From b6f5553615397655639ea4ed60d429293b634825 Mon Sep 17 00:00:00 2001
From: Charles Coulombe <charles.coulombe@calculquebec.ca>
Date: Tue, 19 Aug 2025 11:06:35 -0400
Subject: [PATCH 01/14] Format with 3 decimals and display seconds

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 94e1c5528a3..41a2665fb02 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -273,7 +273,7 @@ def administrative_delete_datasets(
     stop = time.time()
     print()
     print(f"Marked {deleted_instance_count} dataset instances as deleted")
-    print("Total elapsed time: ", stop - start)
+    print(f"Total elapsed time: {stop - start:.3f} seconds")
     print("##########################################")
 
 

From 39047212083e4c6508bcbd842fd43828ff0183af Mon Sep 17 00:00:00 2001
From: Charles Coulombe <charles.coulombe@calculquebec.ca>
Date: Tue, 19 Aug 2025 19:01:31 -0400
Subject: [PATCH 02/14] Fixed query results mapping for compatibility with
 sqlalchemy 2.x

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 41a2665fb02..1c5284e5560 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -235,14 +235,14 @@ def administrative_delete_datasets(
             .select_from(
                 sa.join(model.User.__table__, model.History.__table__).join(model.HistoryDatasetAssociation.__table__)
             )
-            .set_label_style()
+            .set_label_style(sa.LABEL_STYLE_DEFAULT)
         )
 
         for result in app.sa_session.execute(user_query):
-            user_notifications[result[model.User.__table__.c.email]].append(
+            user_notifications[result._mapping[model.User.__table__.c.email]].append(
                 (
-                    result[model.HistoryDatasetAssociation.__table__.c.name],
-                    result[model.History.__table__.c.name],
+                    result._mapping[model.HistoryDatasetAssociation.__table__.c.name],
+                    result._mapping[model.History.__table__.c.name],
                 )
             )
             deleted_instance_count += 1

From 860e2cda72aba8bb008a309625bbbed0414157cc Mon Sep 17 00:00:00 2001
From: Charles Coulombe <charles.coulombe@calculquebec.ca>
Date: Tue, 19 Aug 2025 19:50:04 -0400
Subject: [PATCH 03/14] Refactored and updated administrative_delete_datasets
 function to be more readable but mainly compatible with sqlalchemy 2.x

---
 .../admin_cleanup_datasets.py                 | 63 ++++++++++---------
 1 file changed, 32 insertions(+), 31 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 1c5284e5560..05c6f90c207 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -55,7 +55,9 @@ from mako.template import Template
 from sqlalchemy import (
     and_,
     false,
+    select,
 )
+from sqlalchemy.orm import aliased
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
 
@@ -196,24 +198,26 @@ def administrative_delete_datasets(
 ):
     # Marks dataset history association deleted and email users
     start = time.time()
+    session = app.sa_session
+
+    # Aliases for ORM‑mapped classes
+    HDA = aliased(app.model.HistoryDatasetAssociation)
+    Hist = aliased(app.model.History)
+    User = aliased(app.model.User)
+    Dataset = aliased(app.model.Dataset)
+
     # Get HDAs older than cutoff time (ignore tool_id at this point)
-    # We really only need the id column here, but sqlalchemy barfs when
-    # trying to select only 1 column
     hda_ids_query = (
-        sa.select(model.HistoryDatasetAssociation.__table__.c.id, model.HistoryDatasetAssociation.__table__.c.deleted)
-        .where(
-            and_(
-                model.Dataset.__table__.c.deleted == false(),
-                model.HistoryDatasetAssociation.__table__.c.update_time < cutoff_time,
-                model.HistoryDatasetAssociation.__table__.c.deleted == false(),
-            )
-        )
-        .select_from(sa.outerjoin(model.Dataset.__table__, model.HistoryDatasetAssociation.__table__))
+        select(HDA.id)
+        .join(Dataset, Dataset.id == HDA.dataset_id, isouter=True)
+        .where(and_(
+            Dataset.deleted.is_(False),
+            HDA.update_time < cutoff_time,
+            HDA.deleted.is_(False)))
     )
 
     # Add all datasets associated with Histories to our list
-    hda_ids = []
-    hda_ids.extend([row.id for row in app.sa_session.execute(hda_ids_query)])
+    hda_ids = session.execute(hda_ids_query).scalars().all()
 
