From a6bdb8b1e0573e609431074a7524e883a50ef67f Mon Sep 17 00:00:00 2001 From: John Davis Date: Wed, 10 Apr 2024 16:22:07 -0400 Subject: [PATCH] Drop redundant model class from relationship call --- lib/galaxy/model/__init__.py | 694 ++++++++++++++--------------------- 1 file changed, 269 insertions(+), 425 deletions(-) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index c34a1e538605..63a495d5a414 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -735,33 +735,27 @@ class User(Base, Dictifiable, RepresentById): activation_token: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True) addresses: Mapped[List["UserAddress"]] = relationship( - "UserAddress", back_populates="user", order_by=lambda: desc(UserAddress.update_time), cascade_backrefs=False + back_populates="user", order_by=lambda: desc(UserAddress.update_time), cascade_backrefs=False ) - cloudauthz: Mapped[List["CloudAuthz"]] = relationship("CloudAuthz", back_populates="user") - custos_auth: Mapped[List["CustosAuthnzToken"]] = relationship("CustosAuthnzToken", back_populates="user") - default_permissions: Mapped[List["DefaultUserPermissions"]] = relationship( - "DefaultUserPermissions", back_populates="user" - ) - groups: Mapped[List["UserGroupAssociation"]] = relationship("UserGroupAssociation", back_populates="user") + cloudauthz: Mapped[List["CloudAuthz"]] = relationship(back_populates="user") + custos_auth: Mapped[List["CustosAuthnzToken"]] = 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( - "History", 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), cascade_backrefs=False # type: ignore[has-type] ) 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: Mapped[List["GalaxySession"]] = relationship( - "GalaxySession", back_populates="user", order_by=lambda: desc(GalaxySession.update_time), cascade_backrefs=False # type: ignore[has-type] - ) - quotas: Mapped[List["UserQuotaAssociation"]] = relationship("UserQuotaAssociation", back_populates="user") - quota_source_usages: Mapped[List["UserQuotaSourceUsage"]] = relationship( - "UserQuotaSourceUsage", back_populates="user" + back_populates="user", order_by=lambda: desc(GalaxySession.update_time), cascade_backrefs=False # type: ignore[has-type] ) - social_auth: Mapped[List["UserAuthnzToken"]] = relationship("UserAuthnzToken", back_populates="user") + quotas: Mapped[List["UserQuotaAssociation"]] = relationship(back_populates="user") + quota_source_usages: Mapped[List["UserQuotaSourceUsage"]] = relationship(back_populates="user") + social_auth: Mapped[List["UserAuthnzToken"]] = relationship(back_populates="user") stored_workflow_menu_entries: Mapped[List["StoredWorkflowMenuEntry"]] = relationship( - "StoredWorkflowMenuEntry", primaryjoin=( lambda: (StoredWorkflowMenuEntry.user_id == User.id) & (StoredWorkflowMenuEntry.stored_workflow_id == StoredWorkflow.id) # type: ignore[has-type] @@ -771,15 +765,12 @@ class User(Base, Dictifiable, RepresentById): cascade="all, delete-orphan", collection_class=ordering_list("order_index"), ) - _preferences: Mapped[Dict[str, "UserPreference"]] = relationship( - "UserPreference", collection_class=attribute_keyed_dict("name") - ) + _preferences: Mapped[Dict[str, "UserPreference"]] = relationship(collection_class=attribute_keyed_dict("name")) values: Mapped[List["FormValues"]] = relationship( - "FormValues", primaryjoin=(lambda: User.form_values_id == FormValues.id) # type: ignore[has-type] + primaryjoin=(lambda: User.form_values_id == FormValues.id) # type: ignore[has-type] ) # Add type hint (will this work w/SA?) api_keys: Mapped[List["APIKeys"]] = relationship( - "APIKeys", back_populates="user", order_by=lambda: desc(APIKeys.create_time), primaryjoin=( @@ -789,21 +780,17 @@ class User(Base, Dictifiable, RepresentById): ) ), ) - data_manager_histories: Mapped[List["DataManagerHistoryAssociation"]] = relationship( - "DataManagerHistoryAssociation", back_populates="user" - ) - roles: Mapped[List["UserRoleAssociation"]] = relationship("UserRoleAssociation", back_populates="user") + data_manager_histories: Mapped[List["DataManagerHistoryAssociation"]] = relationship(back_populates="user") + roles: Mapped[List["UserRoleAssociation"]] = relationship(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: Mapped[List["UserNotificationAssociation"]] = relationship( - "UserNotificationAssociation", back_populates="user", cascade_backrefs=False + back_populates="user", cascade_backrefs=False ) non_private_roles: Mapped[List["UserRoleAssociation"]] = relationship( - "UserRoleAssociation", viewonly=True, primaryjoin=( lambda: (User.id == UserRoleAssociation.user_id) # type: ignore[has-type] @@ -1269,7 +1256,7 @@ class PasswordResetToken(Base): token: Mapped[str] = mapped_column(String(32), primary_key=True, unique=True, index=True) expiration_time: Mapped[Optional[datetime]] user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) - user: Mapped[Optional["User"]] = relationship("User") + user: Mapped[Optional["User"]] = relationship() def __init__(self, user, token=None): if token: @@ -1407,10 +1394,10 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): preferred_object_store_id: Mapped[Optional[str]] = mapped_column(String(255)) object_store_id_overrides: Mapped[Optional[bytes]] = mapped_column(JSONType) - user: Mapped[Optional["User"]] = relationship("User") - galaxy_session: Mapped[Optional["GalaxySession"]] = relationship("GalaxySession") - history: Mapped[Optional["History"]] = relationship("History", back_populates="jobs") - library_folder: Mapped[Optional["LibraryFolder"]] = relationship("LibraryFolder") + user: Mapped[Optional["User"]] = relationship() + galaxy_session: Mapped[Optional["GalaxySession"]] = relationship() + history: Mapped[Optional["History"]] = relationship(back_populates="jobs") + library_folder: Mapped[Optional["LibraryFolder"]] = relationship() parameters = relationship("JobParameter") input_datasets = relationship("JobToInputDatasetAssociation", back_populates="job") input_dataset_collections = relationship("JobToInputDatasetCollectionAssociation", back_populates="job") @@ -1420,20 +1407,18 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): output_dataset_collection_instances = relationship("JobToOutputDatasetCollectionAssociation", back_populates="job") output_dataset_collections = relationship("JobToImplicitOutputDatasetCollectionAssociation", back_populates="job") post_job_actions: Mapped[List["PostJobActionAssociation"]] = relationship( - "PostJobActionAssociation", back_populates="job", cascade_backrefs=False + back_populates="job", cascade_backrefs=False ) input_library_datasets = relationship("JobToInputLibraryDatasetAssociation", back_populates="job") output_library_datasets = relationship("JobToOutputLibraryDatasetAssociation", back_populates="job") - external_output_metadata: Mapped[List["JobExternalOutputMetadata"]] = relationship( - "JobExternalOutputMetadata", back_populates="job" - ) - tasks: Mapped[List["Task"]] = relationship("Task", back_populates="job") + external_output_metadata: Mapped[List["JobExternalOutputMetadata"]] = relationship(back_populates="job") + tasks: Mapped[List["Task"]] = relationship(back_populates="job") output_datasets = relationship("JobToOutputDatasetAssociation", back_populates="job") - state_history: Mapped[List["JobStateHistory"]] = relationship("JobStateHistory") - text_metrics: Mapped[List["JobMetricText"]] = relationship("JobMetricText") - numeric_metrics: Mapped[List["JobMetricNumeric"]] = relationship("JobMetricNumeric") + state_history: Mapped[List["JobStateHistory"]] = relationship() + text_metrics: Mapped[List["JobMetricText"]] = relationship() + numeric_metrics: Mapped[List["JobMetricNumeric"]] = relationship() interactivetool_entry_points: Mapped[List["InteractiveToolEntryPoint"]] = relationship( - "InteractiveToolEntryPoint", back_populates="job", uselist=True + back_populates="job", uselist=True ) implicit_collection_jobs_association = relationship( "ImplicitCollectionJobsJobAssociation", back_populates="job", uselist=False, cascade_backrefs=False @@ -2159,9 +2144,9 @@ class Task(Base, JobLike, RepresentById): 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: Mapped["Job"] = relationship("Job", back_populates="tasks") - text_metrics: Mapped[List["TaskMetricText"]] = relationship("TaskMetricText") - numeric_metrics: Mapped[List["TaskMetricNumeric"]] = relationship("TaskMetricNumeric") + job: Mapped["Job"] = relationship(back_populates="tasks") + text_metrics: Mapped[List["TaskMetricText"]] = relationship() + numeric_metrics: Mapped[List["TaskMetricNumeric"]] = relationship() _numeric_metric = TaskMetricNumeric _text_metric = TaskMetricText @@ -2330,9 +2315,9 @@ class JobToInputDatasetAssociation(Base, RepresentById): dataset_version: Mapped[Optional[int]] name: Mapped[Optional[str]] = mapped_column(String(255)) dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", lazy="joined", back_populates="dependent_jobs" + lazy="joined", back_populates="dependent_jobs" ) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="input_datasets") + job: Mapped[Optional["Job"]] = relationship(back_populates="input_datasets") def __init__(self, name, dataset): self.name = name @@ -2349,9 +2334,9 @@ class JobToOutputDatasetAssociation(Base, RepresentById): dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history_dataset_association.id"), index=True) name: Mapped[Optional[str]] = mapped_column(String(255)) dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", lazy="joined", back_populates="creating_job_associations" + lazy="joined", back_populates="creating_job_associations" ) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="output_datasets") + job: Mapped[Optional["Job"]] = relationship(back_populates="output_datasets") def __init__(self, name, dataset): self.name = name @@ -2372,10 +2357,8 @@ class JobToInputDatasetCollectionAssociation(Base, RepresentById): ForeignKey("history_dataset_collection_association.id"), index=True ) name: Mapped[Optional[str]] = mapped_column(String(255)) - dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", lazy="joined" - ) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="input_dataset_collections") + dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship(lazy="joined") + job: Mapped[Optional["Job"]] = relationship(back_populates="input_dataset_collections") def __init__(self, name, dataset_collection): self.name = name @@ -2391,10 +2374,8 @@ class JobToInputDatasetCollectionElementAssociation(Base, RepresentById): ForeignKey("dataset_collection_element.id"), index=True ) name: Mapped[Optional[str]] = mapped_column(Unicode(255)) - dataset_collection_element: Mapped[Optional["DatasetCollectionElement"]] = relationship( - "DatasetCollectionElement", lazy="joined" - ) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="input_dataset_collection_elements") + dataset_collection_element: Mapped[Optional["DatasetCollectionElement"]] = relationship(lazy="joined") + job: Mapped[Optional["Job"]] = relationship(back_populates="input_dataset_collection_elements") def __init__(self, name, dataset_collection_element): self.name = name @@ -2412,10 +2393,8 @@ class JobToOutputDatasetCollectionAssociation(Base, RepresentById): ForeignKey("history_dataset_collection_association.id"), index=True ) name: Mapped[Optional[str]] = mapped_column(Unicode(255)) - dataset_collection_instance: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", lazy="joined" - ) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="output_dataset_collection_instances") + dataset_collection_instance: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship(lazy="joined") + job: Mapped[Optional["Job"]] = relationship(back_populates="output_dataset_collection_instances") def __init__(self, name, dataset_collection_instance): self.name = name @@ -2436,8 +2415,8 @@ class JobToImplicitOutputDatasetCollectionAssociation(Base, RepresentById): job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True) dataset_collection_id: Mapped[Optional[int]] = mapped_column(ForeignKey("dataset_collection.id"), index=True) name: Mapped[Optional[str]] = mapped_column(Unicode(255)) - dataset_collection: Mapped[Optional["DatasetCollection"]] = relationship("DatasetCollection") - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="output_dataset_collections") + dataset_collection: Mapped[Optional["DatasetCollection"]] = relationship() + job: Mapped[Optional["Job"]] = relationship(back_populates="output_dataset_collections") def __init__(self, name, dataset_collection): self.name = name @@ -2451,9 +2430,9 @@ class JobToInputLibraryDatasetAssociation(Base, RepresentById): job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True) ldda_id: Mapped[Optional[int]] = mapped_column(ForeignKey("library_dataset_dataset_association.id"), index=True) name: Mapped[Optional[str]] = mapped_column(Unicode(255)) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="input_library_datasets") + job: Mapped[Optional["Job"]] = relationship(back_populates="input_library_datasets") dataset: Mapped[Optional["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", lazy="joined", back_populates="dependent_jobs" + lazy="joined", back_populates="dependent_jobs" ) def __init__(self, name, dataset): @@ -2469,9 +2448,9 @@ class JobToOutputLibraryDatasetAssociation(Base, RepresentById): job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True) ldda_id: Mapped[Optional[int]] = mapped_column(ForeignKey("library_dataset_dataset_association.id"), index=True) name: Mapped[Optional[str]] = mapped_column(Unicode(255)) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="output_library_datasets") + job: Mapped[Optional["Job"]] = relationship(back_populates="output_library_datasets") dataset: Mapped[Optional["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", lazy="joined", back_populates="creating_job_associations" + lazy="joined", back_populates="creating_job_associations" ) def __init__(self, name, dataset): @@ -2508,7 +2487,6 @@ class ImplicitlyCreatedDatasetCollectionInput(Base, RepresentById): name: Mapped[Optional[str]] = mapped_column(Unicode(255)) input_dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", primaryjoin=( lambda: HistoryDatasetCollectionAssociation.id # type: ignore[has-type] == ImplicitlyCreatedDatasetCollectionInput.input_dataset_collection_id @@ -2526,7 +2504,7 @@ 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( - "ImplicitCollectionJobsJobAssociation", back_populates="implicit_collection_jobs", cascade_backrefs=False + back_populates="implicit_collection_jobs", cascade_backrefs=False ) class populated_states(str, Enum): @@ -2561,7 +2539,7 @@ class ImplicitCollectionJobsJobAssociation(Base, RepresentById): job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True) # Consider making this nullable... order_index: Mapped[int] implicit_collection_jobs = relationship("ImplicitCollectionJobs", back_populates="jobs") - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="implicit_collection_jobs_association") + job: Mapped[Optional["Job"]] = relationship(back_populates="implicit_collection_jobs_association") class PostJobAction(Base, RepresentById): @@ -2573,7 +2551,6 @@ class PostJobAction(Base, RepresentById): output_name: Mapped[Optional[str]] = mapped_column(String(255)) action_arguments: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) workflow_step: Mapped[Optional["WorkflowStep"]] = relationship( - "WorkflowStep", back_populates="post_job_actions", primaryjoin=(lambda: WorkflowStep.id == PostJobAction.workflow_step_id), # type: ignore[has-type] ) @@ -2592,8 +2569,8 @@ class PostJobActionAssociation(Base, RepresentById): id: Mapped[int] = mapped_column(primary_key=True) job_id: Mapped[int] = mapped_column(ForeignKey("job.id"), index=True) post_job_action_id: Mapped[int] = mapped_column(ForeignKey("post_job_action.id"), index=True) - post_job_action: Mapped["PostJobAction"] = relationship("PostJobAction") - job: Mapped["Job"] = relationship("Job", back_populates="post_job_actions") + post_job_action: Mapped["PostJobAction"] = relationship() + job: Mapped["Job"] = relationship(back_populates="post_job_actions") def __init__(self, pja, job=None, job_id=None): if job is not None: @@ -2624,13 +2601,11 @@ class JobExternalOutputMetadata(Base, RepresentById): 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: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", lazy="joined" - ) + history_dataset_association: Mapped[Optional["HistoryDatasetAssociation"]] = relationship(lazy="joined") library_dataset_dataset_association: Mapped[Optional["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", lazy="joined" + lazy="joined" ) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="external_output_metadata") + job: Mapped[Optional["Job"]] = relationship(back_populates="external_output_metadata") def __init__(self, job=None, dataset=None): add_object_to_object_session(self, job) @@ -2676,9 +2651,9 @@ class JobExportHistoryArchive(Base, RepresentById): dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("dataset.id"), index=True) compressed: Mapped[Optional[bool]] = mapped_column(index=True, default=False) history_attrs_filename: Mapped[Optional[str]] = mapped_column(TEXT) - job: Mapped[Optional["Job"]] = relationship("Job") - dataset: Mapped[Optional["Dataset"]] = relationship("Dataset") - history: Mapped[Optional["History"]] = relationship("History", back_populates="exports") + job: Mapped[Optional["Job"]] = relationship() + dataset: Mapped[Optional["Dataset"]] = relationship() + history: Mapped[Optional["History"]] = relationship(back_populates="exports") ATTRS_FILENAME_HISTORY = "history_attrs.txt" @@ -2762,8 +2737,8 @@ class JobImportHistoryArchive(Base, RepresentById): job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True) history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True) archive_dir: Mapped[Optional[str]] = mapped_column(TEXT) - job: Mapped[Optional["Job"]] = relationship("Job") - history: Mapped[Optional["History"]] = relationship("History") + job: Mapped[Optional["Job"]] = relationship() + history: Mapped[Optional["History"]] = relationship() class StoreExportAssociation(Base, RepresentById): @@ -2788,7 +2763,7 @@ class JobContainerAssociation(Base, RepresentById): container_info: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) created_time: Mapped[Optional[datetime]] = mapped_column(default=now) modified_time: Mapped[Optional[datetime]] = mapped_column(default=now, onupdate=now) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="container") + job: Mapped[Optional["Job"]] = relationship(back_populates="container") def __init__(self, **kwd): if "job" in kwd: @@ -2818,7 +2793,7 @@ class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById): created_time: Mapped[Optional[datetime]] = mapped_column(default=now) modified_time: Mapped[Optional[datetime]] = mapped_column(default=now, onupdate=now) label: Mapped[Optional[str]] = mapped_column(TEXT) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="interactivetool_entry_points", uselist=False) + job: Mapped[Optional["Job"]] = relationship(back_populates="interactivetool_entry_points", uselist=False) dict_collection_visible_keys = [ "id", @@ -2884,9 +2859,9 @@ class GenomeIndexToolData(Base, RepresentById): # TODO: params arg is lost modified_time: Mapped[Optional[datetime]] = mapped_column(default=now, onupdate=now) indexer: Mapped[Optional[str]] = mapped_column(String(64)) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) - job: Mapped[Optional["Job"]] = relationship("Job") - dataset: Mapped[Optional["Dataset"]] = relationship("Dataset") - user: Mapped[Optional["User"]] = relationship("User") + job: Mapped[Optional["Job"]] = relationship() + dataset: Mapped[Optional["Dataset"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class Group(Base, Dictifiable, RepresentById): @@ -2897,10 +2872,8 @@ class Group(Base, Dictifiable, RepresentById): update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) 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("GroupQuotaAssociation", back_populates="group") - roles: Mapped[List["GroupRoleAssociation"]] = relationship( - "GroupRoleAssociation", back_populates="group", cascade_backrefs=False - ) + quotas: Mapped[List["GroupQuotaAssociation"]] = relationship(back_populates="group") + roles: Mapped[List["GroupRoleAssociation"]] = relationship(back_populates="group", cascade_backrefs=False) users = relationship("UserGroupAssociation", back_populates="group") dict_collection_visible_keys = ["id", "name"] @@ -2919,8 +2892,8 @@ class UserGroupAssociation(Base, RepresentById): group_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_group.id"), index=True) create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) - user: Mapped[Optional["User"]] = relationship("User", back_populates="groups") - group: Mapped[Optional["Group"]] = relationship("Group", back_populates="users") + user: Mapped[Optional["User"]] = relationship(back_populates="groups") + group: Mapped[Optional["Group"]] = relationship(back_populates="users") def __init__(self, user, group): add_object_to_object_session(self, user) @@ -2952,7 +2925,7 @@ class Notification(Base, Dictifiable, RepresentById): content: Mapped[Optional[bytes]] = mapped_column(DoubleEncodedJsonType) user_notification_associations: Mapped[List["UserNotificationAssociation"]] = relationship( - "UserNotificationAssociation", back_populates="notification" + back_populates="notification" ) def __init__(self, source: str, category: str, variant: str, content): @@ -2972,10 +2945,8 @@ class UserNotificationAssociation(Base, RepresentById): deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False) update_time: Mapped[Optional[datetime]] = mapped_column(default=now, onupdate=now) - user: Mapped[Optional["User"]] = relationship("User", back_populates="all_notifications") - notification: Mapped[Optional["Notification"]] = relationship( - "Notification", back_populates="user_notification_associations" - ) + user: Mapped[Optional["User"]] = relationship(back_populates="all_notifications") + notification: Mapped[Optional["Notification"]] = relationship(back_populates="user_notification_associations") def __init__(self, user, notification): self.user = user @@ -3054,16 +3025,14 @@ 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( - "HistoryDatasetAssociation", back_populates="history", cascade_backrefs=False, order_by=lambda: asc(HistoryDatasetAssociation.hid) # type: ignore[has-type] + back_populates="history", cascade_backrefs=False, order_by=lambda: asc(HistoryDatasetAssociation.hid) # type: ignore[has-type] ) exports: Mapped[List["JobExportHistoryArchive"]] = relationship( - "JobExportHistoryArchive", back_populates="history", primaryjoin=lambda: JobExportHistoryArchive.history_id == History.id, order_by=lambda: desc(JobExportHistoryArchive.id), ) active_datasets: Mapped[List["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", primaryjoin=( lambda: and_( HistoryDatasetAssociation.history_id == History.id, # type: ignore[arg-type] @@ -3073,11 +3042,8 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable order_by=lambda: asc(HistoryDatasetAssociation.hid), # type: ignore[has-type] viewonly=True, ) - dataset_collections: Mapped[List["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", back_populates="history" - ) + dataset_collections: Mapped[List["HistoryDatasetCollectionAssociation"]] = relationship(back_populates="history") active_dataset_collections: Mapped[List["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", primaryjoin=( lambda: ( and_( @@ -3090,7 +3056,6 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable viewonly=True, ) visible_datasets: Mapped[List["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", primaryjoin=( lambda: and_( HistoryDatasetAssociation.history_id == History.id, # type: ignore[arg-type] @@ -3102,7 +3067,6 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable viewonly=True, ) visible_dataset_collections: Mapped[List["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", primaryjoin=( lambda: and_( HistoryDatasetCollectionAssociation.history_id == History.id, # type: ignore[has-type] @@ -3114,28 +3078,23 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable viewonly=True, ) tags: Mapped[List["HistoryTagAssociation"]] = relationship( - "HistoryTagAssociation", order_by=lambda: HistoryTagAssociation.id, back_populates="history" + order_by=lambda: HistoryTagAssociation.id, back_populates="history" ) annotations: Mapped[List["HistoryAnnotationAssociation"]] = relationship( - "HistoryAnnotationAssociation", order_by=lambda: HistoryAnnotationAssociation.id, back_populates="history" + order_by=lambda: HistoryAnnotationAssociation.id, back_populates="history" ) ratings: Mapped[List["HistoryRatingAssociation"]] = relationship( - "HistoryRatingAssociation", order_by=lambda: HistoryRatingAssociation.id, # type: ignore[has-type] back_populates="history", ) - default_permissions: Mapped[List["DefaultHistoryPermissions"]] = relationship( - "DefaultHistoryPermissions", back_populates="history" - ) - users_shared_with: Mapped[List["HistoryUserShareAssociation"]] = relationship( - "HistoryUserShareAssociation", back_populates="history" - ) + 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( - "WorkflowInvocation", back_populates="history", cascade_backrefs=False + back_populates="history", cascade_backrefs=False ) - user: Mapped[Optional["User"]] = relationship("User", back_populates="histories") - jobs: Mapped[List["Job"]] = relationship("Job", back_populates="history", cascade_backrefs=False) + user: Mapped[Optional["User"]] = relationship(back_populates="histories") + jobs: Mapped[List["Job"]] = relationship(back_populates="history", cascade_backrefs=False) update_time = column_property( select(func.max(HistoryAudit.update_time)).where(HistoryAudit.history_id == id).scalar_subquery(), @@ -3628,8 +3587,8 @@ class HistoryUserShareAssociation(Base, UserShareAssociation): id: Mapped[int] = mapped_column(primary_key=True) history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) - user: Mapped[User] = relationship("User") - history: Mapped[Optional["History"]] = relationship("History", back_populates="users_shared_with") + user: Mapped[User] = relationship() + history: Mapped[Optional["History"]] = relationship(back_populates="users_shared_with") class UserRoleAssociation(Base, RepresentById): @@ -3641,8 +3600,8 @@ class UserRoleAssociation(Base, RepresentById): create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) - user: Mapped[Optional["User"]] = relationship("User", back_populates="roles") - role: Mapped[Optional["Role"]] = relationship("Role", back_populates="users") + user: Mapped[Optional["User"]] = relationship(back_populates="roles") + role: Mapped[Optional["Role"]] = relationship(back_populates="users") def __init__(self, user, role): add_object_to_object_session(self, user) @@ -3658,8 +3617,8 @@ class GroupRoleAssociation(Base, RepresentById): role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True) create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) - group: Mapped[Optional["Group"]] = relationship("Group", back_populates="roles") - role: Mapped[Optional["Role"]] = relationship("Role", back_populates="groups") + group: Mapped[Optional["Group"]] = relationship(back_populates="roles") + role: Mapped[Optional["Role"]] = relationship(back_populates="groups") def __init__(self, group, role): self.group = group @@ -3677,9 +3636,9 @@ class Role(Base, Dictifiable, RepresentById): description: Mapped[Optional[str]] = mapped_column(TEXT) type: Mapped[Optional[str]] = mapped_column(String(40), index=True) deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False) - dataset_actions: Mapped[List["DatasetPermissions"]] = relationship("DatasetPermissions", back_populates="role") - groups: Mapped[List["GroupRoleAssociation"]] = relationship("GroupRoleAssociation", back_populates="role") - users: Mapped[List["UserRoleAssociation"]] = relationship("UserRoleAssociation", back_populates="role") + dataset_actions: Mapped[List["DatasetPermissions"]] = relationship(back_populates="role") + groups: Mapped[List["GroupRoleAssociation"]] = relationship(back_populates="role") + users: Mapped[List["UserRoleAssociation"]] = relationship(back_populates="role") dict_collection_visible_keys = ["id", "name"] dict_element_visible_keys = ["id", "name", "description", "type"] @@ -3710,7 +3669,7 @@ class UserQuotaSourceUsage(Base, Dictifiable, RepresentById): 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: Mapped[Decimal] = mapped_column(Numeric(15, 0), default=0) - user: Mapped[Optional["User"]] = relationship("User", back_populates="quota_source_usages") + user: Mapped[Optional["User"]] = relationship(back_populates="quota_source_usages") class UserQuotaAssociation(Base, Dictifiable, RepresentById): @@ -3721,8 +3680,8 @@ class UserQuotaAssociation(Base, Dictifiable, RepresentById): quota_id: Mapped[Optional[int]] = mapped_column(ForeignKey("quota.id"), index=True) create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) - user: Mapped[Optional["User"]] = relationship("User", back_populates="quotas") - quota: Mapped[Optional["Quota"]] = relationship("Quota", back_populates="users") + user: Mapped[Optional["User"]] = relationship(back_populates="quotas") + quota: Mapped[Optional["Quota"]] = relationship(back_populates="users") dict_element_visible_keys = ["user"] @@ -3740,8 +3699,8 @@ class GroupQuotaAssociation(Base, Dictifiable, RepresentById): quota_id: Mapped[Optional[int]] = mapped_column(ForeignKey("quota.id"), index=True) create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) - group: Mapped[Optional["Group"]] = relationship("Group", back_populates="quotas") - quota: Mapped[Optional["Quota"]] = relationship("Quota", back_populates="groups") + group: Mapped[Optional["Group"]] = relationship(back_populates="quotas") + quota: Mapped[Optional["Quota"]] = relationship(back_populates="groups") dict_element_visible_keys = ["group"] @@ -3765,8 +3724,8 @@ class Quota(Base, Dictifiable, RepresentById): deleted: Mapped[Optional[bool]] = mapped_column(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: Mapped[List["GroupQuotaAssociation"]] = relationship("GroupQuotaAssociation", back_populates="quota") - users: Mapped[List["UserQuotaAssociation"]] = relationship("UserQuotaAssociation", back_populates="quota") + groups: Mapped[List["GroupQuotaAssociation"]] = relationship(back_populates="quota") + users: Mapped[List["UserQuotaAssociation"]] = relationship(back_populates="quota") dict_collection_visible_keys = ["id", "name", "quota_source_label"] dict_element_visible_keys = [ @@ -3822,7 +3781,7 @@ class DefaultQuotaAssociation(Base, Dictifiable, RepresentById): update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) type: Mapped[Optional[str]] = mapped_column(String(32)) quota_id: Mapped[Optional[int]] = mapped_column(ForeignKey("quota.id"), index=True) - quota: Mapped[Optional["Quota"]] = relationship("Quota", back_populates="default") + quota: Mapped[Optional["Quota"]] = relationship(back_populates="default") dict_element_visible_keys = ["type"] @@ -3846,8 +3805,8 @@ class DatasetPermissions(Base, RepresentById): action: Mapped[Optional[str]] = mapped_column(TEXT) dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("dataset.id"), index=True) role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True) - dataset: Mapped[Optional["Dataset"]] = relationship("Dataset", back_populates="actions") - role: Mapped[Optional["Role"]] = relationship("Role", back_populates="dataset_actions") + dataset: Mapped[Optional["Dataset"]] = relationship(back_populates="actions") + role: Mapped[Optional["Role"]] = relationship(back_populates="dataset_actions") def __init__(self, action, dataset, role=None, role_id=None): self.action = action @@ -3868,8 +3827,8 @@ class LibraryPermissions(Base, RepresentById): action: Mapped[Optional[str]] = mapped_column(TEXT) library_id: Mapped[Optional[int]] = mapped_column(ForeignKey("library.id"), index=True) role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True) - library: Mapped[Optional["Library"]] = relationship("Library", back_populates="actions") - role: Mapped[Optional["Role"]] = relationship("Role") + library: Mapped[Optional["Library"]] = relationship(back_populates="actions") + role: Mapped[Optional["Role"]] = relationship() def __init__(self, action, library_item, role): self.action = action @@ -3890,8 +3849,8 @@ class LibraryFolderPermissions(Base, RepresentById): action: Mapped[Optional[str]] = mapped_column(TEXT) library_folder_id: Mapped[Optional[int]] = mapped_column(ForeignKey("library_folder.id"), index=True) role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True) - folder: Mapped[Optional["LibraryFolder"]] = relationship("LibraryFolder", back_populates="actions") - role: Mapped[Optional["Role"]] = relationship("Role") + folder: Mapped[Optional["LibraryFolder"]] = relationship(back_populates="actions") + role: Mapped[Optional["Role"]] = relationship() def __init__(self, action, library_item, role): self.action = action @@ -3912,8 +3871,8 @@ class LibraryDatasetPermissions(Base, RepresentById): action: Mapped[Optional[str]] = mapped_column(TEXT) library_dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("library_dataset.id"), index=True) role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True) - library_dataset: Mapped[Optional["LibraryDataset"]] = relationship("LibraryDataset", back_populates="actions") - role: Mapped[Optional["Role"]] = relationship("Role") + library_dataset: Mapped[Optional["LibraryDataset"]] = relationship(back_populates="actions") + role: Mapped[Optional["Role"]] = relationship() def __init__(self, action, library_item, role): self.action = action @@ -3937,9 +3896,9 @@ class LibraryDatasetDatasetAssociationPermissions(Base, RepresentById): ) role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True) library_dataset_dataset_association: Mapped[Optional["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", back_populates="actions" + back_populates="actions" ) - role: Mapped[Optional["Role"]] = relationship("Role") + role: Mapped[Optional["Role"]] = relationship() def __init__(self, action, library_item, role): self.action = action @@ -3958,8 +3917,8 @@ class DefaultUserPermissions(Base, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) action: Mapped[Optional[str]] = mapped_column(TEXT) role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True) - user: Mapped[Optional["User"]] = relationship("User", back_populates="default_permissions") - role: Mapped[Optional["Role"]] = relationship("Role") + user: Mapped[Optional["User"]] = relationship(back_populates="default_permissions") + role: Mapped[Optional["Role"]] = relationship() def __init__(self, user, action, role): add_object_to_object_session(self, user) @@ -3975,8 +3934,8 @@ class DefaultHistoryPermissions(Base, RepresentById): history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True) action: Mapped[Optional[str]] = mapped_column(TEXT) role_id: Mapped[Optional[int]] = mapped_column(ForeignKey("role.id"), index=True) - history: Mapped[Optional["History"]] = relationship("History", back_populates="default_permissions") - role: Mapped[Optional["Role"]] = relationship("Role") + history: Mapped[Optional["History"]] = relationship(back_populates="default_permissions") + role: Mapped[Optional["Role"]] = relationship() def __init__(self, history, action, role): add_object_to_object_session(self, history) @@ -4011,10 +3970,9 @@ class Dataset(Base, StorableObject, Serializable): total_size: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0)) uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType()) - actions: Mapped[List["DatasetPermissions"]] = relationship("DatasetPermissions", back_populates="dataset") - job: Mapped[Optional["Job"]] = relationship(Job, primaryjoin=(lambda: Dataset.job_id == Job.id)) + actions: Mapped[List["DatasetPermissions"]] = relationship(back_populates="dataset") + job: Mapped[Optional["Job"]] = relationship(primaryjoin=(lambda: Dataset.job_id == Job.id)) active_history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", primaryjoin=( lambda: and_( Dataset.id == HistoryDatasetAssociation.dataset_id, # type: ignore[attr-defined] @@ -4025,7 +3983,6 @@ class Dataset(Base, StorableObject, Serializable): viewonly=True, ) purged_history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", primaryjoin=( lambda: and_( Dataset.id == HistoryDatasetAssociation.dataset_id, # type: ignore[attr-defined] @@ -4035,7 +3992,6 @@ class Dataset(Base, StorableObject, Serializable): viewonly=True, ) active_library_associations: Mapped[List["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", primaryjoin=( lambda: and_( Dataset.id == LibraryDatasetDatasetAssociation.dataset_id, # type: ignore[attr-defined] @@ -4044,13 +4000,12 @@ class Dataset(Base, StorableObject, Serializable): ), viewonly=True, ) - hashes: Mapped[List["DatasetHash"]] = relationship("DatasetHash", back_populates="dataset", cascade_backrefs=False) - sources: Mapped[List["DatasetSource"]] = relationship("DatasetSource", back_populates="dataset") + hashes: Mapped[List["DatasetHash"]] = relationship(back_populates="dataset", cascade_backrefs=False) + sources: Mapped[List["DatasetSource"]] = relationship(back_populates="dataset") history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", back_populates="dataset", cascade_backrefs=False + back_populates="dataset", cascade_backrefs=False ) library_associations: Mapped[List["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", primaryjoin=(lambda: LibraryDatasetDatasetAssociation.table.c.dataset_id == Dataset.id), back_populates="dataset", cascade_backrefs=False, @@ -4382,8 +4337,8 @@ class DatasetSource(Base, Dictifiable, Serializable): source_uri: Mapped[Optional[str]] = mapped_column(TEXT) extra_files_path: Mapped[Optional[str]] = mapped_column(TEXT) transform: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) - dataset: Mapped[Optional["Dataset"]] = relationship("Dataset", back_populates="sources") - hashes: Mapped[List["DatasetSourceHash"]] = relationship("DatasetSourceHash", back_populates="source") + dataset: Mapped[Optional["Dataset"]] = relationship(back_populates="sources") + hashes: Mapped[List["DatasetSourceHash"]] = relationship(back_populates="source") dict_collection_visible_keys = ["id", "source_uri", "extra_files_path", "transform"] dict_element_visible_keys = [ "id", @@ -4419,7 +4374,7 @@ class DatasetSourceHash(Base, Serializable): dataset_source_id: Mapped[Optional[int]] = mapped_column(ForeignKey("dataset_source.id"), index=True) hash_function: Mapped[Optional[str]] = mapped_column(TEXT) hash_value: Mapped[Optional[str]] = mapped_column(TEXT) - source: Mapped[Optional["DatasetSource"]] = relationship("DatasetSource", back_populates="hashes") + source: Mapped[Optional["DatasetSource"]] = relationship(back_populates="hashes") def _serialize(self, id_encoder, serialization_options): rval = dict_for( @@ -4445,7 +4400,7 @@ class DatasetHash(Base, Dictifiable, Serializable): 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: Mapped[Optional["Dataset"]] = relationship("Dataset", back_populates="hashes") + dataset: Mapped[Optional["Dataset"]] = relationship(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"] @@ -5526,10 +5481,8 @@ class HistoryDatasetAssociationDisplayAtAuthorization(Base, RepresentById): ) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) site: Mapped[Optional[str]] = mapped_column(TrimmedString(255)) - history_dataset_association: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation" - ) - user: Mapped[Optional["User"]] = relationship("User") + history_dataset_association: Mapped[Optional["HistoryDatasetAssociation"]] = relationship() + user: Mapped[Optional["User"]] = relationship() def __init__(self, hda=None, user=None, site=None): self.history_dataset_association = hda @@ -5550,13 +5503,11 @@ class HistoryDatasetAssociationSubset(Base, RepresentById): location: Mapped[Optional[str]] = mapped_column(Unicode(255), index=True) hda: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", primaryjoin=( lambda: HistoryDatasetAssociationSubset.history_dataset_association_id == HistoryDatasetAssociation.id ), ) subset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", primaryjoin=( lambda: HistoryDatasetAssociationSubset.history_dataset_association_subset_id == HistoryDatasetAssociation.id @@ -5582,9 +5533,7 @@ 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( - "LibraryPermissions", back_populates="library", cascade_backrefs=False - ) + actions: Mapped[List["LibraryPermissions"]] = relationship(back_populates="library", cascade_backrefs=False) permitted_actions = get_permitted_actions(filter="LIBRARY") dict_collection_visible_keys = ["id", "name"] @@ -5665,17 +5614,13 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable): genome_build: Mapped[Optional[str]] = mapped_column(TrimmedString(40)) folders: Mapped[List["LibraryFolder"]] = relationship( - "LibraryFolder", primaryjoin=(lambda: LibraryFolder.id == LibraryFolder.parent_id), order_by=asc(name), back_populates="parent", ) - parent: Mapped[Optional["LibraryFolder"]] = relationship( - "LibraryFolder", back_populates="folders", remote_side=[id] - ) + parent: Mapped[Optional["LibraryFolder"]] = relationship(back_populates="folders", remote_side=[id]) active_folders: Mapped[List["LibraryFolder"]] = relationship( - "LibraryFolder", primaryjoin=("and_(LibraryFolder.parent_id == LibraryFolder.id, not_(LibraryFolder.deleted))"), order_by=asc(name), # """sqlalchemy.exc.ArgumentError: Error creating eager relationship 'active_folders' @@ -5686,7 +5631,6 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable): ) datasets: Mapped[List["LibraryDataset"]] = relationship( - "LibraryDataset", primaryjoin=( lambda: LibraryDataset.folder_id == LibraryFolder.id and LibraryDataset.library_dataset_dataset_association_id.isnot(None) @@ -5696,7 +5640,6 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable): ) active_datasets: Mapped[List["LibraryDataset"]] = relationship( - "LibraryDataset", primaryjoin=( "and_(LibraryDataset.folder_id == LibraryFolder.id, not_(LibraryDataset.deleted), LibraryDataset.library_dataset_dataset_association_id.isnot(None))" ), @@ -5705,9 +5648,7 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable): ) library_root = relationship("Library", back_populates="root_folder") - actions: Mapped[List["LibraryFolderPermissions"]] = relationship( - "LibraryFolderPermissions", back_populates="folder", cascade_backrefs=False - ) + actions: Mapped[List["LibraryFolderPermissions"]] = relationship(back_populates="folder", cascade_backrefs=False) dict_element_visible_keys = [ "id", @@ -5816,12 +5757,11 @@ class LibraryDataset(Base, Serializable): _info: Mapped[Optional[str]] = mapped_column("info", TrimmedString(255)) deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False) purged: Mapped[Optional[bool]] = mapped_column(index=True, default=False) - folder: Mapped[Optional["LibraryFolder"]] = relationship("LibraryFolder") + folder: Mapped[Optional["LibraryFolder"]] = relationship() library_dataset_dataset_association = relationship( "LibraryDatasetDatasetAssociation", foreign_keys=library_dataset_dataset_association_id, post_update=True ) expired_datasets: Mapped[List["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", foreign_keys=[id, library_dataset_dataset_association_id], primaryjoin=( "and_(LibraryDataset.id == LibraryDatasetDatasetAssociation.library_dataset_id, \ @@ -5831,7 +5771,7 @@ class LibraryDataset(Base, Serializable): uselist=True, ) actions: Mapped[List["LibraryDatasetPermissions"]] = relationship( - "LibraryDatasetPermissions", back_populates="library_dataset", cascade_backrefs=False + back_populates="library_dataset", cascade_backrefs=False ) # This class acts as a proxy to the currently selected LDDA @@ -6100,9 +6040,7 @@ class ExtendedMetadata(Base, RepresentById): id: Mapped[int] = mapped_column(primary_key=True) data: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) - children: Mapped[List["ExtendedMetadataIndex"]] = relationship( - "ExtendedMetadataIndex", back_populates="extended_metadata" - ) + children: Mapped[List["ExtendedMetadataIndex"]] = relationship(back_populates="extended_metadata") def __init__(self, data): self.data = data @@ -6117,9 +6055,7 @@ class ExtendedMetadataIndex(Base, RepresentById): ) path: Mapped[Optional[str]] = mapped_column(String(255)) value: Mapped[Optional[str]] = mapped_column(TEXT) - extended_metadata: Mapped[Optional["ExtendedMetadata"]] = relationship( - "ExtendedMetadata", back_populates="children" - ) + extended_metadata: Mapped[Optional["ExtendedMetadata"]] = relationship(back_populates="children") def __init__(self, extended_metadata, path, value): self.extended_metadata = extended_metadata @@ -6138,7 +6074,6 @@ class LibraryInfoAssociation(Base, RepresentById): deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False) library: Mapped[Optional["Library"]] = relationship( - "Library", primaryjoin=( lambda: and_( LibraryInfoAssociation.library_id == Library.id, @@ -6147,10 +6082,10 @@ class LibraryInfoAssociation(Base, RepresentById): ), ) template: Mapped[Optional["FormDefinition"]] = relationship( - "FormDefinition", primaryjoin=lambda: LibraryInfoAssociation.form_definition_id == FormDefinition.id + primaryjoin=lambda: LibraryInfoAssociation.form_definition_id == FormDefinition.id ) info: Mapped[Optional["FormValues"]] = relationship( - "FormValues", primaryjoin=lambda: LibraryInfoAssociation.form_values_id == FormValues.id # type: ignore[has-type] + primaryjoin=lambda: LibraryInfoAssociation.form_values_id == FormValues.id # type: ignore[has-type] ) def __init__(self, library, form_definition, info, inheritable=False): @@ -6171,17 +6106,16 @@ class LibraryFolderInfoAssociation(Base, RepresentById): deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False) folder: Mapped[Optional["LibraryFolder"]] = relationship( - "LibraryFolder", primaryjoin=( lambda: (LibraryFolderInfoAssociation.library_folder_id == LibraryFolder.id) & (not_(LibraryFolderInfoAssociation.deleted)) ), ) template: Mapped[Optional["FormDefinition"]] = relationship( - "FormDefinition", primaryjoin=(lambda: LibraryFolderInfoAssociation.form_definition_id == FormDefinition.id) + primaryjoin=(lambda: LibraryFolderInfoAssociation.form_definition_id == FormDefinition.id) ) info: Mapped[Optional["FormValues"]] = relationship( - "FormValues", primaryjoin=(lambda: LibraryFolderInfoAssociation.form_values_id == FormValues.id) # type: ignore[has-type] + primaryjoin=(lambda: LibraryFolderInfoAssociation.form_values_id == FormValues.id) # type: ignore[has-type] ) def __init__(self, folder, form_definition, info, inheritable=False): @@ -6203,7 +6137,6 @@ class LibraryDatasetDatasetInfoAssociation(Base, RepresentById): deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False) library_dataset_dataset_association: Mapped[Optional["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", primaryjoin=( lambda: ( LibraryDatasetDatasetInfoAssociation.library_dataset_dataset_association_id @@ -6213,11 +6146,10 @@ class LibraryDatasetDatasetInfoAssociation(Base, RepresentById): ), ) template: Mapped[Optional["FormDefinition"]] = relationship( - "FormDefinition", primaryjoin=(lambda: LibraryDatasetDatasetInfoAssociation.form_definition_id == FormDefinition.id), ) info: Mapped[Optional["FormValues"]] = relationship( - "FormValues", primaryjoin=(lambda: LibraryDatasetDatasetInfoAssociation.form_values_id == FormValues.id) # type: ignore[has-type] + primaryjoin=(lambda: LibraryDatasetDatasetInfoAssociation.form_values_id == FormValues.id) # type: ignore[has-type] ) def __init__(self, library_dataset_dataset_association, form_definition, info): @@ -6248,22 +6180,18 @@ class ImplicitlyConvertedDatasetAssociation(Base, Serializable): type: Mapped[Optional[str]] = mapped_column(TrimmedString(255)) parent_hda: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_parent_id == HistoryDatasetAssociation.id), back_populates="implicitly_converted_datasets", ) dataset_ldda: Mapped[Optional["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.ldda_id == LibraryDatasetDatasetAssociation.id), back_populates="implicitly_converted_parent_datasets", ) dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_id == HistoryDatasetAssociation.id), back_populates="implicitly_converted_parent_datasets", ) parent_ldda: Mapped[Optional["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", primaryjoin=( lambda: ImplicitlyConvertedDatasetAssociation.