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Fix various mypy issues around mapped attributes #19883

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Merged
mvdbeek merged 1 commit into from
Mar 25, 2025
Merged

Fix various mypy issues around mapped attributes #19883

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2 changes: 1 addition & 1 deletion lib/galaxy/datatypes/protocols.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ def creating_job(self): ...


class HasDeleted(Protocol):
deleted: bool
deleted: "Mapped[bool]"


class HasExt(Protocol):
Expand Down
4 changes: 2 additions & 2 deletions lib/galaxy/managers/hdas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -364,7 +364,7 @@ def get_discarded_summary(self, user: model.User) -> CleanableItemsSummary:
.where(
and_(
HistoryDatasetAssociation.deleted == true(),
HistoryDatasetAssociation.purged == false(), # type:ignore[arg-type]
HistoryDatasetAssociation.purged == false(),
model.History.user_id == user.id,
)
)
Expand Down Expand Up @@ -394,7 +394,7 @@ def get_discarded(
.where(
and_(
HistoryDatasetAssociation.deleted == true(),
HistoryDatasetAssociation.purged == false(), # type:ignore[arg-type]
HistoryDatasetAssociation.purged == false(),
model.History.user_id == user.id,
)
)
Expand Down
6 changes: 3 additions & 3 deletions lib/galaxy/managers/jobs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -627,7 +627,7 @@ def _build_stmt_for_hda(self, stmt, data_conditions, used_ids, k, v, identifier)
model.HistoryDatasetAssociation.id == e.history_dataset_association_id
)
# b is the HDA used for the job
stmt = stmt.join(b, a.dataset_id == b.id).join(c, c.dataset_id == b.dataset_id) # type:ignore[attr-defined]
stmt = stmt.join(b, a.dataset_id == b.id).join(c, c.dataset_id == b.dataset_id)
name_condition = []
if identifier:
stmt = stmt.join(d)
Expand Down Expand Up @@ -725,7 +725,7 @@ def _build_stmt_for_dce(self, stmt, data_conditions, used_ids, k, v):
),
)
.outerjoin(d, d.id == c.hda_id)
.outerjoin(e, e.dataset_id == d.dataset_id) # type:ignore[attr-defined]
.outerjoin(e, e.dataset_id == d.dataset_id)
)
data_conditions.append(
and_(
Expand All @@ -735,7 +735,7 @@ def _build_stmt_for_dce(self, stmt, data_conditions, used_ids, k, v):
and_(
c.hda_id == b.hda_id,
d.id == c.hda_id,
e.dataset_id == d.dataset_id, # type:ignore[attr-defined]
e.dataset_id == d.dataset_id,
),
),
c.id == v,
Expand Down
36 changes: 19 additions & 17 deletions lib/galaxy/model/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3216,8 +3216,8 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
active_datasets: Mapped[List["HistoryDatasetAssociation"]] = relationship(
primaryjoin=(
lambda: and_(
HistoryDatasetAssociation.history_id == History.id, # type: ignore[arg-type]
not_(HistoryDatasetAssociation.deleted), # type: ignore[has-type]
HistoryDatasetAssociation.history_id == History.id,
not_(HistoryDatasetAssociation.deleted),
)
),
order_by=lambda: asc(HistoryDatasetAssociation.hid), # type: ignore[has-type]
Expand All @@ -3229,7 +3229,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
lambda: (
and_(
HistoryDatasetCollectionAssociation.history_id == History.id,
not_(HistoryDatasetCollectionAssociation.deleted), # type: ignore[arg-type]
not_(HistoryDatasetCollectionAssociation.deleted),
)
)
),
Expand All @@ -3239,8 +3239,8 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
visible_datasets: Mapped[List["HistoryDatasetAssociation"]] = relationship(
primaryjoin=(
lambda: and_(
HistoryDatasetAssociation.history_id == History.id, # type: ignore[arg-type]
not_(HistoryDatasetAssociation.deleted), # type: ignore[has-type]
HistoryDatasetAssociation.history_id == History.id,
not_(HistoryDatasetAssociation.deleted),
HistoryDatasetAssociation.visible, # type: ignore[has-type]
)
),
Expand All @@ -3251,7 +3251,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
primaryjoin=(
lambda: and_(
HistoryDatasetCollectionAssociation.history_id == History.id,
not_(HistoryDatasetCollectionAssociation.deleted), # type: ignore[arg-type]
not_(HistoryDatasetCollectionAssociation.deleted),
HistoryDatasetCollectionAssociation.visible, # type: ignore[arg-type]
)
),
Expand Down Expand Up @@ -4172,27 +4172,27 @@ class Dataset(Base, StorableObject, Serializable):
active_history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship(
primaryjoin=(
lambda: and_(
Dataset.id == HistoryDatasetAssociation.dataset_id, # type: ignore[attr-defined]
HistoryDatasetAssociation.deleted == false(), # type: ignore[has-type]
HistoryDatasetAssociation.purged == false(), # type: ignore[arg-type]
Dataset.id == HistoryDatasetAssociation.dataset_id,
HistoryDatasetAssociation.deleted == false(),
HistoryDatasetAssociation.purged == false(),
)
),
viewonly=True,
)
purged_history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship(
primaryjoin=(
lambda: and_(
Dataset.id == HistoryDatasetAssociation.dataset_id, # type: ignore[attr-defined]
HistoryDatasetAssociation.purged == true(), # type: ignore[arg-type]
Dataset.id == HistoryDatasetAssociation.dataset_id,
HistoryDatasetAssociation.purged == true(),
)
),
viewonly=True,
)
active_library_associations: Mapped[List["LibraryDatasetDatasetAssociation"]] = relationship(
primaryjoin=(
lambda: and_(
Dataset.id == LibraryDatasetDatasetAssociation.dataset_id, # type: ignore[attr-defined]
LibraryDatasetDatasetAssociation.deleted == false(), # type: ignore[has-type]
Dataset.id == LibraryDatasetDatasetAssociation.dataset_id,
LibraryDatasetDatasetAssociation.deleted == false(),
)
),
viewonly=True,
Expand Down Expand Up @@ -4654,11 +4654,13 @@ def datatype_for_extension(extension, datatypes_registry=None) -> "Data":
class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
"""A base class for all 'dataset instances', HDAs, LDDAs, etc"""

purged: Mapped[Optional[bool]]
deleted: Mapped[bool]
dataset_id: Mapped[Optional[int]]
_state: Mapped[Optional[str]]
states = Dataset.states
_state: Optional[str]
conversion_messages = Dataset.conversion_messages
permitted_actions = Dataset.permitted_actions
purged: bool
creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]
copied_from_history_dataset_association: Optional["HistoryDatasetAssociation"]
copied_from_library_dataset_dataset_association: Optional["LibraryDatasetDatasetAssociation"]
Expand Down Expand Up @@ -5318,7 +5320,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
Resource class that creates a relation between a dataset and a user history.
"""

history_id: Optional[int]
history_id: Mapped[Optional[int]]

def __init__(
self,
Expand Down Expand Up @@ -7000,7 +7002,7 @@ class HistoryDatasetCollectionAssociation(
name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
hid: Mapped[Optional[int]]
visible: Mapped[Optional[bool]]
deleted: Mapped[Optional[bool]] = mapped_column(default=False)
deleted: Mapped[bool] = mapped_column(default=False, nullable=True)
copied_from_history_dataset_collection_association_id: Mapped[Optional[int]] = mapped_column(
ForeignKey("history_dataset_collection_association.id")
)
Expand Down
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