     __tablename__ = "stored_workflow_annotation_association"
     __table_args__ = (Index("ix_stored_workflow_ann_assoc_annotation", "annotation", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    annotation = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    stored_workflow_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    annotation: Mapped[Optional[str]] = mapped_column(TEXT)
     stored_workflow = relationship("StoredWorkflow", back_populates="annotations")
     user = relationship("User")
 
@@ -10500,10 +10634,10 @@ class WorkflowStepAnnotationAssociation(Base, RepresentById):
     __tablename__ = "workflow_step_annotation_association"
     __table_args__ = (Index("ix_workflow_step_ann_assoc_annotation", "annotation", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    annotation = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    annotation: Mapped[Optional[str]] = mapped_column(TEXT)
     workflow_step = relationship("WorkflowStep", back_populates="annotations")
     user = relationship("User")
 
@@ -10512,10 +10646,10 @@ class PageAnnotationAssociation(Base, RepresentById):
     __tablename__ = "page_annotation_association"
     __table_args__ = (Index("ix_page_annotation_association_annotation", "annotation", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    page_id = Column(Integer, ForeignKey("page.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    annotation = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    page_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("page.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    annotation: Mapped[Optional[str]] = mapped_column(TEXT)
     page = relationship("Page", back_populates="annotations")
     user = relationship("User")
 
@@ -10524,10 +10658,10 @@ class VisualizationAnnotationAssociation(Base, RepresentById):
     __tablename__ = "visualization_annotation_association"
     __table_args__ = (Index("ix_visualization_annotation_association_annotation", "annotation", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    annotation = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    visualization_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("visualization.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    annotation: Mapped[Optional[str]] = mapped_column(TEXT)
     visualization = relationship("Visualization", back_populates="annotations")
     user = relationship("User")
 
@@ -10535,10 +10669,12 @@ class VisualizationAnnotationAssociation(Base, RepresentById):
 class HistoryDatasetCollectionAssociationAnnotationAssociation(Base, RepresentById):
     __tablename__ = "history_dataset_collection_annotation_association"
 
-    id = Column(Integer, primary_key=True)
-    history_dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    annotation = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    annotation: Mapped[Optional[str]] = mapped_column(TEXT)
     history_dataset_collection = relationship("HistoryDatasetCollectionAssociation", back_populates="annotations")
     user = relationship("User")
 
@@ -10546,10 +10682,12 @@ class HistoryDatasetCollectionAssociationAnnotationAssociation(Base, RepresentBy
 class LibraryDatasetCollectionAnnotationAssociation(Base, RepresentById):
     __tablename__ = "library_dataset_collection_annotation_association"
 
-    id = Column(Integer, primary_key=True)
-    library_dataset_collection_id = Column(Integer, ForeignKey("library_dataset_collection_association.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    annotation = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    library_dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_collection_association.id"), index=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    annotation: Mapped[Optional[str]] = mapped_column(TEXT)
     dataset_collection = relationship("LibraryDatasetCollectionAssociation", back_populates="annotations")
     user = relationship("User")
 
@@ -10557,13 +10695,13 @@ class LibraryDatasetCollectionAnnotationAssociation(Base, RepresentById):
 class Vault(Base):
     __tablename__ = "vault"
 
-    key = Column(Text, primary_key=True)
-    parent_key = Column(Text, ForeignKey(key), index=True, nullable=True)
+    key: Mapped[str] = mapped_column(Text, primary_key=True)
+    parent_key: Mapped[Optional[str]] = mapped_column(Text, ForeignKey(key), index=True, nullable=True)
     children = relationship("Vault", back_populates="parent")
     parent = relationship("Vault", back_populates="children", remote_side=[key])
-    value = Column(Text, nullable=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    value: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
 
 
 # Item rating classes.
@@ -10583,10 +10721,10 @@ def _set_item(self, item):
 class HistoryRatingAssociation(ItemRatingAssociation, RepresentById):
     __tablename__ = "history_rating_association"
 
-    id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    rating = Column(Integer, index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    rating: Mapped[Optional[int]] = mapped_column(Integer, index=True)
     history = relationship("History", back_populates="ratings")
     user = relationship("User")
 
@@ -10598,10 +10736,12 @@ def _set_item(self, history):
 class HistoryDatasetAssociationRatingAssociation(ItemRatingAssociation, RepresentById):
     __tablename__ = "history_dataset_association_rating_association"
 
-    id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    rating = Column(Integer, index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_dataset_association_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    rating: Mapped[Optional[int]] = mapped_column(Integer, index=True)
     history_dataset_association = relationship("HistoryDatasetAssociation", back_populates="ratings")
     user = relationship("User")
 
@@ -10613,10 +10753,10 @@ def _set_item(self, history_dataset_association):
 class StoredWorkflowRatingAssociation(ItemRatingAssociation, RepresentById):
     __tablename__ = "stored_workflow_rating_association"
 
-    id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    rating = Column(Integer, index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    stored_workflow_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    rating: Mapped[Optional[int]] = mapped_column(Integer, index=True)
     stored_workflow = relationship("StoredWorkflow", back_populates="ratings")
     user = relationship("User")
 
@@ -10628,10 +10768,10 @@ def _set_item(self, stored_workflow):
 class PageRatingAssociation(ItemRatingAssociation, RepresentById):
     __tablename__ = "page_rating_association"
 
-    id = Column(Integer, primary_key=True)
-    page_id = Column(Integer, ForeignKey("page.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    rating = Column(Integer, index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    page_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("page.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    rating: Mapped[Optional[int]] = mapped_column(Integer, index=True)
     page = relationship("Page", back_populates="ratings")
     user = relationship("User")
 
@@ -10643,10 +10783,10 @@ def _set_item(self, page):
 class VisualizationRatingAssociation(ItemRatingAssociation, RepresentById):
     __tablename__ = "visualization_rating_association"
 
-    id = Column(Integer, primary_key=True)
-    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    rating = Column(Integer, index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    visualization_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("visualization.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    rating: Mapped[Optional[int]] = mapped_column(Integer, index=True)
     visualization = relationship("Visualization", back_populates="ratings")
     user = relationship("User")
 
@@ -10658,10 +10798,12 @@ def _set_item(self, visualization):
 class HistoryDatasetCollectionRatingAssociation(ItemRatingAssociation, RepresentById):
     __tablename__ = "history_dataset_collection_rating_association"
 
-    id = Column(Integer, primary_key=True)
-    history_dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    rating = Column(Integer, index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    history_dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    rating: Mapped[Optional[int]] = mapped_column(Integer, index=True)
     dataset_collection = relationship("HistoryDatasetCollectionAssociation", back_populates="ratings")
     user = relationship("User")
 
@@ -10673,10 +10815,12 @@ def _set_item(self, dataset_collection):
 class LibraryDatasetCollectionRatingAssociation(ItemRatingAssociation, RepresentById):
     __tablename__ = "library_dataset_collection_rating_association"
 
-    id = Column(Integer, primary_key=True)
-    library_dataset_collection_id = Column(Integer, ForeignKey("library_dataset_collection_association.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    rating = Column(Integer, index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    library_dataset_collection_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_collection_association.id"), index=True
+    )
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    rating: Mapped[Optional[int]] = mapped_column(Integer, index=True)
     dataset_collection = relationship("LibraryDatasetCollectionAssociation", back_populates="ratings")
     user = relationship("User")
 
@@ -10689,11 +10833,11 @@ def _set_item(self, dataset_collection):
 class DataManagerHistoryAssociation(Base, RepresentById):
     __tablename__ = "data_manager_history_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, index=True, default=now, onupdate=now)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, index=True, default=now, onupdate=now, nullable=True)
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
     history = relationship("History")
     user = relationship("User", back_populates="data_manager_histories")
 
@@ -10702,21 +10846,21 @@ class DataManagerJobAssociation(Base, RepresentById):
     __tablename__ = "data_manager_job_association"
     __table_args__ = (Index("ix_data_manager_job_association_data_manager_id", "data_manager_id", mysql_length=200),)
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, index=True, default=now, onupdate=now)
-    job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    data_manager_id = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, index=True, default=now, onupdate=now, nullable=True)
+    job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
+    data_manager_id: Mapped[Optional[str]] = mapped_column(TEXT)
     job = relationship("Job", back_populates="data_manager_association", uselist=False)
 
 
 class UserPreference(Base, RepresentById):
     __tablename__ = "user_preference"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    name = Column(Unicode(255), index=True)
-    value = Column(Text)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    name: Mapped[Optional[str]] = mapped_column(Unicode(255), index=True)
+    value: Mapped[Optional[str]] = mapped_column(Text)
 
     def __init__(self, name=None, value=None):
         # Do not remove this constructor: it is set as the creator for the User.preferences
@@ -10728,25 +10872,25 @@ def __init__(self, name=None, value=None):
 class UserAction(Base, RepresentById):
     __tablename__ = "user_action"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    session_id = Column(Integer, ForeignKey("galaxy_session.id"), index=True)
-    action = Column(Unicode(255))
-    context = Column(Unicode(512))
-    params = Column(Unicode(1024))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    session_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_session.id"), index=True)
+    action: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    context: Mapped[Optional[str]] = mapped_column(Unicode(512))
+    params: Mapped[Optional[str]] = mapped_column(Unicode(1024))
     user = relationship("User")
 
 
 class APIKeys(Base, RepresentById):
     __tablename__ = "api_keys"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    key = Column(TrimmedString(32), index=True, unique=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    key: Mapped[Optional[str]] = mapped_column(TrimmedString(32), index=True, unique=True)
     user = relationship("User", back_populates="api_keys")
-    deleted = Column(Boolean, index=True, server_default=false(), nullable=False)
+    deleted: Mapped[bool] = mapped_column(Boolean, index=True, server_default=false(), nullable=False)
 
 
 def copy_list(lst, *args, **kwds):
@@ -10779,90 +10923,112 @@ def _prepare_metadata_for_serialization(id_encoder, serialization_options, metad
 class CleanupEvent(Base):
     __tablename__ = "cleanup_event"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    message = Column(TrimmedString(1024))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    message: Mapped[Optional[str]] = mapped_column(TrimmedString(1024))
 
 
 class CleanupEventDatasetAssociation(Base):
     __tablename__ = "cleanup_event_dataset_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset.id"), index=True)
 
 
 class CleanupEventMetadataFileAssociation(Base):
     __tablename__ = "cleanup_event_metadata_file_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    metadata_file_id = Column(Integer, ForeignKey("metadata_file.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    metadata_file_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("metadata_file.id"), index=True)
 
 
 class CleanupEventHistoryAssociation(Base):
     __tablename__ = "cleanup_event_history_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
 
 
 class CleanupEventHistoryDatasetAssociationAssociation(Base):
     __tablename__ = "cleanup_event_hda_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    hda_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history_dataset_association.id"), index=True)
 
 
 class CleanupEventLibraryAssociation(Base):
     __tablename__ = "cleanup_event_library_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    library_id = Column(Integer, ForeignKey("library.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    library_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library.id"), index=True)
 
 
 class CleanupEventLibraryFolderAssociation(Base):
     __tablename__ = "cleanup_event_library_folder_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    library_folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    library_folder_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library_folder.id"), index=True)
 
 
 class CleanupEventLibraryDatasetAssociation(Base):
     __tablename__ = "cleanup_event_library_dataset_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    library_dataset_id = Column(Integer, ForeignKey("library_dataset.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    library_dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("library_dataset.id"), index=True)
 
 
 class CleanupEventLibraryDatasetDatasetAssociationAssociation(Base):
     __tablename__ = "cleanup_event_ldda_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    ldda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True
+    )
 
 
 class CleanupEventImplicitlyConvertedDatasetAssociationAssociation(Base):
     __tablename__ = "cleanup_event_icda_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
-    icda_id = Column(Integer, ForeignKey("implicitly_converted_dataset_association.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    cleanup_event_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True
+    )
+    icda_id: Mapped[Optional[int]] = mapped_column(
+        Integer, ForeignKey("implicitly_converted_dataset_association.id"), index=True
+    )
 
 
 class CeleryUserRateLimit(Base):
@@ -10873,8 +11039,8 @@ class CeleryUserRateLimit(Base):
 
     __tablename__ = "celery_user_rate_limit"
 
-    user_id = Column(Integer, ForeignKey("galaxy_user.id", ondelete="CASCADE"), primary_key=True)
-    last_scheduled_time = Column(DateTime, nullable=False)
+    user_id = mapped_column(Integer, ForeignKey("galaxy_user.id", ondelete="CASCADE"), primary_key=True)
+    last_scheduled_time: Mapped[datetime] = mapped_column(DateTime, nullable=False)
 
     def __repr__(self):
         return (
diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index edec5b1f5c82..edd922600b1d 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -1,5 +1,6 @@
 import logging
 import os
+from datetime import datetime
 from enum import Enum
 from typing import (
     Any,
@@ -19,6 +20,8 @@
     TEXT,
 )
 from sqlalchemy.orm import (
+    Mapped,
+    mapped_column,
     registry,
     relationship,
 )
@@ -75,24 +78,24 @@ def __declare_last__(cls):
 class ToolShedRepository(Base):
     __tablename__ = "tool_shed_repository"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed = Column(TrimmedString(255), index=True)
-    name = Column(TrimmedString(255), index=True)
-    description = Column(TEXT)
-    owner = Column(TrimmedString(255), index=True)
-    installed_changeset_revision = Column(TrimmedString(255))
-    changeset_revision = Column(TrimmedString(255), index=True)
-    ctx_rev = Column(TrimmedString(10))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
+    update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
+    tool_shed: Mapped[str] = mapped_column(TrimmedString(255), index=True, nullable=True)
+    name: Mapped[str] = mapped_column(TrimmedString(255), index=True, nullable=True)
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    owner: Mapped[str] = mapped_column(TrimmedString(255), index=True, nullable=True)
+    installed_changeset_revision: Mapped[str] = mapped_column(TrimmedString(255), nullable=True)
+    changeset_revision: Mapped[str] = mapped_column(TrimmedString(255), index=True, nullable=True)
+    ctx_rev: Mapped[Optional[str]] = mapped_column(TrimmedString(10))
     metadata_ = Column("metadata", MutableJSONType, nullable=True)
-    includes_datatypes = Column(Boolean, index=True, default=False)
+    includes_datatypes: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     tool_shed_status = Column(MutableJSONType, nullable=True)
-    deleted = Column(Boolean, index=True, default=False)
-    uninstalled = Column(Boolean, default=False)
-    dist_to_shed = Column(Boolean, default=False)
-    status = Column(TrimmedString(255))
-    error_message = Column(TEXT)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    uninstalled: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    dist_to_shed: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    status: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    error_message: Mapped[Optional[str]] = mapped_column(TEXT)
     tool_versions = relationship("ToolVersion", back_populates="tool_shed_repository")
     tool_dependencies = relationship(
         "ToolDependency", order_by="ToolDependency.name", back_populates="tool_shed_repository"
@@ -654,11 +657,11 @@ def upgrade_available(self):
 class RepositoryRepositoryDependencyAssociation(Base):
     __tablename__ = "repository_repository_dependency_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(ForeignKey("tool_shed_repository.id"), index=True)
-    repository_dependency_id = Column(ForeignKey("repository_dependency.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    tool_shed_repository_id: Mapped[Optional[int]] = mapped_column(ForeignKey("tool_shed_repository.id"), index=True)
+    repository_dependency_id: Mapped[Optional[int]] = mapped_column(ForeignKey("repository_dependency.id"), index=True)
     repository = relationship("ToolShedRepository", back_populates="required_repositories")
     repository_dependency = relationship("RepositoryDependency")
 
@@ -670,10 +673,12 @@ def __init__(self, tool_shed_repository_id=None, repository_dependency_id=None):
 class RepositoryDependency(Base):
     __tablename__ = "repository_dependency"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(ForeignKey("tool_shed_repository.id"), index=True, nullable=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    tool_shed_repository_id: Mapped[int] = mapped_column(
+        ForeignKey("tool_shed_repository.id"), index=True, nullable=False
+    )
     repository = relationship("ToolShedRepository")
 
     def __init__(self, tool_shed_repository_id=None):
@@ -683,15 +688,17 @@ def __init__(self, tool_shed_repository_id=None):
 class ToolDependency(Base):
     __tablename__ = "tool_dependency"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(ForeignKey("tool_shed_repository.id"), index=True, nullable=False)
-    name = Column(TrimmedString(255))
-    version = Column(TEXT)
-    type = Column(TrimmedString(40))
-    status = Column(TrimmedString(255), nullable=False)
-    error_message = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    tool_shed_repository_id: Mapped[int] = mapped_column(
+        ForeignKey("tool_shed_repository.id"), index=True, nullable=False
+    )
+    name: Mapped[str] = mapped_column(TrimmedString(255), nullable=True)
+    version: Mapped[str] = mapped_column(TEXT, nullable=True)
+    type: Mapped[Optional[str]] = mapped_column(TrimmedString(40))
+    status: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    error_message: Mapped[Optional[str]] = mapped_column(TEXT)
     tool_shed_repository = relationship("ToolShedRepository", back_populates="tool_dependencies")
 
     # converting this one to Enum breaks the tool shed tests,
@@ -773,11 +780,13 @@ def is_installed(self):
 class ToolVersion(Base, Dictifiable):
     __tablename__ = "tool_version"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    tool_id = Column(String(255))
-    tool_shed_repository_id = Column(ForeignKey("tool_shed_repository.id"), index=True, nullable=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    tool_id: Mapped[Optional[str]] = mapped_column(String(255))
+    tool_shed_repository_id: Mapped[Optional[int]] = mapped_column(
+        ForeignKey("tool_shed_repository.id"), index=True, nullable=True
+    )
     parent_tool_association = relationship(
         "ToolVersionAssociation", primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.tool_id)
     )
@@ -801,6 +810,6 @@ def to_dict(self, view="element"):
 class ToolVersionAssociation(Base):
     __tablename__ = "tool_version_association"
 
-    id = Column(Integer, primary_key=True)
-    tool_id = Column(ForeignKey("tool_version.id"), index=True, nullable=False)
-    parent_id = Column(ForeignKey("tool_version.id"), index=True, nullable=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    tool_id: Mapped[int] = mapped_column(ForeignKey("tool_version.id"), index=True, nullable=False)
+    parent_id: Mapped[int] = mapped_column(ForeignKey("tool_version.id"), index=True, nullable=False)
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 3b2003d3e1be..4181757d81f0 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -10,6 +10,7 @@
 from typing import (
     Any,
     Mapping,
+    Optional,
     TYPE_CHECKING,
 )
 
@@ -32,6 +33,8 @@
     UniqueConstraint,
 )
 from sqlalchemy.orm import (
+    Mapped,
+    mapped_column,
     registry,
     relationship,
 )
@@ -87,27 +90,27 @@ def __declare_last__(cls):
 class APIKeys(Base):
     __tablename__ = "api_keys"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
-    key = Column(TrimmedString(32), index=True, unique=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    key: Mapped[Optional[str]] = mapped_column(TrimmedString(32), index=True, unique=True)
     user = relationship("User", back_populates="api_keys")
-    deleted = Column(Boolean, index=True, default=False)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
 
 
 class User(Base, Dictifiable):
     __tablename__ = "galaxy_user"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    email = Column(TrimmedString(255), nullable=False)
-    username = Column(String(255), index=True)
-    password = Column(TrimmedString(40), nullable=False)
-    external = Column(Boolean, default=False)
-    new_repo_alert = Column(Boolean, default=False)
-    deleted = Column(Boolean, index=True, default=False)
-    purged = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    email: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
+    username: Mapped[Optional[str]] = mapped_column(String(255), index=True)
+    password: Mapped[str] = mapped_column(TrimmedString(40), nullable=False)
+    external: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    new_repo_alert: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    purged: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     active_repositories = relationship(
         "Repository",
         primaryjoin=(lambda: (Repository.user_id == User.id) & (not_(Repository.deleted))),  # type: ignore[has-type]
@@ -186,9 +189,9 @@ def set_random_password(self, length=16):
 class PasswordResetToken(Base):
     __tablename__ = "password_reset_token"
 
-    token = Column(String(32), primary_key=True, unique=True, index=True)
-    expiration_time = Column(DateTime)
-    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
+    token: Mapped[str] = mapped_column(String(32), primary_key=True, unique=True, index=True)
+    expiration_time: Mapped[Optional[datetime]] = mapped_column(DateTime)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
     user = relationship("User", back_populates="reset_tokens")
 
     def __init__(self, user, token=None):
@@ -204,11 +207,11 @@ def __init__(self, user, token=None):
 class Group(Base, Dictifiable):
     __tablename__ = "galaxy_group"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(String(255), index=True, unique=True)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    name: Mapped[Optional[str]] = mapped_column(String(255), index=True, unique=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     roles = relationship("GroupRoleAssociation", back_populates="group")
     users = relationship("UserGroupAssociation", back_populates="group")
 
@@ -223,13 +226,13 @@ def __init__(self, name=None):
 class Role(Base, Dictifiable):
     __tablename__ = "role"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(String(255), index=True, unique=True)
-    description = Column(TEXT)
-    type = Column(String(40), index=True)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    name: Mapped[Optional[str]] = mapped_column(String(255), index=True, unique=True)
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    type: Mapped[Optional[str]] = mapped_column(String(40), index=True)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     repositories = relationship("RepositoryRoleAssociation", back_populates="role")
     groups = relationship("GroupRoleAssociation", back_populates="role")
     users = relationship("UserRoleAssociation", back_populates="role")
@@ -258,11 +261,11 @@ def is_repository_admin_role(self):
 class UserGroupAssociation(Base):
     __tablename__ = "user_group_association"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
-    group_id = Column(ForeignKey("galaxy_group.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    group_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_group.id"), index=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
     user = relationship("User", back_populates="groups")
     group = relationship("Group", back_populates="users")
 
@@ -275,11 +278,11 @@ def __init__(self, user, group):
 class UserRoleAssociation(Base):
     __tablename__ = "user_role_association"
 
-    id = Column(Integer, primary_key=True)
-    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
-    role_id = Column(ForeignKey("role.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
     user = relationship("User", back_populates="roles")
     role = relationship("Role", back_populates="users")
 
@@ -293,11 +296,11 @@ def __init__(self, user, role):
 class GroupRoleAssociation(Base):
     __tablename__ = "group_role_association"
 
-    id = Column(Integer, primary_key=True)
-    group_id = Column(ForeignKey("galaxy_group.id"), index=True)
-    role_id = Column(ForeignKey("role.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    group_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_group.id"), index=True)
+    role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
     group = relationship("Group", back_populates="roles")
     role = relationship("Role", back_populates="groups")
 
@@ -309,11 +312,11 @@ def __init__(self, group, role):
 class RepositoryRoleAssociation(Base):
     __tablename__ = "repository_role_association"
 
-    id = Column(Integer, primary_key=True)
-    repository_id = Column(ForeignKey("repository.id"), index=True)
-    role_id = Column(ForeignKey("role.id"), index=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    repository_id: Mapped[Optional[int]] = mapped_column(ForeignKey("repository.id"), index=True)
+    role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
     repository = relationship("Repository", back_populates="roles")
     role = relationship("Role", back_populates="repositories")
 
@@ -326,19 +329,19 @@ def __init__(self, repository, role):
 class GalaxySession(Base):
     __tablename__ = "galaxy_session"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(ForeignKey("galaxy_user.id"), index=True, nullable=True)
-    remote_host = Column(String(255))
-    remote_addr = Column(String(255))
-    referer = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True, nullable=True)
+    remote_host: Mapped[Optional[str]] = mapped_column(String(255))
+    remote_addr: Mapped[Optional[str]] = mapped_column(String(255))
+    referer: Mapped[Optional[str]] = mapped_column(TEXT)
     # unique 128 bit random number coerced to a string
-    session_key = Column(TrimmedString(255), index=True, unique=True)
-    is_valid = Column(Boolean, default=False)
+    session_key: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True, unique=True)
+    is_valid: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     # saves a reference to the previous session so we have a way to chain them together
-    prev_session_id = Column(Integer)
-    last_action = Column(DateTime)
+    prev_session_id: Mapped[Optional[int]] = mapped_column(Integer)
+    last_action: Mapped[Optional[datetime]] = mapped_column(DateTime)
     user = relationship("User", back_populates="galaxy_sessions")
 
     def __init__(self, is_valid=False, **kwd):
@@ -350,21 +353,21 @@ def __init__(self, is_valid=False, **kwd):
 class Repository(Base, Dictifiable):
     __tablename__ = "repository"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(TrimmedString(255), index=True)
-    type = Column(TrimmedString(255), index=True)
-    remote_repository_url = Column(TrimmedString(255))
-    homepage_url = Column(TrimmedString(255))
-    description = Column(TEXT)
-    long_description = Column(TEXT)
-    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
-    private = Column(Boolean, default=False)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    name: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    type: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
+    remote_repository_url: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    homepage_url: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    long_description: Mapped[Optional[str]] = mapped_column(TEXT)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    private: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     email_alerts = Column(MutableJSONType, nullable=True)
-    times_downloaded = Column(Integer)
-    deprecated = Column(Boolean, default=False)
+    times_downloaded: Mapped[Optional[int]] = mapped_column(Integer)
+    deprecated: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     categories = relationship("RepositoryCategoryAssociation", back_populates="repository")
     ratings = relationship(
         "RepositoryRatingAssociation",
@@ -564,13 +567,13 @@ def set_item(self, item):
 class RepositoryRatingAssociation(Base, ItemRatingAssociation):
     __tablename__ = "repository_rating_association"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    repository_id = Column(ForeignKey("repository.id"), index=True)
-    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
-    rating = Column(Integer, index=True)
-    comment = Column(TEXT)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    repository_id: Mapped[Optional[int]] = mapped_column(ForeignKey("repository.id"), index=True)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    rating: Mapped[Optional[int]] = mapped_column(Integer, index=True)
+    comment: Mapped[Optional[str]] = mapped_column(TEXT)
     repository = relationship("Repository", back_populates="ratings")
     user = relationship("User")
 
@@ -581,12 +584,12 @@ def set_item(self, repository):
 class Category(Base, Dictifiable):
     __tablename__ = "category"
 
-    id = Column(Integer, primary_key=True)
-    create_time = Column(DateTime, default=now)
-    update_time = Column(DateTime, default=now, onupdate=now)
-    name = Column(TrimmedString(255), index=True, unique=True)
-    description = Column(TEXT)
-    deleted = Column(Boolean, index=True, default=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    create_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
+    update_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
+    name: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True, unique=True)
+    description: Mapped[Optional[str]] = mapped_column(TEXT)
+    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
     repositories = relationship("RepositoryCategoryAssociation", back_populates="category")
 
     dict_collection_visible_keys = ["id", "name", "description", "deleted"]
@@ -600,9 +603,9 @@ def __init__(self, deleted=False, **kwd):
 class RepositoryCategoryAssociation(Base):
     __tablename__ = "repository_category_association"
 
-    id = Column(Integer, primary_key=True)
-    repository_id = Column(ForeignKey("repository.id"), index=True)
-    category_id = Column(ForeignKey("category.id"), index=True)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    repository_id: Mapped[Optional[int]] = mapped_column(ForeignKey("repository.id"), index=True)
+    category_id: Mapped[Optional[int]] = mapped_column(ForeignKey("category.id"), index=True)
     category = relationship("Category", back_populates="repositories")
     repository = relationship("Repository", back_populates="categories")
 
@@ -615,10 +618,10 @@ class Tag(Base):
     __tablename__ = "tag"
     __table_args__ = (UniqueConstraint("name"),)
 
-    id = Column(Integer, primary_key=True)
-    type = Column(Integer)
-    parent_id = Column(ForeignKey("tag.id"))
-    name = Column(TrimmedString(255))
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    type: Mapped[Optional[int]] = mapped_column(Integer)
+    parent_id: Mapped[Optional[int]] = mapped_column(ForeignKey("tag.id"))
+    name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
     children = relationship("Tag", back_populates="parent")
     parent = relationship("Tag", back_populates="children", remote_side=[id])
 

From f8f2400ba3bcd8db44fe9383b739ffdd1aaba004 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 2 Feb 2024 13:18:14 -0500
Subject: [PATCH 06/71] Add typing to JSON columns, fix related mypy errors

Columns:
MutableJSONType
JSONType
DoubleEncodedJsonType

TODO: I think we need a type alias for json-typed columns: bytes understand
iteration, but not access by key.
---
 lib/galaxy/model/__init__.py              | 74 +++++++++++------------
 lib/galaxy/model/deferred.py              |  4 +-
 lib/galaxy/model/store/discover.py        |  2 +-
 lib/galaxy/tools/actions/upload_common.py |  2 +-
 lib/galaxy/workflow/run_request.py        |  2 +-
 lib/tool_shed/webapp/model/__init__.py    |  2 +-
 6 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 25dcb625cf9f..985ad66c484b 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1244,7 +1244,7 @@ class DynamicTool(Base, Dictifiable, RepresentById):
     tool_directory: Mapped[Optional[str]] = mapped_column(Unicode(255))
     hidden: Mapped[Optional[bool]] = mapped_column(Boolean, default=True)
     active: Mapped[Optional[bool]] = mapped_column(Boolean, default=True)
-    value = Column(MutableJSONType)
+    value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
 
     dict_collection_visible_keys = ("id", "tool_id", "tool_format", "tool_version", "uuid", "active", "hidden")
     dict_element_visible_keys = ("id", "tool_id", "tool_format", "tool_version", "uuid", "active", "hidden")
@@ -1336,8 +1336,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     info: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
     copied_from_job_id: Mapped[Optional[int]] = mapped_column(Integer, nullable=True)
     command_line: Mapped[Optional[str]] = mapped_column(TEXT)
-    dependencies = Column(MutableJSONType, nullable=True)
-    job_messages = Column(MutableJSONType, nullable=True)
+    dependencies: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
+    job_messages: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
     param_filename: Mapped[Optional[str]] = mapped_column(String(1024))
     runner_name: Mapped[Optional[str]] = mapped_column(String(255))
     job_stdout: Mapped[Optional[str]] = mapped_column(TEXT)
@@ -1353,13 +1353,13 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     job_runner_name: Mapped[Optional[str]] = mapped_column(String(255))
     job_runner_external_id: Mapped[Optional[str]] = mapped_column(String(255), index=True)
     destination_id: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
-    destination_params = Column(MutableJSONType, nullable=True)
+    destination_params: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
     object_store_id: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     imported: Mapped[Optional[bool]] = mapped_column(Boolean, default=False, index=True)
     params: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     handler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     preferred_object_store_id: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
-    object_store_id_overrides = Column(JSONType)
+    object_store_id_overrides: Mapped[Optional[bytes]] = mapped_column(JSONType)
 
     user = relationship("User")
     galaxy_session = relationship("GalaxySession")
@@ -2108,7 +2108,7 @@ class Task(Base, JobLike, RepresentById):
     tool_stdout: Mapped[Optional[str]] = mapped_column(TEXT)
     tool_stderr: Mapped[Optional[str]] = mapped_column(TEXT)
     exit_code: Mapped[Optional[int]] = mapped_column(Integer, nullable=True)
-    job_messages = Column(MutableJSONType, nullable=True)
+    job_messages: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
     info: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
     traceback: Mapped[Optional[str]] = mapped_column(TEXT)
     job_id: Mapped[int] = mapped_column(Integer, ForeignKey("job.id"), index=True, nullable=False)
@@ -2526,7 +2526,7 @@ class PostJobAction(Base, RepresentById):
     )
     action_type: Mapped[str] = mapped_column(String(255), nullable=False)
     output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
-    action_arguments = Column(MutableJSONType, nullable=True)
+    action_arguments: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
     workflow_step = relationship(
         "WorkflowStep",
         back_populates="post_job_actions",
@@ -2728,7 +2728,7 @@ class StoreExportAssociation(Base, RepresentById):
     create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
     object_type: Mapped[Optional[str]] = mapped_column(TrimmedString(32))
     object_id: Mapped[Optional[int]] = mapped_column(Integer)
-    export_metadata = Column(JSONType)
+    export_metadata: Mapped[Optional[bytes]] = mapped_column(JSONType)
 
 
 class JobContainerAssociation(Base, RepresentById):
@@ -2738,7 +2738,7 @@ class JobContainerAssociation(Base, RepresentById):
     job_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("job.id"), index=True)
     container_type: Mapped[Optional[str]] = mapped_column(TEXT)
     container_name: Mapped[Optional[str]] = mapped_column(TEXT)
-    container_info = Column(MutableJSONType, nullable=True)
+    container_info: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
     created_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
     modified_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now, onupdate=now)
     job = relationship("Job", back_populates="container")
@@ -2765,7 +2765,7 @@ class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById):
     requires_domain: Mapped[Optional[bool]] = mapped_column(Boolean, default=True)
     requires_path_in_url: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     requires_path_in_header_named: Mapped[Optional[str]] = mapped_column(TEXT)
-    info = Column(MutableJSONType, nullable=True)
+    info: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
     configured: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     deleted: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     created_time: Mapped[Optional[datetime]] = mapped_column(DateTime, default=now)
@@ -2900,7 +2900,7 @@ class Notification(Base, Dictifiable, RepresentById):
     )  # Defines the 'importance' of the notification ('info', 'warning', 'urgent', etc.). Used for filtering, highlight rendering, etc
     # A bug in early 23.1 led to values being stored as json string, so we use this special type to process the result value twice.
     # content should always be a dict
-    content = Column(DoubleEncodedJsonType)
+    content: Mapped[Optional[bytes]] = mapped_column(DoubleEncodedJsonType)
 
     user_notification_associations = relationship("UserNotificationAssociation", back_populates="notification")
 
