From a8d30d4da5747965c4cc614b738036c2f28aeaab Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 1 Dec 2023 17:17:00 -0500
Subject: [PATCH 01/43] Set cascade_backrefs=False on Visualization.revisions

---
 lib/galaxy/model/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index d8a44615771a..0cd289339f5f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -9937,6 +9937,7 @@ class Visualization(Base, HasTags, Dictifiable, RepresentById):
         back_populates="visualization",
         cascade="all, delete-orphan",
         primaryjoin=(lambda: Visualization.id == VisualizationRevision.visualization_id),
+        cascade_backrefs=False,
     )
     latest_revision = relationship(
         "VisualizationRevision",

From 28be6afe5458a9e312358fdf5de9004ae8d31329 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 1 Dec 2023 17:24:51 -0500
Subject: [PATCH 02/43] set cascade_backrefs=False on Dataset.hashes

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 0cd289339f5f..b98258982a68 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3873,7 +3873,7 @@ class Dataset(Base, StorableObject, Serializable):
         ),
         viewonly=True,
     )
-    hashes = relationship("DatasetHash", back_populates="dataset")
+    hashes = relationship("DatasetHash", back_populates="dataset", cascade_backrefs=False)
     sources = relationship("DatasetSource", back_populates="dataset")
     history_associations = relationship("HistoryDatasetAssociation", back_populates="dataset")
     library_associations = relationship(

From 81afea8367a8beac6875b8cfe645bafb55a7eb14 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 1 Dec 2023 17:48:42 -0500
Subject: [PATCH 03/43] set cascade_backrefs=False on User.stored_worfklows

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index b98258982a68..6e6648d892dc 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -739,7 +739,10 @@ class User(Base, Dictifiable, RepresentById):
     data_manager_histories = relationship("DataManagerHistoryAssociation", back_populates="user")
     roles = relationship("UserRoleAssociation", back_populates="user")
     stored_workflows = relationship(
-        "StoredWorkflow", back_populates="user", primaryjoin=(lambda: User.id == StoredWorkflow.user_id)  # type: ignore[has-type]
+        "StoredWorkflow",
+        back_populates="user",
+        primaryjoin=(lambda: User.id == StoredWorkflow.user_id),  # type: ignore[has-type]
+        cascade_backrefs=False,
     )
     all_notifications = relationship("UserNotificationAssociation", back_populates="user")
     non_private_roles = relationship(

From 5c043b3ffaa21c9cc9758fa2a4a963f67e2e223d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 01:31:18 -0500
Subject: [PATCH 04/43] Set cascade_backrefs=False on
 Dataset.history_associations, add safeguard

---
 lib/galaxy/model/__init__.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 6e6648d892dc..895844934309 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3878,7 +3878,7 @@ class Dataset(Base, StorableObject, Serializable):
     )
     hashes = relationship("DatasetHash", back_populates="dataset", cascade_backrefs=False)
     sources = relationship("DatasetSource", back_populates="dataset")
-    history_associations = relationship("HistoryDatasetAssociation", back_populates="dataset")
+    history_associations = relationship("HistoryDatasetAssociation", back_populates="dataset", cascade_backrefs=False)
     library_associations = relationship(
         "LibraryDatasetDatasetAssociation",
         primaryjoin=(lambda: LibraryDatasetDatasetAssociation.table.c.dataset_id == Dataset.id),
@@ -4374,6 +4374,11 @@ def __init__(
         elif dataset:
             add_object_to_object_session(self, dataset)
         self.dataset = dataset
+
+        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if object_session(dataset):
+            object_session(dataset).add(self)
+
         self.parent_id = parent_id
 
     @property

From 913c55aeea53179fff4a921fa4f09eea0db50daa Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 11:41:35 -0500
Subject: [PATCH 05/43] Set cascade_backrefs=False on Library.actions, add
 safeguards

---
 lib/galaxy/model/__init__.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 895844934309..38fb8d04bfdc 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3712,6 +3712,9 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, Library):
             self.library = library_item
+            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(library_item):
+                object_session(library_item).add(self)
         else:
             raise Exception(f"Invalid Library specified: {library_item.__class__.__name__}")
         self.role = role
@@ -3733,6 +3736,9 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, LibraryFolder):
             self.folder = library_item
+            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(library_item):
+                object_session(library_item).add(self)
         else:
             raise Exception(f"Invalid LibraryFolder specified: {library_item.__class__.__name__}")
         self.role = role
@@ -5376,7 +5382,7 @@ class Library(Base, Dictifiable, HasName, Serializable):
     description = Column(TEXT)
     synopsis = Column(TEXT)
     root_folder = relationship("LibraryFolder", back_populates="library_root")
-    actions = relationship("LibraryPermissions", back_populates="library")
+    actions = relationship("LibraryPermissions", back_populates="library", cascade_backrefs=False)
 
     permitted_actions = get_permitted_actions(filter="LIBRARY")
     dict_collection_visible_keys = ["id", "name"]

From 68e502aace00e9fe4a5a8ba588a92b94da27f030 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 12:27:24 -0500
Subject: [PATCH 06/43] Set cascade_backrefs=False on Group.roles, add
 safeguard

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 38fb8d04bfdc..e66041d71339 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2774,7 +2774,7 @@ class Group(Base, Dictifiable, RepresentById):
     name = Column(String(255), index=True, unique=True)
     deleted = Column(Boolean, index=True, default=False)
     quotas = relationship("GroupQuotaAssociation", back_populates="group")
-    roles = relationship("GroupRoleAssociation", back_populates="group")
+    roles = relationship("GroupRoleAssociation", back_populates="group", cascade_backrefs=False)
     users = relationship("UserGroupAssociation", back_populates="group")
 
     dict_collection_visible_keys = ["id", "name"]
@@ -3502,6 +3502,9 @@ class GroupRoleAssociation(Base, RepresentById):
 
     def __init__(self, group, role):
         self.group = group
+        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if object_session(group):
+                object_session(group).add(self)
         self.role = role
 
 

From f8fc5dc613ae18364c25751f36f6b15c4619b884 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 12:28:34 -0500
Subject: [PATCH 07/43] Set cascade_backrefs=False on
 Dataset.library_associations

---
 lib/galaxy/model/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index e66041d71339..7a77f1a1bc9f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3892,6 +3892,7 @@ class Dataset(Base, StorableObject, Serializable):
         "LibraryDatasetDatasetAssociation",
         primaryjoin=(lambda: LibraryDatasetDatasetAssociation.table.c.dataset_id == Dataset.id),
         back_populates="dataset",
+        cascade_backrefs=False,
     )
 
     # failed_metadata is only valid as DatasetInstance state currently

From dffe9e4a239c93c14edac7188c46fd83cbf48247 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:09:04 -0500
Subject: [PATCH 08/43] Set cascade_backrefs=False on
 WorkflowStep.post_job_actions, add safeguard

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 7a77f1a1bc9f..e08c724792fa 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2465,6 +2465,9 @@ def __init__(self, action_type, workflow_step=None, output_name=None, action_arg
         self.output_name = output_name
         self.action_arguments = action_arguments
         self.workflow_step = workflow_step
+        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if object_session(workflow_step):
+            object_session(workflow_step).add(self)
 
 
 class PostJobActionAssociation(Base, RepresentById):
@@ -7658,7 +7661,7 @@ class WorkflowStep(Base, RepresentById):
         order_by=lambda: WorkflowStepAnnotationAssociation.id,
         back_populates="workflow_step",
     )
-    post_job_actions = relationship("PostJobAction", back_populates="workflow_step")
+    post_job_actions = relationship("PostJobAction", back_populates="workflow_step", cascade_backrefs=False)
     inputs = relationship("WorkflowStepInput", back_populates="workflow_step")
     workflow_outputs = relationship("WorkflowOutput", back_populates="workflow_step")
     output_connections = relationship(

From 391888bd9583ecca01376adb98b8b3d462eca3a5 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:12:12 -0500
Subject: [PATCH 09/43] Set cascade_backrefs=False on Job.post_job_actions, add
 safeguard

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index e08c724792fa..0f075460c264 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1331,7 +1331,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     )
     output_dataset_collection_instances = relationship("JobToOutputDatasetCollectionAssociation", back_populates="job")
     output_dataset_collections = relationship("JobToImplicitOutputDatasetCollectionAssociation", back_populates="job")
-    post_job_actions = relationship("PostJobActionAssociation", back_populates="job")
+    post_job_actions = relationship("PostJobActionAssociation", back_populates="job", cascade_backrefs=False)
     input_library_datasets = relationship("JobToInputLibraryDatasetAssociation", back_populates="job")
     output_library_datasets = relationship("JobToOutputLibraryDatasetAssociation", back_populates="job")
     external_output_metadata = relationship("JobExternalOutputMetadata", back_populates="job")
@@ -2482,6 +2482,9 @@ class PostJobActionAssociation(Base, RepresentById):
     def __init__(self, pja, job=None, job_id=None):
         if job is not None:
             self.job = job
+            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(job):
+                object_session(job).add(self)
         elif job_id is not None:
             self.job_id = job_id
         else:

