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Drop nullable=False where it is inferred from Mapped type hint
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@jdavcs
jdavcs committed Apr 5, 2024
1 parent 1e3698d commit b1074de
Showing 1 changed file with 37 additions and 41 deletions.
78 changes: 37 additions & 41 deletions lib/galaxy/model/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -720,9 +720,9 @@ class User(Base, Dictifiable, RepresentById):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
email: Mapped[str] = mapped_column(TrimmedString(255), index=True, nullable=False)
email: Mapped[str] = mapped_column(TrimmedString(255), index=True)
username: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True, unique=True)
password: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
password: Mapped[str] = mapped_column(TrimmedString(255))
last_password_change: Mapped[Optional[datetime]] = mapped_column(default=now)
external: Mapped[Optional[bool]] = mapped_column(default=False)
form_values_id: Mapped[Optional[int]] = mapped_column(ForeignKey("form_values.id"), index=True)
Expand All @@ -731,7 +731,7 @@ class User(Base, Dictifiable, RepresentById):
purged: Mapped[Optional[bool]] = mapped_column(index=True, default=False)
disk_usage: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0), index=True)
# Column("person_metadata", JSONType), # TODO: add persistent, configurable metadata rep for workflow creator
active: Mapped[bool] = mapped_column(index=True, default=True, nullable=False)
active: Mapped[bool] = mapped_column(index=True, default=True)
activation_token: Mapped[Optional[str]] = mapped_column(TrimmedString(64), nullable=True, index=True)

addresses: Mapped[List["UserAddress"]] = relationship(
Expand Down Expand Up @@ -2148,7 +2148,7 @@ class Task(Base, JobLike, RepresentById):
job_messages: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
info: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
traceback: Mapped[Optional[str]] = mapped_column(TEXT)
job_id: Mapped[int] = mapped_column(ForeignKey("job.id"), index=True, nullable=False)
job_id: Mapped[int] = mapped_column(ForeignKey("job.id"), index=True)
working_directory: Mapped[Optional[str]] = mapped_column(String(1024))
task_runner_name: Mapped[Optional[str]] = mapped_column(String(255))
task_runner_external_id: Mapped[Optional[str]] = mapped_column(String(255))
Expand Down Expand Up @@ -2506,7 +2506,7 @@ class ImplicitCollectionJobs(Base, Serializable):
__tablename__ = "implicit_collection_jobs"

id: Mapped[int] = mapped_column(primary_key=True)
populated_state: Mapped[str] = mapped_column(TrimmedString(64), default="new", nullable=False)
populated_state: Mapped[str] = mapped_column(TrimmedString(64), default="new")
jobs = relationship(
"ImplicitCollectionJobsJobAssociation", back_populates="implicit_collection_jobs", cascade_backrefs=False
)
Expand Down Expand Up @@ -2541,7 +2541,7 @@ class ImplicitCollectionJobsJobAssociation(Base, RepresentById):
ForeignKey("implicit_collection_jobs.id"), index=True
)
job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True) # Consider making this nullable...
order_index: Mapped[int] = mapped_column(nullable=False)
order_index: Mapped[int]
implicit_collection_jobs = relationship("ImplicitCollectionJobs", back_populates="jobs")
job = relationship("Job", back_populates="implicit_collection_jobs_association")

Expand All @@ -2551,7 +2551,7 @@ class PostJobAction(Base, RepresentById):

id: Mapped[int] = mapped_column(primary_key=True)
workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True, nullable=True)
action_type: Mapped[str] = mapped_column(String(255), nullable=False)
action_type: Mapped[str] = mapped_column(String(255))
output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
action_arguments: Mapped[Optional[bytes]] = mapped_column(MutableJSONType, nullable=True)
workflow_step = relationship(
Expand All @@ -2572,8 +2572,8 @@ class PostJobActionAssociation(Base, RepresentById):
__tablename__ = "post_job_action_association"

id: Mapped[int] = mapped_column(primary_key=True)
job_id: Mapped[int] = mapped_column(ForeignKey("job.id"), index=True, nullable=False)
post_job_action_id: Mapped[int] = mapped_column(ForeignKey("post_job_action.id"), index=True, nullable=False)
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 = relationship("PostJobAction")
job = relationship("Job", back_populates="post_job_actions")

Expand Down Expand Up @@ -2963,8 +2963,8 @@ class HistoryAudit(Base):
__tablename__ = "history_audit"
__table_args__ = (PrimaryKeyConstraint(sqlite_on_conflict="IGNORE"),)

history_id: Mapped[int] = mapped_column(ForeignKey("history.id"), primary_key=True, nullable=False)
update_time: Mapped[datetime] = mapped_column(default=now, primary_key=True, nullable=False)
history_id: Mapped[int] = mapped_column(ForeignKey("history.id"), primary_key=True)
update_time: Mapped[datetime] = mapped_column(default=now, primary_key=True)