@@ -4312,7 +4312,7 @@ class DatasetSource(Base, Dictifiable, Serializable):
     dataset_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("dataset.id"), index=True)
     source_uri: Mapped[Optional[str]] = mapped_column(TEXT)
     extra_files_path: Mapped[Optional[str]] = mapped_column(TEXT)
-    transform = Column(MutableJSONType)
+    transform: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     dataset = relationship("Dataset", back_populates="sources")
     hashes = relationship("DatasetSourceHash", back_populates="source")
     dict_collection_visible_keys = ["id", "source_uri", "extra_files_path", "transform"]
@@ -6017,7 +6017,7 @@ class ExtendedMetadata(Base, RepresentById):
     __tablename__ = "extended_metadata"
 
     id: Mapped[int] = mapped_column(Integer, primary_key=True)
-    data = Column(MutableJSONType)
+    data: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     children = relationship("ExtendedMetadataIndex", back_populates="extended_metadata")
 
     def __init__(self, data):
@@ -7628,10 +7628,10 @@ class Workflow(Base, Dictifiable, RepresentById):
     name: Mapped[Optional[str]] = mapped_column(TEXT)
     has_cycles: Mapped[Optional[bool]] = mapped_column(Boolean)
     has_errors: Mapped[Optional[bool]] = mapped_column(Boolean)
-    reports_config = Column(JSONType)
-    creator_metadata = Column(JSONType)
+    reports_config: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    creator_metadata: Mapped[Optional[bytes]] = mapped_column(JSONType)
     license: Mapped[Optional[str]] = mapped_column(TEXT)
-    source_metadata = Column(JSONType)
+    source_metadata: Mapped[Optional[bytes]] = mapped_column(JSONType)
     uuid: Mapped[Optional[str]] = mapped_column(UUIDType, nullable=True)
 
     steps = relationship(
@@ -7813,12 +7813,12 @@ class WorkflowStep(Base, RepresentById):
     type: Mapped[Optional[str]] = mapped_column(String(64))
     tool_id: Mapped[Optional[str]] = mapped_column(TEXT)
     tool_version: Mapped[Optional[str]] = mapped_column(TEXT)
-    tool_inputs = Column(JSONType)
-    tool_errors = Column(JSONType)
-    position = Column(MutableJSONType)
-    config = Column(JSONType)
+    tool_inputs: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    tool_errors: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    position: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
+    config: Mapped[Optional[bytes]] = mapped_column(JSONType)
     order_index: Mapped[Optional[int]] = mapped_column(Integer)
-    when_expression = Column(JSONType)
+    when_expression: Mapped[Optional[bytes]] = mapped_column(JSONType)
     uuid: Mapped[Optional[str]] = mapped_column(UUIDType)
     label: Mapped[Optional[str]] = mapped_column(Unicode(255))
     temp_input_connections = None
@@ -8124,9 +8124,9 @@ class WorkflowStepInput(Base, RepresentById):
     name: Mapped[Optional[str]] = mapped_column(TEXT)
     merge_type: Mapped[Optional[str]] = mapped_column(TEXT)
     scatter_type: Mapped[Optional[str]] = mapped_column(TEXT)
-    value_from = Column(MutableJSONType)
+    value_from: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     value_from_type: Mapped[Optional[str]] = mapped_column(TEXT)
-    default_value = Column(MutableJSONType)
+    default_value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     default_value_set: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     runtime_value: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
 
@@ -8267,11 +8267,11 @@ class WorkflowComment(Base, RepresentById):
     id: Mapped[int] = mapped_column(Integer, primary_key=True)
     order_index: Mapped[Optional[int]] = mapped_column(Integer)
     workflow_id: Mapped[int] = mapped_column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
-    position = Column(MutableJSONType)
-    size = Column(JSONType)
+    position: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
+    size: Mapped[Optional[bytes]] = mapped_column(JSONType)
     type: Mapped[Optional[str]] = mapped_column(String(16))
     color: Mapped[Optional[str]] = mapped_column(String(16))
-    data = Column(JSONType)
+    data: Mapped[Optional[bytes]] = mapped_column(JSONType)
     parent_comment_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_comment.id"), nullable=True)
 
     workflow = relationship(
@@ -9036,7 +9036,7 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
     implicit_collection_jobs_id: Mapped[Optional[int]] = mapped_column(
         Integer, ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True
     )
-    action = Column(MutableJSONType, nullable=True)
+    action: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
 
     workflow_step = relationship("WorkflowStep")
     job = relationship("Job", back_populates="workflow_invocation_step", uselist=False)
@@ -9271,7 +9271,7 @@ class WorkflowRequestStepState(Base, Dictifiable, Serializable):
         Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE"), index=True
     )
     workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"))
-    value = Column(MutableJSONType)
+    value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     workflow_step = relationship("WorkflowStep")
     workflow_invocation = relationship("WorkflowInvocation", back_populates="step_states")
 
@@ -9355,7 +9355,7 @@ class WorkflowRequestInputStepParameter(Base, Dictifiable, Serializable):
         Integer, ForeignKey("workflow_invocation.id"), index=True
     )
     workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"))
-    parameter_value = Column(MutableJSONType)
+    parameter_value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
 
     workflow_step = relationship("WorkflowStep")
     workflow_invocation = relationship("WorkflowInvocation", back_populates="input_step_parameters")
@@ -9444,7 +9444,7 @@ class WorkflowInvocationOutputValue(Base, Dictifiable, Serializable):
     )
     workflow_step_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_step.id"))
     workflow_output_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("workflow_output.id"), index=True)
-    value = Column(MutableJSONType)
+    value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
 
     workflow_invocation = relationship("WorkflowInvocation", back_populates="output_values")
 
@@ -9611,9 +9611,9 @@ class FormDefinition(Base, Dictifiable, RepresentById):
     form_definition_current_id: Mapped[int] = mapped_column(
         Integer, ForeignKey("form_definition_current.id", use_alter=True), index=True, nullable=False
     )
-    fields = Column(MutableJSONType)
+    fields: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     type: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
-    layout = Column(MutableJSONType)
+    layout: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     form_definition_current = relationship(
         "FormDefinitionCurrent",
         back_populates="forms",
@@ -9703,7 +9703,7 @@ class FormValues(Base, RepresentById):
     create_time: Mapped[datetime] = mapped_column(DateTime, default=now, nullable=True)
     update_time: Mapped[datetime] = mapped_column(DateTime, default=now, onupdate=now, nullable=True)
     form_definition_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("form_definition.id"), index=True)
-    content = Column(MutableJSONType)
+    content: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     form_definition = relationship(
         "FormDefinition", primaryjoin=(lambda: FormValues.form_definition_id == FormDefinition.id)
     )
@@ -9931,7 +9931,7 @@ class UserAuthnzToken(Base, UserMixin, RepresentById):
     user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
     uid: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
     provider: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
-    extra_data: Mapped[Optional[str]] = mapped_column(MutableJSONType, nullable=True)
+    extra_data: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
     lifetime: Mapped[Optional[int]] = mapped_column(Integer)
     assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))
     user = relationship("User", back_populates="social_auth")
@@ -10108,9 +10108,9 @@ class CloudAuthz(Base):
     id: Mapped[int] = mapped_column(Integer, primary_key=True)
     user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
     provider: Mapped[Optional[str]] = mapped_column(String(255))
-    config = Column(MutableJSONType)
+    config: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     authn_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True)
-    tokens = Column(MutableJSONType)
+    tokens: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     last_update: Mapped[Optional[datetime]] = mapped_column(DateTime)
     last_activity: Mapped[Optional[datetime]] = mapped_column(DateTime)
     description: Mapped[Optional[str]] = mapped_column(TEXT)
@@ -10379,7 +10379,7 @@ class VisualizationRevision(Base, RepresentById):
     visualization_id: Mapped[int] = mapped_column(Integer, ForeignKey("visualization.id"), index=True, nullable=False)
     title: Mapped[Optional[str]] = mapped_column(TEXT)
     dbkey: Mapped[Optional[str]] = mapped_column(TEXT)
-    config = Column(MutableJSONType)
+    config: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     visualization = relationship(
         "Visualization",
         back_populates="revisions",
diff --git a/lib/galaxy/model/deferred.py b/lib/galaxy/model/deferred.py
index e72d4e126aca..18f5804375c8 100644
--- a/lib/galaxy/model/deferred.py
+++ b/lib/galaxy/model/deferred.py
@@ -174,12 +174,12 @@ def ensure_materialized(
 
     def _stream_source(self, target_source: DatasetSource, datatype) -> str:
         path = stream_url_to_file(target_source.source_uri, file_sources=self._file_sources)
-        transform = target_source.transform or []
+        transform = target_source.transform or []  # type:ignore[var-annotated]
         to_posix_lines = False
         spaces_to_tabs = False
         datatype_groom = False
         for transform_action in transform:
-            action = transform_action["action"]
+            action = transform_action["action"]  # type:ignore[index]
             if action == "to_posix_lines":
                 to_posix_lines = True
             elif action == "spaces_to_tabs":
diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py
index 4ec5d103158d..05b30ec97ab4 100644
--- a/lib/galaxy/model/store/discover.py
+++ b/lib/galaxy/model/store/discover.py
@@ -463,7 +463,7 @@ def override_object_store_id(self, output_name: Optional[str] = None) -> Optiona
             return None
         default_object_store_id = job.object_store_id
         object_store_id_overrides = job.object_store_id_overrides or {}
-        return object_store_id_overrides.get(output_name, default_object_store_id)
+        return object_store_id_overrides.get(output_name, default_object_store_id)  # type:ignore[union-attr]
 
     @property
     @abc.abstractmethod
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index a345abde954a..9c7412156499 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -104,7 +104,7 @@ def handle_library_params(
         template = session.get(FormDefinition, template_id)
         assert template
         for field in template.fields:
-            field_name = field["name"]
+            field_name = field["name"]  # type:ignore[index]
             if params.get(field_name, False):
                 field_value = util.restore_text(params.get(field_name, ""))
                 template_field_contents[field_name] = field_value
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index 029b1e7630c6..a45e7e441ec0 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -113,7 +113,7 @@ def _normalize_inputs(
             elif inputs_by_el == "step_uuid":
                 possible_input_keys.append(str(step.uuid))
             elif inputs_by_el == "name":
-                possible_input_keys.append(step.label or step.tool_inputs.get("name"))
+                possible_input_keys.append(step.label or step.tool_inputs.get("name"))  # type:ignore[union-attr]
             else:
                 raise exceptions.MessageException(
                     "Workflow cannot be run because unexpected inputs_by value specified."
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 4181757d81f0..00379b0b9ce4 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -365,7 +365,7 @@ class Repository(Base, Dictifiable):
     user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
     private: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
-    email_alerts = Column(MutableJSONType, nullable=True)
+    email_alerts: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
     times_downloaded: Mapped[Optional[int]] = mapped_column(Integer)
     deprecated: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
     categories = relationship("RepositoryCategoryAssociation", back_populates="repository")

From eb1aa47861a5a693fdec4ff4c5c8a2576cb99b2a Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 19 Jan 2024 10:45:58 -0500
Subject: [PATCH 07/71] Use correct type hints to define common model attrs

---
 lib/galaxy/model/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 985ad66c484b..3421ef8967a6 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -261,7 +261,7 @@ def __declare_last__(cls):
 
 
 class RepresentById:
-    id: int
+    id: Mapped[int]
 
     def __repr__(self):
         try:
@@ -420,7 +420,7 @@ def get_display_name(self):
 
 
 class UsesCreateAndUpdateTime:
-    update_time: DateTime
+    update_time: Mapped[Optional[datetime]]
 
     @property
     def seconds_since_updated(self):

From ab406e7e6b23fc8f945f19c58cdc798f1756da59 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 16 Jan 2024 18:45:39 -0500
Subject: [PATCH 08/71] Start applying Mapped to relationship definitions in
 the model

---
 lib/galaxy/model/__init__.py | 76 +++++++++++++++++++++---------------
 1 file changed, 45 insertions(+), 31 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 3421ef8967a6..156c28ab0a3b 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -307,7 +307,7 @@ def set_datatypes_registry(d_registry):
 class HasTags:
     dict_collection_visible_keys = ["tags"]
     dict_element_visible_keys = ["tags"]
-    tags: List["ItemTagAssociation"]
+    tags: Mapped[List["ItemTagAssociation"]]
 
     def to_dict(self, *args, **kwargs):
         rval = super().to_dict(*args, **kwargs)
@@ -704,29 +704,33 @@ class User(Base, Dictifiable, RepresentById):
     active: Mapped[bool] = mapped_column(Boolean, index=True, default=True, nullable=False)
     activation_token: Mapped[Optional[str]] = mapped_column(TrimmedString(64), nullable=True, index=True)
 
-    addresses = relationship(
+    addresses: Mapped[List["UserAddress"]] = relationship(
         "UserAddress", back_populates="user", order_by=lambda: desc(UserAddress.update_time), cascade_backrefs=False
     )
     cloudauthz = relationship("CloudAuthz", back_populates="user")
     custos_auth = relationship("CustosAuthnzToken", back_populates="user")
-    default_permissions = relationship("DefaultUserPermissions", back_populates="user")
-    groups = relationship("UserGroupAssociation", back_populates="user")
-    histories = relationship(
+    default_permissions: Mapped[List["DefaultUserPermissions"]] = relationship(
+        "DefaultUserPermissions", back_populates="user"
+    )
+    groups: Mapped[List["UserGroupAssociation"]] = relationship("UserGroupAssociation", back_populates="user")
+    histories: Mapped[List["History"]] = relationship(
         "History", back_populates="user", order_by=lambda: desc(History.update_time), cascade_backrefs=False  # type: ignore[has-type]
     )
-    active_histories = relationship(
+    active_histories: Mapped[List["History"]] = relationship(
         "History",
         primaryjoin=(lambda: (History.user_id == User.id) & (not_(History.deleted)) & (not_(History.archived))),  # type: ignore[has-type]
         viewonly=True,
         order_by=lambda: desc(History.update_time),  # type: ignore[has-type]
     )
-    galaxy_sessions = relationship(
+    galaxy_sessions: Mapped[List["GalaxySession"]] = relationship(
         "GalaxySession", back_populates="user", order_by=lambda: desc(GalaxySession.update_time), cascade_backrefs=False  # type: ignore[has-type]
     )
-    quotas = relationship("UserQuotaAssociation", back_populates="user")
-    quota_source_usages = relationship("UserQuotaSourceUsage", back_populates="user")
+    quotas: Mapped[List["UserQuotaAssociation"]] = relationship("UserQuotaAssociation", back_populates="user")
+    quota_source_usages: Mapped[List["UserQuotaSourceUsage"]] = relationship(
+        "UserQuotaSourceUsage", back_populates="user"
+    )
     social_auth = relationship("UserAuthnzToken", back_populates="user")
-    stored_workflow_menu_entries = relationship(
+    stored_workflow_menu_entries: Mapped[List["StoredWorkflowMenuEntry"]] = relationship(
         "StoredWorkflowMenuEntry",
         primaryjoin=(
             lambda: (StoredWorkflowMenuEntry.user_id == User.id)
@@ -737,12 +741,14 @@ class User(Base, Dictifiable, RepresentById):
         cascade="all, delete-orphan",
         collection_class=ordering_list("order_index"),
     )
-    _preferences = relationship("UserPreference", collection_class=attribute_mapped_collection("name"))
-    values = relationship(
+    _preferences: Mapped[List["UserPreference"]] = relationship(
+        "UserPreference", collection_class=attribute_mapped_collection("name")
+    )
+    values: Mapped[List["FormValues"]] = relationship(
         "FormValues", primaryjoin=(lambda: User.form_values_id == FormValues.id)  # type: ignore[has-type]
     )
     # Add type hint (will this work w/SA?)
-    api_keys = relationship(
+    api_keys: Mapped[List["APIKeys"]] = relationship(
         "APIKeys",
         back_populates="user",
         order_by=lambda: desc(APIKeys.create_time),
@@ -753,16 +759,20 @@ class User(Base, Dictifiable, RepresentById):
             )
         ),
     )
-    data_manager_histories = relationship("DataManagerHistoryAssociation", back_populates="user")
-    roles = relationship("UserRoleAssociation", back_populates="user")
-    stored_workflows = relationship(
+    data_manager_histories: Mapped[List["DataManagerHistoryAssociation"]] = relationship(
+        "DataManagerHistoryAssociation", back_populates="user"
+    )
+    roles: Mapped[List["UserRoleAssociation"]] = relationship("UserRoleAssociation", back_populates="user")
+    stored_workflows: Mapped[List["StoredWorkflow"]] = relationship(
         "StoredWorkflow",
         back_populates="user",
         primaryjoin=(lambda: User.id == StoredWorkflow.user_id),  # type: ignore[has-type]
         cascade_backrefs=False,
     )
-    all_notifications = relationship("UserNotificationAssociation", back_populates="user", cascade_backrefs=False)
-    non_private_roles = relationship(
+    all_notifications: Mapped[List["UserNotificationAssociation"]] = relationship(
+        "UserNotificationAssociation", back_populates="user", cascade_backrefs=False
+    )
+    non_private_roles: Mapped[List["UserRoleAssociation"]] = relationship(
         "UserRoleAssociation",
         viewonly=True,
         primaryjoin=(
@@ -3052,7 +3062,9 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         order_by=lambda: asc(HistoryDatasetCollectionAssociation.hid),  # type: ignore[has-type]
         viewonly=True,
     )
-    tags = relationship("HistoryTagAssociation", order_by=lambda: HistoryTagAssociation.id, back_populates="history")
+    tags: Mapped[List["HistoryTagAssociation"]] = relationship(
+        "HistoryTagAssociation", order_by=lambda: HistoryTagAssociation.id, back_populates="history"
+    )
     annotations = relationship(
         "HistoryAnnotationAssociation", order_by=lambda: HistoryAnnotationAssociation.id, back_populates="history"
     )
@@ -3550,7 +3562,7 @@ def __filter_contents(self, content_class, **kwds):
 
 
 class UserShareAssociation(RepresentById):
-    user: Optional[User]
+    user: Mapped[User]
 
 
 class HistoryUserShareAssociation(Base, UserShareAssociation):
@@ -3559,7 +3571,7 @@ class HistoryUserShareAssociation(Base, UserShareAssociation):
     id: Mapped[int] = mapped_column(Integer, primary_key=True)
     history_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("history.id"), index=True)
     user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user = relationship("User")
+    user: Mapped[User] = relationship("User")
     history = relationship("History", back_populates="users_shared_with")
 
 
@@ -6768,7 +6780,7 @@ class HistoryDatasetCollectionAssociation(
         back_populates="history_dataset_collection_associations",
         uselist=False,
     )
-    tags = relationship(
+    tags: Mapped[List["HistoryDatasetCollectionTagAssociation"]] = relationship(
         "HistoryDatasetCollectionTagAssociation",
         order_by=lambda: HistoryDatasetCollectionTagAssociation.id,
         back_populates="dataset_collection",
@@ -7114,7 +7126,7 @@ class LibraryDatasetCollectionAssociation(Base, DatasetCollectionInstance, Repre
     collection = relationship("DatasetCollection")
     folder = relationship("LibraryFolder")
 
-    tags = relationship(
+    tags: Mapped[List["LibraryDatasetCollectionTagAssociation"]] = relationship(
         "LibraryDatasetCollectionTagAssociation",
         order_by=lambda: LibraryDatasetCollectionTagAssociation.id,
         back_populates="dataset_collection",
@@ -7474,12 +7486,12 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
         primaryjoin=(lambda: StoredWorkflow.latest_workflow_id == Workflow.id),  # type: ignore[has-type]
         lazy=False,
     )
-    tags = relationship(
+    tags: Mapped[List["StoredWorkflowTagAssociation"]] = relationship(
         "StoredWorkflowTagAssociation",
         order_by=lambda: StoredWorkflowTagAssociation.id,
         back_populates="stored_workflow",
     )
-    owner_tags = relationship(
+    owner_tags: Mapped[List["StoredWorkflowTagAssociation"]] = relationship(
         "StoredWorkflowTagAssociation",
         primaryjoin=(
             lambda: and_(
@@ -7836,7 +7848,7 @@ class WorkflowStep(Base, RepresentById):
         back_populates="parent_workflow_steps",
     )
     dynamic_tool = relationship("DynamicTool", primaryjoin=(lambda: DynamicTool.id == WorkflowStep.dynamic_tool_id))
-    tags = relationship(
+    tags: Mapped[List["WorkflowStepTagAssociation"]] = relationship(
         "WorkflowStepTagAssociation", order_by=lambda: WorkflowStepTagAssociation.id, back_populates="workflow_step"
     )
     annotations = relationship(
@@ -8338,7 +8350,7 @@ class StoredWorkflowUserShareAssociation(Base, UserShareAssociation):
     id: Mapped[int] = mapped_column(Integer, primary_key=True)
     stored_workflow_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("stored_workflow.id"), index=True)
     user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user = relationship("User")
+    user: Mapped[User] = relationship("User")
     stored_workflow = relationship("StoredWorkflow", back_populates="users_shared_with")
 
 
@@ -10167,7 +10179,9 @@ class Page(Base, HasTags, Dictifiable, RepresentById):
         primaryjoin=(lambda: Page.latest_revision_id == PageRevision.id),  # type: ignore[has-type]
         lazy=False,
     )
-    tags = relationship("PageTagAssociation", order_by=lambda: PageTagAssociation.id, back_populates="page")
+    tags: Mapped[List["PageTagAssociation"]] = relationship(
+        "PageTagAssociation", order_by=lambda: PageTagAssociation.id, back_populates="page"
+    )
     annotations = relationship(
         "PageAnnotationAssociation", order_by=lambda: PageAnnotationAssociation.id, back_populates="page"
     )
@@ -10248,7 +10262,7 @@ class PageUserShareAssociation(Base, UserShareAssociation):
     id: Mapped[int] = mapped_column(Integer, primary_key=True)
     page_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("page.id"), index=True)
     user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user = relationship("User")
+    user: Mapped[User] = relationship("User")
     page = relationship("Page", back_populates="users_shared_with")
 
 
@@ -10290,7 +10304,7 @@ class Visualization(Base, HasTags, Dictifiable, RepresentById):
         primaryjoin=(lambda: Visualization.latest_revision_id == VisualizationRevision.id),
         lazy=False,
     )
-    tags = relationship(
+    tags: Mapped[List["VisualizationTagAssociation"]] = relationship(
         "VisualizationTagAssociation", order_by=lambda: VisualizationTagAssociation.id, back_populates="visualization"
     )
     annotations = relationship(
@@ -10404,7 +10418,7 @@ class VisualizationUserShareAssociation(Base, UserShareAssociation):
     id: Mapped[int] = mapped_column(Integer, primary_key=True)
     visualization_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("visualization.id"), index=True)
     user_id: Mapped[Optional[int]] = mapped_column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user = relationship("User")
+    user: Mapped[User] = relationship("User")
     visualization = relationship("Visualization", back_populates="users_shared_with")
 
 

From 3441e9609637e6c805c76d82a6026c686d4dab57 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 24 Jan 2024 16:10:42 -0500
Subject: [PATCH 09/71] Remove column declaration from HasTags parent class

---
 lib/galaxy/model/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 156c28ab0a3b..5f3f83a7edca 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -307,7 +307,6 @@ def set_datatypes_registry(d_registry):
 class HasTags:
     dict_collection_visible_keys = ["tags"]
     dict_element_visible_keys = ["tags"]
-    tags: Mapped[List["ItemTagAssociation"]]
 
     def to_dict(self, *args, **kwargs):
         rval = super().to_dict(*args, **kwargs)

From 84f9fb7e18d72a3c5490865796293c9b17b34db0 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 19 Dec 2023 13:44:25 -0500
Subject: [PATCH 10/71] Fix SA2.0 error: wrap sql in text()

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 5f3f83a7edca..d7d1f3f73518 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -942,7 +942,7 @@ def get_disk_usage(self, nice_size=False, quota_source_label=None):
                 "user_id": self.id,
                 "label": quota_source_label,
             }
-            row = sa_session.execute(statement, params).fetchone()
+            row = sa_session.execute(text(statement), params).fetchone()
             if row is not None:
                 rval = row[0]
             else:

From 595af2efabf08161c0128f70ca1abe2b6b31b218 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 19 Dec 2023 15:43:49 -0500
Subject: [PATCH 11/71] Fix SA2.0 error: pass bind to create_all

---
 lib/tool_shed/webapp/model/mapping.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/lib/tool_shed/webapp/model/mapping.py b/lib/tool_shed/webapp/model/mapping.py
index 0da07ef195c1..0ef27ff7f8b9 100644
--- a/lib/tool_shed/webapp/model/mapping.py
+++ b/lib/tool_shed/webapp/model/mapping.py
@@ -35,13 +35,11 @@ def init(
     engine_options = engine_options or {}
     # Create the database engine
     engine = build_engine(url, engine_options)
-    # Connect the metadata to the database.
-    metadata.bind = engine
 
     result = ToolShedModelMapping([tool_shed.webapp.model], engine=engine)
 
     if create_tables:
-        metadata.create_all()
+        metadata.create_all(bind=engine)
 
     result.create_tables = create_tables
 

From d08a047b508a27b5d2384b17b61a4950855781da Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 19 Dec 2023 15:57:59 -0500
Subject: [PATCH 12/71] Fix SA2.0 error: use Row._mapping for keyed attribute
 access

Ref: https://docs.sqlalchemy.org/en/20/changelog/migration_20.html#result-rows-act-like-named-tuples
---
 test/unit/app/managers/test_NotificationManager.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/unit/app/managers/test_NotificationManager.py b/test/unit/app/managers/test_NotificationManager.py
index 82b339f05792..c8c011160a83 100644
--- a/test/unit/app/managers/test_NotificationManager.py
+++ b/test/unit/app/managers/test_NotificationManager.py
@@ -264,8 +264,8 @@ def test_get_user_notification(self):
         actual_user_notification = self.notification_manager.get_user_notification(user, notification.id)
 
         self._assert_notification_expected(actual_user_notification, expected_user_notification)
-        assert actual_user_notification["seen_time"] is None
-        assert actual_user_notification["deleted"] is False
+        assert actual_user_notification._mapping["seen_time"] is None
+        assert actual_user_notification._mapping["deleted"] is False
 
     def test_update_user_notifications(self):
         user = self._create_test_user()

From 03ad73ccecb4616ac47cb629018c8aaa14500272 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 20 Dec 2023 11:39:46 -0500
Subject: [PATCH 13/71] Fix SA2.0 error: show password in url

SA 1.4: str(url) renders connection string with password
SA 2.0: str(url) renders connection string WITHOUT password
Solution: Use render_as_string(hide_password=False)
---
 lib/galaxy/model/unittest_utils/model_testing_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/unittest_utils/model_testing_utils.py b/lib/galaxy/model/unittest_utils/model_testing_utils.py
index 3f13dd79f731..2f8d71babc54 100644
--- a/lib/galaxy/model/unittest_utils/model_testing_utils.py
+++ b/lib/galaxy/model/unittest_utils/model_testing_utils.py
@@ -263,4 +263,4 @@ def _make_sqlite_db_url(tmpdir: str, database: str) -> DbUrl:
 def _make_postgres_db_url(connection_url: DbUrl, database: str) -> DbUrl:
     url = make_url(connection_url)
     url = url.set(database=database)
-    return DbUrl(str(url))
+    return DbUrl(url.render_as_string(hide_password=False))

From 0c46858a57c59f0f75cb892b1a31f8904a0f1387 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 24 Jan 2024 11:52:45 -0500
Subject: [PATCH 14/71] Fix SA2.0 error: use attribute_keyed_dict

Replaces attribute_mapped_collection (SA20)
---
 lib/galaxy/model/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index d7d1f3f73518..ffd1d37540bd 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -113,7 +113,7 @@
     relationship,
 )
 from sqlalchemy.orm.attributes import flag_modified
-from sqlalchemy.orm.collections import attribute_mapped_collection
+from sqlalchemy.orm.collections import attribute_keyed_dict
 from sqlalchemy.sql import exists
 from typing_extensions import (
     Literal,
@@ -741,7 +741,7 @@ class User(Base, Dictifiable, RepresentById):
         collection_class=ordering_list("order_index"),
     )
     _preferences: Mapped[List["UserPreference"]] = relationship(
-        "UserPreference", collection_class=attribute_mapped_collection("name")
+        "UserPreference", collection_class=attribute_keyed_dict("name")
     )
     values: Mapped[List["FormValues"]] = relationship(
         "FormValues", primaryjoin=(lambda: User.form_values_id == FormValues.id)  # type: ignore[has-type]

From b9d2886dacad699dae7fce83a5cc9e1e3251ec02 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 25 Jan 2024 13:06:09 -0500
Subject: [PATCH 15/71] Fix SA2.0 error: make select stmt a subquery

Rename varable to fix mypy
---
 lib/galaxy/managers/jobs.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 102d8b04f591..97073e9df46d 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -360,7 +360,7 @@ def replace_dataset_ids(path, key, value):
 
         # build one subquery that selects a job with correct job parameters
 
-        subq = select(model.Job.id).where(
+        stmt = select(model.Job.id).where(
             and_(
                 model.Job.tool_id == tool_id,
                 model.Job.user_id == user.id,
@@ -368,22 +368,22 @@ def replace_dataset_ids(path, key, value):
             )
         )
         if tool_version:
-            subq = subq.where(Job.tool_version == str(tool_version))
+            stmt = stmt.where(Job.tool_version == str(tool_version))
 
         if job_state is None:
-            subq = subq.where(
+            stmt = stmt.where(
                 Job.state.in_(
                     [Job.states.NEW, Job.states.QUEUED, Job.states.WAITING, Job.states.RUNNING, Job.states.OK]
                 )
             )
         else:
             if isinstance(job_state, str):
-                subq = subq.where(Job.state == job_state)
+                stmt = stmt.where(Job.state == job_state)
             elif isinstance(job_state, list):
-                subq = subq.where(or_(*[Job.state == s for s in job_state]))
+                stmt = stmt.where(or_(*[Job.state == s for s in job_state]))
 
         # exclude jobs with deleted outputs
-        subq = subq.where(
+        stmt = stmt.where(
             and_(
                 model.Job.any_output_dataset_collection_instances_deleted == false(),
                 model.Job.any_output_dataset_deleted == false(),
@@ -403,7 +403,7 @@ def replace_dataset_ids(path, key, value):
             wildcard_value = value_dump.replace('"id": "__id_wildcard__"', '"id": %')
             a = aliased(JobParameter)
             if value_dump == wildcard_value:
-                subq = subq.join(a).where(
+                stmt = stmt.join(a).where(
                     and_(
                         Job.id == a.job_id,
                         a.name == k,
@@ -411,7 +411,7 @@ def replace_dataset_ids(path, key, value):
                     )
                 )
             else:
-                subq = subq.join(a).where(
+                stmt = stmt.join(a).where(
                     and_(
                         Job.id == a.job_id,
                         a.name == k,
@@ -419,7 +419,8 @@ def replace_dataset_ids(path, key, value):
                     )
                 )
 
-        query = select(Job.id).select_from(Job.table.join(subq, subq.c.id == Job.id))
+        stmt_sq = stmt.subquery()
+        query = select(Job.id).select_from(Job.table.join(stmt_sq, stmt_sq.c.id == Job.id))
 
         data_conditions = []
 

From 6b3bca48b5df8ee3d926b0b6933972dd88fc1ca1 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 7 Feb 2024 14:16:46 -0500
Subject: [PATCH 16/71] Fix SA2.0 error: explicitly use subquery() for
 select-from argument

---
 lib/galaxy/model/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index ffd1d37540bd..3cdfa1f3eb4b 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1216,8 +1216,8 @@ def quota_source_usage_for(self, quota_source_label: Optional[str]) -> Optional[
         return None
 
     def count_stored_workflow_user_assocs(self, stored_workflow) -> int:
-        stmt = select(StoredWorkflowUserShareAssociation).filter_by(user=self, stored_workflow=stored_workflow)
-        stmt = select(func.count()).select_from(stmt)
+        sq = select(StoredWorkflowUserShareAssociation).filter_by(user=self, stored_workflow=stored_workflow).subquery()
+        stmt = select(func.count()).select_from(sq)
         session = object_session(self)
         return session.scalar(stmt)
 