     # Now find the tool_id that generated the dataset (even if it was copied)
     tool_matched_ids = []
@@ -229,32 +233,29 @@ def administrative_delete_datasets(
 
     # Process each of the Dataset objects
     for hda_id in hda_ids:
-        user_query = (
-            sa.select(model.HistoryDatasetAssociation.__table__, model.History.__table__, model.User.__table__)
-            .where(and_(model.HistoryDatasetAssociation.__table__.c.id == hda_id))
-            .select_from(
-                sa.join(model.User.__table__, model.History.__table__).join(model.HistoryDatasetAssociation.__table__)
-            )
-            .set_label_style(sa.LABEL_STYLE_DEFAULT)
-        )
+        # Bind hda_id for current iteration
+        rows = session.execute(
+            select(User.email, HDA.name, Hist.name)
+            .join(Hist, Hist.user_id == User.id)
+            .join(HDA, HDA.history_id == Hist.id)
+            .where(HDA.id == hda_id)
+        ).all()
 
-        for result in app.sa_session.execute(user_query):
-            user_notifications[result._mapping[model.User.__table__.c.email]].append(
-                (
-                    result._mapping[model.HistoryDatasetAssociation.__table__.c.name],
-                    result._mapping[model.History.__table__.c.name],
-                )
-            )
+        for email, dataset_name, history_name in rows:
+            user_notifications[email].append((dataset_name, history_name))
             deleted_instance_count += 1
+
             if not info_only and not email_only:
                 # Get the HistoryDatasetAssociation objects
-                hda = app.sa_session.query(model.HistoryDatasetAssociation).get(hda_id)
+                hda = session.get(app.model.HistoryDatasetAssociation, hda_id)
                 if not hda.deleted:
                     # Mark the HistoryDatasetAssociation as deleted
                     hda.deleted = True
-                    app.sa_session.add(hda)
+                    session.add(hda)
                     print(f"Marked HistoryDatasetAssociation id {hda.id} as deleted")
-                app.sa_session().commit()
+
+        if not info_only and not email_only:
+            session.commit()
 
     emailtemplate = Template(filename=template_file)
     for email, dataset_list in user_notifications.items():

From 651426ae39ba305e927cc8649eda7b2812a7f797 Mon Sep 17 00:00:00 2001
From: Charles Coulombe <charles.coulombe@calculquebec.ca>
Date: Wed, 20 Aug 2025 08:57:04 -0400
Subject: [PATCH 04/14] Updated _get_tool_id_for_hda function to be more
 readable but mainly compatible with sqlalchemy 2.x

---
 .../admin_cleanup_datasets.py                 | 33 ++++++++++++-------
 1 file changed, 22 insertions(+), 11 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 05c6f90c207..9399ca456ac 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -279,20 +279,31 @@ def administrative_delete_datasets(
 
 
 def _get_tool_id_for_hda(app, hda_id):
-    # TODO Some datasets don't seem to have an entry in jtod or a copied_from
     if hda_id is None:
         return None
-    job = (
-        app.sa_session.query(model.Job)
-        .join(model.JobToOutputDatasetAssociation)
-        .filter(model.JobToOutputDatasetAssociation.__table__.c.dataset_id == hda_id)
-        .first()
+
+    # Aliases for ORM‑mapped classes
+    Job = aliased(app.model.Job)
+    JTODA = aliased(app.model.JobToOutputDatasetAssociation)
+    HDA = aliased(app.model.HistoryDatasetAssociation)
+
+    session = app.sa_session
+
+    job_query = (
+        select(Job.tool_id)
+        .join(JTODA, JTODA.job_id == Job.id)
+        .where(JTODA.dataset_id == hda_id)
     )
-    if job is not None:
-        return job.tool_id
-    else:
-        hda = app.sa_session.query(model.HistoryDatasetAssociation).get(hda_id)
-        return _get_tool_id_for_hda(app, hda.copied_from_history_dataset_association_id)
+
+    tool_id = session.execute(job_query).scalars().first()
+    if tool_id is not None:
+        return tool_id
+
+    hda = session.get(app.model.HistoryDatasetAssociation, hda_id)
+    if hda is None:
+        return None
+
+    return _get_tool_id_for_hda(app, hda.copied_from_history_dataset_association_id)
 
 
 if __name__ == "__main__":

