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SQLAlchemy 2.0 follow-up #19388

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Jan 10, 2025
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SQLAlchemy 2.0 follow-up #19388

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9e38cae
Remove cascade_backrefs=False
jdavcs Jan 8, 2025
5f4090b
Try to disable transaction helper
jdavcs Jan 8, 2025
2ba17ff
Fix spelling
jdavcs Jan 8, 2025
0acf625
Remove commented out block, edit comment
jdavcs Jan 9, 2025
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96 changes: 29 additions & 67 deletions lib/galaxy/model/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -803,22 +803,22 @@ class User(Base, Dictifiable, RepresentById):
activation_token: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True)

addresses: Mapped[List["UserAddress"]] = relationship(
back_populates="user", order_by=lambda: desc(UserAddress.update_time), cascade_backrefs=False
back_populates="user", order_by=lambda: desc(UserAddress.update_time)
)
custos_auth: Mapped[List["CustosAuthnzToken"]] = relationship(back_populates="user")
chat_exchanges: Mapped[List["ChatExchange"]] = relationship(back_populates="user")
default_permissions: Mapped[List["DefaultUserPermissions"]] = relationship(back_populates="user")
groups: Mapped[List["UserGroupAssociation"]] = relationship(back_populates="user")
histories: Mapped[List["History"]] = relationship(
back_populates="user", order_by=lambda: desc(History.update_time), cascade_backrefs=False # type: ignore[has-type]
back_populates="user", order_by=lambda: desc(History.update_time) # type: ignore[has-type]
)
active_histories: Mapped[List["History"]] = relationship(
primaryjoin=(lambda: (History.user_id == User.id) & (not_(History.deleted)) & (not_(History.archived))),
viewonly=True,
order_by=lambda: desc(History.update_time), # type: ignore[has-type]
)
galaxy_sessions: Mapped[List["GalaxySession"]] = relationship(
back_populates="user", order_by=lambda: desc(GalaxySession.update_time), cascade_backrefs=False
back_populates="user", order_by=lambda: desc(GalaxySession.update_time)
)
object_stores: Mapped[List["UserObjectStore"]] = relationship(back_populates="user")
file_sources: Mapped[List["UserFileSource"]] = relationship(back_populates="user")
Expand Down Expand Up @@ -853,11 +853,8 @@ class User(Base, Dictifiable, RepresentById):
stored_workflows: Mapped[List["StoredWorkflow"]] = relationship(
back_populates="user",
primaryjoin=(lambda: User.id == StoredWorkflow.user_id),
cascade_backrefs=False,
)
all_notifications: Mapped[List["UserNotificationAssociation"]] = relationship(
back_populates="user", cascade_backrefs=False
)
all_notifications: Mapped[List["UserNotificationAssociation"]] = relationship(back_populates="user")

preferences: AssociationProxy[Any]

Expand Down Expand Up @@ -1507,9 +1504,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
output_dataset_collections: Mapped[List["JobToImplicitOutputDatasetCollectionAssociation"]] = relationship(
back_populates="job"
)
post_job_actions: Mapped[List["PostJobActionAssociation"]] = relationship(
back_populates="job", cascade_backrefs=False
)
post_job_actions: Mapped[List["PostJobActionAssociation"]] = relationship(back_populates="job")
input_library_datasets: Mapped[List["JobToInputLibraryDatasetAssociation"]] = relationship(back_populates="job")
output_library_datasets: Mapped[List["JobToOutputLibraryDatasetAssociation"]] = relationship(back_populates="job")
external_output_metadata: Mapped[List["JobExternalOutputMetadata"]] = relationship(back_populates="job")
Expand All @@ -1522,17 +1517,17 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
back_populates="job", uselist=True
)
implicit_collection_jobs_association: Mapped[List["ImplicitCollectionJobsJobAssociation"]] = relationship(
back_populates="job", uselist=False, cascade_backrefs=False
back_populates="job", uselist=False
)
container: Mapped[Optional["JobContainerAssociation"]] = relationship(back_populates="job", uselist=False)
data_manager_association: Mapped[Optional["DataManagerJobAssociation"]] = relationship(
back_populates="job", uselist=False, cascade_backrefs=False
back_populates="job", uselist=False
)
history_dataset_collection_associations: Mapped[List["HistoryDatasetCollectionAssociation"]] = relationship(
back_populates="job"
)
workflow_invocation_step: Mapped[Optional["WorkflowInvocationStep"]] = relationship(
back_populates="job", uselist=False, cascade_backrefs=False
back_populates="job", uselist=False
)