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id ), @@ -6355,7 +6283,6 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable): update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) elements: Mapped[List["DatasetCollectionElement"]] = relationship( - "DatasetCollectionElement", primaryjoin=(lambda: DatasetCollection.id == DatasetCollectionElement.dataset_collection_id), # type: ignore[has-type] back_populates="collection", order_by=lambda: DatasetCollectionElement.element_index, # type: ignore[has-type] @@ -6823,7 +6750,7 @@ class HistoryDatasetCollectionAssociation( update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, index=True, nullable=True) collection = relationship("DatasetCollection") - history: Mapped[Optional["History"]] = relationship("History", back_populates="dataset_collections") + history: Mapped[Optional["History"]] = relationship(back_populates="dataset_collections") copied_from_history_dataset_collection_association = relationship( "HistoryDatasetCollectionAssociation", @@ -6837,7 +6764,6 @@ class HistoryDatasetCollectionAssociation( back_populates="copied_from_history_dataset_collection_association", ) implicit_input_collections: Mapped[List["ImplicitlyCreatedDatasetCollectionInput"]] = relationship( - "ImplicitlyCreatedDatasetCollectionInput", primaryjoin=( lambda: HistoryDatasetCollectionAssociation.id == ImplicitlyCreatedDatasetCollectionInput.dataset_collection_id @@ -6845,28 +6771,22 @@ class HistoryDatasetCollectionAssociation( ) implicit_collection_jobs = relationship("ImplicitCollectionJobs", uselist=False) job: Mapped[Optional["Job"]] = relationship( - "Job", back_populates="history_dataset_collection_associations", uselist=False, ) tags: Mapped[List["HistoryDatasetCollectionTagAssociation"]] = relationship( - "HistoryDatasetCollectionTagAssociation", order_by=lambda: HistoryDatasetCollectionTagAssociation.id, back_populates="dataset_collection", ) annotations: Mapped[List["HistoryDatasetCollectionAssociationAnnotationAssociation"]] = relationship( - "HistoryDatasetCollectionAssociationAnnotationAssociation", order_by=lambda: HistoryDatasetCollectionAssociationAnnotationAssociation.id, back_populates="history_dataset_collection", ) ratings: Mapped[List["HistoryDatasetCollectionRatingAssociation"]] = relationship( - "HistoryDatasetCollectionRatingAssociation", order_by=lambda: HistoryDatasetCollectionRatingAssociation.id, # type: ignore[has-type] back_populates="dataset_collection", ) - creating_job_associations: Mapped[List["JobToOutputDatasetCollectionAssociation"]] = relationship( - "JobToOutputDatasetCollectionAssociation", viewonly=True - ) + creating_job_associations: Mapped[List["JobToOutputDatasetCollectionAssociation"]] = relationship(viewonly=True) dict_dbkeysandextensions_visible_keys = ["dbkeys", "extensions"] editable_keys = ("name", "deleted", "visible") @@ -7210,17 +7130,14 @@ class LibraryDatasetCollectionAssociation(Base, DatasetCollectionInstance, Repre folder = relationship("LibraryFolder") tags: Mapped[List["LibraryDatasetCollectionTagAssociation"]] = relationship( - "LibraryDatasetCollectionTagAssociation", order_by=lambda: LibraryDatasetCollectionTagAssociation.id, back_populates="dataset_collection", ) annotations: Mapped[List["LibraryDatasetCollectionAnnotationAssociation"]] = relationship( - "LibraryDatasetCollectionAnnotationAssociation", order_by=lambda: LibraryDatasetCollectionAnnotationAssociation.id, back_populates="dataset_collection", ) ratings: Mapped[List["LibraryDatasetCollectionRatingAssociation"]] = relationship( - "LibraryDatasetCollectionRatingAssociation", order_by=lambda: LibraryDatasetCollectionRatingAssociation.id, # type: ignore[has-type] back_populates="dataset_collection", ) @@ -7443,9 +7360,9 @@ class Event(Base, RepresentById): session_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_session.id"), index=True) tool_id: Mapped[Optional[str]] = mapped_column(String(255)) - history: Mapped[Optional["History"]] = relationship("History") - user: Mapped[Optional["User"]] = relationship("User") - galaxy_session: Mapped[Optional["GalaxySession"]] = relationship("GalaxySession") + history: Mapped[Optional["History"]] = relationship() + user: Mapped[Optional["User"]] = relationship() + galaxy_session: Mapped[Optional["GalaxySession"]] = relationship() class GalaxySession(Base, RepresentById): @@ -7466,11 +7383,11 @@ class GalaxySession(Base, RepresentById): prev_session_id: Mapped[Optional[int]] disk_usage: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0), index=True) last_action: Mapped[Optional[datetime]] - current_history: Mapped[Optional["History"]] = relationship("History") + current_history: Mapped[Optional["History"]] = relationship() histories: Mapped[List["GalaxySessionToHistoryAssociation"]] = relationship( - "GalaxySessionToHistoryAssociation", back_populates="galaxy_session", cascade_backrefs=False + back_populates="galaxy_session", cascade_backrefs=False ) - user: Mapped[Optional["User"]] = relationship("User", back_populates="galaxy_sessions") + user: Mapped[Optional["User"]] = relationship(back_populates="galaxy_sessions") def __init__(self, is_valid=False, **kwd): super().__init__(**kwd) @@ -7501,8 +7418,8 @@ class GalaxySessionToHistoryAssociation(Base, RepresentById): create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) session_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_session.id"), index=True) history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True) - galaxy_session: Mapped[Optional["GalaxySession"]] = relationship("GalaxySession", back_populates="histories") - history: Mapped[Optional["History"]] = relationship("History", back_populates="galaxy_sessions") + galaxy_session: Mapped[Optional["GalaxySession"]] = relationship(back_populates="histories") + history: Mapped[Optional["History"]] = relationship(back_populates="galaxy_sessions") def __init__(self, galaxy_session, history): self.galaxy_session = galaxy_session @@ -7539,10 +7456,9 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById): published: Mapped[Optional[bool]] = mapped_column(index=True, default=False) user: Mapped["User"] = relationship( - "User", primaryjoin=(lambda: User.id == StoredWorkflow.user_id), back_populates="stored_workflows" + primaryjoin=(lambda: User.id == StoredWorkflow.user_id), back_populates="stored_workflows" ) workflows: Mapped[List["Workflow"]] = relationship( - "Workflow", back_populates="stored_workflow", cascade="all, delete-orphan", primaryjoin=(lambda: StoredWorkflow.id == Workflow.stored_workflow_id), # type: ignore[has-type] @@ -7556,12 +7472,10 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById): lazy=False, ) tags: Mapped[List["StoredWorkflowTagAssociation"]] = relationship( - "StoredWorkflowTagAssociation", order_by=lambda: StoredWorkflowTagAssociation.id, back_populates="stored_workflow", ) owner_tags: Mapped[List["StoredWorkflowTagAssociation"]] = relationship( - "StoredWorkflowTagAssociation", primaryjoin=( lambda: and_( StoredWorkflow.id == StoredWorkflowTagAssociation.stored_workflow_id, @@ -7572,17 +7486,15 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById): order_by=lambda: StoredWorkflowTagAssociation.id, ) annotations: Mapped[List["StoredWorkflowAnnotationAssociation"]] = relationship( - "StoredWorkflowAnnotationAssociation", order_by=lambda: StoredWorkflowAnnotationAssociation.id, back_populates="stored_workflow", ) ratings: Mapped[List["StoredWorkflowRatingAssociation"]] = relationship( - "StoredWorkflowRatingAssociation", order_by=lambda: StoredWorkflowRatingAssociation.id, # type: ignore[has-type] back_populates="stored_workflow", ) users_shared_with: Mapped[List["StoredWorkflowUserShareAssociation"]] = relationship( - "StoredWorkflowUserShareAssociation", back_populates="stored_workflow" + back_populates="stored_workflow" ) average_rating = None @@ -7723,7 +7635,6 @@ class Workflow(Base, Dictifiable, RepresentById): lazy=False, ) comments: Mapped[List["WorkflowComment"]] = relationship( - "WorkflowComment", back_populates="workflow", primaryjoin=(lambda: Workflow.id == WorkflowComment.workflow_id), # type: ignore[has-type] cascade="all, delete-orphan", @@ -7903,37 +7814,33 @@ class WorkflowStep(Base, RepresentById): parent_comment_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_comment.id"), index=True) parent_comment: Mapped[Optional["WorkflowComment"]] = relationship( - "WorkflowComment", primaryjoin=(lambda: WorkflowComment.id == WorkflowStep.parent_comment_id), back_populates="child_steps", ) subworkflow: Mapped[Optional["Workflow"]] = relationship( - "Workflow", primaryjoin=(lambda: Workflow.id == WorkflowStep.subworkflow_id), back_populates="parent_workflow_steps", ) dynamic_tool: Mapped[Optional["DynamicTool"]] = relationship( - "DynamicTool", primaryjoin=(lambda: DynamicTool.id == WorkflowStep.dynamic_tool_id) + primaryjoin=(lambda: DynamicTool.id == WorkflowStep.dynamic_tool_id) ) tags: Mapped[List["WorkflowStepTagAssociation"]] = relationship( - "WorkflowStepTagAssociation", order_by=lambda: WorkflowStepTagAssociation.id, back_populates="workflow_step" + order_by=lambda: WorkflowStepTagAssociation.id, back_populates="workflow_step" ) annotations: Mapped[List["WorkflowStepAnnotationAssociation"]] = relationship( - "WorkflowStepAnnotationAssociation", order_by=lambda: WorkflowStepAnnotationAssociation.id, back_populates="workflow_step", ) post_job_actions = relationship("PostJobAction", back_populates="workflow_step", cascade_backrefs=False) inputs = relationship("WorkflowStepInput", back_populates="workflow_step") workflow_outputs: Mapped[List["WorkflowOutput"]] = relationship( - "WorkflowOutput", back_populates="workflow_step", cascade_backrefs=False + back_populates="workflow_step", cascade_backrefs=False ) output_connections: Mapped[List["WorkflowStepConnection"]] = relationship( - "WorkflowStepConnection", primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id) + primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id) ) workflow: Mapped["Workflow"] = relationship( - "Workflow", primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id), back_populates="steps", cascade_backrefs=False, @@ -8213,13 +8120,11 @@ class WorkflowStepInput(Base, RepresentById): runtime_value: Mapped[Optional[bool]] = mapped_column(default=False) workflow_step: Mapped[Optional["WorkflowStep"]] = relationship( - "WorkflowStep", back_populates="inputs", cascade="all", primaryjoin=(lambda: WorkflowStepInput.workflow_step_id == WorkflowStep.id), ) connections: Mapped[List["WorkflowStepConnection"]] = relationship( - "WorkflowStepConnection", back_populates="input_step_input", primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id), cascade_backrefs=False, @@ -8307,7 +8212,6 @@ class WorkflowOutput(Base, Serializable): label: Mapped[Optional[str]] = mapped_column(Unicode(255)) uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType) workflow_step: Mapped["WorkflowStep"] = relationship( - "WorkflowStep", back_populates="workflow_outputs", primaryjoin=(lambda: WorkflowStep.id == WorkflowOutput.workflow_step_id), ) @@ -8353,7 +8257,6 @@ class WorkflowComment(Base, RepresentById): parent_comment_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_comment.id"), index=True) workflow: Mapped["Workflow"] = relationship( - "Workflow", primaryjoin=(lambda: Workflow.id == WorkflowComment.workflow_id), back_populates="comments", ) @@ -8365,14 +8268,12 @@ class WorkflowComment(Base, RepresentById): ) parent_comment: Mapped[Optional["WorkflowComment"]] = relationship( - "WorkflowComment", primaryjoin=(lambda: WorkflowComment.id == WorkflowComment.parent_comment_id), back_populates="child_comments", remote_side=[id], ) child_comments: Mapped[List["WorkflowComment"]] = relationship( - "WorkflowComment", primaryjoin=(lambda: WorkflowComment.parent_comment_id == WorkflowComment.id), back_populates="parent_comment", ) @@ -8416,10 +8317,8 @@ class StoredWorkflowUserShareAssociation(Base, UserShareAssociation): id: Mapped[int] = mapped_column(primary_key=True) stored_workflow_id: Mapped[Optional[int]] = mapped_column(ForeignKey("stored_workflow.