Skip to content

Commit

Permalink
Move get_fasta_hdas_by_history into services
Browse files Browse the repository at this point in the history
  • Loading branch information
jdavcs committed Sep 22, 2023
1 parent da8f8ec commit e997338
Show file tree
Hide file tree
Showing 2 changed files with 12 additions and 12 deletions.
11 changes: 0 additions & 11 deletions lib/galaxy/managers/histories.py
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@
select,
true,
)
from sqlalchemy.orm import Session
from typing_extensions import Literal

from galaxy import (
Expand All @@ -44,7 +43,6 @@
StorageCleanerManager,
)
from galaxy.managers.export_tracker import StoreExportTracker
from galaxy.model import HistoryDatasetAssociation
from galaxy.model.base import transaction
from galaxy.schema.fields import DecodedDatabaseIdField
from galaxy.schema.schema import (
Expand Down Expand Up @@ -902,12 +900,3 @@ def username_eq(self, item, val: str) -> bool:

def username_contains(self, item, val: str) -> bool:
return val.lower() in str(item.user.username).lower()


def get_fasta_hdas_by_history(session: Session, history_id: int):
stmt = (
select(HistoryDatasetAssociation)
.filter_by(history_id=history_id, extension="fasta", deleted=False)
.order_by(HistoryDatasetAssociation.hid.desc())
)
return session.scalars(stmt).all()
13 changes: 12 additions & 1 deletion lib/galaxy/webapps/galaxy/services/histories.py
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,10 @@

from sqlalchemy import (
false,
select,
true,
)
from sqlalchemy.orm import Session

from galaxy import (
exceptions as glx_exceptions,
Expand All @@ -32,7 +34,6 @@
from galaxy.managers.citations import CitationsManager
from galaxy.managers.context import ProvidesHistoryContext
from galaxy.managers.histories import (
get_fasta_hdas_by_history,
HistoryDeserializer,
HistoryExportManager,
HistoryFilters,
Expand All @@ -41,6 +42,7 @@
)
from galaxy.managers.notification import NotificationManager
from galaxy.managers.users import UserManager
from galaxy.model import HistoryDatasetAssociation
from galaxy.model.base import transaction
from galaxy.model.store import payload_to_source_uri
from galaxy.schema import (
Expand Down Expand Up @@ -788,3 +790,12 @@ def _get_export_record_data(self, history: model.History) -> Optional[WriteStore
if export_metadata and isinstance(export_metadata.request_data.payload, WriteStoreToPayload):
return export_metadata.request_data.payload
return None


def get_fasta_hdas_by_history(session: Session, history_id: int):
stmt = (
select(HistoryDatasetAssociation)
.filter_by(history_id=history_id, extension="fasta", deleted=False)
.order_by(HistoryDatasetAssociation.hid.desc())
)
return session.scalars(stmt).all()

0 comments on commit e997338

Please sign in to comment.