From 504687422d126e47135faa6981a5f93cd45d4e11 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:13:44 -0500
Subject: [PATCH 10/43] Set cascade_backrefs=False on User.all_notifications,
 add safeguard

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 0f075460c264..75850fe221ae 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -744,7 +744,7 @@ class User(Base, Dictifiable, RepresentById):
         primaryjoin=(lambda: User.id == StoredWorkflow.user_id),  # type: ignore[has-type]
         cascade_backrefs=False,
     )
-    all_notifications = relationship("UserNotificationAssociation", back_populates="user")
+    all_notifications = relationship("UserNotificationAssociation", back_populates="user", cascade_backrefs=False)
     non_private_roles = relationship(
         "UserRoleAssociation",
         viewonly=True,
@@ -2855,6 +2855,9 @@ class UserNotificationAssociation(Base, RepresentById):
 
     def __init__(self, user, notification):
         self.user = user
+        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if object_session(user):
+            object_session(user).add(self)
         self.notification = notification
 
 

From 5b8dba9aa4b0e42611f36ca446cb47b61d4459bf Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:15:22 -0500
Subject: [PATCH 11/43] Set cascade_backrefs=False on Quota.default, add
 safeguard

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 75850fe221ae..33a695f4566f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3614,7 +3614,7 @@ class Quota(Base, Dictifiable, RepresentById):
     operation = Column(String(8))
     deleted = Column(Boolean, index=True, default=False)
     quota_source_label = Column(String(32), default=None)
-    default = relationship("DefaultQuotaAssociation", back_populates="quota")
+    default = relationship("DefaultQuotaAssociation", back_populates="quota", cascade_backrefs=False)
     groups = relationship("GroupQuotaAssociation", back_populates="quota")
     users = relationship("UserQuotaAssociation", back_populates="quota")
 
@@ -3684,6 +3684,9 @@ def __init__(self, type, quota):
         assert type in self.types.__members__.values(), "Invalid type"
         self.type = type
         self.quota = quota
+        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if object_session(quota):
+            object_session(quota).add(self)
 
 
 class DatasetPermissions(Base, RepresentById):

From b4f6a9cd2b82b80b319104b499a8e5acd3a2b84e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:18:15 -0500
Subject: [PATCH 12/43] Set cascade_backrefs=False on LibraryDataset.actions,
 add safeguard

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 33a695f4566f..9277f2096de0 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3775,6 +3775,9 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, LibraryDataset):
             self.library_dataset = library_item
+            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(library_item):
+                object_session(library_item).add(self)
         else:
             raise Exception(f"Invalid LibraryDataset specified: {library_item.__class__.__name__}")
         self.role = role
@@ -5642,7 +5645,7 @@ class LibraryDataset(Base, Serializable):
         viewonly=True,
         uselist=True,
     )
-    actions = relationship("LibraryDatasetPermissions", back_populates="library_dataset")
+    actions = relationship("LibraryDatasetPermissions", back_populates="library_dataset", cascade_backrefs=False)
 
     # This class acts as a proxy to the currently selected LDDA
     upload_options = [

From 1465875f97dd2cf0262f4ff277a793c36a15aed7 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:21:03 -0500
Subject: [PATCH 13/43] Set cascade_backrefs=False on GalaxySession.histories,
 add safeguard

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 9277f2096de0..6c193995e822 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7234,7 +7234,7 @@ class GalaxySession(Base, RepresentById):
     disk_usage = Column(Numeric(15, 0), index=True)
     last_action = Column(DateTime)
     current_history = relationship("History")
-    histories = relationship("GalaxySessionToHistoryAssociation", back_populates="galaxy_session")
+    histories = relationship("GalaxySessionToHistoryAssociation", back_populates="galaxy_session", cascade_backrefs=False)
     user = relationship("User", back_populates="galaxy_sessions")
 
     def __init__(self, is_valid=False, **kwd):
@@ -7271,6 +7271,9 @@ class GalaxySessionToHistoryAssociation(Base, RepresentById):
 
     def __init__(self, galaxy_session, history):
         self.galaxy_session = galaxy_session
+        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if object_session(galaxy_session):
+            object_session(galaxy_session).add(self)
         add_object_to_object_session(self, history)
         self.history = history
 

From f5820d4d381c5a4c7b47f2f3e3186c622c9ed6bb Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:28:19 -0500
Subject: [PATCH 14/43] Set cascade_backrefs=False on
 History.workflow_invocations, add safeguards

---
 lib/galaxy/model/__init__.py       | 2 +-
 lib/galaxy/model/store/__init__.py | 3 +++
 lib/galaxy/workflow/run_request.py | 5 +++++
 3 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 6c193995e822..f53a7a931dbb 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2991,7 +2991,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     default_permissions = relationship("DefaultHistoryPermissions", back_populates="history")
     users_shared_with = relationship("HistoryUserShareAssociation", back_populates="history")
     galaxy_sessions = relationship("GalaxySessionToHistoryAssociation", back_populates="history")
-    workflow_invocations = relationship("WorkflowInvocation", back_populates="history")
+    workflow_invocations = relationship("WorkflowInvocation", back_populates="history", cascade_backrefs=False)
     user = relationship("User", back_populates="histories")
     jobs = relationship("Job", back_populates="history")
 
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index e18fa9ba71a5..ee4819a02f74 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1024,6 +1024,9 @@ def _import_workflow_invocations(
             imported_invocation = model.WorkflowInvocation()
             imported_invocation.user = self.user
             imported_invocation.history = history
+            # Safeguard: imported_invocation was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(history):
+                object_session(history).add(imported_invocation)
             workflow_key = invocation_attrs["workflow"]
             if workflow_key not in object_import_tracker.workflows_by_key:
                 raise Exception(f"Failed to find key {workflow_key} in {object_import_tracker.workflows_by_key.keys()}")
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index 8797b1fb8fe1..b6ce3070e549 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -9,6 +9,8 @@
     TYPE_CHECKING,
 )
 
+from sqlalchemy.orm import object_session
+
 from galaxy import exceptions
 from galaxy.model import (
     EffectiveOutput,
@@ -486,6 +488,9 @@ def workflow_run_config_to_request(
     workflow_invocation = WorkflowInvocation()
     workflow_invocation.uuid = uuid.uuid1()
     workflow_invocation.history = run_config.target_history
+    # Safeguard: workflow_invocation was implicitly merged into this Session prior to SQLAlchemy 2.0.
+    if run_config.target_history and object_session(run_config.target_history):
+        object_session(run_config.target_history).add(workflow_invocation)
 
     def add_parameter(name: str, value: str, type: WorkflowRequestInputParameter.types) -> None:
         parameter = WorkflowRequestInputParameter(

From 98cf269bf57f4743c5c9a9c85f5b6f9d951289e1 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:30:45 -0500
Subject: [PATCH 15/43] Set cascade_backrefs=False on WorflowInvocation.steps,
 add safeguards

---
 lib/galaxy/model/__init__.py       | 1 +
 lib/galaxy/model/store/__init__.py | 3 +++
 lib/galaxy/workflow/run.py         | 4 ++++
 3 files changed, 8 insertions(+)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index f53a7a931dbb..7c3ce283a274 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8218,6 +8218,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         "WorkflowInvocationStep",
         back_populates="workflow_invocation",
         order_by=lambda: WorkflowInvocationStep.order_index,
+        cascade_backrefs=False,
     )
     workflow: Workflow = relationship("Workflow")
     output_dataset_collections = relationship(
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index ee4819a02f74..c905ca62a317 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1048,6 +1048,9 @@ def attach_workflow_step(imported_object, attrs):
             for step_attrs in invocation_attrs["steps"]:
                 imported_invocation_step = model.WorkflowInvocationStep()
                 imported_invocation_step.workflow_invocation = imported_invocation
+                # Safeguard: imported_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                if object_session(imported_invocation):
+                    object_session(imported_invocation).add(imported_invocation_step)
                 attach_workflow_step(imported_invocation_step, step_attrs)
                 restore_times(imported_invocation_step, step_attrs)
                 imported_invocation_step.action = step_attrs["action"]
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 776b4e525803..e50962b8a27f 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -10,6 +10,7 @@
     Union,
 )
 