From f0e63ff652e7dd75386381b3dcbc577a19be3b3a Mon Sep 17 00:00:00 2001
From: Charles Coulombe <charles.coulombe@calculquebec.ca>
Date: Mon, 25 Aug 2025 15:38:57 -0400
Subject: [PATCH 05/14] Added `state` to email subject. Differentiate between
 the information and the actual deletion email

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 9399ca456ac..ae23fb83d4a 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -260,7 +260,8 @@ def administrative_delete_datasets(
     emailtemplate = Template(filename=template_file)
     for email, dataset_list in user_notifications.items():
         msgtext = emailtemplate.render(email=email, datasets=dataset_list, cutoff=cutoff_days)
-        subject = f"Galaxy Server Cleanup - {len(dataset_list)} datasets DELETED"
+        state = "" if info_only or email_only else " DELETED"
+        subject = f"Galaxy Server Cleanup - {len(dataset_list)} datasets{state}"
         fromaddr = config.email_from
         print()
         print(f"From: {fromaddr}")

From 85d8e6a78f2e2ccff71db761bde4a18274fcce34 Mon Sep 17 00:00:00 2001
From: Charles Coulombe <charles.coulombe@calculquebec.ca>
Date: Tue, 26 Aug 2025 10:29:34 -0400
Subject: [PATCH 06/14] Added --no-send option, to allow not sending an email
 upon deletion

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index ae23fb83d4a..a966542fbcd 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -22,6 +22,7 @@ Optional Arguments:
     -i --info_only - Print results, but don't email or delete anything
     -e --email_only - Email notifications, but don't delete anything
         Useful for notifying users of pending deletion
+    --no-send - Do no send email (Default: false)
 
     --smtp - Specify smtp server
         If not specified, use smtp settings specified in config file
@@ -121,6 +122,7 @@ def main():
         help="Send emails only, don't delete",
         default=False,
     )
+    parser.add_argument("--no-send", action="store_true", help="Do not send email", default=False)
     parser.add_argument(
         "--smtp", default=None, help="SMTP Server to use to send email. Default: [read from galaxy config file]"
     )
@@ -188,13 +190,14 @@ def main():
         config=config,
         email_only=args.email_only,
         info_only=args.info_only,
+        no_send=args.no_send,
     )
     app.shutdown()
     sys.exit(0)
 
 
 def administrative_delete_datasets(
-    app, cutoff_time, cutoff_days, tool_id, template_file, config, email_only=False, info_only=False
+    app, cutoff_time, cutoff_days, tool_id, template_file, config, email_only=False, info_only=False, no_send=False
 ):
     # Marks dataset history association deleted and email users
     start = time.time()
@@ -269,7 +272,7 @@ def administrative_delete_datasets(
         print(f"Subject: {subject}")
         print("----------")
         print(msgtext)
-        if not info_only:
+        if not no_send and not info_only:
             galaxy.util.send_mail(fromaddr, email, subject, msgtext, config)
 
     stop = time.time()

From f14f34dca72df143a7fae6ea1078a4cfe77a7d66 Mon Sep 17 00:00:00 2001
From: Charles Coulombe <charles.coulombe@calculquebec.ca>
Date: Tue, 26 Aug 2025 13:18:46 -0400
Subject: [PATCH 07/14] Removed unsused imports

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index a966542fbcd..c593ffa000d 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -51,11 +51,9 @@ from datetime import (
 )
 from time import strftime
 
-import sqlalchemy as sa
 from mako.template import Template
 from sqlalchemy import (
     and_,
-    false,
     select,
 )
 from sqlalchemy.orm import aliased
@@ -66,7 +64,6 @@ from cleanup_datasets import CleanupDatasetsApplication
 
 import galaxy.config
 import galaxy.util
-from galaxy import model
 from galaxy.util.script import (
     app_properties_from_args,
     populate_config_args,
@@ -289,7 +286,6 @@ def _get_tool_id_for_hda(app, hda_id):
     # Aliases for ORM‑mapped classes
     Job = aliased(app.model.Job)
     JTODA = aliased(app.model.JobToOutputDatasetAssociation)
-    HDA = aliased(app.model.HistoryDatasetAssociation)
 
     session = app.sa_session
 

From 1bd316e9518267524949f5221c640e8c65fc4400 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 27 Jan 2026 11:20:42 -0500
Subject: [PATCH 08/14] Use == false() instead of is_(False)