any_output_dataset_collection_instances_deleted = None
Expand Down Expand Up @@ -2607,9 +2602,7 @@ class ImplicitCollectionJobs(Base, Serializable):

id: Mapped[int] = mapped_column(primary_key=True)
populated_state: Mapped[str] = mapped_column(TrimmedString(64), default="new")
jobs: Mapped[List["ImplicitCollectionJobsJobAssociation"]] = relationship(
back_populates="implicit_collection_jobs", cascade_backrefs=False
)
jobs: Mapped[List["ImplicitCollectionJobsJobAssociation"]] = relationship(back_populates="implicit_collection_jobs")

class populated_states(str, Enum):
NEW = "new" # New implicit jobs object, unpopulated job associations
Expand Down Expand Up @@ -3029,7 +3022,7 @@ class Group(Base, Dictifiable, RepresentById):
name: Mapped[Optional[str]] = mapped_column(String(255), index=True, unique=True)
deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False)
quotas: Mapped[List["GroupQuotaAssociation"]] = relationship(back_populates="group")
roles: Mapped[List["GroupRoleAssociation"]] = relationship(back_populates="group", cascade_backrefs=False)
roles: Mapped[List["GroupRoleAssociation"]] = relationship(back_populates="group")
users: Mapped[List["UserGroupAssociation"]] = relationship("UserGroupAssociation", back_populates="group")

dict_collection_visible_keys = ["id", "name"]
Expand Down Expand Up @@ -3190,7 +3183,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
archive_export_id: Mapped[Optional[int]] = mapped_column(ForeignKey("store_export_association.id"), default=None)

datasets: Mapped[List["HistoryDatasetAssociation"]] = relationship(
back_populates="history", cascade_backrefs=False, order_by=lambda: asc(HistoryDatasetAssociation.hid) # type: ignore[has-type]
back_populates="history", order_by=lambda: asc(HistoryDatasetAssociation.hid) # type: ignore[has-type]
)
exports: Mapped[List["JobExportHistoryArchive"]] = relationship(
back_populates="history",
Expand Down Expand Up @@ -3255,11 +3248,9 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
default_permissions: Mapped[List["DefaultHistoryPermissions"]] = relationship(back_populates="history")
users_shared_with: Mapped[List["HistoryUserShareAssociation"]] = relationship(back_populates="history")
galaxy_sessions = relationship("GalaxySessionToHistoryAssociation", back_populates="history")
workflow_invocations: Mapped[List["WorkflowInvocation"]] = relationship(
back_populates="history", cascade_backrefs=False
)
workflow_invocations: Mapped[List["WorkflowInvocation"]] = relationship(back_populates="history")
user: Mapped[Optional["User"]] = relationship(back_populates="histories")
jobs: Mapped[List["Job"]] = relationship(back_populates="history", cascade_backrefs=False)
jobs: Mapped[List["Job"]] = relationship(back_populates="history")
tool_requests: Mapped[List["ToolRequest"]] = relationship(back_populates="history")

update_time = column_property(
Expand Down Expand Up @@ -3916,9 +3907,7 @@ class Quota(Base, Dictifiable, RepresentById):
operation: Mapped[Optional[str]] = mapped_column(String(8))
deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False)
quota_source_label: Mapped[Optional[str]] = mapped_column(String(32), default=None)
default: Mapped[List["DefaultQuotaAssociation"]] = relationship(
"DefaultQuotaAssociation", back_populates="quota", cascade_backrefs=False
)
default: Mapped[List["DefaultQuotaAssociation"]] = relationship("DefaultQuotaAssociation", back_populates="quota")
groups: Mapped[List["GroupQuotaAssociation"]] = relationship(back_populates="quota")
users: Mapped[List["UserQuotaAssociation"]] = relationship(back_populates="quota")

Expand Down Expand Up @@ -4200,15 +4189,12 @@ class Dataset(Base, StorableObject, Serializable):
),
viewonly=True,
)
hashes: Mapped[List["DatasetHash"]] = relationship(back_populates="dataset", cascade_backrefs=False)
hashes: Mapped[List["DatasetHash"]] = relationship(back_populates="dataset")
sources: Mapped[List["DatasetSource"]] = relationship(back_populates="dataset")
history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship(
back_populates="dataset", cascade_backrefs=False
)
history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship(back_populates="dataset")
library_associations: Mapped[List["LibraryDatasetDatasetAssociation"]] = relationship(
primaryjoin=(lambda: LibraryDatasetDatasetAssociation.table.c.dataset_id == Dataset.id),
back_populates="dataset",
cascade_backrefs=False,
)