+from sqlalchemy.orm import object_session
 from typing_extensions import Protocol
 
 from galaxy import model
@@ -225,6 +226,9 @@ def invoke(self) -> Dict[int, Any]:
                     workflow_invocation_step = WorkflowInvocationStep()
                     assert workflow_invocation_step
                     workflow_invocation_step.workflow_invocation = workflow_invocation
+                    # Safeguard: workflow_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                    if workflow_invocation and object_session(workflow_invocation):
+                        object_session(workflow_invocation).add(workflow_invocation_step)
                     workflow_invocation_step.workflow_step = step
                     workflow_invocation_step.state = "new"
 

From 015a62e1f3d18c5659f30dcc329e344620a88099 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:33:26 -0500
Subject: [PATCH 16/43] Set cascade_backrefs=False on
 WorflowInvocation.input_parameters, add safeguard; lint

---
 lib/galaxy/model/__init__.py       | 10 +++++++---
 lib/galaxy/model/store/__init__.py |  8 +++++++-
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 7c3ce283a274..6342d97ea910 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3513,7 +3513,7 @@ def __init__(self, group, role):
         self.group = group
         # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
         if object_session(group):
-                object_session(group).add(self)
+            object_session(group).add(self)
         self.role = role
 
 
@@ -7234,7 +7234,9 @@ class GalaxySession(Base, RepresentById):
     disk_usage = Column(Numeric(15, 0), index=True)
     last_action = Column(DateTime)
     current_history = relationship("History")
-    histories = relationship("GalaxySessionToHistoryAssociation", back_populates="galaxy_session", cascade_backrefs=False)
+    histories = relationship(
+        "GalaxySessionToHistoryAssociation", back_populates="galaxy_session", cascade_backrefs=False
+    )
     user = relationship("User", back_populates="galaxy_sessions")
 
     def __init__(self, is_valid=False, **kwd):
@@ -8199,7 +8201,9 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
     history_id = Column(Integer, ForeignKey("history.id"), index=True)
 
     history = relationship("History", back_populates="workflow_invocations")
-    input_parameters = relationship("WorkflowRequestInputParameter", back_populates="workflow_invocation")
+    input_parameters = relationship(
+        "WorkflowRequestInputParameter", back_populates="workflow_invocation", cascade_backrefs=False
+    )
     step_states = relationship("WorkflowRequestStepState", back_populates="workflow_invocation")
     input_step_parameters = relationship("WorkflowRequestInputStepParameter", back_populates="workflow_invocation")
     input_datasets = relationship("WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation")
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index c905ca62a317..f416242ebe2c 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -40,7 +40,10 @@
 )
 from rocrate.rocrate import ROCrate
 from sqlalchemy import select
-from sqlalchemy.orm import joinedload
+from sqlalchemy.orm import (
+    joinedload,
+    object_session,
+)
 from sqlalchemy.orm.scoping import scoped_session
 from sqlalchemy.sql import expression
 from typing_extensions import Protocol
@@ -1105,6 +1108,9 @@ def attach_workflow_step(imported_object, attrs):
                 input_parameter.name = input_parameter_attrs["name"]
                 input_parameter.type = input_parameter_attrs["type"]
                 input_parameter.workflow_invocation = imported_invocation
+                # Safeguard: input_parameter was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                if object_session(imported_invocation):
+                    object_session(imported_invocation).add(input_parameter)
                 self._session_add(input_parameter)
                 input_parameters.append(input_parameter)
 

From bec69fcaadbf326c81f4b996c8272875dba82c76 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sat, 2 Dec 2023 13:47:04 -0500
Subject: [PATCH 17/43] Check if object is not None before checking its session

---
 lib/galaxy/model/__init__.py       | 20 ++++++++++----------
 lib/galaxy/model/store/__init__.py |  6 +++---
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 6342d97ea910..d1cc9361f97d 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2466,7 +2466,7 @@ def __init__(self, action_type, workflow_step=None, output_name=None, action_arg
         self.action_arguments = action_arguments
         self.workflow_step = workflow_step
         # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if object_session(workflow_step):
+        if workflow_step and object_session(workflow_step):
             object_session(workflow_step).add(self)
 
 
@@ -2483,7 +2483,7 @@ def __init__(self, pja, job=None, job_id=None):
         if job is not None:
             self.job = job
             # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(job):
+            if job and object_session(job):
                 object_session(job).add(self)
         elif job_id is not None:
             self.job_id = job_id
@@ -2856,7 +2856,7 @@ class UserNotificationAssociation(Base, RepresentById):
     def __init__(self, user, notification):
         self.user = user
         # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if object_session(user):
+        if user and object_session(user):
             object_session(user).add(self)
         self.notification = notification
 
@@ -3512,7 +3512,7 @@ class GroupRoleAssociation(Base, RepresentById):
     def __init__(self, group, role):
         self.group = group
         # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if object_session(group):
+        if group and object_session(group):
             object_session(group).add(self)
         self.role = role
 
@@ -3685,7 +3685,7 @@ def __init__(self, type, quota):
         self.type = type
         self.quota = quota
         # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if object_session(quota):
+        if quota and object_session(quota):
             object_session(quota).add(self)
 
 
@@ -3728,7 +3728,7 @@ def __init__(self, action, library_item, role):
         if isinstance(library_item, Library):
             self.library = library_item
             # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(library_item):
+            if library_item and object_session(library_item):
                 object_session(library_item).add(self)
         else:
             raise Exception(f"Invalid Library specified: {library_item.__class__.__name__}")
@@ -3752,7 +3752,7 @@ def __init__(self, action, library_item, role):
         if isinstance(library_item, LibraryFolder):
             self.folder = library_item
             # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(library_item):
+            if library_item and object_session(library_item):
                 object_session(library_item).add(self)
         else:
             raise Exception(f"Invalid LibraryFolder specified: {library_item.__class__.__name__}")
@@ -3776,7 +3776,7 @@ def __init__(self, action, library_item, role):
         if isinstance(library_item, LibraryDataset):
             self.library_dataset = library_item
             # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(library_item):
+            if library_item and object_session(library_item):
                 object_session(library_item).add(self)
         else:
             raise Exception(f"Invalid LibraryDataset specified: {library_item.__class__.__name__}")
@@ -4401,7 +4401,7 @@ def __init__(
         self.dataset = dataset
 
         # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if object_session(dataset):
+        if dataset and object_session(dataset):
             object_session(dataset).add(self)
 
         self.parent_id = parent_id
@@ -7274,7 +7274,7 @@ class GalaxySessionToHistoryAssociation(Base, RepresentById):
     def __init__(self, galaxy_session, history):
         self.galaxy_session = galaxy_session
         # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if object_session(galaxy_session):
+        if galaxy_session and object_session(galaxy_session):
             object_session(galaxy_session).add(self)
         add_object_to_object_session(self, history)
         self.history = history
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index f416242ebe2c..a8bbfabcd335 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1028,7 +1028,7 @@ def _import_workflow_invocations(
             imported_invocation.user = self.user
             imported_invocation.history = history
             # Safeguard: imported_invocation was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(history):
+            if history and object_session(history):
                 object_session(history).add(imported_invocation)
             workflow_key = invocation_attrs["workflow"]
             if workflow_key not in object_import_tracker.workflows_by_key:
@@ -1052,7 +1052,7 @@ def attach_workflow_step(imported_object, attrs):
                 imported_invocation_step = model.WorkflowInvocationStep()
                 imported_invocation_step.workflow_invocation = imported_invocation
                 # Safeguard: imported_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                if object_session(imported_invocation):
+                if imported_invocation and object_session(imported_invocation):
                     object_session(imported_invocation).add(imported_invocation_step)
                 attach_workflow_step(imported_invocation_step, step_attrs)
                 restore_times(imported_invocation_step, step_attrs)
@@ -1109,7 +1109,7 @@ def attach_workflow_step(imported_object, attrs):
                 input_parameter.type = input_parameter_attrs["type"]
                 input_parameter.workflow_invocation = imported_invocation
                 # Safeguard: input_parameter was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                if object_session(imported_invocation):
+                if imported_invocation and object_session(imported_invocation):
                     object_session(imported_invocation).add(input_parameter)
                 self._session_add(input_parameter)
                 input_parameters.append(input_parameter)

From ccb51e4a91ea550e5614a14bab09b2d0953496e0 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sun, 3 Dec 2023 11:09:51 -0500
Subject: [PATCH 18/43] Set cascade_backrefs=Flase on
 WorkflowInvocation.step_states, add safeguard

---
 lib/galaxy/model/__init__.py       | 2 +-
 lib/galaxy/model/store/__init__.py | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index d1cc9361f97d..f060a2572001 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8204,7 +8204,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
     input_parameters = relationship(
         "WorkflowRequestInputParameter", back_populates="workflow_invocation", cascade_backrefs=False
     )
-    step_states = relationship("WorkflowRequestStepState", back_populates="workflow_invocation")
+    step_states = relationship("WorkflowRequestStepState", back_populates="workflow_invocation", cascade_backrefs=False)
     input_step_parameters = relationship("WorkflowRequestInputStepParameter", back_populates="workflow_invocation")
     input_datasets = relationship("WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation")
     input_dataset_collections = relationship(
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index a8bbfabcd335..c1b283ff2648 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1122,6 +1122,8 @@ def attach_workflow_step(imported_object, attrs):
                 step_state.value = step_state_attrs["value"]
                 attach_workflow_step(step_state, step_state_attrs)
                 step_state.workflow_invocation = imported_invocation
+                # Safeguard: step_state was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                self.sa_session.add(step_state)
                 self._session_add(step_state)
                 step_states.append(step_state)
 

From 819dce604902f6ffe05669307df4302fa79d6c64 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sun, 3 Dec 2023 11:32:30 -0500
Subject: [PATCH 19/43] Set cascade_backrefs=False on
 WorflowInvocation.input_datasets, add safeguard.

