diff --git a/lib/galaxy/datatypes/protocols.py b/lib/galaxy/datatypes/protocols.py index 07d2c04d379f..35eac996595a 100644 --- a/lib/galaxy/datatypes/protocols.py +++ b/lib/galaxy/datatypes/protocols.py @@ -23,7 +23,7 @@ def creating_job(self): ... class HasDeleted(Protocol): - deleted: bool + deleted: "Mapped[bool]" class HasExt(Protocol): diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index e2871369589d..84534c2d107e 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -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, ) ) @@ -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, ) ) diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py index c3cc82f9b663..f821ba152057 100644 --- a/lib/galaxy/managers/jobs.py +++ b/lib/galaxy/managers/jobs.py @@ -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) @@ -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_( @@ -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, diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 28a4b56286f5..04957abaf6e6 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -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] @@ -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), ) ) ), @@ -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] ) ), @@ -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] ) ), @@ -4172,9 +4172,9 @@ 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, @@ -4182,8 +4182,8 @@ class Dataset(Base, StorableObject, Serializable): 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, @@ -4191,8 +4191,8 @@ class Dataset(Base, StorableObject, Serializable): 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, @@ -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"] @@ -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, @@ -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") )