# failed_metadata is only valid as DatasetInstance state currently
Expand Down Expand Up @@ -5779,7 +5765,7 @@ class Library(Base, Dictifiable, HasName, Serializable):
description: Mapped[Optional[str]] = mapped_column(TEXT)
synopsis: Mapped[Optional[str]] = mapped_column(TEXT)
root_folder = relationship("LibraryFolder", back_populates="library_root")
actions: Mapped[List["LibraryPermissions"]] = relationship(back_populates="library", cascade_backrefs=False)
actions: Mapped[List["LibraryPermissions"]] = relationship(back_populates="library")

permitted_actions = get_permitted_actions(filter="LIBRARY")
dict_collection_visible_keys = ["id", "name"]
Expand Down Expand Up @@ -5894,7 +5880,7 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
)

library_root = relationship("Library", back_populates="root_folder")
actions: Mapped[List["LibraryFolderPermissions"]] = relationship(back_populates="folder", cascade_backrefs=False)
actions: Mapped[List["LibraryFolderPermissions"]] = relationship(back_populates="folder")

dict_element_visible_keys = [
"id",
Expand Down Expand Up @@ -6016,9 +6002,7 @@ class LibraryDataset(Base, Serializable):
viewonly=True,
uselist=True,
)
actions: Mapped[List["LibraryDatasetPermissions"]] = relationship(
back_populates="library_dataset", cascade_backrefs=False
)
actions: Mapped[List["LibraryDatasetPermissions"]] = relationship(back_populates="library_dataset")

# This class acts as a proxy to the currently selected LDDA
upload_options = [
Expand Down Expand Up @@ -7651,7 +7635,7 @@ class GalaxySession(Base, RepresentById):
last_action: Mapped[Optional[datetime]]
current_history: Mapped[Optional["History"]] = relationship()
histories: Mapped[List["GalaxySessionToHistoryAssociation"]] = relationship(
back_populates="galaxy_session", cascade_backrefs=False
back_populates="galaxy_session",
)
user: Mapped[Optional["User"]] = relationship(back_populates="galaxy_sessions")

Expand Down Expand Up @@ -7729,7 +7713,6 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
cascade="all, delete-orphan",
primaryjoin=(lambda: StoredWorkflow.id == Workflow.stored_workflow_id),
order_by=lambda: -Workflow.id,
cascade_backrefs=False,
)
latest_workflow: Mapped["Workflow"] = relationship(
"Workflow",
Expand Down Expand Up @@ -7922,7 +7905,6 @@ class Workflow(Base, Dictifiable, RepresentById):
"WorkflowStep",
primaryjoin=(lambda: Workflow.id == WorkflowStep.subworkflow_id),
back_populates="subworkflow",
cascade_backrefs=False,
)
stored_workflow = relationship(
"StoredWorkflow",
Expand Down Expand Up @@ -8129,18 +8111,15 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
order_by=lambda: WorkflowStepAnnotationAssociation.id,
back_populates="workflow_step",
)
post_job_actions = relationship("PostJobAction", back_populates="workflow_step", cascade_backrefs=False)
post_job_actions = relationship("PostJobAction", back_populates="workflow_step")
inputs = relationship("WorkflowStepInput", back_populates="workflow_step")
workflow_outputs: Mapped[List["WorkflowOutput"]] = relationship(
back_populates="workflow_step", cascade_backrefs=False
)
workflow_outputs: Mapped[List["WorkflowOutput"]] = relationship(back_populates="workflow_step")
output_connections: Mapped[List["WorkflowStepConnection"]] = relationship(
primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id)
)
workflow: Mapped["Workflow"] = relationship(
primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id),
back_populates="steps",
cascade_backrefs=False,
)