---
 lib/galaxy/model/__init__.py       | 4 +++-
 lib/galaxy/model/store/__init__.py | 2 ++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index f060a2572001..a778ac4341ba 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8206,7 +8206,9 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
     )
     step_states = relationship("WorkflowRequestStepState", back_populates="workflow_invocation", cascade_backrefs=False)
     input_step_parameters = relationship("WorkflowRequestInputStepParameter", back_populates="workflow_invocation")
-    input_datasets = relationship("WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation")
+    input_datasets = relationship(
+        "WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation", cascade_backrefs=False
+    )
     input_dataset_collections = relationship(
         "WorkflowRequestToInputDatasetCollectionAssociation", back_populates="workflow_invocation"
     )
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index c1b283ff2648..5624810647c0 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1141,6 +1141,8 @@ def attach_workflow_step(imported_object, attrs):
                 input_dataset = model.WorkflowRequestToInputDatasetAssociation()
                 attach_workflow_step(input_dataset, input_dataset_attrs)
                 input_dataset.workflow_invocation = imported_invocation
+                # Safeguard: input_dataset was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                self.sa_session.add(input_dataset)
                 input_dataset.name = input_dataset_attrs["name"]
                 dataset_link_attrs = input_dataset_attrs["dataset"]
                 if dataset_link_attrs:

From e47c56155988d445bdd776f9554ae50c68559e0f Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sun, 3 Dec 2023 11:35:18 -0500
Subject: [PATCH 20/43] Simplify logic: remove unnecessary checks

---
 lib/galaxy/model/store/__init__.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 5624810647c0..b03777fabcc4 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1052,8 +1052,7 @@ def attach_workflow_step(imported_object, attrs):
                 imported_invocation_step = model.WorkflowInvocationStep()
                 imported_invocation_step.workflow_invocation = imported_invocation
                 # Safeguard: imported_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                if imported_invocation and object_session(imported_invocation):
-                    object_session(imported_invocation).add(imported_invocation_step)
+                self.sa_session.add(imported_invocation_step)
                 attach_workflow_step(imported_invocation_step, step_attrs)
                 restore_times(imported_invocation_step, step_attrs)
                 imported_invocation_step.action = step_attrs["action"]
@@ -1109,8 +1108,7 @@ def attach_workflow_step(imported_object, attrs):
                 input_parameter.type = input_parameter_attrs["type"]
                 input_parameter.workflow_invocation = imported_invocation
                 # Safeguard: input_parameter was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                if imported_invocation and object_session(imported_invocation):
-                    object_session(imported_invocation).add(input_parameter)
+                self.sa_session.add(input_parameter)
                 self._session_add(input_parameter)
                 input_parameters.append(input_parameter)
 

From f762f26bc4c64dcec8822c74e502ead956dc1ef9 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sun, 3 Dec 2023 11:41:26 -0500
Subject: [PATCH 21/43] Set cascade_backrefs=False on
 WorflowInvocation.input/output_datasets_collections, add safeguards

---
 lib/galaxy/model/__init__.py       | 10 ++++++++--
 lib/galaxy/model/store/__init__.py |  4 ++++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index a778ac4341ba..53cbd0e48007 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8210,7 +8210,9 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         "WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation", cascade_backrefs=False
     )
     input_dataset_collections = relationship(
-        "WorkflowRequestToInputDatasetCollectionAssociation", back_populates="workflow_invocation"
+        "WorkflowRequestToInputDatasetCollectionAssociation",
+        back_populates="workflow_invocation",
+        cascade_backrefs=False,
     )
     subworkflow_invocations = relationship(
         "WorkflowInvocationToSubworkflowInvocationAssociation",
@@ -8228,7 +8230,9 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
     )
     workflow: Workflow = relationship("Workflow")
     output_dataset_collections = relationship(
-        "WorkflowInvocationOutputDatasetCollectionAssociation", back_populates="workflow_invocation"
+        "WorkflowInvocationOutputDatasetCollectionAssociation",
+        back_populates="workflow_invocation",
+        cascade_backrefs=False,
     )
     output_datasets = relationship("WorkflowInvocationOutputDatasetAssociation", back_populates="workflow_invocation")
     output_values = relationship("WorkflowInvocationOutputValue", back_populates="workflow_invocation")
@@ -8454,6 +8458,8 @@ def add_output(self, workflow_output, step, output_object):
         elif output_object.history_content_type == "dataset_collection":
             output_assoc = WorkflowInvocationOutputDatasetCollectionAssociation()
             output_assoc.workflow_invocation = self
+            if object_session(self):
+                object_session(self).add(output_assoc)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.dataset_collection = output_object
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index b03777fabcc4..9ef5a82b9d2e 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1155,6 +1155,8 @@ def attach_workflow_step(imported_object, attrs):
                 input_dataset_collection = model.WorkflowRequestToInputDatasetCollectionAssociation()
                 attach_workflow_step(input_dataset_collection, input_dataset_collection_attrs)
                 input_dataset_collection.workflow_invocation = imported_invocation
+                # Safeguard: input_dataset_collection was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                self.sa_session.add(input_dataset_collection)
                 input_dataset_collection.name = input_dataset_collection_attrs["name"]
                 dataset_collection_link_attrs = input_dataset_collection_attrs["dataset_collection"]
                 if dataset_collection_link_attrs:
@@ -1169,6 +1171,8 @@ def attach_workflow_step(imported_object, attrs):
             for output_dataset_collection_attrs in invocation_attrs["output_dataset_collections"]:
                 output_dataset_collection = model.WorkflowInvocationOutputDatasetCollectionAssociation()
                 output_dataset_collection.workflow_invocation = imported_invocation
+                # Safeguard: output_dataset_collection was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                self.sa_session.add(output_dataset_collection)
                 attach_workflow_step(output_dataset_collection, output_dataset_collection_attrs)
                 workflow_output = output_dataset_collection_attrs["workflow_output"]
                 label = workflow_output.get("label")

From ed9c72b906722349a7dba4be957b30b807f64e17 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sun, 3 Dec 2023 11:49:33 -0500
Subject: [PATCH 22/43] Set cascade_backrefs=False on
 WorflowInvocation.output_datasets, add safeguards

---
 lib/galaxy/model/__init__.py       | 7 ++++++-
 lib/galaxy/model/store/__init__.py | 2 ++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 53cbd0e48007..f4dacac50e65 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8234,7 +8234,9 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         back_populates="workflow_invocation",
         cascade_backrefs=False,
     )
-    output_datasets = relationship("WorkflowInvocationOutputDatasetAssociation", back_populates="workflow_invocation")
+    output_datasets = relationship(
+        "WorkflowInvocationOutputDatasetAssociation", back_populates="workflow_invocation", cascade_backrefs=False
+    )
     output_values = relationship("WorkflowInvocationOutputValue", back_populates="workflow_invocation")
     messages = relationship("WorkflowInvocationMessage", back_populates="workflow_invocation")
 
@@ -8451,6 +8453,9 @@ def add_output(self, workflow_output, step, output_object):
         elif output_object.history_content_type == "dataset":
             output_assoc = WorkflowInvocationOutputDatasetAssociation()
             output_assoc.workflow_invocation = self
+            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(self):
+                object_session(self).add(output_assoc)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.dataset = output_object
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 9ef5a82b9d2e..6f014568a490 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1185,6 +1185,8 @@ def attach_workflow_step(imported_object, attrs):
             for output_dataset_attrs in invocation_attrs["output_datasets"]:
                 output_dataset = model.WorkflowInvocationOutputDatasetAssociation()
                 output_dataset.workflow_invocation = imported_invocation
+                # Safeguard: output_dataset was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                self.sa_session.add(output_dataset)
                 attach_workflow_step(output_dataset, output_dataset_attrs)
                 workflow_output = output_dataset_attrs["workflow_output"]
                 label = workflow_output.get("label")