From d478e0800d48d7b52e6fdd9e87f5f3d66ed3dc5e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 12 Feb 2024 13:41:12 -0500
Subject: [PATCH 17/71] Fix SA2.0 error: replase session.bind with
 session.get_bind()

---
 lib/galaxy/quota/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/quota/__init__.py b/lib/galaxy/quota/__init__.py
index 0c81d75f9466..3f0b55cda645 100644
--- a/lib/galaxy/quota/__init__.py
+++ b/lib/galaxy/quota/__init__.py
@@ -4,7 +4,6 @@
 from typing import Optional
 
 from sqlalchemy import select
-from sqlalchemy.orm import object_session
 from sqlalchemy.sql import text
 
 import galaxy.util
@@ -198,7 +197,7 @@ def relabel_quota_for_dataset(self, dataset, from_label: Optional[str], to_label
     WHERE
         dataset_id = :dataset_id
 )"""
-        engine = object_session(dataset).bind
+        engine = self.sa_session.get_bind()
 
         # Hack for older sqlite, would work on newer sqlite - 3.24.0
         for_sqlite = "sqlite" in engine.dialect.name

From 2d49d6995ef09ab35a0c17624fe7d8802152c70a Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 12 Feb 2024 14:18:02 -0500
Subject: [PATCH 18/71] Fix SA2.0 error: joinedload does not take str args

---
 scripts/cleanup_datasets/cleanup_datasets.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/cleanup_datasets/cleanup_datasets.py b/scripts/cleanup_datasets/cleanup_datasets.py
index a373e551ff14..81fd7801f5da 100755
--- a/scripts/cleanup_datasets/cleanup_datasets.py
+++ b/scripts/cleanup_datasets/cleanup_datasets.py
@@ -261,7 +261,7 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
         histories = (
             app.sa_session.query(app.model.History)
             .filter(and_(app.model.History.__table__.c.deleted == true(), app.model.History.update_time < cutoff_time))
-            .options(joinedload("datasets"))
+            .options(joinedload(app.model.History.datasets))
         )
     else:
         histories = (
@@ -273,7 +273,7 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
                     app.model.History.update_time < cutoff_time,
                 )
             )
-            .options(joinedload("datasets"))
+            .options(joinedload(app.model.History.datasets))
         )
     for history in histories:
         log.info("### Processing history id %d (%s)", history.id, unicodify(history.name))

From fb526d45d3d19d1f2065160d1d0055eff11a6549 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 17 Jan 2024 10:42:33 -0500
Subject: [PATCH 19/71] Fix use of table model attribute

- Use __table__ (SA attr) instead of table (galaxy attr) on mapped classes
- Drop .table and .table.c where redundant
---
 lib/galaxy/model/__init__.py                  | 22 ++++-----
 lib/galaxy/model/item_attrs.py                |  6 +--
 .../galaxy_install/install_manager.py         |  2 +-
 .../installed_repository_metadata_manager.py  |  8 ++--
 .../update_repository_manager.py              |  2 +-
 lib/galaxy/tool_shed/util/repository_util.py  | 26 +++++------
 lib/galaxy/web/framework/helpers/grids.py     |  2 +-
 lib/galaxy/web/legacy_framework/grids.py      | 10 ++--
 .../galaxy/services/tool_shed_repositories.py |  2 +-
 lib/tool_shed/grids/repository_grids.py       | 46 +++++++++----------
 lib/tool_shed/webapp/model/__init__.py        |  2 +
 11 files changed, 63 insertions(+), 65 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 3cdfa1f3eb4b..24701f176c29 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1700,7 +1700,7 @@ def set_state(self, state: JobState) -> bool:
         if session and self.id and state not in Job.finished_states:
             # generate statement that will not revert DELETING or DELETED back to anything non-terminal
             rval = session.execute(
-                update(Job.table)
+                update(Job)
                 .where(Job.id == self.id, ~Job.state.in_((Job.states.DELETING, Job.states.DELETED)))
                 .values(state=state)
             )
@@ -1941,12 +1941,12 @@ def update_hdca_update_time_for_job(self, update_time, sa_session, supports_skip
             subq = subq.with_for_update(skip_locked=True).subquery()
         implicit_statement = (
             HistoryDatasetCollectionAssociation.table.update()
-            .where(HistoryDatasetCollectionAssociation.table.c.id.in_(select(subq)))
+            .where(HistoryDatasetCollectionAssociation.id.in_(select(subq)))
             .values(update_time=update_time)
         )
         explicit_statement = (
             HistoryDatasetCollectionAssociation.table.update()
-            .where(HistoryDatasetCollectionAssociation.table.c.job_id == self.id)
+            .where(HistoryDatasetCollectionAssociation.job_id == self.id)
             .values(update_time=update_time)
         )
         sa_session.execute(explicit_statement)
@@ -3429,17 +3429,17 @@ def disk_size(cls):
         # .expression acts as a column_property and should return a scalar
         # first, get the distinct datasets within a history that are not purged
         hda_to_dataset_join = join(
-            HistoryDatasetAssociation, Dataset, HistoryDatasetAssociation.table.c.dataset_id == Dataset.table.c.id
+            HistoryDatasetAssociation, Dataset, HistoryDatasetAssociation.dataset_id == Dataset.id
         )
         distinct_datasets = (
             select(
                 # use labels here to better access from the query above
-                HistoryDatasetAssociation.table.c.history_id.label("history_id"),
+                HistoryDatasetAssociation.history_id.label("history_id"),
                 Dataset.total_size.label("dataset_size"),
                 Dataset.id.label("dataset_id"),
             )
-            .where(HistoryDatasetAssociation.table.c.purged != true())
-            .where(Dataset.table.c.purged != true())
+            .where(HistoryDatasetAssociation.purged != true())
+            .where(Dataset.purged != true())
             .select_from(hda_to_dataset_join)
             # TODO: slow (in general) but most probably here - index total_size for easier sorting/distinct?
             .distinct()
@@ -8498,7 +8498,7 @@ def set_state(self, state: InvocationState):
         if session and self.id and state not in priority_states:
             # generate statement that will not revert CANCELLING or CANCELLED back to anything non-terminal
             session.execute(
-                update(WorkflowInvocation.table)
+                update(WorkflowInvocation)
                 .where(
                     WorkflowInvocation.id == self.id,
                     or_(~WorkflowInvocation.state.in_(priority_states), WorkflowInvocation.state.is_(None)),
@@ -8527,7 +8527,7 @@ def cancel_invocation_steps(self):
             .filter(~Job.state.in_(Job.finished_states))
             .with_for_update()
         )
-        sa_session.execute(update(Job.table).where(Job.id.in_(job_subq)).values({"state": Job.states.DELETING}))
+        sa_session.execute(update(Job).where(Job.id.in_(job_subq)).values({"state": Job.states.DELETING}))
 
         job_collection_subq = (
             select(Job.id)
@@ -8543,9 +8543,7 @@ def cancel_invocation_steps(self):
         )
 
         sa_session.execute(
-            update(Job.table)
-            .where(Job.table.c.id.in_(job_collection_subq.element))
-            .values({"state": Job.states.DELETING})
+            update(Job).where(Job.id.in_(job_collection_subq.element)).values({"state": Job.states.DELETING})
         )
 
         for invocation in self.subworkflow_invocations:
diff --git a/lib/galaxy/model/item_attrs.py b/lib/galaxy/model/item_attrs.py
index e361d5458441..37a467f5dde7 100644
--- a/lib/galaxy/model/item_attrs.py
+++ b/lib/galaxy/model/item_attrs.py
@@ -180,12 +180,12 @@ def _get_annotation_assoc_class(item):
 def get_foreign_key(source_class, target_class):
     """Returns foreign key in source class that references target class."""
     target_fk = None
-    for fk in source_class.table.foreign_keys:
-        if fk.references(target_class.table):
+    for fk in source_class.__table__.foreign_keys:
+        if fk.references(target_class.__table__):
             target_fk = fk
             break
     if not target_fk:
-        raise Exception(f"No foreign key found between objects: {source_class.table}, {target_class.table}")
+        raise Exception(f"No foreign key found between objects: {source_class.__table__}, {target_class.__table__}")
     return target_fk
 
 
diff --git a/lib/galaxy/tool_shed/galaxy_install/install_manager.py b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
index d97a586c08f0..9c45ea79e7fc 100644
--- a/lib/galaxy/tool_shed/galaxy_install/install_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
@@ -328,7 +328,7 @@ def initiate_repository_installation(self, installation_dict):
             tool_shed_repositories.append(tsr)
         clause_list = []
         for tsr_id in tsr_ids:
-            clause_list.append(self.install_model.ToolShedRepository.table.c.id == tsr_id)
+            clause_list.append(self.install_model.ToolShedRepository.id == tsr_id)
         query = self.install_model.context.query(self.install_model.ToolShedRepository).filter(or_(*clause_list))
         return encoded_kwd, query, tool_shed_repositories, encoded_repository_ids
 
diff --git a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
index aea14cacdd93..bf7e3ccbd33e 100644
--- a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
@@ -86,15 +86,15 @@ def get_query_for_setting_metadata_on_repositories(self, order=True):
         if order:
             return (
                 self.app.install_model.context.query(self.app.install_model.ToolShedRepository)
-                .filter(self.app.install_model.ToolShedRepository.table.c.uninstalled == false())
+                .filter(self.app.install_model.ToolShedRepository.uninstalled == false())
                 .order_by(
-                    self.app.install_model.ToolShedRepository.table.c.name,
-                    self.app.install_model.ToolShedRepository.table.c.owner,
+                    self.app.install_model.ToolShedRepository.name,
+                    self.app.install_model.ToolShedRepository.owner,
                 )
             )
         else:
             return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).filter(
-                self.app.install_model.ToolShedRepository.table.c.uninstalled == false()
+                self.app.install_model.ToolShedRepository.uninstalled == false()
             )
 
     def get_repository_tools_tups(self):
diff --git a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
index 42f86250f563..e7ac8399b88b 100644
--- a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
@@ -75,7 +75,7 @@ def __restarter(self) -> None:
             # the repository revision is the latest installable revision, and whether the repository
             # has been deprecated in the Tool Shed.
             for repository in self.context.query(self.app.install_model.ToolShedRepository).filter(
-                self.app.install_model.ToolShedRepository.table.c.deleted == false()
+                self.app.install_model.ToolShedRepository.deleted == false()
             ):
                 tool_shed_status_dict = get_tool_shed_status_for_installed_repository(self.app, repository)
                 if tool_shed_status_dict:
diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
index 11e9a675039d..dc5734a089aa 100644
--- a/lib/galaxy/tool_shed/util/repository_util.py
+++ b/lib/galaxy/tool_shed/util/repository_util.py
@@ -48,9 +48,7 @@ def check_for_updates(
         success_count = 0
         repository_names_not_updated = []
         updated_count = 0
-        for repository in install_model_context.query(ToolShedRepository).filter(
-            ToolShedRepository.table.c.deleted == false()
-        ):
+        for repository in install_model_context.query(ToolShedRepository).filter(ToolShedRepository.deleted == false()):
             ok, updated = _check_or_update_tool_shed_status_for_installed_repository(
                 tool_shed_registry, install_model_context, repository
             )
@@ -298,18 +296,18 @@ def get_installed_repository(
             )
     query = app.install_model.context.query(app.install_model.ToolShedRepository)
     if repository_id:
-        clause_list = [app.install_model.ToolShedRepository.table.c.id == repository_id]
+        clause_list = [app.install_model.ToolShedRepository.id == repository_id]
     else:
         clause_list = [
-            app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
-            app.install_model.ToolShedRepository.table.c.name == name,
-            app.install_model.ToolShedRepository.table.c.owner == owner,
+            app.install_model.ToolShedRepository.tool_shed == tool_shed,
+            app.install_model.ToolShedRepository.name == name,
+            app.install_model.ToolShedRepository.owner == owner,
         ]
     if changeset_revision is not None:
-        clause_list.append(app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision)
+        clause_list.append(app.install_model.ToolShedRepository.changeset_revision == changeset_revision)
     if installed_changeset_revision is not None:
         clause_list.append(
-            app.install_model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision
+            app.install_model.ToolShedRepository.installed_changeset_revision == installed_changeset_revision
         )
     return query.filter(and_(*clause_list)).first()
 
@@ -443,16 +441,16 @@ def get_repository_by_name_and_owner(app, name, owner, eagerload_columns=None):
     if is_tool_shed_client(app):
         return repository_query.filter(
             and_(
-                app.install_model.ToolShedRepository.table.c.name == name,
-                app.install_model.ToolShedRepository.table.c.owner == owner,
+                app.install_model.ToolShedRepository.name == name,
+                app.install_model.ToolShedRepository.owner == owner,
             )
         ).first()
     # We're in the tool shed.
     q = repository_query.filter(
         and_(
-            app.model.Repository.table.c.name == name,
-            app.model.User.table.c.username == owner,
-            app.model.Repository.table.c.user_id == app.model.User.table.c.id,
+            app.model.Repository.name == name,
+            app.model.User.username == owner,
+            app.model.Repository.user_id == app.model.User.id,
         )
     )
     if eagerload_columns:
diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py
index 98795511186d..ea01f1efd098 100644
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -52,7 +52,7 @@ def sort(self, trans, query, ascending, column_name=None):
             column_name = self.key
         column = getattr(self.model_class, column_name)
         if column is None:
-            column = self.model_class.table.c.get(column_name)
+            column = self.model_class.__table__.c.get(column_name)
         if ascending:
             query = query.order_by(column.asc())
         else:
diff --git a/lib/galaxy/web/legacy_framework/grids.py b/lib/galaxy/web/legacy_framework/grids.py
index 3b62e8665012..dcaff6fa12e6 100644
--- a/lib/galaxy/web/legacy_framework/grids.py
+++ b/lib/galaxy/web/legacy_framework/grids.py
@@ -112,9 +112,9 @@ def sort(self, trans, query, ascending, column_name=None):
         if column_name is None:
             column_name = self.key
         if ascending:
-            query = query.order_by(self.model_class.table.c.get(column_name).asc())
+            query = query.order_by(self.model_class.__table__.c.get(column_name).asc())
         else:
-            query = query.order_by(self.model_class.table.c.get(column_name).desc())
+            query = query.order_by(self.model_class.__table__.c.get(column_name).desc())
         return query
 
 
@@ -165,9 +165,9 @@ def sort(self, trans, query, ascending, column_name=None):
         if column_name is None:
             column_name = self.key
         if ascending:
-            query = query.order_by(func.lower(self.model_class.table.c.get(column_name)).asc())
+            query = query.order_by(func.lower(self.model_class.__table__.c.get(column_name)).asc())
         else:
-            query = query.order_by(func.lower(self.model_class.table.c.get(column_name)).desc())
+            query = query.order_by(func.lower(self.model_class.__table__.c.get(column_name)).desc())
         return query
 
 
@@ -236,7 +236,7 @@ def sort(self, trans, query, ascending, column_name=None):
         item_rating_assoc_class = getattr(trans.model, f"{self.model_class.__name__}RatingAssociation")
         foreign_key = get_foreign_key(item_rating_assoc_class, self.model_class)
         fk_col = foreign_key.parent
-        referent_col = foreign_key.get_referent(self.model_class.table)
+        referent_col = foreign_key.get_referent(self.model_class.__table__)
         # Do sorting using a subquery.
         # Subquery to get average rating for each item.
         ave_rating_subquery = (
diff --git a/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
index 630ad5325bd9..f827c0ee999b 100644
--- a/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
@@ -74,7 +74,7 @@ def _get_tool_shed_repositories(self, **kwd):
         stmt = select(ToolShedRepository)
         for key, value in kwd.items():
             if value is not None:
-                column = ToolShedRepository.table.c[key]
+                column = ToolShedRepository.__table__.c[key]
                 stmt = stmt.filter(column == value)
         stmt = stmt.order_by(ToolShedRepository.name).order_by(cast(ToolShedRepository.ctx_rev, Integer).desc())
         session = self._install_model_context
diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index 5c80c185ff38..691959f32916 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -237,7 +237,7 @@ def build_initial_query(self, trans, **kwd):
                 .join(model.RepositoryMetadata.table)
                 .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
@@ -247,7 +247,7 @@ def build_initial_query(self, trans, **kwd):
                 .join(model.RepositoryMetadata.table)
                 .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
         else:
@@ -258,7 +258,7 @@ def build_initial_query(self, trans, **kwd):
                     and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())
                 )
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
 
@@ -458,7 +458,7 @@ def build_initial_query(self, trans, **kwd):
                 .join(model.RepositoryMetadata.table)
                 .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
@@ -473,7 +473,7 @@ def build_initial_query(self, trans, **kwd):
                 .join(model.RepositoryMetadata.table)
                 .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
         else:
@@ -488,7 +488,7 @@ def build_initial_query(self, trans, **kwd):
                     )
                 )
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
 
@@ -538,7 +538,7 @@ def build_initial_query(self, trans, **kwd):
                         .join(model.RepositoryMetadata.table)
                         .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                         .join(model.User.table)
-                        .outerjoin(model.RepositoryCategoryAssociation.table)
+                        .outerjoin(model.RepositoryCategoryAssociation)
                         .outerjoin(model.Category.table)
                         .filter(model.Category.table.c.name == category.name)
                     )
@@ -547,7 +547,7 @@ def build_initial_query(self, trans, **kwd):
                 .join(model.RepositoryMetadata.table)
                 .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
@@ -560,7 +560,7 @@ def build_initial_query(self, trans, **kwd):
                         .join(model.RepositoryMetadata.table)
                         .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                         .join(model.User.table)
-                        .outerjoin(model.RepositoryCategoryAssociation.table)
+                        .outerjoin(model.RepositoryCategoryAssociation)
                         .outerjoin(model.Category.table)
                         .filter(model.Category.table.c.name == category.name)
                     )
@@ -570,7 +570,7 @@ def build_initial_query(self, trans, **kwd):
                 .join(model.RepositoryMetadata.table)
                 .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
         else:
@@ -587,7 +587,7 @@ def build_initial_query(self, trans, **kwd):
                             )
                         )
                         .join(model.User.table)
-                        .outerjoin(model.RepositoryCategoryAssociation.table)
+                        .outerjoin(model.RepositoryCategoryAssociation)
                         .outerjoin(model.Category.table)
                         .filter(model.Category.table.c.name == category.name)
                     )
@@ -597,7 +597,7 @@ def build_initial_query(self, trans, **kwd):
                     and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())
                 )
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
             )
 
@@ -632,7 +632,7 @@ def build_initial_query(self, trans, **kwd):
                 and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.user_id == trans.user.id)
             )
             .join(model.User.table)
-            .outerjoin(model.RepositoryCategoryAssociation.table)
+            .outerjoin(model.RepositoryCategoryAssociation)
             .outerjoin(model.Category.table)
         )
 
@@ -680,11 +680,11 @@ def build_initial_query(self, trans, **kwd):
         return (
             trans.sa_session.query(model.Repository)
             .filter(model.Repository.table.c.deleted == false())
-            .outerjoin(model.RepositoryRoleAssociation.table)
+            .outerjoin(model.RepositoryRoleAssociation)
             .outerjoin(model.Role.table)
             .filter(or_(*clause_list))
             .join(model.User.table)
-            .outerjoin(model.RepositoryCategoryAssociation.table)
+            .outerjoin(model.RepositoryCategoryAssociation)
             .outerjoin(model.Category.table)
         )
 
@@ -835,7 +835,7 @@ def build_initial_query(self, trans, **kwd):
                 )
             )
             .join(model.User.table)
-            .outerjoin(model.RepositoryCategoryAssociation.table)
+            .outerjoin(model.RepositoryCategoryAssociation)
             .outerjoin(model.Category.table)
         )
 
@@ -1477,11 +1477,11 @@ def build_initial_query(self, trans, **kwd):
                     .join(model.RepositoryMetadata.table)
                     .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                     .join(model.User.table)
-                    .join(model.RepositoryCategoryAssociation.table)
+                    .join(model.RepositoryCategoryAssociation)
                     .join(model.Category.table)
                     .filter(
                         and_(
-                            model.Category.table.c.id == trans.security.decode_id(kwd["id"]),
+                            model.Category.__table__.c.id == trans.security.decode_id(kwd["id"]),
                             model.RepositoryMetadata.table.c.downloadable == true(),
                         )
                     )
@@ -1493,7 +1493,7 @@ def build_initial_query(self, trans, **kwd):
                     .join(model.RepositoryMetadata.table)
                     .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                     .join(model.User.table)
-                    .join(model.RepositoryCategoryAssociation.table)
+                    .join(model.RepositoryCategoryAssociation)
                     .join(model.Category.table)
                     .filter(
                         and_(
@@ -1513,7 +1513,7 @@ def build_initial_query(self, trans, **kwd):
                     )
                     .join(model.RepositoryMetadata.table)
                     .join(model.User.table)
-                    .join(model.RepositoryCategoryAssociation.table)
+                    .join(model.RepositoryCategoryAssociation)
                     .join(model.Category.table)
                     .filter(
                         and_(
@@ -1529,7 +1529,7 @@ def build_initial_query(self, trans, **kwd):
                 .join(model.RepositoryMetadata.table)
                 .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
                 .filter(model.RepositoryMetadata.table.c.downloadable == true())
             )
@@ -1540,7 +1540,7 @@ def build_initial_query(self, trans, **kwd):
                 .join(model.RepositoryMetadata.table)
                 .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
                 .filter(model.RepositoryMetadata.table.c.downloadable == true())
             )
@@ -1553,7 +1553,7 @@ def build_initial_query(self, trans, **kwd):
                 )
                 .join(model.RepositoryMetadata.table)
                 .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.RepositoryCategoryAssociation)
                 .outerjoin(model.Category.table)
                 .filter(model.RepositoryMetadata.table.c.downloadable == true())
             )
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 00379b0b9ce4..84dee54ccf93 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -81,6 +81,8 @@ class Base(metaclass=DeclarativeMeta):
     registry = mapper_registry
     metadata = mapper_registry.metadata
     __init__ = mapper_registry.constructor
+    table: Table
+    __table__: Table
 
     @classmethod
     def __declare_last__(cls):

From e2ded65701b8eb32bfa02893ea36c1f87e9f7f66 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 19 Jan 2024 12:08:29 -0500
Subject: [PATCH 20/71] Fix bug: fix HistoryAudit model

It is not a child of RepresentById becuase it does not and should not have an id attr.

Duplicating the __repr__ definition in the HistoryAudit class is a
temporary fix: a proper fix requires changing all models (id and
__repr__ should be split into 2 mixins): to be done in a follow-up PR.
---
 lib/galaxy/model/__init__.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 24701f176c29..3320a8297b4f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2943,7 +2943,7 @@ def is_hda(d):
     return isinstance(d, HistoryDatasetAssociation)
 
 
-class HistoryAudit(Base, RepresentById):
+class HistoryAudit(Base):
     __tablename__ = "history_audit"
     __table_args__ = (PrimaryKeyConstraint(sqlite_on_conflict="IGNORE"),)
 
@@ -2954,6 +2954,14 @@ class HistoryAudit(Base, RepresentById):
     # See https://github.com/galaxyproject/galaxy/pull/11914 for details.
     __init__ = None  # type: ignore[assignment]
 
+    def __repr__(self):
+        try:
+            r = f"<galaxy.model.{self.__class__.__name__}({cached_id(self)}) at {hex(id(self))}>"
+        except Exception:
+            r = object.__repr__(self)
+            log.exception("Caught exception attempting to generate repr for: %s", r)
+        return r
+
     @classmethod
     def prune(cls, sa_session):
         latest_subq = (

From d679453feea2401e6c64f1ac440989477923efae Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 5 Feb 2024 11:59:16 -0500
Subject: [PATCH 21/71] Fix bug: check if template.fields is not null before
 iterating

---
 lib/galaxy/tools/actions/upload_common.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index 9c7412156499..ab7cc544f787 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -102,12 +102,12 @@ def handle_library_params(
     template: Optional[FormDefinition] = None
     if template_id not in [None, "None"]:
         template = session.get(FormDefinition, template_id)
-        assert template
-        for field in template.fields:
-            field_name = field["name"]  # type:ignore[index]
-            if params.get(field_name, False):
-                field_value = util.restore_text(params.get(field_name, ""))
-                template_field_contents[field_name] = field_value
+        if template and template.fields:
+            for field in template.fields:
+                field_name = field["name"]  # type:ignore[index]
+                if params.get(field_name, False):
+                    field_value = util.restore_text(params.get(field_name, ""))
+                    template_field_contents[field_name] = field_value
     roles: List[Role] = []
     for role_id in util.listify(params.get("roles", [])):
         role = session.get(Role, role_id)

From 1551a23f80e77ae96386026a5e5a48d10a6f3dad Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 9 Feb 2024 16:07:03 -0500
Subject: [PATCH 22/71] Fix bug: call unique() on result, not select stmt

---
 lib/galaxy/tools/actions/upload_common.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index ab7cc544f787..b1f9a8f22a44 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -441,7 +441,6 @@ def active_folders(trans, folder):
         select(LibraryFolder)
         .filter_by(parent=folder, deleted=False)
         .options(joinedload(LibraryFolder.actions))
-        .unique()
         .order_by(LibraryFolder.name)
     )
-    return trans.sa_session.scalars(stmt).all()
+    return trans.sa_session.scalars(stmt).unique().all()

From fbdfaa6027fe079e7a4f9e51e9563055f51206bf Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 9 Feb 2024 16:12:56 -0500
Subject: [PATCH 23/71] Fix bug: do not pass subquery to in_

---
 lib/galaxy/managers/notification.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/notification.py b/lib/galaxy/managers/notification.py
index e2e78a793029..4f11742dec69 100644
--- a/lib/galaxy/managers/notification.py
+++ b/lib/galaxy/managers/notification.py
@@ -304,7 +304,7 @@ def cleanup_expired_notifications(self) -> CleanupResultSummary:
 
         expired_notifications_stmt = select(Notification.id).where(notification_has_expired)
         delete_stmt = delete(UserNotificationAssociation).where(
-            UserNotificationAssociation.notification_id.in_(expired_notifications_stmt.subquery())
+            UserNotificationAssociation.notification_id.in_(expired_notifications_stmt)
         )
         result = self.sa_session.execute(delete_stmt, execution_options={"synchronize_session": False})
         deleted_associations_count = result.rowcount

From 3883f34f996e5b88f1587055de76ce41dc905332 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 9 Feb 2024 16:16:18 -0500
Subject: [PATCH 24/71] Fix bug/typo: use select_from

---
 lib/galaxy/webapps/galaxy/controllers/tag.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/tag.py b/lib/galaxy/webapps/galaxy/controllers/tag.py
index 04f315202da9..05dda97f1ebe 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tag.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tag.py
@@ -140,7 +140,7 @@ def _get_tag_autocomplete_values(self, trans, q, limit, timestamp, user=None, it
         # Do query and get result set.
         query = (
             select(item_tag_assoc_class.table.c.value, func.count())
-            .select_from_obj(from_obj)
+            .select_from(from_obj)
             .where(where_clause)
             .group_by(item_tag_assoc_class.table.c.value)
             .order_by(func.count().desc(), item_tag_assoc_class.table.c.value)

From 4a8cf032df7af1c9cacd84c24b3720dec1b7e593 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 9 Feb 2024 16:40:52 -0500
Subject: [PATCH 25/71] Fix bug: if using alias on ORM entity, use __table__ as
 valid FromClause

---
 lib/galaxy/model/__init__.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 3320a8297b4f..afde68ca3fe9 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -6338,8 +6338,8 @@ def _build_nested_collection_attributes_stmt(
         dataset_permission_attributes = dataset_permission_attributes or ()
         return_entities = return_entities or ()
         dataset_collection = self
-        dc = alias(DatasetCollection)
-        dce = alias(DatasetCollectionElement)
+        dc = alias(DatasetCollection.__table__)
+        dce = alias(DatasetCollectionElement.__table__)
         depth_collection_type = dataset_collection.collection_type
         order_by_columns = [dce.c.element_index]
         nesting_level = 0
@@ -6360,8 +6360,8 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
 
         while ":" in depth_collection_type:
             nesting_level += 1
-            inner_dc = alias(DatasetCollection)
-            inner_dce = alias(DatasetCollectionElement)
+            inner_dc = alias(DatasetCollection.__table__)
+            inner_dce = alias(DatasetCollectionElement.__table__)
             order_by_columns.append(inner_dce.c.element_index)
             q = q.join(
                 inner_dc, and_(inner_dc.c.id == dce.c.child_collection_id, dce.c.dataset_collection_id == dc.c.id)

From efce1c71d54d8c08981be2c0fb2aeb739194a7c9 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 25 Jan 2024 17:06:47 -0500
Subject: [PATCH 26/71] Fix bug: HDAH model is not serializable (caught by
 mypy)

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index afde68ca3fe9..31ac81b25969 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -5417,7 +5417,7 @@ def type_id(cls):
         return (type_coerce(cls.content_type, Unicode) + "-" + type_coerce(cls.id, Unicode)).label("type_id")
 
 
-class HistoryDatasetAssociationHistory(Base, Serializable):
+class HistoryDatasetAssociationHistory(Base):
     __tablename__ = "history_dataset_association_history"
 
     id: Mapped[int] = mapped_column(Integer, primary_key=True)

From f6b22691426cf7cd8156365f7756666c0fd4b5c1 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 23 Jan 2024 14:57:13 -0500
Subject: [PATCH 27/71] Fix typing error: migrations.base

---
 lib/galaxy/model/migrations/base.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/migrations/base.py b/lib/galaxy/model/migrations/base.py
index 973f12224936..e03257d3f522 100644
--- a/lib/galaxy/model/migrations/base.py
+++ b/lib/galaxy/model/migrations/base.py
@@ -33,7 +33,6 @@
 )
 from sqlalchemy.engine import (
     Connection,
-    CursorResult,
     Engine,
 )
 
@@ -398,10 +397,11 @@ def _load_db_metadata(self, conn: Connection) -> MetaData:
         metadata.reflect(bind=conn)
         return metadata
 
-    def _load_sqlalchemymigrate_version(self, conn: Connection) -> CursorResult:
+    def _load_sqlalchemymigrate_version(self, conn: Connection) -> Optional[int]:
         if self.has_sqlalchemymigrate_version_table():
             sql = text(f"select version from {SQLALCHEMYMIGRATE_TABLE}")
             return conn.execute(sql).scalar()
+        return None
 
 
 def pop_arg_from_args(args: List[str], arg_name) -> Optional[str]:

From 28b25eabe5b969f1b2026dd50dbcce4ee599c12c Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 24 Jan 2024 16:27:39 -0500
Subject: [PATCH 28/71] Fix typing error: managers.secured

This fixed 58 mypy errors!
---
 lib/galaxy/managers/secured.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/secured.py b/lib/galaxy/managers/secured.py
index 30958ceb8c92..20d95b8a8217 100644
--- a/lib/galaxy/managers/secured.py
+++ b/lib/galaxy/managers/secured.py
@@ -40,7 +40,7 @@ def is_accessible(self, item: "Query", user: model.User, **kwargs: Any) -> bool:
         # override in subclasses
         raise exceptions.NotImplemented("Abstract interface Method")
 
-    def get_accessible(self, id: int, user: model.User, **kwargs: Any) -> "Query":
+    def get_accessible(self, id: int, user: model.User, **kwargs: Any):
         """
         Return the item with the given id if it's accessible to user,
         otherwise raise an error.