# This class should never be instantiated.
# See https://github.com/galaxyproject/galaxy/pull/11914 for details.
Expand Down Expand Up @@ -3675,7 +3675,7 @@ class UserQuotaSourceUsage(Base, Dictifiable, RepresentById):
user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
quota_source_label: Mapped[Optional[str]] = mapped_column(String(32), index=True)
# user had an index on disk_usage - does that make any sense? -John
disk_usage: Mapped[Decimal] = mapped_column(Numeric(15, 0), default=0, nullable=False)
disk_usage: Mapped[Decimal] = mapped_column(Numeric(15, 0), default=0)
user = relationship("User", back_populates="quota_source_usages")


Expand Down Expand Up @@ -6298,8 +6298,8 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
__tablename__ = "dataset_collection"

id: Mapped[int] = mapped_column(primary_key=True)
collection_type: Mapped[str] = mapped_column(Unicode(255), nullable=False)
populated_state: Mapped[str] = mapped_column(TrimmedString(64), default="ok", nullable=False)
collection_type: Mapped[str] = mapped_column(Unicode(255))
populated_state: Mapped[str] = mapped_column(TrimmedString(64), default="ok")
populated_state_message: Mapped[Optional[str]] = mapped_column(TEXT)
element_count: Mapped[Optional[int]] = mapped_column(nullable=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
Expand Down Expand Up @@ -7186,7 +7186,7 @@ class DatasetCollectionElement(Base, Dictifiable, Serializable):

id: Mapped[int] = mapped_column(primary_key=True)
# Parent collection id describing what collection this element belongs to.
dataset_collection_id: Mapped[int] = mapped_column(ForeignKey("dataset_collection.id"), index=True, nullable=False)
dataset_collection_id: Mapped[int] = mapped_column(ForeignKey("dataset_collection.id"), index=True)
# Child defined by this association - HDA, LDDA, or another dataset association...
hda_id: Mapped[Optional[int]] = mapped_column(
ForeignKey("history_dataset_association.id"), index=True, nullable=True
Expand Down Expand Up @@ -7478,7 +7478,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, index=True, nullable=True)
user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True, nullable=False)
user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
latest_workflow_id: Mapped[Optional[int]] = mapped_column(
ForeignKey("workflow.id", use_alter=True, name="stored_workflow_latest_workflow_id_fk"), index=True
)
Expand Down Expand Up @@ -7837,7 +7837,7 @@ class WorkflowStep(Base, RepresentById):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
workflow_id: Mapped[int] = mapped_column(ForeignKey("workflow.id"), index=True, nullable=False)
workflow_id: Mapped[int] = mapped_column(ForeignKey("workflow.id"), index=True)
subworkflow_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow.id"), index=True, nullable=True)
dynamic_tool_id: Mapped[Optional[int]] = mapped_column(ForeignKey("dynamic_tool.id"), index=True, nullable=True)
type: Mapped[Optional[str]] = mapped_column(String(64))
Expand Down Expand Up @@ -8250,7 +8250,7 @@ class WorkflowOutput(Base, Serializable):
__tablename__ = "workflow_output"

id: Mapped[int] = mapped_column(primary_key=True)
workflow_step_id: Mapped[int] = mapped_column(ForeignKey("workflow_step.id"), index=True, nullable=False)
workflow_step_id: Mapped[int] = mapped_column(ForeignKey("workflow_step.id"), index=True)
output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
label: Mapped[Optional[str]] = mapped_column(Unicode(255))
uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType)
Expand Down Expand Up @@ -8292,7 +8292,7 @@ class WorkflowComment(Base, RepresentById):