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) - user: Mapped[User] = relationship("User") - stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship( - "StoredWorkflow", back_populates="users_shared_with" - ) + user: Mapped[User] = relationship() + stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship(back_populates="users_shared_with") class StoredWorkflowMenuEntry(Base, RepresentById): @@ -8430,9 +8329,8 @@ class StoredWorkflowMenuEntry(Base, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) order_index: Mapped[Optional[int]] - stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship("StoredWorkflow") + stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship() user: Mapped[Optional["User"]] = relationship( - "User", back_populates="stored_workflow_menu_entries", primaryjoin=( lambda: (StoredWorkflowMenuEntry.user_id == User.id) @@ -9032,14 +8930,10 @@ class WorkflowInvocationMessage(Base, Dictifiable, Serializable): hda_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history_dataset_association.id")) hdca_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history_dataset_collection_association.id")) - workflow_invocation: Mapped["WorkflowInvocation"] = relationship( - "WorkflowInvocation", back_populates="messages", lazy=True - ) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship( - "WorkflowStep", foreign_keys=workflow_step_id, lazy=True - ) + workflow_invocation: Mapped["WorkflowInvocation"] = relationship(back_populates="messages", lazy=True) + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship(foreign_keys=workflow_step_id, lazy=True) dependent_workflow_step: Mapped[Optional["WorkflowStep"]] = relationship( - "WorkflowStep", foreign_keys=dependent_workflow_step_id, lazy=True + foreign_keys=dependent_workflow_step_id, lazy=True ) @property @@ -9113,7 +9007,7 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable): action: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) workflow_step = relationship("WorkflowStep") - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="workflow_invocation_step", uselist=False) + job: Mapped[Optional["Job"]] = relationship(back_populates="workflow_invocation_step", uselist=False) implicit_collection_jobs = relationship("ImplicitCollectionJobs", uselist=False) output_dataset_collections = relationship( "WorkflowInvocationStepOutputDatasetCollectionAssociation", @@ -9125,7 +9019,7 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable): back_populates="workflow_invocation_step", cascade_backrefs=False, ) - workflow_invocation: Mapped["WorkflowInvocation"] = relationship("WorkflowInvocation", back_populates="steps") + workflow_invocation: Mapped["WorkflowInvocation"] = relationship(back_populates="steps") output_value = relationship( "WorkflowInvocationOutputValue", foreign_keys="[WorkflowInvocationStep.workflow_invocation_id, WorkflowInvocationStep.workflow_step_id]", @@ -9317,9 +9211,7 @@ class WorkflowRequestInputParameter(Base, Dictifiable, Serializable): 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: Mapped[Optional["WorkflowInvocation"]] = relationship( - "WorkflowInvocation", back_populates="input_parameters" - ) + workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="input_parameters") dict_collection_visible_keys = ["id", "name", "value", "type"] @@ -9348,10 +9240,8 @@ class WorkflowRequestStepState(Base, Dictifiable, Serializable): ) workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id")) value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep") - workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship( - "WorkflowInvocation", back_populates="step_states" - ) + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship() + workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="step_states") dict_collection_visible_keys = ["id", "name", "value", "workflow_step_id"] @@ -9373,11 +9263,9 @@ class WorkflowRequestToInputDatasetAssociation(Base, Dictifiable, Serializable): workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id")) dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history_dataset_association.id"), index=True) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep") - dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship("HistoryDatasetAssociation") - workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship( - "WorkflowInvocation", back_populates="input_datasets" - ) + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship() + dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship() + workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="input_datasets") history_content_type = "dataset" dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "dataset_id", "name"] @@ -9404,12 +9292,10 @@ class WorkflowRequestToInputDatasetCollectionAssociation(Base, Dictifiable, Seri dataset_collection_id: Mapped[Optional[int]] = mapped_column( ForeignKey("history_dataset_collection_association.id"), index=True ) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep") - dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation" - ) + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship() + dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship() workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship( - "WorkflowInvocation", back_populates="input_dataset_collections" + back_populates="input_dataset_collections" ) history_content_type = "dataset_collection" @@ -9435,10 +9321,8 @@ class WorkflowRequestInputStepParameter(Base, Dictifiable, Serializable): workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id")) parameter_value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep") - workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship( - "WorkflowInvocation", back_populates="input_step_parameters" - ) + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship() + workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="input_step_parameters") dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "parameter_value"] @@ -9460,12 +9344,10 @@ class WorkflowInvocationOutputDatasetAssociation(Base, Dictifiable, Serializable dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history_dataset_association.id"), index=True) workflow_output_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_output.id"), index=True) - workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship( - "WorkflowInvocation", back_populates="output_datasets" - ) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep") - dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship("HistoryDatasetAssociation") - workflow_output: Mapped[Optional["WorkflowOutput"]] = relationship("WorkflowOutput") + workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="output_datasets") + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship() + dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship() + workflow_output: Mapped[Optional["WorkflowOutput"]] = relationship() history_content_type = "dataset" dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "dataset_id", "name"] @@ -9498,13 +9380,11 @@ class WorkflowInvocationOutputDatasetCollectionAssociation(Base, Dictifiable, Se ) workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship( - "WorkflowInvocation", back_populates="output_dataset_collections" - ) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep") - dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation" + back_populates="output_dataset_collections" ) - workflow_output: Mapped[Optional["WorkflowOutput"]] = relationship("WorkflowOutput") + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship() + dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship() + workflow_output: Mapped[Optional["WorkflowOutput"]] = relationship() history_content_type = "dataset_collection" dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "dataset_collection_id", "name"] @@ -9530,12 +9410,9 @@ class WorkflowInvocationOutputValue(Base, Dictifiable, Serializable): workflow_output_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_output.id"), index=True) value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) - workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship( - "WorkflowInvocation", back_populates="output_values" - ) + workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="output_values") workflow_invocation_step: Mapped[Optional["WorkflowInvocationStep"]] = relationship( - "WorkflowInvocationStep", foreign_keys="[WorkflowInvocationStep.workflow_invocation_id, WorkflowInvocationStep.workflow_step_id]", primaryjoin=( lambda: and_( @@ -9547,8 +9424,8 @@ class WorkflowInvocationOutputValue(Base, Dictifiable, Serializable): viewonly=True, ) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep") - workflow_output: Mapped[Optional["WorkflowOutput"]] = relationship("WorkflowOutput") + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship() + workflow_output: Mapped[Optional["WorkflowOutput"]] = relationship() dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "value"] @@ -9572,9 +9449,9 @@ class WorkflowInvocationStepOutputDatasetAssociation(Base, Dictifiable, Represen dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history_dataset_association.id"), index=True) output_name: Mapped[Optional[str]] = mapped_column(String(255)) workflow_invocation_step: Mapped[Optional["WorkflowInvocationStep"]] = relationship( - "WorkflowInvocationStep", back_populates="output_datasets" + back_populates="output_datasets" ) - dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship("HistoryDatasetAssociation") + dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship() dict_collection_visible_keys = ["id", "workflow_invocation_step_id", "dataset_id", "output_name"] @@ -9597,11 +9474,9 @@ class WorkflowInvocationStepOutputDatasetCollectionAssociation(Base, Dictifiable output_name: Mapped[Optional[str]] = mapped_column(String(255)) workflow_invocation_step: Mapped[Optional["WorkflowInvocationStep"]] = relationship( - "WorkflowInvocationStep", back_populates="output_dataset_collections" - ) - dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation" + back_populates="output_dataset_collections" ) + dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship() dict_collection_visible_keys = ["id", "workflow_invocation_step_id", "dataset_collection_id", "output_name"] @@ -9620,7 +9495,7 @@ class MetadataFile(Base, StorableObject, Serializable): deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False) purged: Mapped[Optional[bool]] = mapped_column(index=True, default=False) - history_dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship("HistoryDatasetAssociation") + history_dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship() library_dataset = relationship("LibraryDatasetDatasetAssociation") def __init__(self, dataset=None, name=None, uuid=None): @@ -9703,7 +9578,6 @@ class FormDefinition(Base, Dictifiable, RepresentById): type: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True) layout: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) form_definition_current: Mapped["FormDefinitionCurrent"] = relationship( - "FormDefinitionCurrent", back_populates="forms", primaryjoin=(lambda: FormDefinitionCurrent.id == FormDefinition.form_definition_current_id), # type: ignore[has-type] ) @@ -9769,13 +9643,11 @@ class FormDefinitionCurrent(Base, RepresentById): latest_form_id: Mapped[Optional[int]] = mapped_column(ForeignKey("form_definition.id"), index=True) deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False) forms: Mapped[List["FormDefinition"]] = relationship( - "FormDefinition", back_populates="form_definition_current", cascade="all, delete-orphan", primaryjoin=(lambda: FormDefinitionCurrent.id == FormDefinition.form_definition_current_id), ) latest_form: Mapped[Optional["FormDefinition"]] = relationship( - "FormDefinition", post_update=True, primaryjoin=(lambda: FormDefinitionCurrent.latest_form_id == FormDefinition.id), ) @@ -9793,7 +9665,7 @@ class FormValues(Base, RepresentById): form_definition_id: Mapped[Optional[int]] = mapped_column(ForeignKey("form_definition.id"), index=True) content: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) form_definition: Mapped[Optional["FormDefinition"]] = relationship( - "FormDefinition", primaryjoin=(lambda: FormValues.form_definition_id == FormDefinition.id) + primaryjoin=(lambda: FormValues.form_definition_id == FormDefinition.id) ) def __init__(self, form_def=None, content=None): @@ -9821,9 +9693,7 @@ class UserAddress(Base, RepresentById): purged: Mapped[Optional[bool]] = mapped_column(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: Mapped[Optional["User"]] = relationship( - "User", back_populates="addresses", order_by=sqlalchemy.desc("update_time") - ) + user: Mapped[Optional["User"]] = relationship(back_populates="addresses", order_by=sqlalchemy.desc("update_time")) def to_dict(self, trans): return { @@ -10024,7 +9894,7 @@ class UserAuthnzToken(Base, UserMixin, RepresentById): extra_data: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) lifetime: Mapped[Optional[int]] assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64)) - user: Mapped[Optional["User"]] = relationship("User", back_populates="social_auth") + user: Mapped[Optional["User"]] = relationship(back_populates="social_auth") # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz sa_session = None @@ -10205,8 +10075,8 @@ class CloudAuthz(Base): last_activity: Mapped[Optional[datetime]] description: Mapped[Optional[str]] = mapped_column(TEXT) create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) - user: Mapped[Optional["User"]] = relationship("User", back_populates="cloudauthz") - authn: Mapped[Optional["UserAuthnzToken"]] = relationship("UserAuthnzToken") + user: Mapped[Optional["User"]] = relationship(back_populates="cloudauthz") + authn: Mapped[Optional["UserAuthnzToken"]] = relationship() def __init__(self, user_id, provider, config, authn_id, description=None): self.user_id = user_id @@ -10244,33 +10114,28 @@ class Page(Base, HasTags, Dictifiable, RepresentById): importable: Mapped[Optional[bool]] = mapped_column(index=True, default=False) slug: Mapped[Optional[str]] = mapped_column(TEXT) published: Mapped[Optional[bool]] = mapped_column(index=True, default=False) - user: Mapped["User"] = relationship("User") + user: Mapped["User"] = relationship() revisions: Mapped[List["PageRevision"]] = relationship( - "PageRevision", cascade="all, delete-orphan", primaryjoin=(lambda: Page.id == PageRevision.page_id), # type: ignore[has-type] back_populates="page", ) latest_revision: Mapped[Optional["PageRevision"]] = relationship( - "PageRevision", post_update=True, primaryjoin=(lambda: Page.latest_revision_id == PageRevision.id), # type: ignore[has-type] lazy=False, ) tags: Mapped[List["PageTagAssociation"]] = relationship( - "PageTagAssociation", order_by=lambda: PageTagAssociation.id, back_populates="page" + order_by=lambda: PageTagAssociation.id, back_populates="page" ) annotations: Mapped[List["PageAnnotationAssociation"]] = relationship( - "PageAnnotationAssociation", order_by=lambda: PageAnnotationAssociation.id, back_populates="page" + order_by=lambda: PageAnnotationAssociation.id, back_populates="page" ) ratings: Mapped[List["PageRatingAssociation"]] = relationship( - "PageRatingAssociation", order_by=lambda: PageRatingAssociation.id, # type: ignore[has-type] back_populates="page", ) - users_shared_with: Mapped[List["PageUserShareAssociation"]] = relationship( - "PageUserShareAssociation", back_populates="page" - ) + users_shared_with: Mapped[List["PageUserShareAssociation"]] = relationship(back_populates="page") average_rating = None @@ -10322,7 +10187,7 @@ class PageRevision(Base, Dictifiable, RepresentById): title: Mapped[Optional[str]] = mapped_column(TEXT) content: Mapped[Optional[str]] = mapped_column(TEXT) content_format: Mapped[Optional[str]] = mapped_column(TrimmedString(32)) - page: Mapped["Page"] = relationship("Page", primaryjoin=(lambda: Page.id == PageRevision.page_id)) + page: Mapped["Page"] = relationship(primaryjoin=(lambda: Page.id == PageRevision.page_id)) DEFAULT_CONTENT_FORMAT = "html" dict_element_visible_keys = ["id", "page_id", "title", "content", "content_format"] @@ -10342,8 +10207,8 @@ class PageUserShareAssociation(Base, UserShareAssociation): id: Mapped[int] = mapped_column(primary_key=True) page_id: Mapped[Optional[int]] = mapped_column(ForeignKey("page.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) - user: Mapped[User] = relationship("User") - page: Mapped[Optional["Page"]] = relationship("Page", back_populates="users_shared_with") + user: Mapped[User] = relationship() + page: Mapped[Optional["Page"]] = relationship(back_populates="users_shared_with") class Visualization(Base, HasTags, Dictifiable, RepresentById): @@ -10369,36 +10234,30 @@ class Visualization(Base, HasTags, Dictifiable, RepresentById): slug: Mapped[Optional[str]] = mapped_column(TEXT) published: Mapped[Optional[bool]] = mapped_column(default=False, index=True) - user: Mapped["User"] = relationship("User") + user: Mapped["User"] = relationship() revisions: Mapped[List["VisualizationRevision"]] = relationship( - "VisualizationRevision", back_populates="visualization", cascade="all, delete-orphan", primaryjoin=(lambda: Visualization.id == VisualizationRevision.visualization_id), cascade_backrefs=False, ) latest_revision: Mapped[Optional["VisualizationRevision"]] = relationship( - "VisualizationRevision", post_update=True, primaryjoin=(lambda: Visualization.latest_revision_id == VisualizationRevision.id), lazy=False, ) tags: Mapped[List["VisualizationTagAssociation"]] = relationship( - "VisualizationTagAssociation", order_by=lambda: VisualizationTagAssociation.id, back_populates="visualization" + order_by=lambda: VisualizationTagAssociation.id, back_populates="visualization" ) annotations: Mapped[List["VisualizationAnnotationAssociation"]] = relationship( - "VisualizationAnnotationAssociation", order_by=lambda: VisualizationAnnotationAssociation.id, back_populates="visualization", ) ratings: Mapped[List["VisualizationRatingAssociation"]] = relationship( - "VisualizationRatingAssociation", order_by=lambda: VisualizationRatingAssociation.id, # type: ignore[has-type] back_populates="visualization", ) - users_shared_with: Mapped[List["VisualizationUserShareAssociation"]] = relationship( - "VisualizationUserShareAssociation", back_populates="visualization" - ) + users_shared_with: Mapped[List["VisualizationUserShareAssociation"]] = relationship(back_populates="visualization") average_rating = None @@ -10476,7 +10335,6 @@ class VisualizationRevision(Base, RepresentById): dbkey: Mapped[Optional[str]] = mapped_column(TEXT) config: Mapped[Optional[bytes]] = mapped_column(MutableJSONType) visualization: Mapped["Visualization"] = relationship( - "Visualization", back_populates="revisions", primaryjoin=(lambda: Visualization.id == VisualizationRevision.visualization_id), ) @@ -10499,8 +10357,8 @@ class VisualizationUserShareAssociation(Base, UserShareAssociation): id: Mapped[int] = mapped_column(primary_key=True) visualization_id: Mapped[Optional[int]] = mapped_column(ForeignKey("visualization.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) - user: Mapped[User] = relationship("User") - visualization: Mapped[Optional["Visualization"]] = relationship("Visualization", back_populates="users_shared_with") + user: Mapped[User] = relationship() + visualization: Mapped[Optional["Visualization"]] = relationship(back_populates="users_shared_with") class Tag(Base, RepresentById): @@ -10511,8 +10369,8 @@ class Tag(Base, RepresentById): type: Mapped[Optional[int]] parent_id: Mapped[Optional[int]] = mapped_column(ForeignKey("tag.id")) name: Mapped[Optional[str]] = mapped_column(TrimmedString(255)) - children: Mapped[List["Tag"]] = relationship("Tag", back_populates="parent") - parent: Mapped[Optional["Tag"]] = relationship("Tag", back_populates="children", remote_side=[id]) + children: Mapped[List["Tag"]] = relationship(back_populates="parent") + parent: Mapped[Optional["Tag"]] = relationship(back_populates="children", remote_side=[id]) def __str__(self): return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % (self.id, self.type or -1, self.parent_id, self.name) @@ -10548,9 +10406,9 @@ class HistoryTagAssociation(Base, ItemTagAssociation, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["History"]] = relationship("History", back_populates="tags") - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + history: Mapped[Optional["History"]] = relationship(back_populates="tags") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class HistoryDatasetAssociationTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10564,11 +10422,9 @@ class HistoryDatasetAssociationTagAssociation(Base, ItemTagAssociation, Represen user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", back_populates="tags" - ) - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + history_dataset_association: Mapped[Optional["HistoryDatasetAssociation"]] = relationship(back_populates="tags") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class LibraryDatasetDatasetAssociationTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10583,10 +10439,10 @@ class LibraryDatasetDatasetAssociationTagAssociation(Base, ItemTagAssociation, R 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: Mapped[Optional["LibraryDatasetDatasetAssociation"]] = relationship( - "LibraryDatasetDatasetAssociation", back_populates="tags" + back_populates="tags" ) - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class PageTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10598,9 +10454,9 @@ class PageTagAssociation(Base, ItemTagAssociation, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["Page"]] = relationship("Page", back_populates="tags") - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + page: Mapped[Optional["Page"]] = relationship(back_populates="tags") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class WorkflowStepTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10612,9 +10468,9 @@ class WorkflowStepTagAssociation(Base, ItemTagAssociation, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep", back_populates="tags") - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship(back_populates="tags") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class StoredWorkflowTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10626,9 +10482,9 @@ class StoredWorkflowTagAssociation(Base, ItemTagAssociation, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["StoredWorkflow"]] = relationship("StoredWorkflow", back_populates="tags") - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship(back_populates="tags") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class VisualizationTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10640,9 +10496,9 @@ class VisualizationTagAssociation(Base, ItemTagAssociation, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["Visualization"]] = relationship("Visualization", back_populates="tags") - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + visualization: Mapped[Optional["Visualization"]] = relationship(back_populates="tags") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class HistoryDatasetCollectionTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10656,11 +10512,9 @@ class HistoryDatasetCollectionTagAssociation(Base, ItemTagAssociation, Represent user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", back_populates="tags" - ) - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship(back_populates="tags") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class LibraryDatasetCollectionTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10674,11 +10528,9 @@ class LibraryDatasetCollectionTagAssociation(Base, ItemTagAssociation, Represent user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["LibraryDatasetCollectionAssociation"]] = relationship( - "LibraryDatasetCollectionAssociation", back_populates="tags" - ) - tag: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + dataset_collection: Mapped[Optional["LibraryDatasetCollectionAssociation"]] = relationship(back_populates="tags") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() class ToolTagAssociation(Base, ItemTagAssociation, RepresentById): @@ -10690,8 +10542,8 @@ class ToolTagAssociation(Base, ItemTagAssociation, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(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: Mapped[Optional["Tag"]] = relationship("Tag") - user: Mapped[Optional["User"]] = relationship("User") + tag: Mapped[Optional["Tag"]] = relationship() + user: Mapped[Optional["User"]] = relationship() # Item annotation classes. @@ -10703,8 +10555,8 @@ class HistoryAnnotationAssociation(Base, RepresentById): history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) annotation: Mapped[Optional[str]] = mapped_column(TEXT) - history: Mapped[Optional["History"]] = relationship("History", back_populates="annotations") - user: Mapped[Optional["User"]] = relationship("User") + history: Mapped[Optional["History"]] = relationship(back_populates="annotations") + user: Mapped[Optional["User"]] = relationship() class HistoryDatasetAssociationAnnotationAssociation(Base, RepresentById): @@ -10717,10 +10569,8 @@ class HistoryDatasetAssociationAnnotationAssociation(Base, RepresentById): ) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) annotation: Mapped[Optional[str]] = mapped_column(TEXT) - hda: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", back_populates="annotations" - ) - user: Mapped[Optional["User"]] = relationship("User") + hda: Mapped[Optional["HistoryDatasetAssociation"]] = relationship(back_populates="annotations") + user: Mapped[Optional["User"]] = relationship() class StoredWorkflowAnnotationAssociation(Base, RepresentById): @@ -10731,8 +10581,8 @@ class StoredWorkflowAnnotationAssociation(Base, RepresentById): stored_workflow_id: Mapped[Optional[int]] = mapped_column(ForeignKey("stored_workflow.