From 0f4ad52bf757737e700fe79d04bd58dd5bf94b6b Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 25 Jan 2024 10:07:46 -0500
Subject: [PATCH 29/71] Fix typing error: session type

---
 lib/galaxy/celery/base_task.py                  |  7 +++----
 lib/galaxy/managers/dbkeys.py                   |  4 ++--
 lib/galaxy/managers/group_roles.py              |  4 ++--
 lib/galaxy/managers/group_users.py              |  4 ++--
 lib/galaxy/managers/groups.py                   |  5 ++---
 lib/galaxy/managers/jobs.py                     |  7 ++-----
 lib/galaxy/managers/pages.py                    | 14 ++++++--------
 lib/galaxy/managers/roles.py                    |  8 +++-----
 lib/galaxy/managers/users.py                    |  4 ++--
 lib/galaxy/webapps/galaxy/services/histories.py |  4 ++--
 lib/galaxy/webapps/galaxy/services/quotas.py    |  4 ++--
 11 files changed, 28 insertions(+), 37 deletions(-)

diff --git a/lib/galaxy/celery/base_task.py b/lib/galaxy/celery/base_task.py
index 410d6d4d2bfe..af032fec1821 100644
--- a/lib/galaxy/celery/base_task.py
+++ b/lib/galaxy/celery/base_task.py
@@ -11,7 +11,6 @@
 )
 from sqlalchemy.dialects.postgresql import insert as ps_insert
 from sqlalchemy.exc import IntegrityError
-from sqlalchemy.orm import Session
 
 from galaxy.model import CeleryUserRateLimit
 from galaxy.model.base import transaction
@@ -70,7 +69,7 @@ def __call__(self, task: Task, task_id, args, kwargs):
 
     @abstractmethod
     def calculate_task_start_time(
-        self, user_id: int, sa_session: Session, task_interval_secs: float, now: datetime.datetime
+        self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         return now
 
@@ -99,7 +98,7 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
     )
 
     def calculate_task_start_time(  # type: ignore
-        self, user_id: int, sa_session: Session, task_interval_secs: float, now: datetime.datetime
+        self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         with transaction(sa_session):
             result = sa_session.execute(
@@ -138,7 +137,7 @@ class GalaxyTaskBeforeStartUserRateLimitStandard(GalaxyTaskBeforeStartUserRateLi
     )
 
     def calculate_task_start_time(
-        self, user_id: int, sa_session: Session, task_interval_secs: float, now: datetime.datetime
+        self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         last_scheduled_time = None
         with transaction(sa_session):
diff --git a/lib/galaxy/managers/dbkeys.py b/lib/galaxy/managers/dbkeys.py
index 8ec01e3d57bd..99168133a69e 100644
--- a/lib/galaxy/managers/dbkeys.py
+++ b/lib/galaxy/managers/dbkeys.py
@@ -14,9 +14,9 @@
 )
 
 from sqlalchemy import select
-from sqlalchemy.orm import Session
 
 from galaxy.model import HistoryDatasetAssociation
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.util import (
     galaxy_directory,
     sanitize_lists_to_string,
@@ -166,6 +166,6 @@ def get_chrom_info(self, dbkey, trans=None, custom_build_hack_get_len_from_fasta
         return (chrom_info, db_dataset)
 
 
-def get_len_files_by_history(session: Session, history_id: int):
+def get_len_files_by_history(session: galaxy_scoped_session, history_id: int):
     stmt = select(HistoryDatasetAssociation).filter_by(history_id=history_id, extension="len", deleted=False)
     return session.scalars(stmt)
diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index 984a5c48f9ab..c942bbe7431a 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -5,13 +5,13 @@
 )
 
 from sqlalchemy import select
-from sqlalchemy.orm import Session
 
 from galaxy import model
 from galaxy.exceptions import ObjectNotFound
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.model import GroupRoleAssociation
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.structured_app import MinimalManagerApp
 
 log = logging.getLogger(__name__)
@@ -93,7 +93,7 @@ def _remove_role_from_group(self, trans: ProvidesAppContext, group_role: model.G
             trans.sa_session.commit()
 
 
-def get_group_role(session: Session, group, role) -> Optional[GroupRoleAssociation]:
+def get_group_role(session: galaxy_scoped_session, group, role) -> Optional[GroupRoleAssociation]:
     stmt = (
         select(GroupRoleAssociation).where(GroupRoleAssociation.group == group).where(GroupRoleAssociation.role == role)
     )
diff --git a/lib/galaxy/managers/group_users.py b/lib/galaxy/managers/group_users.py
index e71eb8ecadcf..6bcd088fcc3f 100644
--- a/lib/galaxy/managers/group_users.py
+++ b/lib/galaxy/managers/group_users.py
@@ -5,7 +5,6 @@
 )
 
 from sqlalchemy import select
-from sqlalchemy.orm import Session
 
 from galaxy import model
 from galaxy.exceptions import ObjectNotFound
@@ -15,6 +14,7 @@
     UserGroupAssociation,
 )
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.structured_app import MinimalManagerApp
 
 log = logging.getLogger(__name__)
@@ -96,7 +96,7 @@ def _remove_user_from_group(self, trans: ProvidesAppContext, group_user: model.U
             trans.sa_session.commit()
 
 
-def get_group_user(session: Session, user, group) -> Optional[UserGroupAssociation]:
+def get_group_user(session: galaxy_scoped_session, user, group) -> Optional[UserGroupAssociation]:
     stmt = (
         select(UserGroupAssociation).where(UserGroupAssociation.user == user).where(UserGroupAssociation.group == group)
     )
diff --git a/lib/galaxy/managers/groups.py b/lib/galaxy/managers/groups.py
index 33de69670cf5..f600369e3184 100644
--- a/lib/galaxy/managers/groups.py
+++ b/lib/galaxy/managers/groups.py
@@ -2,7 +2,6 @@
     false,
     select,
 )
-from sqlalchemy.orm import Session
 
 from galaxy import model
 from galaxy.exceptions import (
@@ -152,11 +151,11 @@ def _get_group(self, sa_session: galaxy_scoped_session, group_id: int) -> model.
         return group
 
 
-def get_group_by_name(session: Session, name: str):
+def get_group_by_name(session: galaxy_scoped_session, name: str):
     stmt = select(Group).filter(Group.name == name).limit(1)
     return session.scalars(stmt).first()
 
 
-def get_not_deleted_groups(session: Session):
+def get_not_deleted_groups(session: galaxy_scoped_session):
     stmt = select(Group).where(Group.deleted == false())
     return session.scalars(stmt)
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 97073e9df46d..7b11d63f7d26 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -20,10 +20,7 @@
     or_,
     true,
 )
-from sqlalchemy.orm import (
-    aliased,
-    Session,
-)
+from sqlalchemy.orm import aliased
 from sqlalchemy.sql import select
 
 from galaxy import model
@@ -1069,7 +1066,7 @@ def summarize_job_outputs(job: model.Job, tool, params):
     return outputs
 
 
-def get_jobs_to_check_at_startup(session: Session, track_jobs_in_database: bool, config):
+def get_jobs_to_check_at_startup(session: galaxy_scoped_session, track_jobs_in_database: bool, config):
     if track_jobs_in_database:
         in_list = (Job.states.QUEUED, Job.states.RUNNING, Job.states.STOPPED)
     else:
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index da0d076305b0..e37866a61fb1 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -24,10 +24,7 @@
     select,
     true,
 )
-from sqlalchemy.orm import (
-    aliased,
-    Session,
-)
+from sqlalchemy.orm import aliased
 
 from galaxy import (
     exceptions,
@@ -64,6 +61,7 @@
     text_column_filter,
 )
 from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.schema import (
     CreatePagePayload,
     PageContentFormat,
@@ -644,12 +642,12 @@ def placeholderRenderForSave(trans: ProvidesHistoryContext, item_class, item_id,
     )
 
 
-def get_page_revision(session: Session, page_id: int):
+def get_page_revision(session: galaxy_scoped_session, page_id: int):
     stmt = select(PageRevision).filter_by(page_id=page_id)
     return session.scalars(stmt)
 
 
-def get_shared_pages(session: Session, user: User):
+def get_shared_pages(session: galaxy_scoped_session, user: User):
     stmt = (
         select(PageUserShareAssociation)
         .where(PageUserShareAssociation.user == user)
@@ -660,12 +658,12 @@ def get_shared_pages(session: Session, user: User):
     return session.scalars(stmt)
 
 
-def get_page(session: Session, user: User, slug: str):
+def get_page(session: galaxy_scoped_session, user: User, slug: str):
     stmt = _build_page_query(select(Page), user, slug)
     return session.scalars(stmt).first()
 
 
-def page_exists(session: Session, user: User, slug: str) -> bool:
+def page_exists(session: galaxy_scoped_session, user: User, slug: str) -> bool:
     stmt = _build_page_query(select(Page.id), user, slug)
     return session.scalars(stmt).first() is not None
 
diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index 89bf69815e2c..a12de13be181 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -9,10 +9,7 @@
     false,
     select,
 )
-from sqlalchemy.orm import (
-    exc as sqlalchemy_exceptions,
-    Session,
-)
+from sqlalchemy.orm import exc as sqlalchemy_exceptions
 
 from galaxy import model
 from galaxy.exceptions import (
@@ -26,6 +23,7 @@
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model import Role
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.schema import RoleDefinitionModel
 from galaxy.util import unicodify
 
@@ -162,6 +160,6 @@ def undelete(self, trans: ProvidesUserContext, role: model.Role) -> model.Role:
         return role
 
 
-def get_roles_by_ids(session: Session, role_ids):
+def get_roles_by_ids(session: galaxy_scoped_session, role_ids):
     stmt = select(Role).where(Role.id.in_(role_ids))
     return session.scalars(stmt).all()
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 8f4b9c428e82..40c32292f9fa 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -24,7 +24,6 @@
     select,
     true,
 )
-from sqlalchemy.orm import Session
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import (
@@ -46,6 +45,7 @@
     UserQuotaUsage,
 )
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.security.validate_user_input import (
     VALID_EMAIL_RE,
     validate_email,
@@ -873,7 +873,7 @@ def _add_parsers(self):
         self.fn_filter_parsers.update({})
 
 
-def get_users_by_ids(session: Session, user_ids):
+def get_users_by_ids(session: galaxy_scoped_session, user_ids):
     stmt = select(User).where(User.id.in_(user_ids))
     return session.scalars(stmt).all()
 
diff --git a/lib/galaxy/webapps/galaxy/services/histories.py b/lib/galaxy/webapps/galaxy/services/histories.py
index ab3fe0e69dc0..dd192b860f21 100644
--- a/lib/galaxy/webapps/galaxy/services/histories.py
+++ b/lib/galaxy/webapps/galaxy/services/histories.py
@@ -20,7 +20,6 @@
     select,
     true,
 )
-from sqlalchemy.orm import Session
 
 from galaxy import (
     exceptions as glx_exceptions,
@@ -45,6 +44,7 @@
 from galaxy.managers.users import UserManager
 from galaxy.model import HistoryDatasetAssociation
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.model.store import payload_to_source_uri
 from galaxy.schema import (
     FilterQueryParams,
@@ -820,7 +820,7 @@ def _get_export_record_data(self, history: model.History) -> Optional[WriteStore
         return None
 
 
-def get_fasta_hdas_by_history(session: Session, history_id: int):
+def get_fasta_hdas_by_history(session: galaxy_scoped_session, history_id: int):
     stmt = (
         select(HistoryDatasetAssociation)
         .filter_by(history_id=history_id, extension="fasta", deleted=False)
diff --git a/lib/galaxy/webapps/galaxy/services/quotas.py b/lib/galaxy/webapps/galaxy/services/quotas.py
index 290ee8056668..37ac0a3ceaf8 100644
--- a/lib/galaxy/webapps/galaxy/services/quotas.py
+++ b/lib/galaxy/webapps/galaxy/services/quotas.py
@@ -6,7 +6,6 @@
     select,
     true,
 )
-from sqlalchemy.orm import Session
 
 from galaxy import util
 from galaxy.managers.context import ProvidesUserContext
@@ -14,6 +13,7 @@
 from galaxy.managers.quotas import QuotaManager
 from galaxy.managers.users import get_user_by_email
 from galaxy.model import Quota
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.quota._schema import (
     CreateQuotaParams,
     CreateQuotaResult,
@@ -161,7 +161,7 @@ def get_group_id(item):
         payload["in_groups"] = list(map(str, new_in_groups))
 
 
-def get_quotas(session: Session, deleted: bool = False):
+def get_quotas(session: galaxy_scoped_session, deleted: bool = False):
     is_deleted = true()
     if not deleted:
         is_deleted = false()

From 36f3051fc36ce277ec9963c7695da7e46e4ec8d5 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 2 Feb 2024 11:05:22 -0500
Subject: [PATCH 30/71] Fix typing error: use Session instead of scoped_session

No need to pass around scoped_session as arguments
---
 lib/galaxy/managers/hdas.py                    | 2 +-
 lib/galaxy/model/deferred.py                   | 3 +--
 test/unit/data/test_dataset_materialization.py | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index c6176e2cac8d..863d6d9986c7 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -178,7 +178,7 @@ def materialize(self, request: MaterializeDatasetInstanceTaskRequest) -> None:
             True,  # attached...
             object_store=self.app.object_store,
             file_sources=self.app.file_sources,
-            sa_session=self.app.model.context,
+            sa_session=self.app.model.session(),
         )
         user = self.user_manager.by_id(request_user.user_id)
         if request.source == DatasetSourceType.hda:
diff --git a/lib/galaxy/model/deferred.py b/lib/galaxy/model/deferred.py
index 18f5804375c8..66a4c23f1d4a 100644
--- a/lib/galaxy/model/deferred.py
+++ b/lib/galaxy/model/deferred.py
@@ -11,7 +11,6 @@
 
 from sqlalchemy.orm import object_session
 from sqlalchemy.orm.exc import DetachedInstanceError
-from sqlalchemy.orm.scoping import scoped_session
 
 from galaxy.datatypes.sniff import (
     convert_function,
@@ -278,7 +277,7 @@ def materializer_factory(
     transient_path_mapper: Optional[TransientPathMapper] = None,
     transient_directory: Optional[str] = None,
     file_sources: Optional[ConfiguredFileSources] = None,
-    sa_session: Optional[scoped_session] = None,
+    sa_session: Optional[Session] = None,
 ) -> DatasetInstanceMaterializer:
     if object_store_populator is None and object_store is not None:
         object_store_populator = ObjectStorePopulator(object_store, None)
diff --git a/test/unit/data/test_dataset_materialization.py b/test/unit/data/test_dataset_materialization.py
index c107f2eb6bc8..9015b107539f 100644
--- a/test/unit/data/test_dataset_materialization.py
+++ b/test/unit/data/test_dataset_materialization.py
@@ -134,7 +134,7 @@ def test_deferred_hdas_basic_attached_from_detached_hda():
 
     assert deferred_hda.dataset.state == "deferred"
     materializer = materializer_factory(
-        True, object_store=fixture_context.app.object_store, sa_session=fixture_context.sa_session
+        True, object_store=fixture_context.app.object_store, sa_session=fixture_context.sa_session()
     )
     materialized_hda = materializer.ensure_materialized(deferred_hda)
     materialized_dataset = materialized_hda.dataset

From 6dde02fa5adacf2d651fe14b843e501784ff9892 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 9 Feb 2024 14:08:07 -0500
Subject: [PATCH 31/71] Fix typing error: sharable

---
 lib/galaxy/managers/sharable.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 0d106a9ae1b7..053c11562fe4 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -28,7 +28,10 @@
     true,
 )
 
-from galaxy import exceptions
+from galaxy import (
+    exceptions,
+    model,
+)
 from galaxy.managers import (
     annotatable,
     base,
@@ -91,7 +94,7 @@ def by_user(self, user: User, **kwargs: Any) -> List[Any]:
         return self.list(filters=filters, **kwargs)
 
     # .... owned/accessible interfaces
-    def is_owner(self, item: "Query", user: Optional[User], **kwargs: Any) -> bool:
+    def is_owner(self, item: model.Base, user: Optional[User], **kwargs: Any) -> bool:
         """
         Return true if this sharable belongs to `user` (or `user` is an admin).
         """

From 5aca5b425f3936802f4ccc4708378a9765ab5545 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 5 Feb 2024 23:23:39 -0500
Subject: [PATCH 32/71] Fix SA2.0 error: sqlalchemy exceptions import; minor
 mypy fix

---
 lib/galaxy/managers/base.py                   | 4 ++--
 lib/galaxy/managers/export_tracker.py         | 2 +-
 lib/galaxy/managers/folders.py                | 4 ++--
 lib/galaxy/managers/forms.py                  | 9 ++++++---
 lib/galaxy/managers/libraries.py              | 4 ++--
 lib/galaxy/managers/roles.py                  | 9 ++++++---
 lib/galaxy/managers/users.py                  | 2 +-
 lib/galaxy/model/store/_bco_convert_utils.py  | 1 +
 lib/galaxy/model/tags.py                      | 1 +
 lib/galaxy/tool_shed/util/repository_util.py  | 4 +++-
 lib/galaxy/webapps/base/webapp.py             | 2 +-
 lib/galaxy/webapps/galaxy/controllers/user.py | 2 +-
 lib/tool_shed/managers/groups.py              | 2 +-
 13 files changed, 28 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index c151852ee054..be487b4da675 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -318,9 +318,9 @@ def _one_with_recast_errors(self, query: Query) -> U:
         # overridden to raise serializable errors
         try:
             return query.one()
-        except sqlalchemy.orm.exc.NoResultFound:
+        except sqlalchemy.exc.NoResultFound:
             raise exceptions.ObjectNotFound(f"{self.model_class.__name__} not found")
-        except sqlalchemy.orm.exc.MultipleResultsFound:
+        except sqlalchemy.exc.MultipleResultsFound:
             raise exceptions.InconsistentDatabase(f"found more than one {self.model_class.__name__}")
 
     # NOTE: at this layer, all ids are expected to be decoded and in int form
diff --git a/lib/galaxy/managers/export_tracker.py b/lib/galaxy/managers/export_tracker.py
index 29ec780e0261..f0d6ae0d33f5 100644
--- a/lib/galaxy/managers/export_tracker.py
+++ b/lib/galaxy/managers/export_tracker.py
@@ -8,7 +8,7 @@
     and_,
     select,
 )
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.exc import NoResultFound
 from sqlalchemy.orm.scoping import scoped_session
 
 from galaxy.exceptions import ObjectNotFound
diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py
index 97f0f3ad4cac..29c465e95566 100644
--- a/lib/galaxy/managers/folders.py
+++ b/lib/galaxy/managers/folders.py
@@ -20,11 +20,11 @@
     or_,
     select,
 )
-from sqlalchemy.orm import aliased
-from sqlalchemy.orm.exc import (
+from sqlalchemy.exc import (
     MultipleResultsFound,
     NoResultFound,
 )
+from sqlalchemy.orm import aliased
 
 from galaxy import (
     model,
diff --git a/lib/galaxy/managers/forms.py b/lib/galaxy/managers/forms.py
index 989a7310fe65..fdbbd4985e7c 100644
--- a/lib/galaxy/managers/forms.py
+++ b/lib/galaxy/managers/forms.py
@@ -1,5 +1,8 @@
 from sqlalchemy import select
-from sqlalchemy.orm import exc as sqlalchemy_exceptions
+from sqlalchemy.exc import (
+    MultipleResultsFound,
+    NoResultFound,
+)
 
 from galaxy.exceptions import (
     InconsistentDatabase,
@@ -59,9 +62,9 @@ def get(self, trans: ProvidesUserContext, form_id: int) -> FormDefinitionCurrent
         try:
             stmt = select(FormDefinitionCurrent).where(FormDefinitionCurrent.id == form_id)
             form = self.session().execute(stmt).scalar_one()
-        except sqlalchemy_exceptions.MultipleResultsFound:
+        except MultipleResultsFound:
             raise InconsistentDatabase("Multiple forms found with the same id.")
-        except sqlalchemy_exceptions.NoResultFound:
+        except NoResultFound:
             raise RequestParameterInvalidException("No accessible form found with the id provided.")
         except Exception as e:
             raise InternalServerError(f"Error loading from the database.{unicodify(e)}")
diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py
index 45c1c582a074..2e7ff0efa128 100644
--- a/lib/galaxy/managers/libraries.py
+++ b/lib/galaxy/managers/libraries.py
@@ -19,11 +19,11 @@
     select,
     true,
 )
-from sqlalchemy.orm import Query
-from sqlalchemy.orm.exc import (
+from sqlalchemy.exc import (
     MultipleResultsFound,
     NoResultFound,
 )
+from sqlalchemy.orm import Query
 
 from galaxy import exceptions
 from galaxy.managers.folders import FolderManager
diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index a12de13be181..8dfdc7e2f11b 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -9,7 +9,10 @@
     false,
     select,
 )
-from sqlalchemy.orm import exc as sqlalchemy_exceptions
+from sqlalchemy.exc import (
+    MultipleResultsFound,
+    NoResultFound,
+)
 
 from galaxy import model
 from galaxy.exceptions import (
@@ -56,9 +59,9 @@ def get(self, trans: ProvidesUserContext, role_id: int) -> model.Role:
         try:
             stmt = select(self.model_class).where(self.model_class.id == role_id)
             role = self.session().execute(stmt).scalar_one()
-        except sqlalchemy_exceptions.MultipleResultsFound:
+        except MultipleResultsFound:
             raise InconsistentDatabase("Multiple roles found with the same id.")
-        except sqlalchemy_exceptions.NoResultFound:
+        except NoResultFound:
             raise ObjectNotFound("No accessible role found with the id provided.")
         except Exception as e:
             raise InternalServerError(f"Error loading from the database.{unicodify(e)}")
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 40c32292f9fa..f92b82b68c10 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -24,7 +24,7 @@
     select,
     true,
 )
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.exc import NoResultFound
 
 from galaxy import (
     exceptions,
diff --git a/lib/galaxy/model/store/_bco_convert_utils.py b/lib/galaxy/model/store/_bco_convert_utils.py
index 82bb952b47f5..1763b2851665 100644
--- a/lib/galaxy/model/store/_bco_convert_utils.py
+++ b/lib/galaxy/model/store/_bco_convert_utils.py
@@ -27,6 +27,7 @@ def register_step(self, step: WorkflowStep) -> None:
             return
 
         tool_version = step.tool_version
+        assert tool_id
         self._recorded_tools.add(tool_id)
         uri_safe_tool_id = urllib.parse.quote(tool_id)
         if "repos/" in tool_id:
diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py
index a62051b79eef..f62b3cbb3b67 100644
--- a/lib/galaxy/model/tags.py
+++ b/lib/galaxy/model/tags.py
@@ -194,6 +194,7 @@ def _ensure_user_owns_item(self, user: Optional["User"], item):
     def item_has_tag(self, user, item, tag):
         """Returns true if item is has a given tag."""
         # Get tag name.
+        tag_name = None
         if isinstance(tag, str):
             tag_name = tag
         elif isinstance(tag, galaxy.model.Tag):
diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
index dc5734a089aa..ce03847a7aa9 100644
--- a/lib/galaxy/tool_shed/util/repository_util.py
+++ b/lib/galaxy/tool_shed/util/repository_util.py
@@ -635,7 +635,9 @@ def get_tool_shed_repository_by_id(app, repository_id) -> ToolShedRepository:
 def get_tool_shed_status_for(tool_shed_registry: Registry, repository: ToolShedRepository):
     tool_shed_url = tool_shed_registry.get_tool_shed_url(str(repository.tool_shed))
     assert tool_shed_url
-    params = dict(name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision)
+    params: Dict[str, Any] = dict(
+        name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision
+    )
     pathspec = ["repository", "status_for_installed_repository"]
     try:
         encoded_tool_shed_status_dict = util.url_get(
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 155511afb585..9191d6a65913 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -25,7 +25,7 @@
     select,
     true,
 )
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.exc import NoResultFound
 
 from galaxy import util
 from galaxy.exceptions import (
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index e661f3c40afe..f0a82c7f7519 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -10,7 +10,7 @@
 from urllib.parse import unquote
 
 from markupsafe import escape
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.exc import NoResultFound
 
 from galaxy import (
     util,
diff --git a/lib/tool_shed/managers/groups.py b/lib/tool_shed/managers/groups.py
index 280f1e685995..21f2a6ce0e62 100644
--- a/lib/tool_shed/managers/groups.py
+++ b/lib/tool_shed/managers/groups.py
@@ -9,7 +9,7 @@
     select,
     true,
 )
-from sqlalchemy.orm.exc import (
+from sqlalchemy.exc import (
     MultipleResultsFound,
     NoResultFound,
 )

From e8a9e6e3fcb07fc4d74766d93d94712558b5b30d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 23 Jan 2024 15:02:54 -0500
Subject: [PATCH 33/71] Mypy: type-ignore: this is never SessionlessContext

---
 lib/galaxy/model/base.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/base.py b/lib/galaxy/model/base.py
index 707dc486a734..8890349e9b9c 100644
--- a/lib/galaxy/model/base.py
+++ b/lib/galaxy/model/base.py
@@ -53,8 +53,8 @@ def transaction(session: Union[scoped_session, Session, "SessionlessContext"]):
         yield
         return  # exit: can't use as a Session
 
-    if not session.in_transaction():
-        with session.begin():
+    if not session.in_transaction():  # type:ignore[union-attr]
+        with session.begin():  # type:ignore[union-attr]
             yield
     else:
         yield

From 25d91eb00ba4df1e1f735f126f80202874dce0d1 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 23 Jan 2024 15:07:04 -0500
Subject: [PATCH 34/71] Mypy: use verbose assignment to help mypy

---
 lib/galaxy/model/base.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/model/base.py b/lib/galaxy/model/base.py
index 8890349e9b9c..8cfe259a4dc0 100644
--- a/lib/galaxy/model/base.py
+++ b/lib/galaxy/model/base.py
@@ -197,7 +197,9 @@ def ensure_object_added_to_session(object_to_add, *, object_in_session=None, ses
     if session:
         session.add(object_to_add)
         return True
-    if object_in_session and object_session(object_in_session):
-        object_session(object_in_session).add(object_to_add)
-        return True
+    if object_in_session:
+        session = object_session(object_in_session)
+        if session:
+            session.add(object_to_add)
+            return True
     return False

From 1a2eb39f8938baa61c5c9544bb0921bcaf60f5f4 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 23 Jan 2024 15:37:42 -0500
Subject: [PATCH 35/71] Mypy: add assert stmt

---
 lib/galaxy/tool_shed/util/repository_util.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
index ce03847a7aa9..dae1c02ccd6c 100644
--- a/lib/galaxy/tool_shed/util/repository_util.py
+++ b/lib/galaxy/tool_shed/util/repository_util.py
@@ -64,7 +64,8 @@ def check_for_updates(
             message += "Unable to retrieve status from the tool shed for the following repositories:\n"
             message += ", ".join(repository_names_not_updated)
     else:
-        repository = install_model_context.get(ToolShedRepository, repository_id)
+        repository = install_model_context.get(ToolShedRepository, repository_id)  # type:ignore[assignment]
+        assert repository
         ok, updated = _check_or_update_tool_shed_status_for_installed_repository(
             tool_shed_registry, install_model_context, repository
         )

From f960416c018dc5feea2c813aff327fa4f83b19d0 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 24 Jan 2024 15:27:56 -0500
Subject: [PATCH 36/71] Mypy: add assert to ensure seesion is not None

Calling that method when a User obj is not attached to a session should
not happen.
---
 lib/galaxy/model/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 31ac81b25969..719203ce27b2 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1219,6 +1219,7 @@ def count_stored_workflow_user_assocs(self, stored_workflow) -> int:
         sq = select(StoredWorkflowUserShareAssociation).filter_by(user=self, stored_workflow=stored_workflow).subquery()
         stmt = select(func.count()).select_from(sq)
         session = object_session(self)
+        assert session
         return session.scalar(stmt)
 
 

From 4c2b4d67e3362e34453a1028a8522f892bc1e54e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 24 Jan 2024 15:48:13 -0500
Subject: [PATCH 37/71] Mypy: return 0 if no results

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 719203ce27b2..2ed0e2d796e2 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1220,7 +1220,7 @@ def count_stored_workflow_user_assocs(self, stored_workflow) -> int:
         stmt = select(func.count()).select_from(sq)
         session = object_session(self)
         assert session
-        return session.scalar(stmt)
+        return session.scalar(stmt) or 0
 
 
 class PasswordResetToken(Base):

From dd090bf39383301a509537ad8e161f484a1377d4 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 24 Jan 2024 17:10:54 -0500
Subject: [PATCH 38/71] Mypy: type-ignore: scoped_session vs.
 install_model_session

We use the disctinction for DI.
---
 test/unit/app/test_galaxy_install.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/app/test_galaxy_install.py b/test/unit/app/test_galaxy_install.py
index 1695e8faebc2..f7c44908ff58 100644
--- a/test/unit/app/test_galaxy_install.py
+++ b/test/unit/app/test_galaxy_install.py
@@ -57,7 +57,7 @@ def test_against_production_shed(tmp_path: Path):
     assert tsr
     message, status = check_for_updates(
         install_target.tool_shed_registry,
-        install_model_context,
+        install_model_context,  # type:ignore[arg-type]
         tsr.id,
     )
     assert status

From fae5ed7d09cc5eea22d2e34821aed8a5d2e9aff9 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 25 Jan 2024 10:18:25 -0500
Subject: [PATCH 39/71] Mypy: refactor to one-liner

---
 lib/galaxy/webapps/galaxy/services/quotas.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/services/quotas.py b/lib/galaxy/webapps/galaxy/services/quotas.py
index 37ac0a3ceaf8..38b6a69fe849 100644
--- a/lib/galaxy/webapps/galaxy/services/quotas.py
+++ b/lib/galaxy/webapps/galaxy/services/quotas.py
@@ -162,8 +162,6 @@ def get_group_id(item):
 
 
 def get_quotas(session: galaxy_scoped_session, deleted: bool = False):
-    is_deleted = true()
-    if not deleted:
-        is_deleted = false()
+    is_deleted = true() if deleted else false()
     stmt = select(Quota).where(Quota.deleted == is_deleted)
     return session.scalars(stmt)

From 2270d1758b9ff9931b237f815d0ba9936ace18a1 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 25 Jan 2024 11:13:33 -0500
Subject: [PATCH 40/71] Mypy: add assert stmts where we know session returns an
 object

---
 lib/galaxy/managers/model_stores.py                | 1 +
 lib/galaxy/managers/pages.py                       | 4 ++++
 lib/galaxy/webapps/galaxy/api/tool_entry_points.py | 1 +
 lib/galaxy/webapps/galaxy/api/users.py             | 1 +
 lib/galaxy/webapps/galaxy/services/tools.py        | 1 +
 lib/galaxy/workflow/run_request.py                 | 2 ++
 6 files changed, 10 insertions(+)

diff --git a/lib/galaxy/managers/model_stores.py b/lib/galaxy/managers/model_stores.py
index 48a70117604f..395d9dbade4c 100644
--- a/lib/galaxy/managers/model_stores.py
+++ b/lib/galaxy/managers/model_stores.py
@@ -100,6 +100,7 @@ def setup_history_export_job(self, request: SetupHistoryExportJob):
         with DirectoryModelExportStore(store_directory, app=self._app, export_files="symlink") as export_store:
             export_store.export_history(history, include_hidden=include_hidden, include_deleted=include_deleted)
         job = self._sa_session.get(model.Job, job_id)
+        assert job
         job.state = model.Job.states.NEW
         with transaction(self._sa_session):
             self._sa_session.commit()
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index e37866a61fb1..c773786c4d2b 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -614,19 +614,23 @@ def placeholderRenderForSave(trans: ProvidesHistoryContext, item_class, item_id,
     if item_class == "History":
         history = trans.sa_session.get(History, decoded_item_id)
         history = base.security_check(trans, history, False, True)
+        assert history
         item_name = history.name
     elif item_class == "HistoryDatasetAssociation":
         hda = trans.sa_session.get(HistoryDatasetAssociation, decoded_item_id)
         hda_manager = trans.app.hda_manager
         hda = hda_manager.get_accessible(decoded_item_id, trans.user)
+        assert hda
         item_name = hda.name
     elif item_class == "StoredWorkflow":
         wf = trans.sa_session.get(StoredWorkflow, decoded_item_id)
         wf = base.security_check(trans, wf, False, True)
+        assert wf
         item_name = wf.name
     elif item_class == "Visualization":
         visualization = trans.sa_session.get(Visualization, decoded_item_id)
         visualization = base.security_check(trans, visualization, False, True)
+        assert visualization
         item_name = visualization.title
     class_shorthand = PAGE_CLASS_MAPPING[item_class]
     if encode:
diff --git a/lib/galaxy/webapps/galaxy/api/tool_entry_points.py b/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
index fcaffd3049de..f173a8b46ecf 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
@@ -54,6 +54,7 @@ def index(self, trans: ProvidesUserContext, running=False, job_id=None, **kwd):
 
         if job_id is not None:
             job = trans.sa_session.get(Job, self.decode_id(job_id))
+            assert job
             if not self.interactivetool_manager.can_access_job(trans, job):
                 raise exceptions.ItemAccessibilityException()
             entry_points = job.interactivetool_entry_points
diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py
index 03e1511c732d..bf74edf20f58 100644
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -515,6 +515,7 @@ def add_custom_builds(
             else:
                 build_dict["fasta"] = trans.security.decode_id(len_value)
                 dataset = trans.sa_session.get(HistoryDatasetAssociation, int(build_dict["fasta"]))
+                assert dataset
                 try:
                     new_len = dataset.get_converted_dataset(trans, "len")
                     new_linecount = new_len.get_converted_dataset(trans, "linecount")
diff --git a/lib/galaxy/webapps/galaxy/services/tools.py b/lib/galaxy/webapps/galaxy/services/tools.py
index 2266c6c58597..3b2e3ff9f6dc 100644
--- a/lib/galaxy/webapps/galaxy/services/tools.py
+++ b/lib/galaxy/webapps/galaxy/services/tools.py
@@ -280,6 +280,7 @@ def _patch_library_inputs(self, trans: ProvidesHistoryContext, inputs, target_hi
     def _patch_library_dataset(self, trans: ProvidesHistoryContext, v, target_history):
         if isinstance(v, dict) and "id" in v and v.get("src") == "ldda":
             ldda = trans.sa_session.get(LibraryDatasetDatasetAssociation, self.decode_id(v["id"]))
+            assert ldda
             if trans.user_is_admin or trans.app.security_agent.can_access_dataset(
                 trans.get_current_user_roles(), ldda.dataset
             ):
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index a45e7e441ec0..dd041531bd1c 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -379,6 +379,7 @@ def build_workflow_run_configs(
             try:
                 if input_source == "ldda":
                     ldda = trans.sa_session.get(LibraryDatasetDatasetAssociation, trans.security.decode_id(input_id))
+                    assert ldda
                     assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
                         trans.get_current_user_roles(), ldda.dataset
                     )
@@ -387,6 +388,7 @@ def build_workflow_run_configs(
                     ldda = trans.sa_session.get(
                         LibraryDataset, trans.security.decode_id(input_id)
                     ).library_dataset_dataset_association
+                    assert ldda
                     assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
                         trans.get_current_user_roles(), ldda.dataset
                     )