id: Mapped[int] = mapped_column(primary_key=True)
order_index: Mapped[Optional[int]]
workflow_id: Mapped[int] = mapped_column(ForeignKey("workflow.id"), index=True, nullable=False)
workflow_id: Mapped[int] = mapped_column(ForeignKey("workflow.id"), index=True)
position: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
size: Mapped[Optional[bytes]] = mapped_column(JSONType)
type: Mapped[Optional[str]] = mapped_column(String(16))
Expand Down Expand Up @@ -8394,7 +8394,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, index=True, nullable=True)
workflow_id: Mapped[int] = mapped_column(ForeignKey("workflow.id"), index=True, nullable=False)
workflow_id: Mapped[int] = mapped_column(ForeignKey("workflow.id"), index=True)
state: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True)
scheduler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
handler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
Expand Down Expand Up @@ -8968,9 +8968,7 @@ class WorkflowInvocationToSubworkflowInvocationAssociation(Base, Dictifiable, Re
class WorkflowInvocationMessage(Base, Dictifiable):
__tablename__ = "workflow_invocation_message"
id: Mapped[int] = mapped_column(primary_key=True)
workflow_invocation_id: Mapped[int] = mapped_column(
ForeignKey("workflow_invocation.id"), index=True, nullable=False
)
workflow_invocation_id: Mapped[int] = mapped_column(ForeignKey("workflow_invocation.id"), index=True)
reason: Mapped[Optional[str]] = mapped_column(String(32))
details: Mapped[Optional[str]] = mapped_column(TrimmedString(255), nullable=True)
output_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
Expand Down Expand Up @@ -9047,10 +9045,8 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
workflow_invocation_id: Mapped[int] = mapped_column(
ForeignKey("workflow_invocation.id"), index=True, nullable=False
)
workflow_step_id: Mapped[int] = mapped_column(ForeignKey("workflow_step.id"), index=True, nullable=False)
workflow_invocation_id: Mapped[int] = mapped_column(ForeignKey("workflow_invocation.id"), index=True)
workflow_step_id: Mapped[int] = mapped_column(ForeignKey("workflow_step.id"), index=True)
state: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True)
job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True, nullable=True)
implicit_collection_jobs_id: Mapped[Optional[int]] = mapped_column(
Expand Down Expand Up @@ -9616,10 +9612,10 @@ class FormDefinition(Base, Dictifiable, RepresentById):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[Optional[datetime]] = mapped_column(default=now)
update_time: Mapped[Optional[datetime]] = mapped_column(default=now, onupdate=now)
name: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
name: Mapped[str] = mapped_column(TrimmedString(255))
desc: Mapped[Optional[str]] = mapped_column(TEXT)
form_definition_current_id: Mapped[int] = mapped_column(
ForeignKey("form_definition_current.id", use_alter=True), index=True, nullable=False
ForeignKey("form_definition_current.id", use_alter=True), index=True
)
fields: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
type: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
Expand Down Expand Up @@ -9731,13 +9727,13 @@ class UserAddress(Base, RepresentById):
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
desc: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
name: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
name: Mapped[str] = mapped_column(TrimmedString(255))
institution: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
address: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
city: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
state: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
postal_code: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
country: Mapped[str] = mapped_column(TrimmedString(255), nullable=False)
address: Mapped[str] = mapped_column(TrimmedString(255))
city: Mapped[str] = mapped_column(TrimmedString(255))
state: Mapped[str] = mapped_column(TrimmedString(255))
postal_code: Mapped[str] = mapped_column(TrimmedString(255))
country: Mapped[str] = mapped_column(TrimmedString(255))
phone: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False)
purged: Mapped[Optional[bool]] = mapped_column(index=True, default=False)
Expand Down Expand Up @@ -10155,7 +10151,7 @@ class Page(Base, HasTags, Dictifiable, RepresentById):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True, nullable=False)
user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
latest_revision_id: Mapped[Optional[int]] = mapped_column(
ForeignKey("page_revision.id", use_alter=True, name="page_latest_revision_id_fk"), index=True
)
Expand Down Expand Up @@ -10236,7 +10232,7 @@ class PageRevision(Base, Dictifiable, RepresentById):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
page_id: Mapped[int] = mapped_column(ForeignKey("page.id"), index=True, nullable=False)
page_id: Mapped[int] = mapped_column(ForeignKey("page.id"), index=True)
title: Mapped[Optional[str]] = mapped_column(TEXT)
content: Mapped[Optional[str]] = mapped_column(TEXT)
content_format: Mapped[Optional[str]] = mapped_column(TrimmedString(32))
Expand Down Expand Up @@ -10274,7 +10270,7 @@ class Visualization(Base, HasTags, Dictifiable, RepresentById):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True, nullable=False)
user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
latest_revision_id: Mapped[Optional[int]] = mapped_column(
ForeignKey("visualization_revision.id", use_alter=True, name="visualization_latest_revision_id_fk"),
index=True,
Expand Down Expand Up @@ -10387,7 +10383,7 @@ class VisualizationRevision(Base, RepresentById):
id: Mapped[int] = mapped_column(primary_key=True)
create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
visualization_id: Mapped[int] = mapped_column(ForeignKey("visualization.id"), index=True, nullable=False)
visualization_id: Mapped[int] = mapped_column(ForeignKey("visualization.id"), index=True)
title: Mapped[Optional[str]] = mapped_column(TEXT)
dbkey: Mapped[Optional[str]] = mapped_column(TEXT)
config: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
Expand Down Expand Up @@ -10901,7 +10897,7 @@ class APIKeys(Base, RepresentById):
user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
key: Mapped[Optional[str]] = mapped_column(TrimmedString(32), index=True, unique=True)
user = relationship("User", back_populates="api_keys")
deleted: Mapped[bool] = mapped_column(index=True, server_default=false(), nullable=False)
deleted: Mapped[bool] = mapped_column(index=True, server_default=false())


def copy_list(lst, *args, **kwds):
Expand Down Expand Up @@ -11031,7 +11027,7 @@ class CeleryUserRateLimit(Base):
__tablename__ = "celery_user_rate_limit"

user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id", ondelete="CASCADE"), primary_key=True)
last_scheduled_time: Mapped[datetime] = mapped_column(nullable=False)
last_scheduled_time: Mapped[datetime]

def __repr__(self):
return (
Expand Down

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