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index c593ffa000d..2c11ef92f93 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -211,9 +211,9 @@ def administrative_delete_datasets(
         select(HDA.id)
         .join(Dataset, Dataset.id == HDA.dataset_id, isouter=True)
         .where(and_(
-            Dataset.deleted.is_(False),
+            Dataset.deleted == false(),
             HDA.update_time < cutoff_time,
-            HDA.deleted.is_(False)))
+            HDA.deleted == false()))
     )
 
     # Add all datasets associated with Histories to our list

From cce6f59c1c31d82461084bc64fbf54d54c2931ac Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 27 Jan 2026 11:28:27 -0500
Subject: [PATCH 09/14] Do not use aliased on models for readability: just
 import them

---
 .../admin_cleanup_datasets.py                 | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 2c11ef92f93..6154821d72c 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -64,6 +64,12 @@ from cleanup_datasets import CleanupDatasetsApplication
 
 import galaxy.config
 import galaxy.util
+from galaxy.model import (
+    Dataset,
+    History,
+    HistoryDatasetAssociation,
+    User,
+)
 from galaxy.util.script import (
     app_properties_from_args,
     populate_config_args,
@@ -200,20 +206,14 @@ def administrative_delete_datasets(
     start = time.time()
     session = app.sa_session
 
-    # Aliases for ORM‑mapped classes
-    HDA = aliased(app.model.HistoryDatasetAssociation)
-    Hist = aliased(app.model.History)
-    User = aliased(app.model.User)
-    Dataset = aliased(app.model.Dataset)
-
     # Get HDAs older than cutoff time (ignore tool_id at this point)
     hda_ids_query = (
-        select(HDA.id)
-        .join(Dataset, Dataset.id == HDA.dataset_id, isouter=True)
+        select(HistoryDatasetAssociation.id)
+        .join(Dataset, Dataset.id == HistoryDatasetAssociation.dataset_id, isouter=True)
         .where(and_(
             Dataset.deleted == false(),
-            HDA.update_time < cutoff_time,
-            HDA.deleted == false()))
+            HistoryDatasetAssociation.update_time < cutoff_time,
+            HistoryDatasetAssociation.deleted == false()))
     )
 
     # Add all datasets associated with Histories to our list
@@ -235,10 +235,10 @@ def administrative_delete_datasets(
     for hda_id in hda_ids:
         # Bind hda_id for current iteration
         rows = session.execute(
-            select(User.email, HDA.name, Hist.name)
-            .join(Hist, Hist.user_id == User.id)
-            .join(HDA, HDA.history_id == Hist.id)
-            .where(HDA.id == hda_id)
+            select(User.email, HistoryDatasetAssociation.name, History.name)
+            .join(History, History.user_id == User.id)
+            .join(HistoryDatasetAssociation, HistoryDatasetAssociation.history_id == History.id)
+            .where(HistoryDatasetAssociation.id == hda_id)
         ).all()
 
         for email, dataset_name, history_name in rows:
@@ -247,7 +247,7 @@ def administrative_delete_datasets(
 
             if not info_only and not email_only:
                 # Get the HistoryDatasetAssociation objects
-                hda = session.get(app.model.HistoryDatasetAssociation, hda_id)
+                hda = session.get(HistoryDatasetAssociation, hda_id)
                 if not hda.deleted:
                     # Mark the HistoryDatasetAssociation as deleted
                     hda.deleted = True
@@ -299,7 +299,7 @@ def _get_tool_id_for_hda(app, hda_id):
     if tool_id is not None:
         return tool_id
 
-    hda = session.get(app.model.HistoryDatasetAssociation, hda_id)
+    hda = session.get(HistoryDatasetAssociation, hda_id)
     if hda is None:
         return None
 

From 3a59617837e8fffb4ee794903f72713f75fb453e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 27 Jan 2026 11:30:40 -0500
Subject: [PATCH 10/14] Restore old comment