From ddb3101527d28a1adc98bddd16b121f0393c8f06 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 25 Jan 2024 11:24:37 -0500
Subject: [PATCH 41/71] Mypy: rename wfi_step > wfi_step_sq when it becomes a
 subquery

---
 lib/galaxy/managers/jobs.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 7b11d63f7d26..ce0688eec41b 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -137,13 +137,13 @@ def add_workflow_jobs():
                 )
             elif invocation_id is not None:
                 wfi_step = wfi_step.where(WorkflowInvocationStep.workflow_invocation_id == invocation_id)
-            wfi_step = wfi_step.subquery()
+            wfi_step_sq = wfi_step.subquery()
 
-            stmt1 = stmt.join(wfi_step)
+            stmt1 = stmt.join(wfi_step_sq)
             stmt2 = stmt.join(ImplicitCollectionJobsJobAssociation).join(
-                wfi_step,
+                wfi_step_sq,
                 ImplicitCollectionJobsJobAssociation.implicit_collection_jobs_id
-                == wfi_step.c.implicit_collection_jobs_id,
+                == wfi_step_sq.c.implicit_collection_jobs_id,
             )
             # Ensure the result is models, not tuples
             sq = stmt1.union(stmt2).subquery()

From 4e84e83e8087e287a77c3ce3d133c0a3d12d7462 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 26 Jan 2024 18:18:27 -0500
Subject: [PATCH 42/71] Job search refactor: factor out build_job_subquery

---
 lib/galaxy/managers/jobs.py | 125 ++++++++++++++++++------------------
 1 file changed, 64 insertions(+), 61 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index ce0688eec41b..da01b666cda4 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -355,68 +355,8 @@ def replace_dataset_ids(path, key, value):
                 return key, value
             return key, value
 
-        # build one subquery that selects a job with correct job parameters
+        stmt_sq = self._build_job_subquery(tool_id, user.id, tool_version, job_state, wildcard_param_dump)
 
-        stmt = select(model.Job.id).where(
-            and_(
-                model.Job.tool_id == tool_id,
-                model.Job.user_id == user.id,
-                model.Job.copied_from_job_id.is_(None),  # Always pick original job
-            )
-        )
-        if tool_version:
-            stmt = stmt.where(Job.tool_version == str(tool_version))
-
-        if job_state is None:
-            stmt = stmt.where(
-                Job.state.in_(
-                    [Job.states.NEW, Job.states.QUEUED, Job.states.WAITING, Job.states.RUNNING, Job.states.OK]
-                )
-            )
-        else:
-            if isinstance(job_state, str):
-                stmt = stmt.where(Job.state == job_state)
-            elif isinstance(job_state, list):
-                stmt = stmt.where(or_(*[Job.state == s for s in job_state]))
-
-        # exclude jobs with deleted outputs
-        stmt = stmt.where(
-            and_(
-                model.Job.any_output_dataset_collection_instances_deleted == false(),
-                model.Job.any_output_dataset_deleted == false(),
-            )
-        )
-
-        for k, v in wildcard_param_dump.items():
-            if v == {"__class__": "RuntimeValue"}:
-                # TODO: verify this is always None. e.g. run with runtime input input
-                v = None
-            elif k.endswith("|__identifier__"):
-                # We've taken care of this while constructing the conditions based on ``input_data`` above
-                continue
-            elif k == "chromInfo" and "?.len" in v:
-                continue
-            value_dump = json.dumps(v, sort_keys=True)
-            wildcard_value = value_dump.replace('"id": "__id_wildcard__"', '"id": %')
-            a = aliased(JobParameter)
-            if value_dump == wildcard_value:
-                stmt = stmt.join(a).where(
-                    and_(
-                        Job.id == a.job_id,
-                        a.name == k,
-                        a.value == value_dump,
-                    )
-                )
-            else:
-                stmt = stmt.join(a).where(
-                    and_(
-                        Job.id == a.job_id,
-                        a.name == k,
-                        a.value.like(wildcard_value),
-                    )
-                )
-
-        stmt_sq = stmt.subquery()
         query = select(Job.id).select_from(Job.table.join(stmt_sq, stmt_sq.c.id == Job.id))
 
         data_conditions = []
@@ -627,6 +567,69 @@ def replace_dataset_ids(path, key, value):
         log.info("No equivalent jobs found %s", search_timer)
         return None
 
+    def _build_job_subquery(self, tool_id, user_id, tool_version, job_state, wildcard_param_dump):
+        """Build subquery that selects a job with correct job parameters."""
+        stmt = select(model.Job.id).where(
+            and_(
+                model.Job.tool_id == tool_id,
+                model.Job.user_id == user_id,
+                model.Job.copied_from_job_id.is_(None),  # Always pick original job
+            )
+        )
+        if tool_version:
+            stmt = stmt.where(Job.tool_version == str(tool_version))
+
+        if job_state is None:
+            stmt = stmt.where(
+                Job.state.in_(
+                    [Job.states.NEW, Job.states.QUEUED, Job.states.WAITING, Job.states.RUNNING, Job.states.OK]
+                )
+            )
+        else:
+            if isinstance(job_state, str):
+                stmt = stmt.where(Job.state == job_state)
+            elif isinstance(job_state, list):
+                stmt = stmt.where(or_(*[Job.state == s for s in job_state]))
+
+        # exclude jobs with deleted outputs
+        stmt = stmt.where(
+            and_(
+                model.Job.any_output_dataset_collection_instances_deleted == false(),
+                model.Job.any_output_dataset_deleted == false(),
+            )
+        )
+
+        for k, v in wildcard_param_dump.items():
+            if v == {"__class__": "RuntimeValue"}:
+                # TODO: verify this is always None. e.g. run with runtime input input
+                v = None
+            elif k.endswith("|__identifier__"):
+                # We've taken care of this while constructing the conditions based on ``input_data`` above
+                continue
+            elif k == "chromInfo" and "?.len" in v:
+                continue
+            value_dump = json.dumps(v, sort_keys=True)
+            wildcard_value = value_dump.replace('"id": "__id_wildcard__"', '"id": %')
+            a = aliased(JobParameter)
+            if value_dump == wildcard_value:
+                stmt = stmt.join(a).where(
+                    and_(
+                        Job.id == a.job_id,
+                        a.name == k,
+                        a.value == value_dump,
+                    )
+                )
+            else:
+                stmt = stmt.join(a).where(
+                    and_(
+                        Job.id == a.job_id,
+                        a.name == k,
+                        a.value.like(wildcard_value),
+                    )
+                )
+
+        return stmt.subquery()
+
 
 def view_show_job(trans, job: Job, full: bool) -> typing.Dict:
     is_admin = trans.user_is_admin

From 295da0c459da39a7038a25ff95e04ee0e9132d6f Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 26 Jan 2024 20:43:53 -0500
Subject: [PATCH 43/71] Job search refactor: build_stmt_for_hda

---
 lib/galaxy/managers/jobs.py | 118 +++++++++++++++++++-----------------
 1 file changed, 61 insertions(+), 57 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index da01b666cda4..4ae4eed3f636 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -379,63 +379,7 @@ def replace_dataset_ids(path, key, value):
                 data_types.append(t)
                 identifier = type_values["identifier"]
                 if t == "hda":
-                    a = aliased(model.JobToInputDatasetAssociation)
-                    b = aliased(model.HistoryDatasetAssociation)
-                    c = aliased(model.HistoryDatasetAssociation)
-                    d = aliased(model.JobParameter)
-                    e = aliased(model.HistoryDatasetAssociationHistory)
-                    query = query.add_columns(a.dataset_id)
-                    used_ids.append(a.dataset_id)
-                    query = query.join(a, a.job_id == model.Job.id)
-                    stmt = select(model.HistoryDatasetAssociation.id).where(
-                        model.HistoryDatasetAssociation.id == e.history_dataset_association_id
-                    )
-                    # b is the HDA used for the job
-                    query = query.join(b, a.dataset_id == b.id).join(c, c.dataset_id == b.dataset_id)
-                    name_condition = []
-                    if identifier:
-                        query = query.join(d)
-                        data_conditions.append(
-                            and_(
-                                d.name.in_({f"{_}|__identifier__" for _ in k}),
-                                d.value == json.dumps(identifier),
-                            )
-                        )
-                    else:
-                        stmt = stmt.where(e.name == c.name)
-                        name_condition.append(b.name == c.name)
-                    stmt = (
-                        stmt.where(
-                            e.extension == c.extension,
-                        )
-                        .where(
-                            a.dataset_version == e.version,
-                        )
-                        .where(
-                            e._metadata == c._metadata,
-                        )
-                    )
-                    data_conditions.append(
-                        and_(
-                            a.name.in_(k),
-                            c.id == v,  # c is the requested job input HDA
-                            # We need to make sure that the job we are looking for has been run with identical inputs.
-                            # Here we deal with 3 requirements:
-                            #  - the jobs' input dataset (=b) version is 0, meaning the job's input dataset is not yet ready
-                            #  - b's update_time is older than the job create time, meaning no changes occurred
-                            #  - the job has a dataset_version recorded, and that versions' metadata matches c's metadata.
-                            or_(
-                                and_(
-                                    or_(a.dataset_version.in_([0, b.version]), b.update_time < model.Job.create_time),
-                                    b.extension == c.extension,
-                                    b.metadata == c.metadata,
-                                    *name_condition,
-                                ),
-                                b.id.in_(stmt),
-                            ),
-                            or_(b.deleted == false(), c.deleted == false()),
-                        )
-                    )
+                    query = self._build_stmt_for_hda(query, data_conditions, used_ids, k, v, identifier)
                 elif t == "ldda":
                     a = aliased(model.JobToInputLibraryDatasetAssociation)
                     query = query.add_columns(a.ldda_id)
@@ -630,6 +574,66 @@ def _build_job_subquery(self, tool_id, user_id, tool_version, job_state, wildcar
 
         return stmt.subquery()
 
+    def _build_stmt_for_hda(self, stmt, data_conditions, used_ids, k, v, identifier):
+        a = aliased(model.JobToInputDatasetAssociation)
+        b = aliased(model.HistoryDatasetAssociation)
+        c = aliased(model.HistoryDatasetAssociation)
+        d = aliased(model.JobParameter)
+        e = aliased(model.HistoryDatasetAssociationHistory)
+        stmt = stmt.add_columns(a.dataset_id)
+        used_ids.append(a.dataset_id)
+        stmt = stmt.join(a, a.job_id == model.Job.id)
+        hda_stmt = select(model.HistoryDatasetAssociation.id).where(
+            model.HistoryDatasetAssociation.id == e.history_dataset_association_id
+        )
+        # b is the HDA used for the job
+        stmt = stmt.join(b, a.dataset_id == b.id).join(c, c.dataset_id == b.dataset_id)
+        name_condition = []
+        if identifier:
+            stmt = stmt.join(d)
+            data_conditions.append(
+                and_(
+                    d.name.in_({f"{_}|__identifier__" for _ in k}),
+                    d.value == json.dumps(identifier),
+                )
+            )
+        else:
+            hda_stmt = hda_stmt.where(e.name == c.name)
+            name_condition.append(b.name == c.name)
+        hda_stmt = (
+            hda_stmt.where(
+                e.extension == c.extension,
+            )
+            .where(
+                a.dataset_version == e.version,
+            )
+            .where(
+                e._metadata == c._metadata,
+            )
+        )
+        data_conditions.append(
+            and_(
+                a.name.in_(k),
+                c.id == v,  # c is the requested job input HDA
+                # We need to make sure that the job we are looking for has been run with identical inputs.
+                # Here we deal with 3 requirements:
+                #  - the jobs' input dataset (=b) version is 0, meaning the job's input dataset is not yet ready
+                #  - b's update_time is older than the job create time, meaning no changes occurred
+                #  - the job has a dataset_version recorded, and that versions' metadata matches c's metadata.
+                or_(
+                    and_(
+                        or_(a.dataset_version.in_([0, b.version]), b.update_time < model.Job.create_time),
+                        b.extension == c.extension,
+                        b.metadata == c.metadata,
+                        *name_condition,
+                    ),
+                    b.id.in_(hda_stmt),
+                ),
+                or_(b.deleted == false(), c.deleted == false()),
+            )
+        )
+        return stmt
+
 
 def view_show_job(trans, job: Job, full: bool) -> typing.Dict:
     is_admin = trans.user_is_admin

From 78f26fd9acf344bf44f312b837c5c3449fbfe1c5 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 26 Jan 2024 20:50:42 -0500
Subject: [PATCH 44/71] Job search refactor: build_stmt_for_ldda

---
 lib/galaxy/managers/jobs.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 4ae4eed3f636..298d105b52e9 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -381,11 +381,7 @@ def replace_dataset_ids(path, key, value):
                 if t == "hda":
                     query = self._build_stmt_for_hda(query, data_conditions, used_ids, k, v, identifier)
                 elif t == "ldda":
-                    a = aliased(model.JobToInputLibraryDatasetAssociation)
-                    query = query.add_columns(a.ldda_id)
-                    query = query.join(a, a.job_id == model.Job.id)
-                    data_conditions.append(and_(a.name.in_(k), a.ldda_id == v))
-                    used_ids.append(a.ldda_id)
+                    query = self._build_stmt_for_ldda(query, data_conditions, used_ids, k, v)
                 elif t == "hdca":
                     a = aliased(model.JobToInputDatasetCollectionAssociation)
                     b = aliased(model.HistoryDatasetCollectionAssociation)
@@ -634,6 +630,14 @@ def _build_stmt_for_hda(self, stmt, data_conditions, used_ids, k, v, identifier)
         )
         return stmt
 
+    def _build_stmt_for_ldda(self, stmt, data_conditions, used_ids, k, v):
+        a = aliased(model.JobToInputLibraryDatasetAssociation)
+        stmt = stmt.add_columns(a.ldda_id)
+        stmt = stmt.join(a, a.job_id == model.Job.id)
+        data_conditions.append(and_(a.name.in_(k), a.ldda_id == v))
+        used_ids.append(a.ldda_id)
+        return stmt
+
 
 def view_show_job(trans, job: Job, full: bool) -> typing.Dict:
     is_admin = trans.user_is_admin

From 03925e2a1a3b58a3b6982e131114b3c1d58414cc Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 26 Jan 2024 21:06:00 -0500
Subject: [PATCH 45/71] Job search refactor: build_stmt_for_hdca

---
 lib/galaxy/managers/jobs.py | 52 ++++++++++++++++++-------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 298d105b52e9..5253b3c3b34e 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -383,32 +383,7 @@ def replace_dataset_ids(path, key, value):
                 elif t == "ldda":
                     query = self._build_stmt_for_ldda(query, data_conditions, used_ids, k, v)
                 elif t == "hdca":
-                    a = aliased(model.JobToInputDatasetCollectionAssociation)
-                    b = aliased(model.HistoryDatasetCollectionAssociation)
-                    c = aliased(model.HistoryDatasetCollectionAssociation)
-                    query = query.add_columns(a.dataset_collection_id)
-                    query = (
-                        query.join(a, a.job_id == model.Job.id)
-                        .join(b, b.id == a.dataset_collection_id)
-                        .join(c, b.name == c.name)
-                    )
-                    data_conditions.append(
-                        and_(
-                            a.name.in_(k),
-                            c.id == v,
-                            or_(
-                                and_(b.deleted == false(), b.id == v),
-                                and_(
-                                    or_(
-                                        c.copied_from_history_dataset_collection_association_id == b.id,
-                                        b.copied_from_history_dataset_collection_association_id == c.id,
-                                    ),
-                                    c.deleted == false(),
-                                ),
-                            ),
-                        )
-                    )
-                    used_ids.append(a.dataset_collection_id)
+                    query = self._build_stmt_for_hdca(query, data_conditions, used_ids, k, v)
                 elif t == "dce":
                     a = aliased(model.JobToInputDatasetCollectionElementAssociation)
                     b = aliased(model.DatasetCollectionElement)
@@ -638,6 +613,31 @@ def _build_stmt_for_ldda(self, stmt, data_conditions, used_ids, k, v):
         used_ids.append(a.ldda_id)
         return stmt
 
+    def _build_stmt_for_hdca(self, stmt, data_conditions, used_ids, k, v):
+        a = aliased(model.JobToInputDatasetCollectionAssociation)
+        b = aliased(model.HistoryDatasetCollectionAssociation)
+        c = aliased(model.HistoryDatasetCollectionAssociation)
+        stmt = stmt.add_columns(a.dataset_collection_id)
+        stmt = stmt.join(a, a.job_id == model.Job.id).join(b, b.id == a.dataset_collection_id).join(c, b.name == c.name)
+        data_conditions.append(
+            and_(
+                a.name.in_(k),
+                c.id == v,
+                or_(
+                    and_(b.deleted == false(), b.id == v),
+                    and_(
+                        or_(
+                            c.copied_from_history_dataset_collection_association_id == b.id,
+                            b.copied_from_history_dataset_collection_association_id == c.id,
+                        ),
+                        c.deleted == false(),
+                    ),
+                ),
+            )
+        )
+        used_ids.append(a.dataset_collection_id)
+        return stmt
+
 
 def view_show_job(trans, job: Job, full: bool) -> typing.Dict:
     is_admin = trans.user_is_admin

From ad9023cac7cd2bb3f5a399de730f9eb349c0b900 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 26 Jan 2024 21:09:10 -0500
Subject: [PATCH 46/71] Job search refactor: build_stmt_for_dce

---
 lib/galaxy/managers/jobs.py | 72 +++++++++++++++++++------------------
 1 file changed, 38 insertions(+), 34 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 5253b3c3b34e..3a3304cf6caf 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -385,40 +385,7 @@ def replace_dataset_ids(path, key, value):
                 elif t == "hdca":
                     query = self._build_stmt_for_hdca(query, data_conditions, used_ids, k, v)
                 elif t == "dce":
-                    a = aliased(model.JobToInputDatasetCollectionElementAssociation)
-                    b = aliased(model.DatasetCollectionElement)
-                    c = aliased(model.DatasetCollectionElement)
-                    d = aliased(model.HistoryDatasetAssociation)
-                    e = aliased(model.HistoryDatasetAssociation)
-                    query = query.add_columns(a.dataset_collection_element_id)
-                    query = (
-                        query.join(a, a.job_id == model.Job.id)
-                        .join(b, b.id == a.dataset_collection_element_id)
-                        .join(
-                            c,
-                            and_(
-                                c.element_identifier == b.element_identifier,
-                                or_(c.hda_id == b.hda_id, c.child_collection_id == b.child_collection_id),
-                            ),
-                        )
-                        .outerjoin(d, d.id == c.hda_id)
-                        .outerjoin(e, e.dataset_id == d.dataset_id)
-                    )
-                    data_conditions.append(
-                        and_(
-                            a.name.in_(k),
-                            or_(
-                                c.child_collection_id == b.child_collection_id,
-                                and_(
-                                    c.hda_id == b.hda_id,
-                                    d.id == c.hda_id,
-                                    e.dataset_id == d.dataset_id,
-                                ),
-                            ),
-                            c.id == v,
-                        )
-                    )
-                    used_ids.append(a.dataset_collection_element_id)
+                    query = self._build_stmt_for_dce(query, data_conditions, used_ids, k, v)
                 else:
                     return []
 
@@ -638,6 +605,43 @@ def _build_stmt_for_hdca(self, stmt, data_conditions, used_ids, k, v):
         used_ids.append(a.dataset_collection_id)
         return stmt
 
+    def _build_stmt_for_dce(self, stmt, data_conditions, used_ids, k, v):
+        a = aliased(model.JobToInputDatasetCollectionElementAssociation)
+        b = aliased(model.DatasetCollectionElement)
+        c = aliased(model.DatasetCollectionElement)
+        d = aliased(model.HistoryDatasetAssociation)
+        e = aliased(model.HistoryDatasetAssociation)
+        stmt = stmt.add_columns(a.dataset_collection_element_id)
+        stmt = (
+            stmt.join(a, a.job_id == model.Job.id)
+            .join(b, b.id == a.dataset_collection_element_id)
+            .join(
+                c,
+                and_(
+                    c.element_identifier == b.element_identifier,
+                    or_(c.hda_id == b.hda_id, c.child_collection_id == b.child_collection_id),
+                ),
+            )
+            .outerjoin(d, d.id == c.hda_id)
+            .outerjoin(e, e.dataset_id == d.dataset_id)
+        )
+        data_conditions.append(
+            and_(
+                a.name.in_(k),
+                or_(
+                    c.child_collection_id == b.child_collection_id,
+                    and_(
+                        c.hda_id == b.hda_id,
+                        d.id == c.hda_id,
+                        e.dataset_id == d.dataset_id,
+                    ),
+                ),
+                c.id == v,
+            )
+        )
+        used_ids.append(a.dataset_collection_element_id)
+        return stmt
+
 
 def view_show_job(trans, job: Job, full: bool) -> typing.Dict:
     is_admin = trans.user_is_admin

From 55dd20f2320b013aa3747dc4df3c203e003b6f0b Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 26 Jan 2024 21:11:04 -0500
Subject: [PATCH 47/71] Job search refactor: rename query >> stmt

---
 lib/galaxy/managers/jobs.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 3a3304cf6caf..91c770c387f2 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -357,11 +357,11 @@ def replace_dataset_ids(path, key, value):
 
         stmt_sq = self._build_job_subquery(tool_id, user.id, tool_version, job_state, wildcard_param_dump)
 
-        query = select(Job.id).select_from(Job.table.join(stmt_sq, stmt_sq.c.id == Job.id))
+        stmt = select(Job.id).select_from(Job.table.join(stmt_sq, stmt_sq.c.id == Job.id))
 
         data_conditions = []
 
-        # We now build the query filters that relate to the input datasets
+        # We now build the stmt filters that relate to the input datasets
         # that this job uses. We keep track of the requested dataset id in `requested_ids`,
         # the type (hda, hdca or lda) in `data_types`
         # and the ids that have been used in the job that has already been run in `used_ids`.
@@ -379,19 +379,19 @@ def replace_dataset_ids(path, key, value):
                 data_types.append(t)
                 identifier = type_values["identifier"]
                 if t == "hda":
-                    query = self._build_stmt_for_hda(query, data_conditions, used_ids, k, v, identifier)
+                    stmt = self._build_stmt_for_hda(stmt, data_conditions, used_ids, k, v, identifier)
                 elif t == "ldda":
-                    query = self._build_stmt_for_ldda(query, data_conditions, used_ids, k, v)
+                    stmt = self._build_stmt_for_ldda(stmt, data_conditions, used_ids, k, v)
                 elif t == "hdca":
-                    query = self._build_stmt_for_hdca(query, data_conditions, used_ids, k, v)
+                    stmt = self._build_stmt_for_hdca(stmt, data_conditions, used_ids, k, v)
                 elif t == "dce":
-                    query = self._build_stmt_for_dce(query, data_conditions, used_ids, k, v)
+                    stmt = self._build_stmt_for_dce(stmt, data_conditions, used_ids, k, v)
                 else:
                     return []
 
-            query = query.where(*data_conditions).group_by(model.Job.id, *used_ids).order_by(model.Job.id.desc())
+            stmt = stmt.where(*data_conditions).group_by(model.Job.id, *used_ids).order_by(model.Job.id.desc())
 
-        for job in self.sa_session.execute(query):
+        for job in self.sa_session.execute(stmt):
             # We found a job that is equal in terms of tool_id, user, state and input datasets,
             # but to be able to verify that the parameters match we need to modify all instances of
             # dataset_ids (HDA, LDDA, HDCA) in the incoming param_dump to point to those used by the

From 7d4a46739444ef6b3c90add674895735a21338ff Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 26 Jan 2024 21:13:37 -0500
Subject: [PATCH 48/71] Mypy: add anno for Lists; type-ignore for HDAs

Note: type-ignore is due to imperative mapping of HDAs (and LDDAs). This
will be removed once we map those models declaratively
---
 lib/galaxy/managers/jobs.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 91c770c387f2..70957f89e076 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -5,6 +5,7 @@
     date,
     datetime,
 )
+from typing import List
 
 import sqlalchemy
 from boltons.iterutils import remap
@@ -359,7 +360,7 @@ def replace_dataset_ids(path, key, value):
 
         stmt = select(Job.id).select_from(Job.table.join(stmt_sq, stmt_sq.c.id == Job.id))
 
-        data_conditions = []
+        data_conditions: List = []
 
         # We now build the stmt filters that relate to the input datasets
         # that this job uses. We keep track of the requested dataset id in `requested_ids`,
@@ -367,7 +368,7 @@ def replace_dataset_ids(path, key, value):
         # and the ids that have been used in the job that has already been run in `used_ids`.
         requested_ids = []
         data_types = []
-        used_ids = []
+        used_ids: List = []
         for k, input_list in input_data.items():
             # k will be matched against the JobParameter.name column. This can be prefixed depending on whethter
             # the input is in a repeat, or not (section and conditional)
@@ -525,7 +526,7 @@ def _build_stmt_for_hda(self, stmt, data_conditions, used_ids, k, v, identifier)
             model.HistoryDatasetAssociation.id == e.history_dataset_association_id
         )
         # b is the HDA used for the job
-        stmt = stmt.join(b, a.dataset_id == b.id).join(c, c.dataset_id == b.dataset_id)
+        stmt = stmt.join(b, a.dataset_id == b.id).join(c, c.dataset_id == b.dataset_id)  # type:ignore[attr-defined]
         name_condition = []
         if identifier:
             stmt = stmt.join(d)
@@ -623,7 +624,7 @@ def _build_stmt_for_dce(self, stmt, data_conditions, used_ids, k, v):
                 ),
             )
             .outerjoin(d, d.id == c.hda_id)
-            .outerjoin(e, e.dataset_id == d.dataset_id)
+            .outerjoin(e, e.dataset_id == d.dataset_id)  # type:ignore[attr-defined]
         )
         data_conditions.append(
             and_(
@@ -633,7 +634,7 @@ def _build_stmt_for_dce(self, stmt, data_conditions, used_ids, k, v):
                     and_(
                         c.hda_id == b.hda_id,
                         d.id == c.hda_id,
-                        e.dataset_id == d.dataset_id,
+                        e.dataset_id == d.dataset_id,  # type:ignore[attr-defined]
                     ),
                 ),
                 c.id == v,

From c7948516016c6bc342ac02bed0bc7cfc663581d0 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 2 Feb 2024 01:15:45 -0500
Subject: [PATCH 49/71] Mypy: managers.histories

---
 lib/galaxy/managers/histories.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index bebd03446786..4e5b20bf5ba8 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -213,6 +213,8 @@ def p_tag_filter(term_text: str, quoted: bool):
             total_matches = get_count(trans.sa_session, stmt)
         else:
             total_matches = None
+
+        sort_column: Any
         if payload.sort_by == "username":
             sort_column = model.User.username
         else:
@@ -220,6 +222,7 @@ def p_tag_filter(term_text: str, quoted: bool):
         if payload.sort_desc:
             sort_column = sort_column.desc()
         stmt = stmt.order_by(sort_column)
+
         if payload.limit is not None:
             stmt = stmt.limit(payload.limit)
         if payload.offset is not None:
@@ -479,7 +482,7 @@ def is_history_shared_with(self, history: model.History, user: model.User) -> bo
             .where(HistoryUserShareAssociation.user_id == user.id)
             .where(HistoryUserShareAssociation.history_id == history.id)
         )
-        return self.session().scalar(stmt)
+        return bool(self.session().scalar(stmt))
 
     def make_members_public(self, trans, item):
         """Make the non-purged datasets in history public.
@@ -560,6 +563,7 @@ def get_discarded_summary(self, user: model.User) -> CleanableItemsSummary:
             model.History.purged == false(),
         )
         result = self.history_manager.session().execute(stmt).fetchone()
+        assert result
         total_size = 0 if result[0] is None else result[0]
         return CleanableItemsSummary(total_size=total_size, total_items=result[1])
 
@@ -594,6 +598,7 @@ def get_archived_summary(self, user: model.User) -> CleanableItemsSummary:
             model.History.purged == false(),
         )
         result = self.history_manager.session().execute(stmt).fetchone()
+        assert result
         total_size = 0 if result[0] is None else result[0]
         return CleanableItemsSummary(total_size=total_size, total_items=result[1])
 

From bc329c58916527bcdfe3bf1d7a5ba0d6c6bc340f Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 2 Feb 2024 10:56:38 -0500
Subject: [PATCH 50/71] Mypy: model.deferred

---
 lib/galaxy/model/deferred.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/deferred.py b/lib/galaxy/model/deferred.py
index 66a4c23f1d4a..d57622f700ba 100644
--- a/lib/galaxy/model/deferred.py
+++ b/lib/galaxy/model/deferred.py
@@ -9,7 +9,10 @@
     Union,
 )
 
-from sqlalchemy.orm import object_session
+from sqlalchemy.orm import (
+    object_session,
+    Session,
+)
 from sqlalchemy.orm.exc import DetachedInstanceError
 
 from galaxy.datatypes.sniff import (
@@ -74,7 +77,7 @@ def __init__(
         object_store_populator: Optional[ObjectStorePopulator] = None,
         transient_path_mapper: Optional[TransientPathMapper] = None,
         file_sources: Optional[ConfiguredFileSources] = None,
-        sa_session: Optional[scoped_session] = None,
+        sa_session: Optional[Session] = None,
     ):
         """Constructor for DatasetInstanceMaterializer.
 