From ae82102e652c2800ed56a16f331710fb04db80f5 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Sun, 3 Dec 2023 11:50:48 -0500
Subject: [PATCH 23/43] Set cascade_backrefs=False on
 WorflowInvocation.output_values, add safeguards

---
 lib/galaxy/model/__init__.py       | 7 ++++++-
 lib/galaxy/model/store/__init__.py | 2 ++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index f4dacac50e65..51cf6a2344e6 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8237,7 +8237,9 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
     output_datasets = relationship(
         "WorkflowInvocationOutputDatasetAssociation", back_populates="workflow_invocation", cascade_backrefs=False
     )
-    output_values = relationship("WorkflowInvocationOutputValue", back_populates="workflow_invocation")
+    output_values = relationship(
+        "WorkflowInvocationOutputValue", back_populates="workflow_invocation", cascade_backrefs=False
+    )
     messages = relationship("WorkflowInvocationMessage", back_populates="workflow_invocation")
 
     dict_collection_visible_keys = [
@@ -8446,6 +8448,9 @@ def add_output(self, workflow_output, step, output_object):
             # dispatch on actual object and not step type.
             output_assoc = WorkflowInvocationOutputValue()
             output_assoc.workflow_invocation = self
+            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(self):
+                object_session(self).add(output_assoc)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.value = output_object
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 6f014568a490..00f04b426afa 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1199,6 +1199,8 @@ def attach_workflow_step(imported_object, attrs):
             for output_value_attrs in invocation_attrs["output_values"]:
                 output_value = model.WorkflowInvocationOutputValue()
                 output_value.workflow_invocation = imported_invocation
+                # Safeguard: output_value was implicitly merged into this Session prior to SQLAlchemy 2.0.
+                self.sa_session.add(output_value)
                 output_value.value = output_value_attrs["value"]
                 attach_workflow_step(output_value, output_value_attrs)
                 workflow_output = output_value_attrs["workflow_output"]

From 5ee7287fd0e2713ab6ea7900af8e2508d4160ba7 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 10:54:48 -0500
Subject: [PATCH 24/43] Set cascade_backrefs=False on
 Job.data_manager_association

---
 lib/galaxy/model/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 51cf6a2344e6..beb9b1e284f1 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1345,7 +1345,9 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
         "ImplicitCollectionJobsJobAssociation", back_populates="job", uselist=False
     )
     container = relationship("JobContainerAssociation", back_populates="job", uselist=False)
-    data_manager_association = relationship("DataManagerJobAssociation", back_populates="job", uselist=False)
+    data_manager_association = relationship(
+        "DataManagerJobAssociation", back_populates="job", uselist=False, cascade_backrefs=False
+    )
     history_dataset_collection_associations = relationship("HistoryDatasetCollectionAssociation", back_populates="job")
     workflow_invocation_step = relationship("WorkflowInvocationStep", back_populates="job", uselist=False)
 

From ecbbb56da71ade396727a55a4ccd9b7db84a7a72 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 10:57:41 -0500
Subject: [PATCH 25/43] Set cascade_backrefs=False on
 ImiplicitCollectionJobs.jobs

---
 lib/galaxy/model/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index beb9b1e284f1..1c431e362d55 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2413,7 +2413,9 @@ class ImplicitCollectionJobs(Base, Serializable):
 
     id = Column(Integer, primary_key=True)
     populated_state = Column(TrimmedString(64), default="new", nullable=False)
-    jobs = relationship("ImplicitCollectionJobsJobAssociation", back_populates="implicit_collection_jobs")
+    jobs = relationship(
+        "ImplicitCollectionJobsJobAssociation", back_populates="implicit_collection_jobs", cascade_backrefs=False
+    )
 
     class populated_states(str, Enum):
         NEW = "new"  # New implicit jobs object, unpopulated job associations

From 1b8c68b08a834bffe62bd5338c7a3f08aa9ce9a6 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 11:20:09 -0500
Subject: [PATCH 26/43] Set cascade_backrefs=False on User.galaxy_sessions, add
 safeguard

---
 lib/galaxy/model/__init__.py      | 2 +-
 lib/galaxy/webapps/base/webapp.py | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 1c431e362d55..0188584fde42 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -704,7 +704,7 @@ class User(Base, Dictifiable, RepresentById):
         order_by=lambda: desc(History.update_time),  # type: ignore[has-type]
     )
     galaxy_sessions = relationship(
-        "GalaxySession", back_populates="user", order_by=lambda: desc(GalaxySession.update_time)  # type: ignore[has-type]
+        "GalaxySession", back_populates="user", order_by=lambda: desc(GalaxySession.update_time), cascade_backrefs=False  # type: ignore[has-type]
     )
     quotas = relationship("UserQuotaAssociation", back_populates="user")
     quota_source_usages = relationship("UserQuotaSourceUsage", back_populates="user")
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 97bd22c768d1..d9766abf3fea 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -24,6 +24,7 @@
     select,
     true,
 )
+from sqlalchemy.orm import object_session
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import util
@@ -1119,6 +1120,9 @@ def create_new_session(trans, prev_galaxy_session=None, user_for_new_session=Non
     if user_for_new_session:
         # The new session should be associated with the user
         galaxy_session.user = user_for_new_session
+        # Safeguard: galaxy_session was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if user_for_new_session and object_session(user_for_new_session):
+            object_session(user_for_new_session).add(galaxy_session)
     return galaxy_session
 
 

From 040f31513a067ab33b8ed74bd6f3e6754c9322cb Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 11:24:08 -0500
Subject: [PATCH 27/43] Set cascade_backrefs=False on User.addresses

---
 lib/galaxy/model/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 0188584fde42..250154331039 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -689,7 +689,9 @@ class User(Base, Dictifiable, RepresentById):
     active = Column(Boolean, index=True, default=True, nullable=False)
     activation_token = Column(TrimmedString(64), nullable=True, index=True)
 
-    addresses = relationship("UserAddress", back_populates="user", order_by=lambda: desc(UserAddress.update_time))
+    addresses = relationship(
+        "UserAddress", back_populates="user", order_by=lambda: desc(UserAddress.update_time), cascade_backrefs=False
+    )
     cloudauthz = relationship("CloudAuthz", back_populates="user")
     custos_auth = relationship("CustosAuthnzToken", back_populates="user")
     default_permissions = relationship("DefaultUserPermissions", back_populates="user")

From 3e70f587eab4d45b2fab3032a1985a177f5ac572 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 11:26:13 -0500
Subject: [PATCH 28/43] Set cascade_backrefs=False on StoredWorkflow.workflows,
 add safeguard.

---
 lib/galaxy/model/__init__.py   | 1 +
 lib/galaxy/workflow/extract.py | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 250154331039..ed1054202e94 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7328,6 +7328,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
         cascade="all, delete-orphan",
         primaryjoin=(lambda: StoredWorkflow.id == Workflow.stored_workflow_id),  # type: ignore[has-type]
         order_by=lambda: -Workflow.id,  # type: ignore[has-type]
+        cascade_backrefs=False,
     )
     latest_workflow = relationship(
         "Workflow",
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 199c096e1133..064b15f7efd9 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -71,6 +71,8 @@ def extract_workflow(
     workflow.stored_workflow = stored
     stored.latest_workflow = workflow
     trans.sa_session.add(stored)
+    # Safeguard: workflow was implicitly merged into this Session prior to SQLAlchemy 2.0.
+    trans.sa_session.add(workflow)
     with transaction(trans.sa_session):
         trans.sa_session.commit()
     return stored

From a21cc2d1cd87f45fd0c70fcc662d6ac09f85d1f0 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 11:28:35 -0500
Subject: [PATCH 29/43] Set cascade_backrefs=False on User.histories

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index ed1054202e94..24dc01bf3c61 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -697,7 +697,7 @@ class User(Base, Dictifiable, RepresentById):
     default_permissions = relationship("DefaultUserPermissions", back_populates="user")
     groups = relationship("UserGroupAssociation", back_populates="user")
     histories = relationship(
-        "History", back_populates="user", order_by=lambda: desc(History.update_time)  # type: ignore[has-type]
+        "History", back_populates="user", order_by=lambda: desc(History.update_time), cascade_backrefs=False  # type: ignore[has-type]
     )
     active_histories = relationship(
         "History",