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) annotation: Mapped[Optional[str]] = mapped_column(TEXT) - stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship("StoredWorkflow", back_populates="annotations") - user: Mapped[Optional["User"]] = relationship("User") + stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship(back_populates="annotations") + user: Mapped[Optional["User"]] = relationship() class WorkflowStepAnnotationAssociation(Base, RepresentById): @@ -10743,8 +10593,8 @@ class WorkflowStepAnnotationAssociation(Base, RepresentById): workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) annotation: Mapped[Optional[str]] = mapped_column(TEXT) - workflow_step: Mapped[Optional["WorkflowStep"]] = relationship("WorkflowStep", back_populates="annotations") - user: Mapped[Optional["User"]] = relationship("User") + workflow_step: Mapped[Optional["WorkflowStep"]] = relationship(back_populates="annotations") + user: Mapped[Optional["User"]] = relationship() class PageAnnotationAssociation(Base, RepresentById): @@ -10755,8 +10605,8 @@ class PageAnnotationAssociation(Base, RepresentById): page_id: Mapped[Optional[int]] = mapped_column(ForeignKey("page.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) annotation: Mapped[Optional[str]] = mapped_column(TEXT) - page: Mapped[Optional["Page"]] = relationship("Page", back_populates="annotations") - user: Mapped[Optional["User"]] = relationship("User") + page: Mapped[Optional["Page"]] = relationship(back_populates="annotations") + user: Mapped[Optional["User"]] = relationship() class VisualizationAnnotationAssociation(Base, RepresentById): @@ -10767,8 +10617,8 @@ class VisualizationAnnotationAssociation(Base, RepresentById): visualization_id: Mapped[Optional[int]] = mapped_column(ForeignKey("visualization.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) annotation: Mapped[Optional[str]] = mapped_column(TEXT) - visualization: Mapped[Optional["Visualization"]] = relationship("Visualization", back_populates="annotations") - user: Mapped[Optional["User"]] = relationship("User") + visualization: Mapped[Optional["Visualization"]] = relationship(back_populates="annotations") + user: Mapped[Optional["User"]] = relationship() class HistoryDatasetCollectionAssociationAnnotationAssociation(Base, RepresentById): @@ -10781,9 +10631,9 @@ class HistoryDatasetCollectionAssociationAnnotationAssociation(Base, RepresentBy user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) annotation: Mapped[Optional[str]] = mapped_column(TEXT) history_dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", back_populates="annotations" + back_populates="annotations" ) - user: Mapped[Optional["User"]] = relationship("User") + user: Mapped[Optional["User"]] = relationship() class LibraryDatasetCollectionAnnotationAssociation(Base, RepresentById): @@ -10796,9 +10646,9 @@ class LibraryDatasetCollectionAnnotationAssociation(Base, RepresentById): user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) annotation: Mapped[Optional[str]] = mapped_column(TEXT) dataset_collection: Mapped[Optional["LibraryDatasetCollectionAssociation"]] = relationship( - "LibraryDatasetCollectionAssociation", back_populates="annotations" + back_populates="annotations" ) - user: Mapped[Optional["User"]] = relationship("User") + user: Mapped[Optional["User"]] = relationship() class Vault(Base): @@ -10806,8 +10656,8 @@ class Vault(Base): key: Mapped[str] = mapped_column(Text, primary_key=True) parent_key: Mapped[Optional[str]] = mapped_column(Text, ForeignKey(key), index=True) - children: Mapped[List["Vault"]] = relationship("Vault", back_populates="parent") - parent: Mapped[Optional["Vault"]] = relationship("Vault", back_populates="children", remote_side=[key]) + children: Mapped[List["Vault"]] = relationship(back_populates="parent") + parent: Mapped[Optional["Vault"]] = relationship(back_populates="children", remote_side=[key]) value: Mapped[Optional[str]] = mapped_column(Text) create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True) @@ -10834,8 +10684,8 @@ class HistoryRatingAssociation(ItemRatingAssociation, RepresentById): history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) rating: Mapped[Optional[int]] = mapped_column(index=True) - history: Mapped[Optional["History"]] = relationship("History", back_populates="ratings") - user: Mapped[Optional["User"]] = relationship("User") + history: Mapped[Optional["History"]] = relationship(back_populates="ratings") + user: Mapped[Optional["User"]] = relationship() def _set_item(self, history): add_object_to_object_session(self, history) @@ -10851,10 +10701,8 @@ class HistoryDatasetAssociationRatingAssociation(ItemRatingAssociation, Represen ) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) rating: Mapped[Optional[int]] = mapped_column(index=True) - history_dataset_association: Mapped[Optional["HistoryDatasetAssociation"]] = relationship( - "HistoryDatasetAssociation", back_populates="ratings" - ) - user: Mapped[Optional["User"]] = relationship("User") + history_dataset_association: Mapped[Optional["HistoryDatasetAssociation"]] = relationship(back_populates="ratings") + user: Mapped[Optional["User"]] = relationship() def _set_item(self, history_dataset_association): add_object_to_object_session(self, history_dataset_association) @@ -10868,8 +10716,8 @@ class StoredWorkflowRatingAssociation(ItemRatingAssociation, RepresentById): stored_workflow_id: Mapped[Optional[int]] = mapped_column(ForeignKey("stored_workflow.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) rating: Mapped[Optional[int]] = mapped_column(index=True) - stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship("StoredWorkflow", back_populates="ratings") - user: Mapped[Optional["User"]] = relationship("User") + stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship(back_populates="ratings") + user: Mapped[Optional["User"]] = relationship() def _set_item(self, stored_workflow): add_object_to_object_session(self, stored_workflow) @@ -10883,8 +10731,8 @@ class PageRatingAssociation(ItemRatingAssociation, RepresentById): page_id: Mapped[Optional[int]] = mapped_column(ForeignKey("page.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) rating: Mapped[Optional[int]] = mapped_column(index=True) - page: Mapped[Optional["Page"]] = relationship("Page", back_populates="ratings") - user: Mapped[Optional["User"]] = relationship("User") + page: Mapped[Optional["Page"]] = relationship(back_populates="ratings") + user: Mapped[Optional["User"]] = relationship() def _set_item(self, page): add_object_to_object_session(self, page) @@ -10898,8 +10746,8 @@ class VisualizationRatingAssociation(ItemRatingAssociation, RepresentById): visualization_id: Mapped[Optional[int]] = mapped_column(ForeignKey("visualization.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) rating: Mapped[Optional[int]] = mapped_column(index=True) - visualization: Mapped[Optional["Visualization"]] = relationship("Visualization", back_populates="ratings") - user: Mapped[Optional["User"]] = relationship("User") + visualization: Mapped[Optional["Visualization"]] = relationship(back_populates="ratings") + user: Mapped[Optional["User"]] = relationship() def _set_item(self, visualization): add_object_to_object_session(self, visualization) @@ -10915,10 +10763,8 @@ class HistoryDatasetCollectionRatingAssociation(ItemRatingAssociation, Represent ) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) rating: Mapped[Optional[int]] = mapped_column(index=True) - dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship( - "HistoryDatasetCollectionAssociation", back_populates="ratings" - ) - user: Mapped[Optional["User"]] = relationship("User") + dataset_collection: Mapped[Optional["HistoryDatasetCollectionAssociation"]] = relationship(back_populates="ratings") + user: Mapped[Optional["User"]] = relationship() def _set_item(self, dataset_collection): add_object_to_object_session(self, dataset_collection) @@ -10934,10 +10780,8 @@ class LibraryDatasetCollectionRatingAssociation(ItemRatingAssociation, Represent ) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) rating: Mapped[Optional[int]] = mapped_column(index=True) - dataset_collection: Mapped[Optional["LibraryDatasetCollectionAssociation"]] = relationship( - "LibraryDatasetCollectionAssociation", back_populates="ratings" - ) - user: Mapped[Optional["User"]] = relationship("User") + dataset_collection: Mapped[Optional["LibraryDatasetCollectionAssociation"]] = relationship(back_populates="ratings") + user: Mapped[Optional["User"]] = relationship() def _set_item(self, dataset_collection): add_object_to_object_session(self, dataset_collection) @@ -10953,8 +10797,8 @@ class DataManagerHistoryAssociation(Base, RepresentById): update_time: Mapped[datetime] = mapped_column(index=True, default=now, onupdate=now, nullable=True) history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True) user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True) - history: Mapped[Optional["History"]] = relationship("History") - user: Mapped[Optional["User"]] = relationship("User", back_populates="data_manager_histories") + history: Mapped[Optional["History"]] = relationship() + user: Mapped[Optional["User"]] = relationship(back_populates="data_manager_histories") class DataManagerJobAssociation(Base, RepresentById): @@ -10966,7 +10810,7 @@ class DataManagerJobAssociation(Base, RepresentById): update_time: Mapped[datetime] = mapped_column(index=True, default=now, onupdate=now, nullable=True) job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True) data_manager_id: Mapped[Optional[str]] = mapped_column(TEXT) - job: Mapped[Optional["Job"]] = relationship("Job", back_populates="data_manager_association", uselist=False) + job: Mapped[Optional["Job"]] = relationship(back_populates="data_manager_association", uselist=False) class UserPreference(Base, RepresentById): @@ -10994,7 +10838,7 @@ class UserAction(Base, RepresentById): 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: Mapped[Optional["User"]] = relationship("User") + user: Mapped[Optional["User"]] = relationship() class APIKeys(Base, RepresentById): @@ -11004,7 +10848,7 @@ class APIKeys(Base, RepresentById): create_time: Mapped[datetime] = mapped_column(default=now, nullable=True) 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: Mapped[Optional["User"]] = relationship("User", back_populates="api_keys") + user: Mapped[Optional["User"]] = relationship(back_populates="api_keys") deleted: Mapped[bool] = mapped_column(index=True, server_default=false())