@@ -122,6 +125,7 @@ def ensure_materialized(
                 sa_session = self._sa_session
                 if sa_session is None:
                     sa_session = object_session(dataset_instance)
+                assert sa_session
                 sa_session.add(materialized_dataset)
                 with transaction(sa_session):
                     sa_session.commit()
@@ -152,6 +156,7 @@ def ensure_materialized(
             sa_session = self._sa_session
             if sa_session is None:
                 sa_session = object_session(dataset_instance)
+            assert sa_session
             sa_session.add(materialized_dataset_instance)
         materialized_dataset_instance.copy_from(
             dataset_instance, new_dataset=materialized_dataset, include_tags=attached, include_metadata=True

From c84f52b51fc0449a0b27530dc0decd3608ca1769 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 5 Feb 2024 11:52:30 -0500
Subject: [PATCH 51/71] Mypy: arg passed to template can be None

---
 lib/galaxy/managers/pages.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index c773786c4d2b..5e058a623a13 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -12,6 +12,7 @@
 from html.parser import HTMLParser
 from typing import (
     Callable,
+    Optional,
     Tuple,
 )
 
@@ -610,7 +611,7 @@ def placeholderRenderForEdit(trans: ProvidesHistoryContext, item_class, item_id)
 
 def placeholderRenderForSave(trans: ProvidesHistoryContext, item_class, item_id, encode=False):
     encoded_item_id, decoded_item_id = get_page_identifiers(item_id, trans.app)
-    item_name = ""
+    item_name: Optional[str] = ""
     if item_class == "History":
         history = trans.sa_session.get(History, decoded_item_id)
         history = base.security_check(trans, history, False, True)

From 51d94931676cacd95facaf9b43e3ac0b7b8fdc6a Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 5 Feb 2024 12:17:33 -0500
Subject: [PATCH 52/71] Mypy: celery tasks

type ignore arg: we need to map DatasetInstance classes declaratively
for that to work correctly.
---
 lib/galaxy/celery/tasks.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index fc60f6921327..e49008fb9cec 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -195,7 +195,7 @@ def set_metadata(
     try:
         if overwrite:
             hda_manager.overwrite_metadata(dataset_instance)
-        dataset_instance.datatype.set_meta(dataset_instance)
+        dataset_instance.datatype.set_meta(dataset_instance)  # type:ignore [arg-type]
         dataset_instance.set_peek()
         # Reset SETTING_METADATA state so the dataset instance getter picks the dataset state
         dataset_instance.set_metadata_success_state()
@@ -228,6 +228,7 @@ def setup_fetch_data(
 ):
     tool = cached_create_tool_from_representation(app=app, raw_tool_source=raw_tool_source)
     job = sa_session.get(Job, job_id)
+    assert job
     # self.request.hostname is the actual worker name given by the `-n` argument, not the hostname as you might think.
     job.handler = self.request.hostname
     job.job_runner_name = "celery"
@@ -260,6 +261,7 @@ def finish_job(
 ):
     tool = cached_create_tool_from_representation(app=app, raw_tool_source=raw_tool_source)
     job = sa_session.get(Job, job_id)
+    assert job
     # TODO: assert state ?
     mini_job_wrapper = MinimalJobWrapper(job=job, app=app, tool=tool)
     mini_job_wrapper.finish("", "")
@@ -320,6 +322,7 @@ def fetch_data(
     task_user_id: Optional[int] = None,
 ) -> str:
     job = sa_session.get(Job, job_id)
+    assert job
     mini_job_wrapper = MinimalJobWrapper(job=job, app=app)
     mini_job_wrapper.change_state(model.Job.states.RUNNING, flush=True, job=job)
     return abort_when_job_stops(_fetch_data, session=sa_session, job_id=job_id, setup_return=setup_return)

From f19f65b0a14cea013851ca9ceea333d7321e5131 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 6 Feb 2024 00:00:14 -0500
Subject: [PATCH 53/71] Mypy: type-ignore hda attr-defined error

Need to map declaratively to remove this
---
 lib/galaxy/managers/hdas.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 863d6d9986c7..00196dc61597 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -201,7 +201,7 @@ def copy(
         if not isinstance(item, model.HistoryDatasetAssociation):
             raise TypeError()
         hda = item
-        copy = hda.copy(parent_id=kwargs.get("parent_id"), copy_hid=False, copy_tags=hda.tags, flush=flush)
+        copy = hda.copy(parent_id=kwargs.get("parent_id"), copy_hid=False, copy_tags=hda.tags, flush=flush)  # type:ignore[attr-defined]
         if hide_copy:
             copy.visible = False
         if history:

From 41b737fb906ce0b2a7a597007a3c9f757755b4a6 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 6 Feb 2024 00:25:01 -0500
Subject: [PATCH 54/71] Convert visualization manager index query to SA Core

---
 lib/galaxy/managers/hdas.py           |  4 ++-
 lib/galaxy/managers/visualizations.py | 49 +++++++++++++++------------
 2 files changed, 31 insertions(+), 22 deletions(-)

diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 00196dc61597..04adacb687ea 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -201,7 +201,9 @@ def copy(
         if not isinstance(item, model.HistoryDatasetAssociation):
             raise TypeError()
         hda = item
-        copy = hda.copy(parent_id=kwargs.get("parent_id"), copy_hid=False, copy_tags=hda.tags, flush=flush)  # type:ignore[attr-defined]
+        copy = hda.copy(
+            parent_id=kwargs.get("parent_id"), copy_hid=False, copy_tags=hda.tags, flush=flush
+        )  # type:ignore[attr-defined]
         if hide_copy:
             copy.visible = False
         if history:
diff --git a/lib/galaxy/managers/visualizations.py b/lib/galaxy/managers/visualizations.py
index 1f03e3900ff1..bd097b99e9cc 100644
--- a/lib/galaxy/managers/visualizations.py
+++ b/lib/galaxy/managers/visualizations.py
@@ -14,7 +14,9 @@
 
 from sqlalchemy import (
     false,
+    func,
     or_,
+    select,
     true,
 )
 from sqlalchemy.orm import aliased
@@ -86,7 +88,7 @@ def index_query(
             message = "Requires user to log in."
             raise exceptions.RequestParameterInvalidException(message)
 
-        query = trans.sa_session.query(self.model_class)
+        stmt = select(self.model_class)
 
         filters = []
         if show_own or (not show_published and not show_shared and not is_admin):
@@ -95,20 +97,20 @@ def index_query(
             filters.append(self.model_class.published == true())
         if user and show_shared:
             filters.append(self.user_share_model.user == user)
-            query = query.outerjoin(self.model_class.users_shared_with)
-        query = query.filter(or_(*filters))
+            stmt = stmt.outerjoin(self.model_class.users_shared_with)
+        stmt = stmt.where(or_(*filters))
 
         if payload.user_id:
-            query = query.filter(self.model_class.user_id == payload.user_id)
+            stmt = stmt.where(self.model_class.user_id == payload.user_id)
 
         if payload.search:
             search_query = payload.search
             parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS)
 
             def p_tag_filter(term_text: str, quoted: bool):
-                nonlocal query
+                nonlocal stmt
                 alias = aliased(model.VisualizationTagAssociation)
-                query = query.outerjoin(self.model_class.tags.of_type(alias))
+                stmt = stmt.outerjoin(self.model_class.tags.of_type(alias))
                 return tag_filter(alias, term_text, quoted)
 
             for term in parsed_search.terms:
@@ -117,30 +119,30 @@ def p_tag_filter(term_text: str, quoted: bool):
                     q = term.text
                     if key == "tag":
                         pg = p_tag_filter(term.text, term.quoted)
-                        query = query.filter(pg)
+                        stmt = stmt.where(pg)
                     elif key == "title":
-                        query = query.filter(text_column_filter(self.model_class.title, term))
+                        stmt = stmt.where(text_column_filter(self.model_class.title, term))
                     elif key == "slug":
-                        query = query.filter(text_column_filter(self.model_class.slug, term))
+                        stmt = stmt.where(text_column_filter(self.model_class.slug, term))
                     elif key == "user":
-                        query = append_user_filter(query, self.model_class, term)
+                        stmt = append_user_filter(stmt, self.model_class, term)
                     elif key == "is":
                         if q == "deleted":
                             show_deleted = True
                         if q == "published":
-                            query = query.filter(self.model_class.published == true())
+                            stmt = stmt.where(self.model_class.published == true())
                         if q == "importable":
-                            query = query.filter(self.model_class.importable == true())
+                            stmt = stmt.where(self.model_class.importable == true())
                         elif q == "shared_with_me":
                             if not show_shared:
                                 message = "Can only use tag is:shared_with_me if show_shared parameter also true."
                                 raise exceptions.RequestParameterInvalidException(message)
-                            query = query.filter(self.user_share_model.user == user)
+                            stmt = stmt.where(self.user_share_model.user == user)
                 elif isinstance(term, RawTextTerm):
                     tf = p_tag_filter(term.text, False)
                     alias = aliased(model.User)
-                    query = query.outerjoin(self.model_class.user.of_type(alias))
-                    query = query.filter(
+                    stmt = stmt.outerjoin(self.model_class.user.of_type(alias))
+                    stmt = stmt.where(
                         raw_text_column_filter(
                             [
                                 self.model_class.title,
@@ -155,21 +157,21 @@ def p_tag_filter(term_text: str, quoted: bool):
         if (show_published or show_shared) and not is_admin:
             show_deleted = False
 
-        query = query.filter(self.model_class.deleted == (true() if show_deleted else false())).distinct()
+        stmt = stmt.where(self.model_class.deleted == (true() if show_deleted else false())).distinct()
 
         if include_total_count:
-            total_matches = query.count()
+            total_matches = get_count(trans.sa_session, stmt)
         else:
             total_matches = None
         sort_column = getattr(model.Visualization, payload.sort_by)
         if payload.sort_desc:
             sort_column = sort_column.desc()
-        query = query.order_by(sort_column)
+        stmt = stmt.order_by(sort_column)
         if payload.limit is not None:
-            query = query.limit(payload.limit)
+            stmt = stmt.limit(payload.limit)
         if payload.offset is not None:
-            query = query.offset(payload.offset)
-        return query, total_matches
+            stmt = stmt.offset(payload.offset)
+        return trans.sa_session.scalars(stmt), total_matches
 
 
 class VisualizationSerializer(sharable.SharableModelSerializer):
@@ -210,3 +212,8 @@ def add_deserializers(self):
         super().add_deserializers()
         self.deserializers.update({})
         self.deserializable_keyset.update(self.deserializers.keys())
+
+
+def get_count(session, statement):
+    stmt = select(func.count()).select_from(statement)
+    return session.scalar(stmt)

From 3bb43ec6545e5e76e3e6e90f2383d2a51267e035 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 6 Feb 2024 01:15:00 -0500
Subject: [PATCH 55/71] Mypy: session is not none

---
 lib/galaxy/managers/hdas.py        | 2 ++
 lib/galaxy/model/__init__.py       | 2 +-
 lib/galaxy/model/database_utils.py | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 04adacb687ea..f0acddc138b4 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -217,6 +217,7 @@ def copy(
             if history:
                 history.add_pending_items()
             session = object_session(copy)
+            assert session
             with transaction(session):
                 session.commit()
 
@@ -253,6 +254,7 @@ def _purge(self, hda, flush=True):
             user.adjust_total_disk_usage(-quota_amount_reduction, quota_source_info.label)
             # TODO: don't flush above if we're going to re-flush here
             session = object_session(user)
+            assert session
             with transaction(session):
                 session.commit()
 
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 2ed0e2d796e2..5f99411be19d 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -6492,7 +6492,7 @@ def element_identifiers_extensions_paths_and_metadata_files(
                 hda_attributes=("extension",),
                 return_entities=(HistoryDatasetAssociation, Dataset),
             )
-            tuples = object_session(self).execute(stmt)
+            tuples = object_session(self).execute(stmt)  # type:ignore[union-attr]
             # element_identifiers, extension, path
             for row in tuples:
                 result = [row[:-3], row.extension, row.Dataset.get_file_name()]
diff --git a/lib/galaxy/model/database_utils.py b/lib/galaxy/model/database_utils.py
index 123bd22a12e6..a3ec08cd46dc 100644
--- a/lib/galaxy/model/database_utils.py
+++ b/lib/galaxy/model/database_utils.py
@@ -192,6 +192,6 @@ def ensure_object_added_to_session(object_to_add, *, object_in_session=None, ses
         session.add(object_to_add)
         return True
     if object_in_session and object_session(object_in_session):
-        object_session(object_in_session).add(object_to_add)
+        object_session(object_in_session).add(object_to_add)  # type:ignore[union-attr]
         return True
     return False

From 9b4080a2ff41ae16018bdc992ed2f5acd6280f32 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 6 Feb 2024 01:40:33 -0500
Subject: [PATCH 56/71] Mypy: type-ignore what requires more refactoring

---
 lib/galaxy/managers/collections.py      |  2 +-
 lib/galaxy/managers/hdas.py             |  7 +++++--
 lib/galaxy/managers/history_contents.py | 12 ++++++------
 lib/galaxy/model/store/discover.py      |  2 +-
 lib/galaxy/tools/parameters/basic.py    |  1 +
 5 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 8db9037b55a5..772009aa6464 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -839,7 +839,7 @@ def get_collection_contents(self, trans: ProvidesAppContext, parent_id, limit=No
     def _get_collection_contents_qry(self, parent_id, limit=None, offset=None):
         """Build query to find first level of collection contents by containing collection parent_id"""
         DCE = model.DatasetCollectionElement
-        qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)
+        qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)  # type:ignore[var-annotated]
         qry = qry.order_by(DCE.element_index)
         qry = qry.options(
             joinedload(model.DatasetCollectionElement.child_collection), joinedload(model.DatasetCollectionElement.hda)
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index f0acddc138b4..9b6bd50222c8 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -202,8 +202,11 @@ def copy(
             raise TypeError()
         hda = item
         copy = hda.copy(
-            parent_id=kwargs.get("parent_id"), copy_hid=False, copy_tags=hda.tags, flush=flush
-        )  # type:ignore[attr-defined]
+            parent_id=kwargs.get("parent_id"),
+            copy_hid=False,
+            copy_tags=hda.tags,  # type:ignore[attr-defined]
+            flush=flush,
+        )
         if hide_copy:
             copy.visible = False
         if history:
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index 0a4a09f08f00..b8380f3f31f3 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -22,8 +22,10 @@
     nullsfirst,
     nullslast,
     select,
+    Select,
     sql,
     true,
+    UnaryExpression,
 )
 from sqlalchemy.orm import (
     joinedload,
@@ -134,7 +136,7 @@ def parse_order_by(self, order_by_string, default=None):
             attribute_dsc = f"{attribute}-dsc"
             attribute_asc = f"{attribute}-asc"
             if order_by_string in (attribute, attribute_dsc):
-                order_by = desc(attribute)
+                order_by: UnaryExpression = desc(attribute)
                 if attribute == "size":
                     return nullslast(order_by)
                 return order_by
@@ -163,12 +165,10 @@ def state_counts(self, history):
             base.ModelFilterParser.parsed_filter("orm", sql.column("visible") == true()),
         ]
         contents_subquery = self._union_of_contents_query(history, filters=filters).subquery()
-        statement = (
-            sql.select(sql.column("state"), func.count("*"))
-            .select_from(contents_subquery)
-            .group_by(sql.column("state"))
+        statement: Select = (
+            select(sql.column("state"), func.count("*")).select_from(contents_subquery).group_by(sql.column("state"))
         )
-        counts = self.app.model.context.execute(statement).fetchall()
+        counts = self.app.model.session().execute(statement).fetchall()
         return dict(counts)
 
     def active_counts(self, history):
diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py
index 05b30ec97ab4..8664e09adca0 100644
--- a/lib/galaxy/model/store/discover.py
+++ b/lib/galaxy/model/store/discover.py
@@ -462,7 +462,7 @@ def override_object_store_id(self, output_name: Optional[str] = None) -> Optiona
         if not job:
             return None
         default_object_store_id = job.object_store_id
-        object_store_id_overrides = job.object_store_id_overrides or {}
+        object_store_id_overrides = job.object_store_id_overrides or {}  # type:ignore[var-annotated]
         return object_store_id_overrides.get(output_name, default_object_store_id)  # type:ignore[union-attr]
 
     @property
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index b5a8c30a8754..57084e3c5b4b 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2044,6 +2044,7 @@ def src_id_to_item(
         item = sa_session.get(src_to_class[value["src"]], decoded_id)
     except KeyError:
         raise ValueError(f"Unknown input source {value['src']} passed to job submission API.")
+    assert item
     item.extra_params = {k: v for k, v in value.items() if k not in ("src", "id")}
     return item
 

From 575279e080607d0ec623ded4a3f5a07fecf5acee Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 6 Feb 2024 02:01:25 -0500
Subject: [PATCH 57/71] Mypy: type-ignore hda, ldda attrs: need declarative
 mapping

Also, minor SA2.0 syntax fix
---
 lib/galaxy/managers/folders.py          | 2 +-
 lib/galaxy/managers/history_contents.py | 2 +-
 lib/galaxy/managers/roles.py            | 3 ++-
 lib/galaxy/tools/wrappers.py            | 4 +++-
 lib/galaxy/workflow/run_request.py      | 6 +++---
 5 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py
index 29c465e95566..04762990cf9b 100644
--- a/lib/galaxy/managers/folders.py
+++ b/lib/galaxy/managers/folders.py
@@ -505,7 +505,7 @@ def _get_contained_datasets_statement(
             stmt = stmt.where(
                 or_(
                     func.lower(ldda.name).contains(search_text, autoescape=True),
-                    func.lower(ldda.message).contains(search_text, autoescape=True),
+                    func.lower(ldda.message).contains(search_text, autoescape=True),  # type:ignore[attr-defined]
                 )
             )
         sort_column = LDDA_SORT_COLUMN_MAP[payload.order_by](ldda, associated_dataset)
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index b8380f3f31f3..4bf0240ca623 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -418,7 +418,7 @@ def _contained_id_map(self, id_list):
             .where(component_class.id.in_(id_list))  # type: ignore[attr-defined]
             .options(undefer(component_class._metadata))
             .options(joinedload(component_class.dataset).joinedload(model.Dataset.actions))
-            .options(joinedload(component_class.tags))
+            .options(joinedload(component_class.tags))  # type: ignore[attr-defined]
             .options(joinedload(component_class.annotations))  # type: ignore[attr-defined]
         )
         result = self._session().scalars(stmt).unique()
diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index 8dfdc7e2f11b..1f8ef428b101 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -128,7 +128,8 @@ def purge(self, trans: ProvidesUserContext, role: model.Role) -> model.Role:
             raise RequestParameterInvalidException(f"Role '{role.name}' has not been deleted, so it cannot be purged.")
         # Delete UserRoleAssociations
         for ura in role.users:
-            user = sa_session.query(trans.app.model.User).get(ura.user_id)
+            user = sa_session.get(trans.app.model.User, ura.user_id)
+            assert user
             # Delete DefaultUserPermissions for associated users
             for dup in user.default_permissions:
                 if role == dup.role:
diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index b8591ea749d5..0059fc29092a 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -387,7 +387,9 @@ def __init__(
             self.dataset = wrap_with_safe_string(dataset_instance, no_wrap_classes=ToolParameterValueWrapper)
             self.metadata = self.MetadataWrapper(dataset_instance, compute_environment)
             if isinstance(dataset_instance, HasTags):
-                self.groups = {tag.user_value.lower() for tag in dataset_instance.tags if tag.user_tname == "group"}
+                self.groups = {
+                    tag.user_value.lower() for tag in dataset_instance.tags if tag.user_tname == "group"
+                }  # type-ignore[attr-defined]
             else:
                 # May be a 'FakeDatasetAssociation'
                 self.groups = set()
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index dd041531bd1c..516c85d07eb1 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -385,9 +385,9 @@ def build_workflow_run_configs(
                     )
                     content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
                 elif input_source == "ld":
-                    ldda = trans.sa_session.get(
-                        LibraryDataset, trans.security.decode_id(input_id)
-                    ).library_dataset_dataset_association
+                    library_dataset = trans.sa_session.get(LibraryDataset, trans.security.decode_id(input_id))
+                    assert library_dataset
+                    ldda = library_dataset.library_dataset_dataset_association
                     assert ldda
                     assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
                         trans.get_current_user_roles(), ldda.dataset

From a541a10ffecebc4f227d4051b4ea53859f4daa0e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 7 Feb 2024 16:14:56 -0500
Subject: [PATCH 58/71] Mypy: type-ignores to handle late evaluation of
 relationship arguments

---
 lib/galaxy/model/__init__.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 5f99411be19d..da587b59def1 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3039,7 +3039,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
             lambda: (
                 and_(
                     HistoryDatasetCollectionAssociation.history_id == History.id,  # type: ignore[has-type]
-                    not_(HistoryDatasetCollectionAssociation.deleted),  # type: ignore[has-type]
+                    not_(HistoryDatasetCollectionAssociation.deleted),  # type: ignore[has-type, arg-type]
                 )
             )
         ),
@@ -3063,8 +3063,8 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         primaryjoin=(
             lambda: and_(
                 HistoryDatasetCollectionAssociation.history_id == History.id,  # type: ignore[has-type]
-                not_(HistoryDatasetCollectionAssociation.deleted),  # type: ignore[has-type]
-                HistoryDatasetCollectionAssociation.visible,  # type: ignore[has-type]
+                not_(HistoryDatasetCollectionAssociation.deleted),  # type: ignore[has-type, arg-type]
+                HistoryDatasetCollectionAssociation.visible,  # type: ignore[has-type, arg-type]
             )
         ),
         order_by=lambda: asc(HistoryDatasetCollectionAssociation.hid),  # type: ignore[has-type]
@@ -3972,7 +3972,7 @@ class Dataset(Base, StorableObject, Serializable):
             lambda: and_(
                 Dataset.id == HistoryDatasetAssociation.dataset_id,  # type: ignore[attr-defined]
                 HistoryDatasetAssociation.deleted == false(),  # type: ignore[has-type]
-                HistoryDatasetAssociation.purged == false(),  # type: ignore[attr-defined]
+                HistoryDatasetAssociation.purged == false(),  # type: ignore[attr-defined, arg-type]
             )
         ),
         viewonly=True,
@@ -3982,7 +3982,7 @@ class Dataset(Base, StorableObject, Serializable):
         primaryjoin=(
             lambda: and_(
                 Dataset.id == HistoryDatasetAssociation.dataset_id,  # type: ignore[attr-defined]
-                HistoryDatasetAssociation.purged == true(),  # type: ignore[attr-defined]
+                HistoryDatasetAssociation.purged == true(),  # type: ignore[attr-defined, arg-type]
             )
         ),
         viewonly=True,
@@ -6074,7 +6074,10 @@ class LibraryInfoAssociation(Base, RepresentById):
     library = relationship(
         "Library",
         primaryjoin=(
-            lambda: and_(LibraryInfoAssociation.library_id == Library.id, not_(LibraryInfoAssociation.deleted))
+            lambda: and_(
+                LibraryInfoAssociation.library_id == Library.id,
+                not_(LibraryInfoAssociation.deleted),  # type:ignore[arg-type]
+            )
         ),
     )
     template = relationship(
@@ -6395,7 +6398,7 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
         for entity in return_entities:
             q = q.add_columns(entity)
             if entity == DatasetCollectionElement:
-                q = q.filter(entity.id == dce.c.id)
+                q = q.filter(entity.id == dce.c.id)  # type:ignore[arg-type]
 
         q = q.order_by(*order_by_columns)
         return q

From c58ff7375d1b4c015eee1cf618896c969abaa194 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 8 Feb 2024 15:17:19 -0500
Subject: [PATCH 59/71] Mypy: type-ignore column property assignments (type is
 correct)

---
 lib/galaxy/model/__init__.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index da587b59def1..e6754f14ec83 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -11335,7 +11335,7 @@ def __repr__(self):
 # ----------------------------------------------------------------------------------------
 # The following statements must not precede the mapped models defined above.
 
-Job.any_output_dataset_collection_instances_deleted = column_property(
+Job.any_output_dataset_collection_instances_deleted = column_property(  # type:ignore[assignment]
     exists(HistoryDatasetCollectionAssociation.id).where(
         and_(
             Job.id == JobToOutputDatasetCollectionAssociation.job_id,
@@ -11345,7 +11345,7 @@ def __repr__(self):
     )
 )
 
-Job.any_output_dataset_deleted = column_property(
+Job.any_output_dataset_deleted = column_property(  # type:ignore[assignment]
     exists(HistoryDatasetAssociation.id).where(
         and_(
             Job.id == JobToOutputDatasetAssociation.job_id,
@@ -11355,44 +11355,44 @@ def __repr__(self):
     )
 )
 
-History.average_rating = column_property(
+History.average_rating = column_property(  # type:ignore[assignment]
     select(func.avg(HistoryRatingAssociation.rating))
     .where(HistoryRatingAssociation.history_id == History.id)
     .scalar_subquery(),
     deferred=True,
 )
 
-History.users_shared_with_count = column_property(
+History.users_shared_with_count = column_property(  # type:ignore[assignment]
     select(func.count(HistoryUserShareAssociation.id))
     .where(History.id == HistoryUserShareAssociation.history_id)
     .scalar_subquery(),
     deferred=True,
 )
 
-Page.average_rating = column_property(
+Page.average_rating = column_property(  # type:ignore[assignment]
     select(func.avg(PageRatingAssociation.rating)).where(PageRatingAssociation.page_id == Page.id).scalar_subquery(),
     deferred=True,
 )
 
-StoredWorkflow.average_rating = column_property(
+StoredWorkflow.average_rating = column_property(  # type:ignore[assignment]
     select(func.avg(StoredWorkflowRatingAssociation.rating))
     .where(StoredWorkflowRatingAssociation.stored_workflow_id == StoredWorkflow.id)
     .scalar_subquery(),
     deferred=True,
 )
 
-Visualization.average_rating = column_property(
+Visualization.average_rating = column_property(  # type:ignore[assignment]
     select(func.avg(VisualizationRatingAssociation.rating))
     .where(VisualizationRatingAssociation.visualization_id == Visualization.id)
     .scalar_subquery(),
     deferred=True,
 )
 
-Workflow.step_count = column_property(
+Workflow.step_count = column_property(  # type:ignore[assignment]
     select(func.count(WorkflowStep.id)).where(Workflow.id == WorkflowStep.workflow_id).scalar_subquery(), deferred=True
 )
 
-WorkflowInvocationStep.subworkflow_invocation_id = column_property(
+WorkflowInvocationStep.subworkflow_invocation_id = column_property(  # type:ignore[assignment]
     select(WorkflowInvocationToSubworkflowInvocationAssociation.subworkflow_invocation_id)
     .where(
         and_(

From c1ec3ae1afc4c617d4cd8a3fcfed4f017b9b26a6 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 6 Feb 2024 14:04:15 -0500
Subject: [PATCH 60/71] Mypy: typing errors, misc. fixes

---
 lib/galaxy/app_unittest_utils/galaxy_mock.py   |  2 +-
 lib/galaxy/celery/base_task.py                 |  3 +--
 lib/galaxy/jobs/__init__.py                    |  4 ++--
 lib/galaxy/managers/datasets.py                |  4 ++--
 lib/galaxy/managers/export_tracker.py          |  4 ++--
 lib/galaxy/managers/folders.py                 |  3 ++-
 lib/galaxy/managers/genomes.py                 |  2 +-
 lib/galaxy/managers/hdas.py                    |  5 +++--
 lib/galaxy/managers/histories.py               |  2 +-
 lib/galaxy/managers/history_contents.py        |  2 +-
 lib/galaxy/managers/interactivetool.py         |  4 ++--
 lib/galaxy/managers/job_connections.py         |  2 +-
 lib/galaxy/managers/jobs.py                    |  4 ++--
 lib/galaxy/managers/model_stores.py            |  1 +
 lib/galaxy/managers/notification.py            | 18 +++++++++---------
 lib/galaxy/managers/pages.py                   |  2 +-
 lib/galaxy/managers/users.py                   |  2 +-
 lib/galaxy/managers/visualizations.py          |  2 +-
 lib/galaxy/managers/workflows.py               | 13 ++++++-------
 lib/galaxy/model/__init__.py                   | 13 ++++++++-----
 lib/galaxy/model/database_utils.py             |  4 ++--
 lib/galaxy/model/store/__init__.py             | 12 ++++++------
 lib/galaxy/model/unittest_utils/data_app.py    |  2 +-
 .../migration_scripts_testing_utils.py         |  1 +
 .../unittest_utils/model_testing_utils.py      |  2 +-
 .../installed_repository_manager.py            |  8 +++++---
 .../installed_repository_metadata_manager.py   |  2 +-
 .../update_repository_manager.py               |  2 +-
 .../tool_shed/metadata/metadata_generator.py   |  2 +-
 lib/galaxy/tools/wrappers.py                   |  6 ++++--
 lib/galaxy/visualization/genomes.py            |  2 +-
 .../galaxy/services/tool_shed_repositories.py  |  3 ++-
 lib/galaxy/workflow/extract.py                 |  4 ++--
 lib/galaxy/workflow/modules.py                 |  7 ++++---
 lib/galaxy/workflow/run.py                     |  2 ++
 lib/tool_shed/managers/repositories.py         |  4 +++-
 .../metadata/repository_metadata_manager.py    |  2 +-
 lib/tool_shed/test/base/twilltestcase.py       |  7 +++++--
 lib/tool_shed/util/shed_util_common.py         |  2 +-
 test/unit/app/tools/test_metadata.py           |  2 +-
 .../data/model/test_mapping_testing_utils.py   |  2 +-
 test/unit/data/model/test_model_store.py       |  4 ++--
 test/unit/data/test_mutable_json_column.py     |  2 +-
 43 files changed, 97 insertions(+), 79 deletions(-)

diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
index c33e3b433326..d50842158020 100644
--- a/lib/galaxy/app_unittest_utils/galaxy_mock.py
+++ b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -125,7 +125,7 @@ def __init__(self, config=None, **kwargs) -> None:
         self[ShortTermStorageMonitor] = sts_manager  # type: ignore[type-abstract]
         self[galaxy_scoped_session] = self.model.context
         self.visualizations_registry = MockVisualizationsRegistry()
-        self.tag_handler = tags.GalaxyTagHandler(self.model.context)
+        self.tag_handler = tags.GalaxyTagHandler(self.model.session)
         self[tags.GalaxyTagHandler] = self.tag_handler
         self.quota_agent = quota.DatabaseQuotaAgent(self.model)
         self.job_config = Bunch(
diff --git a/lib/galaxy/celery/base_task.py b/lib/galaxy/celery/base_task.py
index af032fec1821..724472765393 100644
--- a/lib/galaxy/celery/base_task.py
+++ b/lib/galaxy/celery/base_task.py
@@ -86,14 +86,13 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
         .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', " ":now) "))
         .returning(CeleryUserRateLimit.last_scheduled_time)
     )
-
     _insert_stmt = (
         ps_insert(CeleryUserRateLimit)
         .values(user_id=bindparam("userid"), last_scheduled_time=bindparam("now"))
         .returning(CeleryUserRateLimit.last_scheduled_time)
     )
 
-    _upsert_stmt = _insert_stmt.on_conflict_do_update(
+    _upsert_stmt = _insert_stmt.on_conflict_do_update(  # type:ignore[attr-defined]
         index_elements=["user_id"], set_=dict(last_scheduled_time=bindparam("sched_time"))
     )
 
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index ae9a2dddca06..570d1d72b99b 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1181,7 +1181,7 @@ def galaxy_url(self):
         return self.get_destination_configuration("galaxy_infrastructure_url")
 
     def get_job(self) -> model.Job:
-        return self.sa_session.get(Job, self.job_id)
+        return self.sa_session.get(Job, self.job_id)  # type:ignore[return-value]
 
     def get_id_tag(self):
         # For compatibility with drmaa, which uses job_id right now, and TaskWrapper
@@ -1551,7 +1551,7 @@ def change_state(self, state, info=False, flush=True, job=None):
     def get_state(self) -> str:
         job = self.get_job()
         self.sa_session.refresh(job)
-        return job.state
+        return job.state  # type:ignore[return-value]
 
     def set_runner(self, runner_url, external_id):
         log.warning("set_runner() is deprecated, use set_job_destination()")
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index 612a69989deb..fbe82e56e996 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -112,8 +112,8 @@ def purge_datasets(self, request: PurgeDatasetsTaskRequest):
         self.error_unless_dataset_purge_allowed()
         with self.session().begin():
             for dataset_id in request.dataset_ids:
-                dataset: Dataset = self.session().get(Dataset, dataset_id)
-                if dataset.user_can_purge:
+                dataset: Optional[Dataset] = self.session().get(Dataset, dataset_id)
+                if dataset and dataset.user_can_purge:
                     try:
                         dataset.full_delete()
                     except Exception:
diff --git a/lib/galaxy/managers/export_tracker.py b/lib/galaxy/managers/export_tracker.py
index f0d6ae0d33f5..c2f9719f2441 100644
--- a/lib/galaxy/managers/export_tracker.py
+++ b/lib/galaxy/managers/export_tracker.py
@@ -44,7 +44,7 @@ def set_export_association_metadata(self, export_association_id: int, export_met
             export_association: StoreExportAssociation = self.session.execute(stmt).scalars().one()
         except NoResultFound:
             raise ObjectNotFound("Cannot set export metadata. Reason: Export association not found")
-        export_association.export_metadata = export_metadata.json()
+        export_association.export_metadata = export_metadata.json()  # type:ignore[assignment]
         with transaction(self.session):
             self.session.commit()
 
@@ -72,4 +72,4 @@ def get_object_exports(
             stmt = stmt.offset(offset)
         if limit:
             stmt = stmt.limit(limit)
-        return self.session.execute(stmt).scalars()
+        return self.session.execute(stmt).scalars()  # type:ignore[return-value]
diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py
index 04762990cf9b..fcbbed0cb9c5 100644
--- a/lib/galaxy/managers/folders.py
+++ b/lib/galaxy/managers/folders.py
@@ -536,7 +536,7 @@ def _filter_by_include_deleted(
 
     def build_folder_path(
         self, sa_session: galaxy_scoped_session, folder: model.LibraryFolder
-    ) -> List[Tuple[str, str]]:
+    ) -> List[Tuple[int, Optional[str]]]:
         """
         Returns the folder path from root to the given folder.
 