From 1a78d9c0fd9e09d1653d4252d7edebb124020e69 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 11:40:16 -0500
Subject: [PATCH 30/43] Set cascade_backrefs=False on
 Workflow.parent_workflow_steps, add safeguard

---
 lib/galaxy/model/__init__.py   | 1 +
 lib/galaxy/workflow/modules.py | 4 ++++
 2 files changed, 5 insertions(+)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 24dc01bf3c61..1080de81a2dc 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7497,6 +7497,7 @@ class Workflow(Base, Dictifiable, RepresentById):
         "WorkflowStep",
         primaryjoin=(lambda: Workflow.id == WorkflowStep.subworkflow_id),  # type: ignore[has-type]
         back_populates="subworkflow",
+        cascade_backrefs=False,
     )
     stored_workflow = relationship(
         "StoredWorkflow",
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index b0360fc893c8..9a2240b2dd67 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -18,6 +18,7 @@
 )
 
 from cwl_utils.expression import do_eval
+from sqlalchemy.orm import object_session
 from typing_extensions import TypedDict
 
 from galaxy import (
@@ -644,6 +645,9 @@ def from_workflow_step(Class, trans, step, **kwds):
     def save_to_step(self, step, **kwd):
         step.type = self.type
         step.subworkflow = self.subworkflow
+        # Safeguard: step was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if self.subworkflow and object_session(self.subworkflow):
+            object_session(self.subworkflow).add(step)
 
     def get_name(self):
         if hasattr(self.subworkflow, "name"):

From 2fed1313e54769486091465813790ed9ec552c01 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 14:30:39 -0500
Subject: [PATCH 31/43] Set cascade_backrefs=False on
 WorkflowStepInput.connections, add safeguard

---
 lib/galaxy/model/__init__.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 1080de81a2dc..f171d104e7e7 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7790,6 +7790,9 @@ def add_connection(self, input_name, output_name, output_step, input_subworkflow
 
         conn = WorkflowStepConnection()
         conn.input_step_input = step_input
+        # Safeguard: conn was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if step_input and object_session(step_input):
+            object_session(step_input).add(conn)
         conn.output_name = output_name
         add_object_to_object_session(conn, output_step)
         conn.output_step = output_step
@@ -7979,6 +7982,7 @@ class WorkflowStepInput(Base, RepresentById):
         "WorkflowStepConnection",
         back_populates="input_step_input",
         primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id),
+        cascade_backrefs=False,
     )
 
     def __init__(self, workflow_step):

From 657ae1750e4b865ec9509b398973d41fcd553fa0 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 14:54:45 -0500
Subject: [PATCH 32/43] Set cascade_backrefs=False on
 WorkflowInvocationStep.output_datasets, add safeguard

---
 lib/galaxy/model/__init__.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index f171d104e7e7..0a677be0fc3e 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8876,7 +8876,9 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
         "WorkflowInvocationStepOutputDatasetCollectionAssociation", back_populates="workflow_invocation_step"
     )
     output_datasets = relationship(
-        "WorkflowInvocationStepOutputDatasetAssociation", back_populates="workflow_invocation_step"
+        "WorkflowInvocationStepOutputDatasetAssociation",
+        back_populates="workflow_invocation_step",
+        cascade_backrefs=False,
     )
     workflow_invocation = relationship("WorkflowInvocation", back_populates="steps")
     output_value = relationship(
@@ -8931,6 +8933,9 @@ def add_output(self, output_name, output_object):
         if output_object.history_content_type == "dataset":
             output_assoc = WorkflowInvocationStepOutputDatasetAssociation()
             output_assoc.workflow_invocation_step = self
+            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(self):
+                object_session(self).add(output_assoc)
             output_assoc.dataset = output_object
             output_assoc.output_name = output_name
             self.output_datasets.append(output_assoc)

From 855a0c1b3beb200366d1f6af8c6886857148ba9c Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 15:02:28 -0500
Subject: [PATCH 33/43] Set cascade_backrefs=False on
 WorkflowInvocationStep.output_dataset_collections, add safeguard

---
 lib/galaxy/model/__init__.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 0a677be0fc3e..316f188f1af0 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8873,7 +8873,9 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
     job = relationship("Job", back_populates="workflow_invocation_step", uselist=False)
     implicit_collection_jobs = relationship("ImplicitCollectionJobs", uselist=False)
     output_dataset_collections = relationship(
-        "WorkflowInvocationStepOutputDatasetCollectionAssociation", back_populates="workflow_invocation_step"
+        "WorkflowInvocationStepOutputDatasetCollectionAssociation",
+        back_populates="workflow_invocation_step",
+        cascade_backrefs=False,
     )
     output_datasets = relationship(
         "WorkflowInvocationStepOutputDatasetAssociation",
@@ -8942,6 +8944,9 @@ def add_output(self, output_name, output_object):
         elif output_object.history_content_type == "dataset_collection":
             output_assoc = WorkflowInvocationStepOutputDatasetCollectionAssociation()
             output_assoc.workflow_invocation_step = self
+            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
+            if object_session(self):
+                object_session(self).add(output_assoc)
             output_assoc.dataset_collection = output_object
             output_assoc.output_name = output_name
             self.output_dataset_collections.append(output_assoc)

From 5abd3e2b709aa590d15a7c3cfbcf934a08b17a93 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 15:05:23 -0500
Subject: [PATCH 34/43] Set cascade_backrefs=False on
 WorkflowStep.workflow_outputs, add safeguard

---
 lib/galaxy/model/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 316f188f1af0..fd75e87931eb 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7688,7 +7688,7 @@ class WorkflowStep(Base, RepresentById):
     )
     post_job_actions = relationship("PostJobAction", back_populates="workflow_step", cascade_backrefs=False)
     inputs = relationship("WorkflowStepInput", back_populates="workflow_step")
-    workflow_outputs = relationship("WorkflowOutput", back_populates="workflow_step")
+    workflow_outputs = relationship("WorkflowOutput", back_populates="workflow_step", cascade_backrefs=False)
     output_connections = relationship(
         "WorkflowStepConnection", primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id)
     )
@@ -8074,6 +8074,9 @@ class WorkflowOutput(Base, Serializable):
 
     def __init__(self, workflow_step, output_name=None, label=None, uuid=None):
         self.workflow_step = workflow_step
+        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        if object_session(workflow_step):
+            object_session(workflow_step).add(self)
         self.output_name = output_name
         self.label = label
         self.uuid = get_uuid(uuid)

From d275234eb1e51a76f08984a1f37e97fd425ba034 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 4 Dec 2023 15:41:24 -0500
Subject: [PATCH 35/43] Set cascade_backrefs=False on History.jobs, add
 safeguard

---
 lib/galaxy/model/__init__.py       | 2 +-
 test/integration/test_job_files.py | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index fd75e87931eb..32550f11fd93 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2999,7 +2999,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     galaxy_sessions = relationship("GalaxySessionToHistoryAssociation", back_populates="history")
     workflow_invocations = relationship("WorkflowInvocation", back_populates="history", cascade_backrefs=False)
     user = relationship("User", back_populates="histories")
-    jobs = relationship("Job", back_populates="history")
+    jobs = relationship("Job", back_populates="history", cascade_backrefs=False)
 
     update_time = column_property(
         select(func.max(HistoryAudit.update_time)).where(HistoryAudit.history_id == id).scalar_subquery(),
diff --git a/test/integration/test_job_files.py b/test/integration/test_job_files.py
index f45cd6a722e1..f9f6cfaae540 100644
--- a/test/integration/test_job_files.py
+++ b/test/integration/test_job_files.py
@@ -20,6 +20,7 @@
 
 import requests
 from sqlalchemy import select
+from sqlalchemy.orm import object_session
 
 from galaxy import model
 from galaxy.model.base import transaction
@@ -138,6 +139,8 @@ def create_static_job_with_state(self, state):
             sa_session.commit()
         job = model.Job()
         job.history = history
+        # Safeguard: job was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        object_session(history).add(job)
         job.user = user
         job.handler = "unknown-handler"
         job.state = state

From e52e95f4f244d2b697726e510de102126a3e712c Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Dec 2023 08:35:20 -0500
Subject: [PATCH 36/43] Set cascade_backrefs=False on LibraryFolder.actions

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 32550f11fd93..6381ed97a1f1 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -5526,7 +5526,7 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
     )
 
     library_root = relationship("Library", back_populates="root_folder")
-    actions = relationship("LibraryFolderPermissions", back_populates="folder")
+    actions = relationship("LibraryFolderPermissions", back_populates="folder", cascade_backrefs=False)
 
     dict_element_visible_keys = [
         "id",

From 59b9dd17be31f06d653db2a27926b705982b7ba4 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Dec 2023 08:40:17 -0500
Subject: [PATCH 37/43] Set cascade_backrefs=False on
 Job.implicit_collection_jobs_association