STEP_TYPE_TO_INPUT_TYPE = {
Expand Down Expand Up @@ -8444,7 +8423,6 @@ class WorkflowStepInput(Base, RepresentById):
connections: Mapped[List["WorkflowStepConnection"]] = relationship(
back_populates="input_step_input",
primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id),
cascade_backrefs=False,
)

def __init__(self, workflow_step):
Expand Down Expand Up @@ -8694,20 +8672,13 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True)

history = relationship("History", back_populates="workflow_invocations")
input_parameters = relationship(
"WorkflowRequestInputParameter", back_populates="workflow_invocation", cascade_backrefs=False
)
step_states = relationship("WorkflowRequestStepState", back_populates="workflow_invocation", cascade_backrefs=False)
input_step_parameters = relationship(
"WorkflowRequestInputStepParameter", back_populates="workflow_invocation", cascade_backrefs=False
)
input_datasets = relationship(
"WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation", cascade_backrefs=False
)
input_parameters = relationship("WorkflowRequestInputParameter", back_populates="workflow_invocation")
step_states = relationship("WorkflowRequestStepState", back_populates="workflow_invocation")
input_step_parameters = relationship("WorkflowRequestInputStepParameter", back_populates="workflow_invocation")
input_datasets = relationship("WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation")
input_dataset_collections = relationship(
"WorkflowRequestToInputDatasetCollectionAssociation",
back_populates="workflow_invocation",
cascade_backrefs=False,
)
subworkflow_invocations = relationship(
"WorkflowInvocationToSubworkflowInvocationAssociation",
Expand All @@ -8721,20 +8692,14 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
"WorkflowInvocationStep",
back_populates="workflow_invocation",
order_by=lambda: WorkflowInvocationStep.order_index,
cascade_backrefs=False,
)
workflow = relationship("Workflow")
output_dataset_collections = relationship(
"WorkflowInvocationOutputDatasetCollectionAssociation",
back_populates="workflow_invocation",
cascade_backrefs=False,
)
output_datasets = relationship(
"WorkflowInvocationOutputDatasetAssociation", back_populates="workflow_invocation", cascade_backrefs=False
)
output_values = relationship(
"WorkflowInvocationOutputValue", back_populates="workflow_invocation", cascade_backrefs=False
)
output_datasets = relationship("WorkflowInvocationOutputDatasetAssociation", back_populates="workflow_invocation")
output_values = relationship("WorkflowInvocationOutputValue", back_populates="workflow_invocation")
messages = relationship("WorkflowInvocationMessage", back_populates="workflow_invocation")

dict_collection_visible_keys = [
Expand Down Expand Up @@ -9421,12 +9386,10 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
output_dataset_collections = relationship(
"WorkflowInvocationStepOutputDatasetCollectionAssociation",
back_populates="workflow_invocation_step",
cascade_backrefs=False,
)
output_datasets = relationship(
"WorkflowInvocationStepOutputDatasetAssociation",
back_populates="workflow_invocation_step",
cascade_backrefs=False,
)
workflow_invocation: Mapped["WorkflowInvocation"] = relationship(back_populates="steps")
output_value = relationship(
Expand Down Expand Up @@ -10616,7 +10579,6 @@ class Visualization(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpda
back_populates="visualization",
cascade="all, delete-orphan",
primaryjoin=(lambda: Visualization.id == VisualizationRevision.visualization_id),
cascade_backrefs=False,
)
latest_revision: Mapped[Optional["VisualizationRevision"]] = relationship(
post_update=True,
Expand Down Expand Up @@ -11775,7 +11737,7 @@ def __repr__(self):
_metadata=deferred(HistoryDatasetAssociation.table.c._metadata),
dependent_jobs=relationship(JobToInputDatasetAssociation, back_populates="dataset"),
creating_job_associations=relationship(JobToOutputDatasetAssociation, back_populates="dataset"),
history=relationship(History, back_populates="datasets", cascade_backrefs=False),
history=relationship(History, back_populates="datasets"),
implicitly_converted_datasets=relationship(
ImplicitlyConvertedDatasetAssociation,
primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_parent_id == HistoryDatasetAssociation.id),
Expand Down
7 changes: 2 additions & 5 deletions lib/galaxy/model/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@
@contextlib.contextmanager
def transaction(session: Union[scoped_session, Session, "SessionlessContext"]):
"""Start a new transaction only if one is not present."""
# TODO The `session.begin` code has been removed. Once we can verify this does not break SQLAlchemy transactions, remove this helper + all references (561)
# temporary hack; need to fix access to scoped_session callable, not proxy
if isinstance(session, scoped_session):
session = session()
Expand All @@ -52,11 +53,7 @@ def transaction(session: Union[scoped_session, Session, "SessionlessContext"]):
yield
return # exit: can't use as a Session

if not session.in_transaction(): # type:ignore[union-attr]
with session.begin(): # type:ignore[union-attr]
yield
else:
yield
yield


def check_database_connection(session):
Expand Down
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