@@ -546,6 +546,7 @@ def build_folder_path(
         path_to_root = [(current_folder.id, current_folder.name)]
         while current_folder.parent_id is not None:
             parent_folder = sa_session.get(LibraryFolder, current_folder.parent_id)
+            assert parent_folder
             current_folder = parent_folder
             path_to_root.insert(0, (current_folder.id, current_folder.name))
         return path_to_root
diff --git a/lib/galaxy/managers/genomes.py b/lib/galaxy/managers/genomes.py
index 82cd1131d9f4..ce742e7c6d96 100644
--- a/lib/galaxy/managers/genomes.py
+++ b/lib/galaxy/managers/genomes.py
@@ -95,7 +95,7 @@ def _create_genome_filter(model_class=None):
             if self.database_connection.startswith("postgres"):
                 column = text("convert_from(metadata, 'UTF8')::json ->> 'dbkey'")
             else:
-                column = func.json_extract(model_class.table.c._metadata, "$.dbkey")
+                column = func.json_extract(model_class.table.c._metadata, "$.dbkey")  # type:ignore[assignment]
             lower_val = val.lower()  # Ignore case
             # dbkey can either be "hg38" or '["hg38"]', so we need to check both
             if op == "eq":
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 9b6bd50222c8..956f73425bcc 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -364,12 +364,13 @@ def get_discarded_summary(self, user: model.User) -> CleanableItemsSummary:
             .where(
                 and_(
                     model.HistoryDatasetAssociation.deleted == true(),
-                    model.HistoryDatasetAssociation.purged == false(),
+                    model.HistoryDatasetAssociation.purged == false(),  # type:ignore[arg-type]
                     model.History.user_id == user.id,
                 )
             )
         )
         result = self.hda_manager.session().execute(stmt).fetchone()
+        assert result
         total_size = 0 if result[0] is None else result[0]
         return CleanableItemsSummary(total_size=total_size, total_items=result[1])
 
@@ -393,7 +394,7 @@ def get_discarded(
             .where(
                 and_(
                     model.HistoryDatasetAssociation.deleted == true(),
-                    model.HistoryDatasetAssociation.purged == false(),
+                    model.HistoryDatasetAssociation.purged == false(),  # type:ignore[arg-type]
                     model.History.user_id == user.id,
                 )
             )
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index 4e5b20bf5ba8..1f3df4fccf87 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -227,7 +227,7 @@ def p_tag_filter(term_text: str, quoted: bool):
             stmt = stmt.limit(payload.limit)
         if payload.offset is not None:
             stmt = stmt.offset(payload.offset)
-        return trans.sa_session.scalars(stmt), total_matches
+        return trans.sa_session.scalars(stmt), total_matches  # type:ignore[return-value]
 
     def copy(self, history, user, **kwargs):
         """
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index 4bf0240ca623..3dbcecfcdbda 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -166,7 +166,7 @@ def state_counts(self, history):
         ]
         contents_subquery = self._union_of_contents_query(history, filters=filters).subquery()
         statement: Select = (
-            select(sql.column("state"), func.count("*")).select_from(contents_subquery).group_by(sql.column("state"))
+            select(sql.column("state"), func.count()).select_from(contents_subquery).group_by(sql.column("state"))
         )
         counts = self.app.model.session().execute(statement).fetchall()
         return dict(counts)
diff --git a/lib/galaxy/managers/interactivetool.py b/lib/galaxy/managers/interactivetool.py
index ac05892bef7c..4892091eee99 100644
--- a/lib/galaxy/managers/interactivetool.py
+++ b/lib/galaxy/managers/interactivetool.py
@@ -243,8 +243,8 @@ def build_subquery():
             filters = []
             for state in Job.non_ready_states:
                 filters.append(Job.state == state)
-            stmt = stmt.where(or_(*filters)).subquery()
-            return stmt
+            stmt = stmt.where(or_(*filters))
+            return stmt.subquery()
 
         stmt = select(InteractiveToolEntryPoint).where(InteractiveToolEntryPoint.job_id.in_(build_subquery()))
         return trans.sa_session.scalars(stmt)
diff --git a/lib/galaxy/managers/job_connections.py b/lib/galaxy/managers/job_connections.py
index c9000869cce3..c3317a0e8a52 100644
--- a/lib/galaxy/managers/job_connections.py
+++ b/lib/galaxy/managers/job_connections.py
@@ -54,7 +54,7 @@ def get_related_hids(self, history_id, hid: int):
             for val in graph["outputs"] + graph["inputs"]:
                 item_class = get_class(val["src"])
                 item_hid = self.sa_session.execute(select(item_class.hid).where(item_class.id == val["id"])).scalar()
-                result.append(item_hid)
+                result.append(item_hid)  # type:ignore[arg-type]
         return result
 
     def _get_union_results(self, *selects):
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 70957f89e076..f34d8a2dda2e 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -188,7 +188,7 @@ def add_search_criteria(stmt):
                     elif key == "runner":
                         stmt = stmt.where(text_column_filter(Job.job_runner_name, term))
                 elif isinstance(term, RawTextTerm):
-                    columns = [Job.tool_id]
+                    columns: List = [Job.tool_id]
                     if user_details:
                         columns.append(User.email)
                     if is_admin:
@@ -847,7 +847,7 @@ def summarize_jobs_to_dict(sa_session, jobs_source):
                 model.ImplicitCollectionJobsJobAssociation.table.join(model.Job)
             )
             statement = (
-                select(model.Job.state, func.count("*"))
+                select(model.Job.state, func.count())
                 .select_from(join)
                 .where(model.ImplicitCollectionJobs.id == jobs_source.id)
                 .group_by(model.Job.state)
diff --git a/lib/galaxy/managers/model_stores.py b/lib/galaxy/managers/model_stores.py
index 395d9dbade4c..1e4a82c89363 100644
--- a/lib/galaxy/managers/model_stores.py
+++ b/lib/galaxy/managers/model_stores.py
@@ -96,6 +96,7 @@ def setup_history_export_job(self, request: SetupHistoryExportJob):
         store_directory = request.store_directory
 
         history = self._sa_session.get(model.History, history_id)
+        assert history
         # symlink files on export, on worker files will tarred up in a dereferenced manner.
         with DirectoryModelExportStore(store_directory, app=self._app, export_files="symlink") as export_store:
             export_store.export_history(history, include_hidden=include_hidden, include_deleted=include_deleted)
diff --git a/lib/galaxy/managers/notification.py b/lib/galaxy/managers/notification.py
index 4f11742dec69..47b62142a43b 100644
--- a/lib/galaxy/managers/notification.py
+++ b/lib/galaxy/managers/notification.py
@@ -18,6 +18,7 @@
     union,
     update,
 )
+from sqlalchemy.orm import InstrumentedAttribute
 from sqlalchemy.sql import Select
 from typing_extensions import Protocol
 
@@ -64,7 +65,7 @@ def __init__(self, sa_session: galaxy_scoped_session, config: GalaxyAppConfigura
         self.sa_session = sa_session
         self.config = config
         self.recipient_resolver = NotificationRecipientResolver(strategy=DefaultStrategy(sa_session))
-        self.user_notification_columns = [
+        self.user_notification_columns: List[InstrumentedAttribute] = [
             Notification.id,
             Notification.source,
             Notification.category,
@@ -77,7 +78,7 @@ def __init__(self, sa_session: galaxy_scoped_session, config: GalaxyAppConfigura
             UserNotificationAssociation.seen_time,
             UserNotificationAssociation.deleted,
         ]
-        self.broadcast_notification_columns = [
+        self.broadcast_notification_columns: List[InstrumentedAttribute] = [
             Notification.id,
             Notification.source,
             Notification.category,
@@ -126,7 +127,7 @@ def send_notification_to_recipients(self, request: NotificationCreateRequest) ->
     def _send_to_users(self, notification: Notification, users: List[User]):
         # TODO: Move this potentially expensive operation to a task?
         for user in users:
-            if self._user_is_subscribed_to_notification(user, notification.category):
+            if self._user_is_subscribed_to_notification(user, notification.category):  # type:ignore[arg-type]
                 user_notification_association = UserNotificationAssociation(user, notification)
                 self.sa_session.add(user_notification_association)
 
@@ -199,8 +200,7 @@ def get_user_total_unread_notification_count(self, user: User) -> int:
                 )
             )
         )
-        result = self.sa_session.execute(stmt).scalar()
-        return result
+        return self.sa_session.execute(stmt).scalar() or 0
 
     def get_broadcasted_notification(self, notification_id: int, active_only: Optional[bool] = True):
         stmt = (
@@ -275,8 +275,8 @@ def update_broadcasted_notification(self, notification_id: int, request: Notific
     def get_user_notification_preferences(self, user: User) -> UserNotificationPreferences:
         """Gets the user's current notification preferences or the default ones if no preferences are set."""
         current_notification_preferences = (
-            user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME]
-            if NOTIFICATION_PREFERENCES_SECTION_NAME in user.preferences
+            user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME]  # type:ignore[index]
+            if NOTIFICATION_PREFERENCES_SECTION_NAME in user.preferences  # type:ignore[operator]
             else None
         )
         try:
@@ -291,7 +291,7 @@ def update_user_notification_preferences(
         """Updates the user's notification preferences with the requested changes."""
         notification_preferences = self.get_user_notification_preferences(user)
         notification_preferences.update(request.preferences)
-        user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME] = notification_preferences.json()
+        user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME] = notification_preferences.json()  # type:ignore[index]
         with transaction(self.sa_session):
             self.sa_session.commit()
         return notification_preferences
@@ -413,7 +413,7 @@ def resolve_users(self, recipients: NotificationRecipients) -> List[User]:
         unique_user_ids.update(user_ids_from_groups_and_roles)
 
         stmt = select(User).where(User.id.in_(unique_user_ids))
-        return self.sa_session.scalars(stmt).all()
+        return self.sa_session.scalars(stmt).all()  # type:ignore[return-value]
 
     def _get_all_user_ids_from_roles_query(self, role_ids: Set[int]) -> Select:
         stmt = (
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index 5e058a623a13..581b5b93562b 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -239,7 +239,7 @@ def p_tag_filter(term_text: str, quoted: bool):
             stmt = stmt.limit(payload.limit)
         if payload.offset is not None:
             stmt = stmt.offset(payload.offset)
-        return trans.sa_session.scalars(stmt), total_matches
+        return trans.sa_session.scalars(stmt), total_matches  # type:ignore[return-value]
 
     def create_page(self, trans, payload: CreatePagePayload):
         user = trans.get_user()
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index f92b82b68c10..edf557e35a90 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -176,7 +176,7 @@ def _get_all_active_jobs_from_user(self, user: User) -> List[Job]:
         """Get all jobs that are not ready yet and belong to the given user."""
         stmt = select(Job).where(and_(Job.user_id == user.id, Job.state.in_(Job.non_ready_states)))
         jobs = self.session().scalars(stmt)
-        return jobs
+        return jobs  # type:ignore[return-value]
 
     def undelete(self, user, flush=True):
         """Remove the deleted flag for the given user."""
diff --git a/lib/galaxy/managers/visualizations.py b/lib/galaxy/managers/visualizations.py
index bd097b99e9cc..80fbf13348c8 100644
--- a/lib/galaxy/managers/visualizations.py
+++ b/lib/galaxy/managers/visualizations.py
@@ -171,7 +171,7 @@ def p_tag_filter(term_text: str, quoted: bool):
             stmt = stmt.limit(payload.limit)
         if payload.offset is not None:
             stmt = stmt.offset(payload.offset)
-        return trans.sa_session.scalars(stmt), total_matches
+        return trans.sa_session.scalars(stmt), total_matches  # type:ignore[return-value]
 
 
 class VisualizationSerializer(sharable.SharableModelSerializer):
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 054f5f1e78a9..b5085d02fb27 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -39,7 +39,6 @@
 from sqlalchemy.orm import (
     aliased,
     joinedload,
-    Query,
     subqueryload,
 )
 from typing_extensions import Annotated
@@ -192,7 +191,7 @@ def index_query(
 
         latest_workflow_load = joinedload(StoredWorkflow.latest_workflow)
         if not payload.skip_step_counts:
-            latest_workflow_load = latest_workflow_load.undefer(Workflow.step_count)
+            latest_workflow_load = latest_workflow_load.undefer(Workflow.step_count)  # type:ignore[arg-type]
         latest_workflow_load = latest_workflow_load.lazyload(Workflow.steps)
 
         stmt = stmt.options(joinedload(StoredWorkflow.annotations))
@@ -269,7 +268,7 @@ def name_filter(term):
         if payload.offset is not None:
             stmt = stmt.offset(payload.offset)
         result = trans.sa_session.scalars(stmt).unique()
-        return result, total_matches
+        return result, total_matches  # type:ignore[return-value]
 
     def get_stored_workflow(self, trans, workflow_id, by_stored_id=True) -> StoredWorkflow:
         """Use a supplied ID (UUID or encoded stored workflow ID) to find
@@ -488,7 +487,7 @@ def build_invocations_query(
         sort_by=None,
         sort_desc=None,
         include_nested_invocations=True,
-    ) -> Tuple[Query, int]:
+    ) -> Tuple[List, int]:
         """Get invocations owned by the current user."""
 
         stmt = select(WorkflowInvocation)
@@ -536,7 +535,7 @@ def build_invocations_query(
             for inv in trans.sa_session.scalars(stmt)
             if self.check_security(trans, inv, check_ownership=True, check_accessible=False)
         ]
-        return invocations, total_matches
+        return invocations, total_matches  # type:ignore[return-value]
 
 
 MissingToolsT = List[Tuple[str, str, Optional[str], str]]
@@ -792,7 +791,7 @@ def _workflow_from_raw_description(
                 elif not workflow_state_resolution_options.archive_source.startswith("file://"):  # URL import
                     source_metadata["url"] = workflow_state_resolution_options.archive_source
                 workflow_state_resolution_options.archive_source = None  # so trs_id is not set for subworkflows
-                workflow.source_metadata = source_metadata
+                workflow.source_metadata = source_metadata  # type:ignore[assignment]
 
         # Assume no errors until we find a step that has some
         workflow.has_errors = False
@@ -1785,7 +1784,7 @@ def __module_from_dict(
         temp_input_connections: Dict[str, Union[List[DictConnection], DictConnection]] = step_dict.get(
             "input_connections", {}
         )
-        step.temp_input_connections = temp_input_connections
+        step.temp_input_connections = temp_input_connections  # type: ignore[assignment]
 
         # Create the model class for the step
         steps.append(step)
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index e6754f14ec83..29463c29f64b 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -28,6 +28,7 @@
 from string import Template
 from typing import (
     Any,
+    cast,
     Dict,
     Iterable,
     List,
@@ -4199,7 +4200,7 @@ def get_size(self, nice_size: bool = False, calculate_size: bool = True) -> Unio
             if nice_size:
                 return galaxy.util.nice_size(self.file_size)
             else:
-                return self.file_size
+                return cast(int, self.file_size)
         elif calculate_size:
             # Hopefully we only reach this branch in sessionless mode
             if nice_size:
@@ -4207,7 +4208,7 @@ def get_size(self, nice_size: bool = False, calculate_size: bool = True) -> Unio
             else:
                 return self._calculate_size()
         else:
-            return self.file_size or 0
+            return cast(int, self.file_size) or 0
 
     def set_size(self, no_extra_files=False):
         """Sets the size of the data on disk.
@@ -4855,7 +4856,9 @@ def find_conversion_destination(
         self, accepted_formats: List[str], **kwd
     ) -> Tuple[bool, Optional[str], Optional["DatasetInstance"]]:
         """Returns ( target_ext, existing converted dataset )"""
-        return self.datatype.find_conversion_destination(self, accepted_formats, _get_datatypes_registry(), **kwd)
+        return self.datatype.find_conversion_destination(
+            self, accepted_formats, _get_datatypes_registry(), **kwd  # type:ignore[arg-type]
+        )
 
     def add_validation_error(self, validation_error):
         self.validation_errors.append(validation_error)
@@ -6897,7 +6900,7 @@ def build_statement():
                 col = func.sum(case((column(state_label) == state, 1), else_=0)).label(state)
                 stm = stm.add_columns(col)
             # Add aggregate column for all jobs
-            col = func.count("*").label("all_jobs")
+            col = func.count().label("all_jobs")
             stm = stm.add_columns(col)
             return stm
 
@@ -11407,7 +11410,7 @@ def __repr__(self):
 
 # Set up proxy so that this syntax is possible:
 # <user_obj>.preferences[pref_name] = pref_value
-User.preferences = association_proxy("_preferences", "value", creator=UserPreference)
+User.preferences = association_proxy("_preferences", "value", creator=UserPreference)  # type:ignore[assignment]
 
 # Optimized version of getting the current Galaxy session.
 # See https://github.com/sqlalchemy/sqlalchemy/discussions/7638 for approach
diff --git a/lib/galaxy/model/database_utils.py b/lib/galaxy/model/database_utils.py
index a3ec08cd46dc..403be8d1242f 100644
--- a/lib/galaxy/model/database_utils.py
+++ b/lib/galaxy/model/database_utils.py
@@ -15,7 +15,7 @@
 from sqlalchemy.orm import object_session
 from sqlalchemy.sql.compiler import IdentifierPreparer
 from sqlalchemy.sql.expression import (
-    ClauseElement,
+    Executable,
     text,
 )
 
@@ -163,7 +163,7 @@ def supports_skip_locked(engine: Engine) -> bool:
     return _statement_executed_without_error(stmt, engine)
 
 
-def _statement_executed_without_error(statement: ClauseElement, engine: Engine) -> bool:
+def _statement_executed_without_error(statement: Executable, engine: Engine) -> bool:
     # Execute statement against database, then issue a rollback.
     try:
         with engine.connect() as conn, conn.begin() as trans:
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 38564174ab34..32ac1215b6cd 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -704,7 +704,7 @@ def handle_dataset_object_edit(dataset_instance, dataset_attrs):
                                 # Try to set metadata directly. @mvdbeek thinks we should only record the datasets
                                 try:
                                     if dataset_instance.has_metadata_files:
-                                        dataset_instance.datatype.set_meta(dataset_instance)
+                                        dataset_instance.datatype.set_meta(dataset_instance)  # type:ignore[arg-type]
                                 except Exception:
                                     log.debug(f"Metadata setting failed on {dataset_instance}", exc_info=True)
                                     dataset_instance.state = dataset_instance.dataset.states.FAILED_METADATA
@@ -1232,7 +1232,7 @@ def _import_jobs(self, object_import_tracker: "ObjectImportTracker", history: Op
                 continue
 
             imported_job = model.Job()
-            imported_job.id = job_attrs.get("id")
+            imported_job.id = cast(int, job_attrs.get("id"))
             imported_job.user = self.user
             add_object_to_session(imported_job, history_sa_session)
             imported_job.history = history
@@ -2159,12 +2159,12 @@ def export_history(
         sa_session = app.model.session
 
         # Write collections' attributes (including datasets list) to file.
-        stmt = (
+        stmt_hdca = (
             select(model.HistoryDatasetCollectionAssociation)
             .where(model.HistoryDatasetCollectionAssociation.history == history)
             .where(model.HistoryDatasetCollectionAssociation.deleted == expression.false())
         )
-        collections = sa_session.scalars(stmt)
+        collections = sa_session.scalars(stmt_hdca)
 
         for collection in collections:
             # filter this ?
@@ -2178,7 +2178,7 @@ def export_history(
         # Write datasets' attributes to file.
         actions_backref = model.Dataset.actions  # type: ignore[attr-defined]
 
-        stmt = (
+        stmt_hda = (
             select(model.HistoryDatasetAssociation)
             .where(model.HistoryDatasetAssociation.history == history)
             .join(model.Dataset)
@@ -2186,7 +2186,7 @@ def export_history(
             .order_by(model.HistoryDatasetAssociation.hid)
             .where(model.Dataset.purged == expression.false())
         )
-        datasets = sa_session.scalars(stmt).unique()
+        datasets = sa_session.scalars(stmt_hda).unique()
         for dataset in datasets:
             dataset.annotation = get_item_annotation_str(sa_session, history.user, dataset)
             should_include_file = (dataset.visible or include_hidden) and (not dataset.deleted or include_deleted)
diff --git a/lib/galaxy/model/unittest_utils/data_app.py b/lib/galaxy/model/unittest_utils/data_app.py
index 8942af46a4d7..75307163ae3d 100644
--- a/lib/galaxy/model/unittest_utils/data_app.py
+++ b/lib/galaxy/model/unittest_utils/data_app.py
@@ -98,7 +98,7 @@ def __init__(self, config: Optional[GalaxyDataTestConfig] = None, **kwd):
         self.object_store = objectstore.build_object_store_from_config(self.config)
         self.model = init("/tmp", self.config.database_connection, create_tables=True, object_store=self.object_store)
         self.security_agent = self.model.security_agent
-        self.tag_handler = GalaxyTagHandler(self.model.context)
+        self.tag_handler = GalaxyTagHandler(self.model.session)
         self.init_datatypes()
 
     def init_datatypes(self):
diff --git a/lib/galaxy/model/unittest_utils/migration_scripts_testing_utils.py b/lib/galaxy/model/unittest_utils/migration_scripts_testing_utils.py
index 7aad9d474081..0fbfaf947de3 100644
--- a/lib/galaxy/model/unittest_utils/migration_scripts_testing_utils.py
+++ b/lib/galaxy/model/unittest_utils/migration_scripts_testing_utils.py
@@ -75,6 +75,7 @@ def run_command(cmd: str) -> subprocess.CompletedProcess:
 def get_db_heads(config: Config) -> Tuple[str, ...]:
     """Return revision ids (version heads) stored in the database."""
     dburl = config.get_main_option("sqlalchemy.url")
+    assert dburl
     engine = create_engine(dburl, future=True)
     with engine.connect() as conn:
         context = MigrationContext.configure(conn)
diff --git a/lib/galaxy/model/unittest_utils/model_testing_utils.py b/lib/galaxy/model/unittest_utils/model_testing_utils.py
index 2f8d71babc54..960045510abb 100644
--- a/lib/galaxy/model/unittest_utils/model_testing_utils.py
+++ b/lib/galaxy/model/unittest_utils/model_testing_utils.py
@@ -145,7 +145,7 @@ def drop_database(db_url, database):
         _drop_database(db_url, database)
     else:
         url = make_url(db_url)
-        os.remove(url.database)
+        os.remove(url.database)  # type:ignore[arg-type]
 
 
 def dbcleanup_wrapper(session, obj, where_clause=None):
diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
index aff38254d183..792b07abc386 100644
--- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
@@ -117,7 +117,7 @@ def activate_repository(self, repository: ToolShedRepository) -> None:
                 tpm=tpm,
                 repository=repository,
                 changeset_revision=repository.changeset_revision,
-                metadata_dict=repository.metadata_,
+                metadata_dict=repository.metadata_,  # type:ignore[arg-type]
             )
             repository_tools_tups = irmm.get_repository_tools_tups()
             # Reload tools into the appropriate tool panel section.
@@ -139,7 +139,7 @@ def activate_repository(self, repository: ToolShedRepository) -> None:
                 dmh = data_manager.DataManagerHandler(self.app)
                 dmh.install_data_managers(
                     self.app.config.shed_data_manager_config_file,
-                    repository.metadata_,
+                    repository.metadata_,  # type:ignore[arg-type]
                     repository.get_shed_config_dict(self.app),
                     data_manager_relative_install_dir,
                     repository,
@@ -206,7 +206,9 @@ def add_entry_to_repository_dependencies_of_installed_repositories(self, reposit
 
     def get_containing_repository_for_tool_dependency(self, tool_dependency_tup: tuple) -> ToolShedRepository:
         tool_shed_repository_id, name, version, type = tool_dependency_tup
-        return self.context.query(ToolShedRepository).get(tool_shed_repository_id)
+        repository = self.context.query(ToolShedRepository).get(tool_shed_repository_id)
+        assert repository
+        return repository
 
     def get_dependencies_for_repository(
         self,
diff --git a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
index bf7e3ccbd33e..e2ed787bdba2 100644
--- a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
@@ -131,7 +131,7 @@ def reset_all_metadata_on_installed_repository(self):
             original_metadata_dict = self.repository.metadata_
             self.generate_metadata_for_changeset_revision()
             if self.metadata_dict != original_metadata_dict:
-                self.repository.metadata_ = self.metadata_dict
+                self.repository.metadata_ = self.metadata_dict  # type:ignore[assignment]
                 self.update_in_shed_tool_config()
 
                 session = self.app.install_model.context
diff --git a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
index e7ac8399b88b..dfa8bec8b769 100644
--- a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
@@ -116,7 +116,7 @@ def update_repository_record(
         if tool_shed_status_dict:
             repository.tool_shed_status = tool_shed_status_dict
         else:
-            repository.tool_shed_status = None
+            repository.tool_shed_status = None  # type:ignore[assignment]
         session = self.app.install_model.context
         session.add(repository)
         with transaction(session):
diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py
index e040ec0bdf16..b0827bdbf8b0 100644
--- a/lib/galaxy/tool_shed/metadata/metadata_generator.py
+++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py
@@ -854,7 +854,7 @@ class GalaxyMetadataGenerator(BaseMetadataGenerator):
     """A MetadataGenerator building on Galaxy's app and repository constructs."""
 
     app: InstallationTarget
-    repository: Optional[ToolShedRepository]
+    repository: Optional[ToolShedRepository]  # type:ignore[assignment]
 
     def __init__(
         self,
diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index 0059fc29092a..95fbd019e0e6 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -388,8 +388,10 @@ def __init__(
             self.metadata = self.MetadataWrapper(dataset_instance, compute_environment)
             if isinstance(dataset_instance, HasTags):
                 self.groups = {
-                    tag.user_value.lower() for tag in dataset_instance.tags if tag.user_tname == "group"
-                }  # type-ignore[attr-defined]
+                    tag.user_value.lower()
+                    for tag in dataset_instance.tags  # type:ignore[attr-defined]
+                    if tag.user_tname == "group"
+                }
             else:
                 # May be a 'FakeDatasetAssociation'
                 self.groups = set()
diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 98019adec70f..066785feae7a 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -269,7 +269,7 @@ def get_dbkeys(self, user: Optional[User], chrom_info=False):
         dbkeys = []
 
         # Add user's custom keys to dbkeys.
-        if user and "dbkeys" in user.preferences:
+        if user and user.preferences and "dbkeys" in user.preferences:
             user_keys_dict = loads(user.preferences["dbkeys"])
             dbkeys.extend([(attributes["name"], key) for key, attributes in user_keys_dict.items()])
 
diff --git a/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
index f827c0ee999b..594015ca4528 100644
--- a/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
@@ -57,6 +57,7 @@ def index(self, request: InstalledToolShedRepositoryIndexRequest) -> List[Instal
 
     def show(self, repository_id: DecodedDatabaseIdField) -> InstalledToolShedRepository:
         tool_shed_repository = self._install_model_context.get(ToolShedRepository, repository_id)
+        assert tool_shed_repository
         return self._show(tool_shed_repository)
 
     def check_for_updates(self, repository_id: Optional[int]) -> CheckForUpdatesResponse:
@@ -74,7 +75,7 @@ def _get_tool_shed_repositories(self, **kwd):
         stmt = select(ToolShedRepository)
         for key, value in kwd.items():
             if value is not None:
-                column = ToolShedRepository.__table__.c[key]
+                column = ToolShedRepository.__table__.c[key]  # type:ignore[attr-defined]
                 stmt = stmt.filter(column == value)
         stmt = stmt.order_by(ToolShedRepository.name).order_by(cast(ToolShedRepository.ctx_rev, Integer).desc())
         session = self._install_model_context
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 54899414413c..5d10aa8a8a19 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -116,7 +116,7 @@ def extract_steps(
         if name not in step_labels:
             step.label = name
             step_labels.add(name)
-        step.tool_inputs = dict(name=name)
+        step.tool_inputs = dict(name=name)  # type:ignore[assignment]
         hid_to_output_pair[hid] = (step, "output")
         steps.append(step)
     for i, hid in enumerate(dataset_collection_ids):
@@ -132,7 +132,7 @@ def extract_steps(
         if name not in step_labels:
             step.label = name
             step_labels.add(name)
-        step.tool_inputs = dict(name=name, collection_type=collection_type)
+        step.tool_inputs = dict(name=name, collection_type=collection_type)  # type:ignore[assignment]
         hid_to_output_pair[hid] = (step, "output")
         steps.append(step)
     # Tool steps
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index da53d9de6159..6374b1a0ab18 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1376,7 +1376,7 @@ def get_inputs(self):
 
     def restrict_options(self, step, connections: Iterable[WorkflowStepConnection], default_value):
         try:
-            static_options = []
+            static_options = []  # type:ignore[var-annotated]
             # Retrieve possible runtime options for 'select' type inputs
             for connection in connections:
                 # Well this isn't a great assumption...
@@ -2421,6 +2421,7 @@ def from_workflow_step(self, trans, step: WorkflowStep, **kwargs) -> WorkflowMod
         Return module initialized from the WorkflowStep object `step`.
         """
         type = step.type
+        assert type
         return self.module_types[type].from_workflow_step(trans, step, **kwargs)
 
 
@@ -2509,13 +2510,13 @@ def inject(self, step: WorkflowStep, step_args=None, steps=None, **kwargs):
         If step_args is provided from a web form this is applied to generate
         'state' else it is just obtained from the database.
         """
-        step.upgrade_messages = {}
+        step.upgrade_messages = {}  # type: ignore[assignment]
 
         # Make connection information available on each step by input name.
         step.setup_input_connections_by_name()
 
         # Populate module.
-        module = step.module = module_factory.from_workflow_step(self.trans, step, **kwargs)
+        module = step.module = module_factory.from_workflow_step(self.trans, step, **kwargs)  # type: ignore[assignment]
 
         # Any connected input needs to have value DummyDataset (these
         # are not persisted so we need to do it every time)
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index c7eab00a7a1d..02b7a4c8f0c7 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -600,6 +600,7 @@ def set_step_outputs(
                         workflow_output = model.WorkflowOutput(step, output_name=output_name)
                         step.workflow_outputs.append(workflow_output)
             for workflow_output in step.workflow_outputs:
+                assert workflow_output.output_name
                 output_name = workflow_output.output_name
                 if output_name not in outputs:
                     invocation_step.workflow_invocation.add_message(
@@ -632,6 +633,7 @@ def _subworkflow_invocation(self, step: "WorkflowStep") -> WorkflowInvocation:
         workflow_invocation = self.workflow_invocation
         subworkflow_invocation = workflow_invocation.get_subworkflow_invocation_for_step(step)
         if subworkflow_invocation is None:
+            assert step.order_index
             raise MessageException(f"Failed to find persisted subworkflow invocation for step [{step.order_index + 1}]")
         return subworkflow_invocation
 
diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py
index 79fbb68cc0d5..5159c915cd87 100644
--- a/lib/tool_shed/managers/repositories.py
+++ b/lib/tool_shed/managers/repositories.py
@@ -210,7 +210,8 @@ def index_tool_ids(app: ToolShedApp, tool_ids: List[str]) -> Dict[str, Any]:
         repository = guid_to_repository(app, tool_id)
         owner = repository.user.username
         name = repository.name
-        repository = _get_repository_by_name_and_owner(app.model.context.current, name, owner, app.model.User)
+        assert name
+        repository = _get_repository_by_name_and_owner(app.model.session().current, name, owner, app.model.User)
         if not repository:
             log.warning(f"Repository {owner}/{name} does not exist, skipping")
             continue
@@ -527,6 +528,7 @@ def upload_tar_and_set_metadata(
     app = trans.app
     user = trans.user
     assert user
+    assert user.username
     repo_dir = repository.repo_path(app)
     tip = repository.tip()
     tar_response = upload_tar(
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index a5df2eddcf91..bff8d0a21788 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -48,7 +48,7 @@ class ToolShedMetadataGenerator(BaseMetadataGenerator):
     """A MetadataGenerator building on ToolShed's app and repository constructs."""
 
     app: ToolShedApp
-    repository: Optional[Repository]
+    repository: Optional[Repository]  # type:ignore[assignment]
 