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 6381ed97a1f1..c690a7d5e39e 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1344,7 +1344,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     numeric_metrics = relationship("JobMetricNumeric")
     interactivetool_entry_points = relationship("InteractiveToolEntryPoint", back_populates="job", uselist=True)
     implicit_collection_jobs_association = relationship(
-        "ImplicitCollectionJobsJobAssociation", back_populates="job", uselist=False
+        "ImplicitCollectionJobsJobAssociation", back_populates="job", uselist=False, cascade_backrefs=False
     )
     container = relationship("JobContainerAssociation", back_populates="job", uselist=False)
     data_manager_association = relationship(

From 18b7d01cca4563119d686e173856a8d4a034e0e3 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Dec 2023 08:47:08 -0500
Subject: [PATCH 38/43] Set cascade_backrefs=False on
 WorkflowInvocation.input_step_parameters

---
 lib/galaxy/model/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index c690a7d5e39e..2594af7f9ded 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -8220,7 +8220,9 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         "WorkflowRequestInputParameter", back_populates="workflow_invocation", cascade_backrefs=False
     )
     step_states = relationship("WorkflowRequestStepState", back_populates="workflow_invocation", cascade_backrefs=False)
-    input_step_parameters = relationship("WorkflowRequestInputStepParameter", back_populates="workflow_invocation")
+    input_step_parameters = relationship(
+        "WorkflowRequestInputStepParameter", back_populates="workflow_invocation", cascade_backrefs=False
+    )
     input_datasets = relationship(
         "WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation", cascade_backrefs=False
     )

From 303f70e1ef942434d4c921b67cfefb124c2cf40e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Dec 2023 09:01:43 -0500
Subject: [PATCH 39/43] Set cascade_backrefs=False on WorkflowStep.workflow,
 add safeguard

We loop over steps to determine if at least one of them has been added
to the session. If so, we add the workflow.
---
 lib/galaxy/managers/workflows.py | 7 +++++++
 lib/galaxy/model/__init__.py     | 5 ++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 4ca49ca19b02..37c7a748981f 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -35,6 +35,7 @@
 from sqlalchemy.orm import (
     aliased,
     joinedload,
+    object_session,
     Query,
     subqueryload,
 )
@@ -818,6 +819,12 @@ def _workflow_from_raw_description(
 
         workflow.has_cycles = True
         workflow.steps = steps
+        # Safeguard: workflow was implicitly merged into this Session prior to SQLAlchemy 2.0.
+        # when AT LEAST ONE step in steps belonged to a session.
+        for step in steps:
+            if step and object_session(step):
+                object_session(step).add(workflow)
+                break
 
         comments: List[model.WorkflowComment] = []
         comments_by_external_id: Dict[str, model.WorkflowComment] = {}
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 2594af7f9ded..492b8d98c1b4 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7693,7 +7693,10 @@ class WorkflowStep(Base, RepresentById):
         "WorkflowStepConnection", primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id)
     )
     workflow = relationship(
-        "Workflow", primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id), back_populates="steps"
+        "Workflow",
+        primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id),
+        back_populates="steps",
+        cascade_backrefs=False,
     )
 
     # Injected attributes

From 4fac426a812abc2f2abfc84192ff4d2d80bd73ac Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Dec 2023 14:53:45 -0500
Subject: [PATCH 40/43] Remove redundant safeguards (self._session_add()
 called)

---
 lib/galaxy/model/store/__init__.py | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 00f04b426afa..53fe0c99beef 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1107,8 +1107,6 @@ def attach_workflow_step(imported_object, attrs):
                 input_parameter.name = input_parameter_attrs["name"]
                 input_parameter.type = input_parameter_attrs["type"]
                 input_parameter.workflow_invocation = imported_invocation
-                # Safeguard: input_parameter was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(input_parameter)
                 self._session_add(input_parameter)
                 input_parameters.append(input_parameter)
 
@@ -1120,8 +1118,6 @@ def attach_workflow_step(imported_object, attrs):
                 step_state.value = step_state_attrs["value"]
                 attach_workflow_step(step_state, step_state_attrs)
                 step_state.workflow_invocation = imported_invocation
-                # Safeguard: step_state was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(step_state)
                 self._session_add(step_state)
                 step_states.append(step_state)
 
@@ -1139,8 +1135,6 @@ def attach_workflow_step(imported_object, attrs):
                 input_dataset = model.WorkflowRequestToInputDatasetAssociation()
                 attach_workflow_step(input_dataset, input_dataset_attrs)
                 input_dataset.workflow_invocation = imported_invocation
-                # Safeguard: input_dataset was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(input_dataset)
                 input_dataset.name = input_dataset_attrs["name"]
                 dataset_link_attrs = input_dataset_attrs["dataset"]
                 if dataset_link_attrs:
@@ -1155,8 +1149,6 @@ def attach_workflow_step(imported_object, attrs):
                 input_dataset_collection = model.WorkflowRequestToInputDatasetCollectionAssociation()
                 attach_workflow_step(input_dataset_collection, input_dataset_collection_attrs)
                 input_dataset_collection.workflow_invocation = imported_invocation
-                # Safeguard: input_dataset_collection was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(input_dataset_collection)
                 input_dataset_collection.name = input_dataset_collection_attrs["name"]
                 dataset_collection_link_attrs = input_dataset_collection_attrs["dataset_collection"]
                 if dataset_collection_link_attrs:
@@ -1171,8 +1163,6 @@ def attach_workflow_step(imported_object, attrs):
             for output_dataset_collection_attrs in invocation_attrs["output_dataset_collections"]:
                 output_dataset_collection = model.WorkflowInvocationOutputDatasetCollectionAssociation()
                 output_dataset_collection.workflow_invocation = imported_invocation
-                # Safeguard: output_dataset_collection was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(output_dataset_collection)
                 attach_workflow_step(output_dataset_collection, output_dataset_collection_attrs)
                 workflow_output = output_dataset_collection_attrs["workflow_output"]
                 label = workflow_output.get("label")
@@ -1185,8 +1175,6 @@ def attach_workflow_step(imported_object, attrs):
             for output_dataset_attrs in invocation_attrs["output_datasets"]:
                 output_dataset = model.WorkflowInvocationOutputDatasetAssociation()
                 output_dataset.workflow_invocation = imported_invocation
-                # Safeguard: output_dataset was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(output_dataset)
                 attach_workflow_step(output_dataset, output_dataset_attrs)
                 workflow_output = output_dataset_attrs["workflow_output"]
                 label = workflow_output.get("label")
@@ -1199,8 +1187,6 @@ def attach_workflow_step(imported_object, attrs):
             for output_value_attrs in invocation_attrs["output_values"]:
                 output_value = model.WorkflowInvocationOutputValue()
                 output_value.workflow_invocation = imported_invocation
-                # Safeguard: output_value was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(output_value)
                 output_value.value = output_value_attrs["value"]
                 attach_workflow_step(output_value, output_value_attrs)
                 workflow_output = output_value_attrs["workflow_output"]

From 3ef86ebcc8e23a9defa4ad00da37d3f0b415eb41 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Dec 2023 14:09:15 -0500
Subject: [PATCH 41/43] Add utility function

---
 lib/galaxy/model/database_utils.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/lib/galaxy/model/database_utils.py b/lib/galaxy/model/database_utils.py
index ee7d12819edb..0865450d71da 100644
--- a/lib/galaxy/model/database_utils.py
+++ b/lib/galaxy/model/database_utils.py
@@ -12,6 +12,7 @@
 )
 from sqlalchemy.engine import Engine
 from sqlalchemy.engine.url import make_url
+from sqlalchemy.orm import object_session
 from sqlalchemy.sql.compiler import IdentifierPreparer
 from sqlalchemy.sql.expression import (
     ClauseElement,
@@ -175,3 +176,22 @@ def _statement_executed_without_error(statement: ClauseElement, engine: Engine)
 
 def is_postgres(url: DbUrl) -> bool:
     return url.startswith("postgres")
+
+
+def ensure_object_added_to_session(object_to_add, *, object_in_session=None, session=None) -> bool:
+    """
+    This function is intended as a safeguard to mimic pre-SQLAlchemy 2.0 behavior.
+    `object_to_add` was implicitly merged into a Session prior to SQLAlchemy 2.0, which was indicated
+    by `RemovedIn20Warning` warnings logged while running Galaxy's tests. (See https://github.com/galaxyproject/galaxy/issues/12541)
+    As part of the upgrade to 2.0, the `cascade_backrefs=False` argument was added to the relevant relationships that turned off this behavior.
+    This function is called from the code that triggered these warnings, thus emulating the cascading behavior.
+    The intention is to remove all such calls, as well as this function definition, after the move to SQLAlchemy 2.0.
+    # Ref: https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#cascade-backrefs-behavior-deprecated-for-removal-in-2-0
+    """
+    if session:
+        session.add(object_to_add)
+        return True
+    if object_in_session and object_session(object_in_session):
+        object_session(object_in_session).add(object_to_add)
+        return True
+    return False