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 6154821d72c..9a0df0692ea 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -280,6 +280,7 @@ def administrative_delete_datasets(
 
 
 def _get_tool_id_for_hda(app, hda_id):
+    # TODO Some datasets don't seem to have an entry in jtod or a copied_from
     if hda_id is None:
         return None
 

From 5ffdf789c1d4d682147618f708d58d47fcc4db7e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 27 Jan 2026 11:49:22 -0500
Subject: [PATCH 11/14] Remove redundant join criteria

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 9a0df0692ea..89163a7b9f3 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -209,7 +209,7 @@ def administrative_delete_datasets(
     # Get HDAs older than cutoff time (ignore tool_id at this point)
     hda_ids_query = (
         select(HistoryDatasetAssociation.id)
-        .join(Dataset, Dataset.id == HistoryDatasetAssociation.dataset_id, isouter=True)
+        .join(Dataset, isouter=True)
         .where(and_(
             Dataset.deleted == false(),
             HistoryDatasetAssociation.update_time < cutoff_time,
@@ -236,8 +236,8 @@ def administrative_delete_datasets(
         # Bind hda_id for current iteration
         rows = session.execute(
             select(User.email, HistoryDatasetAssociation.name, History.name)
-            .join(History, History.user_id == User.id)
-            .join(HistoryDatasetAssociation, HistoryDatasetAssociation.history_id == History.id)
+            .join(History)
+            .join(HistoryDatasetAssociation)
             .where(HistoryDatasetAssociation.id == hda_id)
         ).all()
 
@@ -292,7 +292,7 @@ def _get_tool_id_for_hda(app, hda_id):
 
     job_query = (
         select(Job.tool_id)
-        .join(JTODA, JTODA.job_id == Job.id)
+        .join(JTODA)
         .where(JTODA.dataset_id == hda_id)
     )
 

From 01a3f2707be77c4ec7666fa5f0078cea70135051 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 27 Jan 2026 11:50:36 -0500
Subject: [PATCH 12/14] Do not change existing behavior; raising error is
 correct

---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 89163a7b9f3..d995cc385ca 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -301,9 +301,6 @@ def _get_tool_id_for_hda(app, hda_id):
         return tool_id
 
     hda = session.get(HistoryDatasetAssociation, hda_id)
-    if hda is None:
-        return None
-
     return _get_tool_id_for_hda(app, hda.copied_from_history_dataset_association_id)
 
 

From 8a40ef19fba2526c9e3c87da6d50b47868b3d6fc Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 27 Jan 2026 11:51:12 -0500
Subject: [PATCH 13/14] Format

---
 .../cleanup_datasets/admin_cleanup_datasets.py  | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index d995cc385ca..097e0f3cedc 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -210,10 +210,13 @@ def administrative_delete_datasets(
     hda_ids_query = (
         select(HistoryDatasetAssociation.id)
         .join(Dataset, isouter=True)
-        .where(and_(
-            Dataset.deleted == false(),
-            HistoryDatasetAssociation.update_time < cutoff_time,
-            HistoryDatasetAssociation.deleted == false()))
+        .where(
+            and_(
+                Dataset.deleted == false(),
+                HistoryDatasetAssociation.update_time < cutoff_time,
+                HistoryDatasetAssociation.deleted == false(),
+            )
+        )
     )
 
     # Add all datasets associated with Histories to our list
@@ -290,11 +293,7 @@ def _get_tool_id_for_hda(app, hda_id):
 
     session = app.sa_session
 
-    job_query = (
-        select(Job.tool_id)
-        .join(JTODA)
-        .where(JTODA.dataset_id == hda_id)
-    )
+    job_query = select(Job.tool_id).join(JTODA).where(JTODA.dataset_id == hda_id)
 
     tool_id = session.execute(job_query).scalars().first()
     if tool_id is not None:

From 4f66c001245503a98c8944c823ddac1b55d52e75 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 27 Jan 2026 15:16:04 -0500
Subject: [PATCH 14/14] Update
 scripts/cleanup_datasets/admin_cleanup_datasets.py

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 scripts/cleanup_datasets/admin_cleanup_datasets.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 097e0f3cedc..d2259823480 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -54,6 +54,7 @@ from time import strftime
 from mako.template import Template
 from sqlalchemy import (
     and_,
+    false,
     select,
 )
 from sqlalchemy.orm import aliased