     # why is mypy making me re-annotate these things from the base class, it didn't
     # when they were in the same file
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 968109ac0235..4579ca1c72f1 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -1300,8 +1300,11 @@ def edit_repository_information(self, repository: Repository, revert=True, **kwd
             self.check_for_strings(strings_displayed)
         if revert:
             strings_displayed = []
+            # assert original_information[input_elem_name]
             for input_elem_name in ["repo_name", "description", "long_description"]:
-                self._browser.fill_form_value("edit_repository", input_elem_name, original_information[input_elem_name])
+                self._browser.fill_form_value(
+                    "edit_repository", input_elem_name, original_information[input_elem_name]  # type:ignore[arg-type]
+                )
                 strings_displayed.append(self.escape_html(original_information[input_elem_name]))
             self._browser.submit_form_with_name("edit_repository", "edit_repository_button")
             if self._browser.is_twill:
@@ -2050,7 +2053,7 @@ def _assert_repo_has_tool_with_id(
         )
         tools = installed_repository.metadata_["tools"]
         found_it = False
-        for tool in tools:
+        for tool in tools:  # type:ignore[attr-defined]
             if "id" not in tool:
                 continue
             if tool["id"] == tool_id:
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 99027ea17fc8..a6cab6cc954d 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -287,7 +287,7 @@ def handle_email_alerts(
                     email_alerts.append(user.email)
         else:
             subject = f"Galaxy tool shed update alert for repository named {str(repository.name)}"
-            email_alerts = json.loads(repository.email_alerts)
+            email_alerts = json.loads(repository.email_alerts)  # type:ignore[arg-type]
         for email in email_alerts:
             to = email.strip()
             # Send it
diff --git a/test/unit/app/tools/test_metadata.py b/test/unit/app/tools/test_metadata.py
index 8f83c6b90ef6..7e1784a84caa 100644
--- a/test/unit/app/tools/test_metadata.py
+++ b/test/unit/app/tools/test_metadata.py
@@ -18,7 +18,7 @@ class TestMetadata(TestCase, tools_support.UsesTools):
     def setUp(self):
         super().setUp()
         self.setup_app()
-        model.Dataset.object_store = self.app.object_store
+        model.Dataset.object_store = self.app.object_store  # type: ignore[assignment]
         job = model.Job()
         sa_session = self.app.model.session
         sa_session.add(job)
diff --git a/test/unit/data/model/test_mapping_testing_utils.py b/test/unit/data/model/test_mapping_testing_utils.py
index 6424632422ab..346ec2421403 100644
--- a/test/unit/data/model/test_mapping_testing_utils.py
+++ b/test/unit/data/model/test_mapping_testing_utils.py
@@ -65,7 +65,7 @@ def test_collection_consists_of_objects(session):
     # contains wrong number of objects
     assert not collection_consists_of_objects([stored_foo1, stored_foo1, stored_foo2], foo1, foo2)
     # if an object's primary key is not set, it cannot be equal to another object
-    foo1.id, stored_foo1.id = None, None
+    foo1.id, stored_foo1.id = None, None  # type:ignore[assignment]
     assert not collection_consists_of_objects([stored_foo1], foo1)
 
 
diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py
index 81c3d9f68b5f..e31511e7c272 100644
--- a/test/unit/data/model/test_model_store.py
+++ b/test/unit/data/model/test_model_store.py
@@ -988,7 +988,7 @@ def _setup_collection_invocation(app):
     workflow_step_1 = model.WorkflowStep()
     workflow_step_1.order_index = 0
     workflow_step_1.type = "data_collection_input"
-    workflow_step_1.tool_inputs = {}
+    workflow_step_1.tool_inputs = {}  # type:ignore[assignment]
     sa_session.add(workflow_step_1)
     workflow_1 = _workflow_from_steps(u, [workflow_step_1])
     workflow_1.license = "MIT"
@@ -1014,7 +1014,7 @@ def _setup_simple_invocation(app):
     workflow_step_1 = model.WorkflowStep()
     workflow_step_1.order_index = 0
     workflow_step_1.type = "data_input"
-    workflow_step_1.tool_inputs = {}
+    workflow_step_1.tool_inputs = {}  # type:ignore[assignment]
     sa_session.add(workflow_step_1)
     workflow = _workflow_from_steps(u, [workflow_step_1])
     workflow.license = "MIT"
diff --git a/test/unit/data/test_mutable_json_column.py b/test/unit/data/test_mutable_json_column.py
index 895438e74b40..9bc67fbc68e0 100644
--- a/test/unit/data/test_mutable_json_column.py
+++ b/test/unit/data/test_mutable_json_column.py
@@ -20,7 +20,7 @@ def test_metadata_mutable_column(self):
         session = self.model.session
         with transaction(session):
             session.commit()
-        w.value = {"x": "z"}
+        w.value = {"x": "z"}  # type:ignore[assignment]
         persisted = self.persist_and_reload(w)
         assert persisted.value == {"x": "z"}
         persisted.value["x"] = "1"

From 69581d1466f16033d258f0c0e4f4cf6446509bad Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 12 Feb 2024 13:47:18 -0500
Subject: [PATCH 61/71] Mypy: all statements are reachable

---
 lib/galaxy/managers/workflows.py    | 2 +-
 lib/galaxy/model/__init__.py        | 2 +-
 lib/galaxy/visualization/genomes.py | 4 ++--
 lib/galaxy/workflow/modules.py      | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index b5085d02fb27..3d454b457f82 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -1882,7 +1882,7 @@ def __connect_workflow_steps(self, steps: List[model.WorkflowStep], steps_by_ext
         for step in steps:
             # Input connections
             if step.temp_input_connections:  # populated by __module_from_dict
-                for input_name, conn_list in step.temp_input_connections.items():
+                for input_name, conn_list in step.temp_input_connections.items():  # type:ignore[unreachable]
                     if not conn_list:
                         continue
                     if not isinstance(conn_list, list):  # Older style singleton connection
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 29463c29f64b..5565bca37f04 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -4186,7 +4186,7 @@ def _calculate_size(self) -> int:
             except OSError:
                 return 0
         assert self.object_store
-        return self.object_store.size(self)
+        return self.object_store.size(self)  # type:ignore[unreachable]
 
     @overload
     def get_size(self, nice_size: Literal[False], calculate_size: bool = True) -> int: ...
diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 066785feae7a..50672c8227b4 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -269,8 +269,8 @@ def get_dbkeys(self, user: Optional[User], chrom_info=False):
         dbkeys = []
 
         # Add user's custom keys to dbkeys.
-        if user and user.preferences and "dbkeys" in user.preferences:
-            user_keys_dict = loads(user.preferences["dbkeys"])
+        if user and user.preferences and "dbkeys" in user.preferences:  # type:ignore[unreachable]
+            user_keys_dict = loads(user.preferences["dbkeys"])  # type:ignore[unreachable]
             dbkeys.extend([(attributes["name"], key) for key, attributes in user_keys_dict.items()])
 
         # Add app keys to dbkeys.
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 6374b1a0ab18..6dfcbc500a68 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1383,7 +1383,7 @@ def restrict_options(self, step, connections: Iterable[WorkflowStepConnection],
                 assert connection.input_step
                 module = connection.input_step.module
                 assert isinstance(module, (ToolModule, SubWorkflowModule))
-                if isinstance(module, ToolModule):
+                if isinstance(module, ToolModule):  # type:ignore[unreachable]
                     assert module.tool
                     tool_inputs = module.tool.inputs  # may not be set, but we're catching the Exception below.
 
@@ -2545,7 +2545,7 @@ def inject_all(self, workflow: Workflow, param_map=None, ignore_tool_missing_exc
 
     def compute_runtime_state(self, step: WorkflowStep, step_args=None):
         assert step.module, "module must be injected before computing runtime state"
-        state, step_errors = step.module.compute_runtime_state(self.trans, step, step_args)
+        state, step_errors = step.module.compute_runtime_state(self.trans, step, step_args)  # type:ignore[unreachable]
         step.state = state
 
         # Fix any missing parameters

From 6396effcb75387d40c7e3d6472ad1e3cb27bb38b Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 12 Feb 2024 13:54:14 -0500
Subject: [PATCH 62/71] Mypy: need to map hda declaratively, then its parent is
 model.Base

---
 lib/galaxy/managers/hdas.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 956f73425bcc..62d8e87e9bc6 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -125,7 +125,7 @@ def is_accessible(self, item: model.HistoryDatasetAssociation, user: Optional[mo
         #     return True
         return super().is_accessible(item, user, **kwargs)
 
-    def is_owner(self, item: model.Base, user: Optional[model.User], current_history=None, **kwargs: Any) -> bool:
+    def is_owner(self, item, user: Optional[model.User], current_history=None, **kwargs: Any) -> bool:
         """
         Use history to see if current user owns HDA.
         """

From 6311c371b6552dfa348c508375f33fb03f113c8b Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 9 Feb 2024 15:07:03 -0500
Subject: [PATCH 63/71] Fix typing errors: sharable, secured

---
 lib/galaxy/managers/secured.py                 |  2 +-
 lib/galaxy/managers/sharable.py                | 10 +++-------
 lib/galaxy/webapps/galaxy/services/sharable.py |  2 +-
 3 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/managers/secured.py b/lib/galaxy/managers/secured.py
index 20d95b8a8217..64721d8b137e 100644
--- a/lib/galaxy/managers/secured.py
+++ b/lib/galaxy/managers/secured.py
@@ -33,7 +33,7 @@ class AccessibleManagerMixin:
     def by_id(self, id: int): ...
 
     # don't want to override by_id since consumers will also want to fetch w/o any security checks
-    def is_accessible(self, item: "Query", user: model.User, **kwargs: Any) -> bool:
+    def is_accessible(self, item, user: model.User, **kwargs: Any) -> bool:
         """
         Return True if the item accessible to user.
         """
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 053c11562fe4..35e1afec570d 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -18,7 +18,6 @@
     Optional,
     Set,
     Type,
-    TYPE_CHECKING,
 )
 
 from sqlalchemy import (
@@ -55,9 +54,6 @@
 from galaxy.util import ready_name_for_url
 from galaxy.util.hash_util import md5_hash_str
 
-if TYPE_CHECKING:
-    from sqlalchemy.orm import Query
-
 log = logging.getLogger(__name__)
 
 
@@ -101,9 +97,9 @@ def is_owner(self, item: model.Base, user: Optional[User], **kwargs: Any) -> boo
         # ... effectively a good fit to have this here, but not semantically
         if self.user_manager.is_admin(user, trans=kwargs.get("trans", None)):
             return True
-        return item.user == user
+        return item.user == user  # type:ignore[attr-defined]
 
-    def is_accessible(self, item: "Query", user: Optional[User], **kwargs: Any) -> bool:
+    def is_accessible(self, item, user: Optional[User], **kwargs: Any) -> bool:
         """
         If the item is importable, is owned by `user`, or (the valid) `user`
         is in 'users shared with' list for the item: return True.
@@ -183,7 +179,7 @@ def share_with(self, item, user: User, flush: bool = True):
         """
         # precondition: user has been validated
         # get or create
-        existing = self.get_share_assocs(item, user=user)
+        existing = self.get_share_assocs(item, user=user)  # type:ignore[dict-item]
         if existing:
             return existing.pop(0)
         return self._create_user_share_assoc(item, user, flush=flush)
diff --git a/lib/galaxy/webapps/galaxy/services/sharable.py b/lib/galaxy/webapps/galaxy/services/sharable.py
index f940ed4e94ea..73724ba6e28e 100644
--- a/lib/galaxy/webapps/galaxy/services/sharable.py
+++ b/lib/galaxy/webapps/galaxy/services/sharable.py
@@ -182,7 +182,7 @@ def _send_notification_to_users(self, users_to_notify: Set[User], item: Sharable
 class SharedItemNotificationFactory:
     source = "galaxy_sharing_system"
 
-    type_map: Dict[SharableItem, SharableItemType] = {
+    type_map: Dict[Type[SharableItem], SharableItemType] = {
         History: "history",
         StoredWorkflow: "workflow",
         Visualization: "visualization",

From 49a2112291524dea35298de86a8c5918dadfd56d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 12 Feb 2024 20:24:24 -0500
Subject: [PATCH 64/71] Fix package mypy errors

---
 lib/galaxy/model/store/__init__.py            | 2 +-
 lib/galaxy/tool_util/toolbox/watcher.py       | 6 +++---
 lib/galaxy/tools/wrappers.py                  | 2 +-
 lib/galaxy/util/watcher.py                    | 6 +++---
 lib/galaxy_test/selenium/framework.py         | 6 +++---
 lib/tool_shed/test/base/playwrightbrowser.py  | 6 +++---
 lib/tool_shed/test/base/twillbrowser.py       | 4 ++--
 test/unit/app/managers/test_HistoryManager.py | 5 ++++-
 8 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 32ac1215b6cd..58a18dea7d13 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2161,7 +2161,7 @@ def export_history(
         # Write collections' attributes (including datasets list) to file.
         stmt_hdca = (
             select(model.HistoryDatasetCollectionAssociation)
-            .where(model.HistoryDatasetCollectionAssociation.history == history)
+            .where(model.HistoryDatasetCollectionAssociation.history == history)  # type:ignore[arg-type]
             .where(model.HistoryDatasetCollectionAssociation.deleted == expression.false())
         )
         collections = sa_session.scalars(stmt_hdca)
diff --git a/lib/galaxy/tool_util/toolbox/watcher.py b/lib/galaxy/tool_util/toolbox/watcher.py
index e570bb58198d..b885ea964e27 100644
--- a/lib/galaxy/tool_util/toolbox/watcher.py
+++ b/lib/galaxy/tool_util/toolbox/watcher.py
@@ -9,9 +9,9 @@
 
     can_watch = True
 except ImportError:
-    Observer = None
-    FileSystemEventHandler = object
-    PollingObserver = None
+    Observer = None  # type:ignore[assignment, misc]
+    FileSystemEventHandler = object  # type:ignore[assignment, misc]
+    PollingObserver = None  # type:ignore[assignment, misc]
     can_watch = False
 
 from galaxy.util.hash_util import md5_hash_file
diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index 95fbd019e0e6..3946baf593a2 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -389,7 +389,7 @@ def __init__(
             if isinstance(dataset_instance, HasTags):
                 self.groups = {
                     tag.user_value.lower()
-                    for tag in dataset_instance.tags  # type:ignore[attr-defined]
+                    for tag in dataset_instance.tags  # type:ignore[unused-ignore, attr-defined]
                     if tag.user_tname == "group"
                 }
             else:
diff --git a/lib/galaxy/util/watcher.py b/lib/galaxy/util/watcher.py
index dd4f0110299a..501a2212201c 100644
--- a/lib/galaxy/util/watcher.py
+++ b/lib/galaxy/util/watcher.py
@@ -13,9 +13,9 @@
 
     can_watch = True
 except ImportError:
-    Observer = None
-    FileSystemEventHandler = object
-    PollingObserver = None
+    Observer = None  # type:ignore[assignment]
+    FileSystemEventHandler = object  # type:ignore[assignment, misc]
+    PollingObserver = None  # type:ignore[assignment, misc]
     can_watch = False
 
 from galaxy.util.hash_util import md5_hash_file
diff --git a/lib/galaxy_test/selenium/framework.py b/lib/galaxy_test/selenium/framework.py
index 5b919286dbc3..a3b298d54c19 100644
--- a/lib/galaxy_test/selenium/framework.py
+++ b/lib/galaxy_test/selenium/framework.py
@@ -536,7 +536,7 @@ def setup_shared_state(self):
     NavigatesGalaxyMixin = object
 
 
-class UsesLibraryAssertions(NavigatesGalaxyMixin):
+class UsesLibraryAssertions(NavigatesGalaxyMixin):  # type:ignore[valid-type, misc]
     @retry_assertion_during_transitions
     def assert_num_displayed_items_is(self, n):
         num_displayed = self.num_displayed_items()
@@ -546,7 +546,7 @@ def num_displayed_items(self) -> int:
         return len(self.libraries_table_elements())
 
 
-class UsesHistoryItemAssertions(NavigatesGalaxyMixin):
+class UsesHistoryItemAssertions(NavigatesGalaxyMixin):  # type:ignore[valid-type, misc]
     def assert_item_peek_includes(self, hid, expected):
         item_body = self.history_panel_item_component(hid=hid)
         peek_text = item_body.peek.wait_for_text()
@@ -584,7 +584,7 @@ def assert_item_hid_text(self, hid):
 )
 
 
-class UsesWorkflowAssertions(NavigatesGalaxyMixin):
+class UsesWorkflowAssertions(NavigatesGalaxyMixin):  # type:ignore[valid-type, misc]
     @retry_assertion_during_transitions
     def _assert_showing_n_workflows(self, n):
         actual_count = len(self.workflow_card_elements())
diff --git a/lib/tool_shed/test/base/playwrightbrowser.py b/lib/tool_shed/test/base/playwrightbrowser.py
index d493e97aa990..4c82a0d7183c 100644
--- a/lib/tool_shed/test/base/playwrightbrowser.py
+++ b/lib/tool_shed/test/base/playwrightbrowser.py
@@ -132,7 +132,7 @@ def _fill_form_value(self, form: Locator, control_name: str, value: FormValueTyp
         input_s = form.locator(f"select[name='{control_name}']")
         if input_i.count():
             if control_name in ["redirect"]:
-                input_i.input_value = value
+                input_i.input_value = value  # type:ignore[method-assign, assignment]
             else:
                 if isinstance(value, bool):
                     if value and not input_i.is_checked():
@@ -142,9 +142,9 @@ def _fill_form_value(self, form: Locator, control_name: str, value: FormValueTyp
                 else:
                     input_i.fill(value)
         if input_t.count():
-            input_t.fill(value)
+            input_t.fill(value)  # type:ignore[arg-type]
         if input_s.count():
-            input_s.select_option(value)
+            input_s.select_option(value)  # type:ignore[arg-type]
 
     def edit_repository_categories(self, categories_to_add: List[str], categories_to_remove: List[str]) -> None:
         multi_select = "form[name='categories'] select[name='category_id']"
diff --git a/lib/tool_shed/test/base/twillbrowser.py b/lib/tool_shed/test/base/twillbrowser.py
index 1f4af8791678..a73cdf85b299 100644
--- a/lib/tool_shed/test/base/twillbrowser.py
+++ b/lib/tool_shed/test/base/twillbrowser.py
@@ -5,7 +5,7 @@
 )
 
 import twill.commands as tc
-from twill.browser import FormElement
+from twill.browser import FormElement  # type:ignore[attr-defined]
 
 from galaxy.util import smart_str
 from .browser import (
@@ -19,7 +19,7 @@
 
 
 def visit_url(url: str, allowed_codes: List[int]) -> str:
-    new_url = tc.go(url)
+    new_url = tc.go(url)  # type:ignore[func-returns-value]
     return_code = tc.browser.code
     assert return_code in allowed_codes, "Invalid HTTP return code {}, allowed codes: {}".format(
         return_code,
diff --git a/test/unit/app/managers/test_HistoryManager.py b/test/unit/app/managers/test_HistoryManager.py
index ba1710740540..c3627c87d166 100644
--- a/test/unit/app/managers/test_HistoryManager.py
+++ b/test/unit/app/managers/test_HistoryManager.py
@@ -85,7 +85,10 @@ def test_base(self):
 
         self.log("should be able to order")
         history3 = self.history_manager.create(name="history3", user=user2)
-        name_first_then_time = (model.History.name, sqlalchemy.desc(model.History.create_time))
+        name_first_then_time = (
+            model.History.name,
+            sqlalchemy.desc(model.History.create_time),
+        )  # type:ignore[var-annotated]
         assert self.history_manager.list(order_by=name_first_then_time) == [history2, history1, history3]
 
     def test_copy(self):

From acdb9c65faac3b013a8ea25e9e4169babea935fd Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 13 Feb 2024 02:50:50 -0500
Subject: [PATCH 65/71] Fix SA2.0 error: celery task

1. In 2.0, when the statement contains "returning", the result type is
   ChunkedIteratorResult, which does not have the rowcount attr,
   becuase:
2. result.rowcount should not be used for statements containting the returning clause

Ref: https://docs.sqlalchemy.org/en/20/core/connections.html#sqlalchemy.engine.CursorResult.rowcount
---
 lib/galaxy/celery/base_task.py | 37 +++++++++++++---------------------
 1 file changed, 14 insertions(+), 23 deletions(-)

diff --git a/lib/galaxy/celery/base_task.py b/lib/galaxy/celery/base_task.py
index 724472765393..6737aba0231c 100644
--- a/lib/galaxy/celery/base_task.py
+++ b/lib/galaxy/celery/base_task.py
@@ -80,37 +80,28 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
     We take advantage of efficiencies in its dialect.
     """
 
-    _update_stmt = (
-        update(CeleryUserRateLimit)
-        .where(CeleryUserRateLimit.user_id == bindparam("userid"))
-        .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', " ":now) "))
-        .returning(CeleryUserRateLimit.last_scheduled_time)
-    )
-    _insert_stmt = (
-        ps_insert(CeleryUserRateLimit)
-        .values(user_id=bindparam("userid"), last_scheduled_time=bindparam("now"))
-        .returning(CeleryUserRateLimit.last_scheduled_time)
-    )
-
-    _upsert_stmt = _insert_stmt.on_conflict_do_update(  # type:ignore[attr-defined]
-        index_elements=["user_id"], set_=dict(last_scheduled_time=bindparam("sched_time"))
-    )
-
     def calculate_task_start_time(  # type: ignore
         self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         with transaction(sa_session):
-            result = sa_session.execute(
-                self._update_stmt, {"userid": user_id, "interval": task_interval_secs, "now": now}
+            update_stmt = (
+                update(CeleryUserRateLimit)
+                .where(CeleryUserRateLimit.user_id == user_id)
+                .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', " ":now) "))
+                .returning(CeleryUserRateLimit.last_scheduled_time)
             )
-            if result.rowcount == 0:
+            result = sa_session.execute(update_stmt, {"interval": task_interval_secs, "now": now}).all()
+            if not result:
                 sched_time = now + datetime.timedelta(seconds=task_interval_secs)
-                result = sa_session.execute(
-                    self._upsert_stmt, {"userid": user_id, "now": now, "sched_time": sched_time}
+                upsert_stmt = (
+                    ps_insert(CeleryUserRateLimit)  # type:ignore[attr-defined]
+                    .values(user_id=user_id, last_scheduled_time=now)
+                    .returning(CeleryUserRateLimit.last_scheduled_time)
+                    .on_conflict_do_update(index_elements=["user_id"], set_=dict(last_scheduled_time=sched_time))
                 )
-            for row in result:
-                return row[0]
+                result = sa_session.execute(upsert_stmt).all()
             sa_session.commit()
+            return result[0][0]
 
 
 class GalaxyTaskBeforeStartUserRateLimitStandard(GalaxyTaskBeforeStartUserRateLimit):

From 036dad5c8b190ef297111ba86331c4f7505daf14 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 20 Feb 2024 00:28:43 -0500
Subject: [PATCH 66/71] Wrap call to ensure session is closed

Otherwise there's an idle transaction left in the database (+locks)
---
 lib/tool_shed/webapp/controllers/admin.py    |  2 +-
 lib/tool_shed/webapp/model/mapping.py        |  5 +++++
 lib/tool_shed/webapp/util/shed_statistics.py | 10 ++--------
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/lib/tool_shed/webapp/controllers/admin.py b/lib/tool_shed/webapp/controllers/admin.py
index 73ddef546528..9b1681bafe24 100644
--- a/lib/tool_shed/webapp/controllers/admin.py
+++ b/lib/tool_shed/webapp/controllers/admin.py
@@ -324,7 +324,7 @@ def regenerate_statistics(self, trans, **kwd):
         message = escape(kwd.get("message", ""))
         status = kwd.get("status", "done")
         if "regenerate_statistics_button" in kwd:
-            trans.app.shed_counter.generate_statistics()
+            trans.app.shed_counter.generate_statistics(trans.sa_session)
             message = "Successfully regenerated statistics"
         return trans.fill_template("/webapps/tool_shed/admin/statistics.mako", message=message, status=status)
 
diff --git a/lib/tool_shed/webapp/model/mapping.py b/lib/tool_shed/webapp/model/mapping.py
index 0ef27ff7f8b9..94ff0317f3c4 100644
--- a/lib/tool_shed/webapp/model/mapping.py
+++ b/lib/tool_shed/webapp/model/mapping.py
@@ -45,4 +45,9 @@ def init(
 
     result.security_agent = CommunityRBACAgent(result)
     result.shed_counter = shed_statistics.ShedCounter(result)
+
+    session = result.session()
+    with session.begin():
+        result.shed_counter.generate_statistics(session)
+
     return result
diff --git a/lib/tool_shed/webapp/util/shed_statistics.py b/lib/tool_shed/webapp/util/shed_statistics.py
index d864420ecb2d..7e21673de19d 100644
--- a/lib/tool_shed/webapp/util/shed_statistics.py
+++ b/lib/tool_shed/webapp/util/shed_statistics.py
@@ -23,14 +23,8 @@ def __init__(self, model):
         self.unique_owners = 0
         self.unique_valid_tools = 0
         self.workflows = 0
-        self.generate_statistics()
 
-    @property
-    def sa_session(self):
-        """Returns a SQLAlchemy session"""
-        return self.model.context
-
-    def generate_statistics(self):
+    def generate_statistics(self, sa_session):
         self.custom_datatypes = 0
         self.deleted_repositories = 0
         self.deprecated_repositories = 0
@@ -42,7 +36,7 @@ def generate_statistics(self):
         self.unique_valid_tools = 0
         self.workflows = 0
         unique_user_ids = []
-        for repository in self.sa_session.scalars(select(Repository)):
+        for repository in sa_session.scalars(select(Repository)):
             self.repositories += 1
             self.total_clones += repository.times_downloaded
             is_deleted = repository.deleted

From a701cde23d0b055479179b6b403ba91b444fd337 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 20 Feb 2024 00:45:51 -0500
Subject: [PATCH 67/71] Ensure session is closed on TS Registry load

Same as prev. commit: otherwise db locks are left
---
 lib/tool_shed/repository_registry.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/repository_registry.py b/lib/tool_shed/repository_registry.py
index 6927b4e68e74..521ae1a06c6f 100644
--- a/lib/tool_shed/repository_registry.py
+++ b/lib/tool_shed/repository_registry.py
@@ -44,8 +44,12 @@ def __init__(self, app):
         self.viewable_suites_by_category = {}
         self.viewable_valid_repositories_and_suites_by_category = {}
         self.viewable_valid_suites_by_category = {}
-        self.load_viewable_repositories_and_suites_by_category()
-        self.load_repository_and_suite_tuples()
+        self.load()
+
+    def load(self):
+        with self.sa_session.begin():
+            self.load_viewable_repositories_and_suites_by_category()
+            self.load_repository_and_suite_tuples()
 
     def add_category_entry(self, category):
         category_name = str(category.name)

From 8c88bf9de1c0df6b19082f69f3703656f2fe6a32 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 20 Feb 2024 01:08:42 -0500
Subject: [PATCH 68/71] Fix SA2.0 error: list arg to select; mypy

---
 lib/galaxy/model/__init__.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 5565bca37f04..a2f860ff26e5 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7611,8 +7611,9 @@ def copy_tags_from(self, target_user, source_workflow):
 
     def invocation_counts(self) -> InvocationsStateCounts:
         sa_session = object_session(self)
+        assert sa_session
         stmt = (
-            select([WorkflowInvocation.state, func.count(WorkflowInvocation.state)])
+            select(WorkflowInvocation.state, func.count(WorkflowInvocation.state))
             .select_from(StoredWorkflow)
             .join(Workflow, Workflow.stored_workflow_id == StoredWorkflow.id)
             .join(WorkflowInvocation, WorkflowInvocation.workflow_id == Workflow.id)
@@ -7620,7 +7621,7 @@ def invocation_counts(self) -> InvocationsStateCounts:
             .where(StoredWorkflow.id == self.id)
         )
         rows = sa_session.execute(stmt).all()
-        rows_as_dict = dict(r for r in rows if r[0] is not None)
+        rows_as_dict = dict(r for r in rows if r[0] is not None)  # type:ignore[arg-type, var-annotated]
         return InvocationsStateCounts(rows_as_dict)
 
     def to_dict(self, view="collection", value_mapper=None):

From b644b1da4e620603e9e6a807c9177ffa46fca86e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 22 Feb 2024 23:51:23 -0500
Subject: [PATCH 69/71] Use NullPool for sqlite engines

This restores the behavior under SQLAlchemy 1.4
(Note that we set the pool for sqlite only if it's not an in-memory db
---
 lib/galaxy/model/orm/engine_factory.py      | 18 +++++++-----
 test/unit/data/model/test_engine_factory.py | 32 ++++++++++-----------
 2 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/lib/galaxy/model/orm/engine_factory.py b/lib/galaxy/model/orm/engine_factory.py
index 886a4e3462ab..374c53219c73 100644
--- a/lib/galaxy/model/orm/engine_factory.py
+++ b/lib/galaxy/model/orm/engine_factory.py
@@ -12,6 +12,7 @@
     exc,
 )
 from sqlalchemy.engine import Engine
+from sqlalchemy.pool import NullPool
 
 log = logging.getLogger(__name__)
 
@@ -101,8 +102,13 @@ def after_cursor_execute(conn, cursor, statement, parameters, context, executema
                     pass
 
     engine_options = engine_options or {}
-    engine_options = set_sqlite_connect_args(engine_options, url)
-    engine = create_engine(url, **engine_options, future=True)
+    if url.startswith("sqlite://"):
+        set_sqlite_connect_args(engine_options, url)
+
+    if url.startswith("sqlite://") and url not in ("sqlite:///:memory:", "sqlite://"):
+        engine = create_engine(url, **engine_options, poolclass=NullPool, future=True)
+    else:
+        engine = create_engine(url, **engine_options, future=True)
 
     # Prevent sharing connection across fork: https://docs.sqlalchemy.org/en/14/core/pooling.html#using-connection-pools-with-multiprocessing-or-os-fork
     register_after_fork(engine, lambda e: e.dispose())
@@ -123,13 +129,11 @@ def checkout(dbapi_connection, connection_record, connection_proxy):
     return engine
 
 
-def set_sqlite_connect_args(engine_options: Dict, url: str):
+def set_sqlite_connect_args(engine_options: Dict, url: str) -> None:
     """
     Add or update `connect_args` in `engine_options` if db is sqlite.
     Set check_same_thread to False for sqlite, handled by request-specific session.
     See https://fastapi.tiangolo.com/tutorial/sql-databases/#note
     """
-    if url.startswith("sqlite://"):
-        connect_args = engine_options.setdefault("connect_args", {})
-        connect_args["check_same_thread"] = False
-    return engine_options
+    connect_args = engine_options.setdefault("connect_args", {})
+    connect_args["check_same_thread"] = False
diff --git a/test/unit/data/model/test_engine_factory.py b/test/unit/data/model/test_engine_factory.py
index 947664865f3e..361fc1f608d3 100644
--- a/test/unit/data/model/test_engine_factory.py
+++ b/test/unit/data/model/test_engine_factory.py
@@ -7,28 +7,28 @@
 class TestSetSqliteConnectArgs:
     def test_engine_options_empty(self):
         engine_options = {}  # type: ignore[var-annotated]
-        updated = set_sqlite_connect_args(engine_options, SQLITE_URL)
-        assert updated == {"connect_args": {"check_same_thread": False}}
+        set_sqlite_connect_args(engine_options, SQLITE_URL)
+        assert engine_options == {"connect_args": {"check_same_thread": False}}
 
     def test_update_nonempty_engine_options(self):
         engine_options = {"foo": "some foo"}
-        updated = set_sqlite_connect_args(engine_options, SQLITE_URL)
-        assert len(updated) == 2
-        assert updated["foo"] == "some foo"
-        assert updated["connect_args"] == {"check_same_thread": False}
+        set_sqlite_connect_args(engine_options, SQLITE_URL)
+        assert len(engine_options) == 2
+        assert engine_options["foo"] == "some foo"
+        assert engine_options["connect_args"] == {"check_same_thread": False}  # type:ignore[comparison-overlap]
 
     def test_overwrite_connect_args(self):
         engine_options = {"foo": "some foo", "connect_args": {"check_same_thread": True}}
-        updated = set_sqlite_connect_args(engine_options, SQLITE_URL)
-        assert len(updated) == 2
-        assert updated["foo"] == "some foo"
-        assert updated["connect_args"] == {"check_same_thread": False}
+        set_sqlite_connect_args(engine_options, SQLITE_URL)
+        assert len(engine_options) == 2
+        assert engine_options["foo"] == "some foo"
+        assert engine_options["connect_args"] == {"check_same_thread": False}
 
     def test_update_nonempty_connect_args(self):
         engine_options = {"foo": "some foo", "connect_args": {"bar": "some bar"}}
-        updated = set_sqlite_connect_args(engine_options, SQLITE_URL)
-        assert len(updated) == 2
-        assert updated["foo"] == "some foo"
-        assert len(updated["connect_args"]) == 2
-        assert updated["connect_args"]["check_same_thread"] is False
-        assert updated["connect_args"]["bar"] == "some bar"
+        set_sqlite_connect_args(engine_options, SQLITE_URL)
+        assert len(engine_options) == 2
+        assert engine_options["foo"] == "some foo"
+        assert len(engine_options["connect_args"]) == 2
+        assert engine_options["connect_args"]["check_same_thread"] is False  # type:ignore[index]
+        assert engine_options["connect_args"]["bar"] == "some bar"  # type:ignore[index]

From 230c4b48b8571f8d064d9ee4ca87a7f8d085c1fb Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 28 Feb 2024 11:40:28 -0600
Subject: [PATCH 70/71] Help mypy: job is never None

---
 lib/galaxy/jobs/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 570d1d72b99b..f15afe2b58e6 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1181,7 +1181,9 @@ def galaxy_url(self):
         return self.get_destination_configuration("galaxy_infrastructure_url")
 
     def get_job(self) -> model.Job:
-        return self.sa_session.get(Job, self.job_id)  # type:ignore[return-value]
+        job = self.sa_session.get(Job, self.job_id)
+        assert job
+        return job
 
     def get_id_tag(self):
         # For compatibility with drmaa, which uses job_id right now, and TaskWrapper

From fd644c3d03cae83ec2f049457159de6517d42431 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Mar 2024 13:40:15 -0500
Subject: [PATCH 71/71] Add Decimal to accpted types by util.nice_size()

---
 lib/galaxy/util/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 4769a6842ba3..53532c6a57ed 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -29,6 +29,7 @@
     datetime,
     timezone,
 )
+from decimal import Decimal
 from email.mime.multipart import MIMEMultipart
 from email.mime.text import MIMEText
 from hashlib import md5
@@ -1519,7 +1520,7 @@ def shorten_with_metric_prefix(amount: int) -> str:
         return str(amount)
 
 
-def nice_size(size: Union[float, int, str]) -> str:
+def nice_size(size: Union[float, int, str, Decimal]) -> str:
     """
     Returns a readably formatted string with the size