From ab2f76c94d89fd9419b1dc0bc5ea606834cdbe2b Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Dec 2023 14:42:17 -0500
Subject: [PATCH 42/43] Use utility function for safeguards

---
 lib/galaxy/managers/workflows.py   |  5 +--
 lib/galaxy/model/__init__.py       | 70 ++++++++----------------------
 lib/galaxy/model/store/__init__.py | 13 ++----
 lib/galaxy/webapps/base/webapp.py  |  6 +--
 lib/galaxy/workflow/extract.py     |  4 +-
 lib/galaxy/workflow/modules.py     |  6 +--
 lib/galaxy/workflow/run.py         |  6 +--
 lib/galaxy/workflow/run_request.py |  7 +--
 test/integration/test_job_files.py |  5 +--
 9 files changed, 36 insertions(+), 86 deletions(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 37c7a748981f..5c1a1481e6e7 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -35,7 +35,6 @@
 from sqlalchemy.orm import (
     aliased,
     joinedload,
-    object_session,
     Query,
     subqueryload,
 )
@@ -67,6 +66,7 @@
     WorkflowInvocationStep,
 )
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.model.index_filter_util import (
     append_user_filter,
     raw_text_column_filter,
@@ -822,8 +822,7 @@ def _workflow_from_raw_description(
         # Safeguard: workflow was implicitly merged into this Session prior to SQLAlchemy 2.0.
         # when AT LEAST ONE step in steps belonged to a session.
         for step in steps:
-            if step and object_session(step):
-                object_session(step).add(workflow)
+            if ensure_object_added_to_session(workflow, object_in_session=step):
                 break
 
         comments: List[model.WorkflowComment] = []
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 492b8d98c1b4..02f1e4985f52 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -129,6 +129,7 @@
     UUIDType,
 )
 from galaxy.model.database_object_names import NAMING_CONVENTION
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.model.item_attrs import (
     get_item_annotation_str,
     UsesAnnotations,
@@ -2471,9 +2472,7 @@ def __init__(self, action_type, workflow_step=None, output_name=None, action_arg
         self.output_name = output_name
         self.action_arguments = action_arguments
         self.workflow_step = workflow_step
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if workflow_step and object_session(workflow_step):
-            object_session(workflow_step).add(self)
+        ensure_object_added_to_session(self, object_in_session=workflow_step)
 
 
 class PostJobActionAssociation(Base, RepresentById):
@@ -2488,9 +2487,7 @@ class PostJobActionAssociation(Base, RepresentById):
     def __init__(self, pja, job=None, job_id=None):
         if job is not None:
             self.job = job
-            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if job and object_session(job):
-                object_session(job).add(self)
+            ensure_object_added_to_session(self, object_in_session=job)
         elif job_id is not None:
             self.job_id = job_id
         else:
@@ -2861,9 +2858,7 @@ class UserNotificationAssociation(Base, RepresentById):
 
     def __init__(self, user, notification):
         self.user = user
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if user and object_session(user):
-            object_session(user).add(self)
+        ensure_object_added_to_session(self, object_in_session=user)
         self.notification = notification
 
 
@@ -3517,9 +3512,7 @@ class GroupRoleAssociation(Base, RepresentById):
 
     def __init__(self, group, role):
         self.group = group
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if group and object_session(group):
-            object_session(group).add(self)
+        ensure_object_added_to_session(self, object_in_session=group)
         self.role = role
 
 
@@ -3690,9 +3683,7 @@ def __init__(self, type, quota):
         assert type in self.types.__members__.values(), "Invalid type"
         self.type = type
         self.quota = quota
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if quota and object_session(quota):
-            object_session(quota).add(self)
+        ensure_object_added_to_session(self, object_in_session=quota)
 
 
 class DatasetPermissions(Base, RepresentById):
@@ -3733,9 +3724,7 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, Library):
             self.library = library_item
-            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if library_item and object_session(library_item):
-                object_session(library_item).add(self)
+            ensure_object_added_to_session(self, object_in_session=library_item)
         else:
             raise Exception(f"Invalid Library specified: {library_item.__class__.__name__}")
         self.role = role
@@ -3757,9 +3746,7 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, LibraryFolder):
             self.folder = library_item
-            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if library_item and object_session(library_item):
-                object_session(library_item).add(self)
+            ensure_object_added_to_session(self, object_in_session=library_item)
         else:
             raise Exception(f"Invalid LibraryFolder specified: {library_item.__class__.__name__}")
         self.role = role
@@ -3781,9 +3768,7 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, LibraryDataset):
             self.library_dataset = library_item
-            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if library_item and object_session(library_item):
-                object_session(library_item).add(self)
+            ensure_object_added_to_session(self, object_in_session=library_item)
         else:
             raise Exception(f"Invalid LibraryDataset specified: {library_item.__class__.__name__}")
         self.role = role
@@ -4405,11 +4390,7 @@ def __init__(
         elif dataset:
             add_object_to_object_session(self, dataset)
         self.dataset = dataset
-
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if dataset and object_session(dataset):
-            object_session(dataset).add(self)
-
+        ensure_object_added_to_session(self, object_in_session=dataset)
         self.parent_id = parent_id
 
     @property
@@ -7279,9 +7260,7 @@ class GalaxySessionToHistoryAssociation(Base, RepresentById):
 
     def __init__(self, galaxy_session, history):
         self.galaxy_session = galaxy_session
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if galaxy_session and object_session(galaxy_session):
-            object_session(galaxy_session).add(self)
+        ensure_object_added_to_session(self, object_in_session=galaxy_session)
         add_object_to_object_session(self, history)
         self.history = history
 
@@ -7793,9 +7772,7 @@ def add_connection(self, input_name, output_name, output_step, input_subworkflow
 
         conn = WorkflowStepConnection()
         conn.input_step_input = step_input
-        # Safeguard: conn was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if step_input and object_session(step_input):
-            object_session(step_input).add(conn)
+        ensure_object_added_to_session(conn, object_in_session=step_input)
         conn.output_name = output_name
         add_object_to_object_session(conn, output_step)
         conn.output_step = output_step
@@ -8077,9 +8054,7 @@ class WorkflowOutput(Base, Serializable):
 
     def __init__(self, workflow_step, output_name=None, label=None, uuid=None):
         self.workflow_step = workflow_step
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if object_session(workflow_step):
-            object_session(workflow_step).add(self)
+        ensure_object_added_to_session(self, object_in_session=workflow_step)
         self.output_name = output_name
         self.label = label
         self.uuid = get_uuid(uuid)
@@ -8468,9 +8443,7 @@ def add_output(self, workflow_output, step, output_object):
             # dispatch on actual object and not step type.
             output_assoc = WorkflowInvocationOutputValue()
             output_assoc.workflow_invocation = self
-            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.value = output_object
@@ -8478,9 +8451,7 @@ def add_output(self, workflow_output, step, output_object):
         elif output_object.history_content_type == "dataset":
             output_assoc = WorkflowInvocationOutputDatasetAssociation()
             output_assoc.workflow_invocation = self
-            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.dataset = output_object
@@ -8488,8 +8459,7 @@ def add_output(self, workflow_output, step, output_object):
         elif output_object.history_content_type == "dataset_collection":
             output_assoc = WorkflowInvocationOutputDatasetCollectionAssociation()
             output_assoc.workflow_invocation = self
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.dataset_collection = output_object
@@ -8943,18 +8913,14 @@ def add_output(self, output_name, output_object):
         if output_object.history_content_type == "dataset":
             output_assoc = WorkflowInvocationStepOutputDatasetAssociation()
             output_assoc.workflow_invocation_step = self
-            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.dataset = output_object
             output_assoc.output_name = output_name
             self.output_datasets.append(output_assoc)
         elif output_object.history_content_type == "dataset_collection":
             output_assoc = WorkflowInvocationStepOutputDatasetCollectionAssociation()
             output_assoc.workflow_invocation_step = self
-            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.dataset_collection = output_object
             output_assoc.output_name = output_name
             self.output_dataset_collections.append(output_assoc)
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 53fe0c99beef..27dbaa6ffa34 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -40,10 +40,7 @@
 )
 from rocrate.rocrate import ROCrate
 from sqlalchemy import select
-from sqlalchemy.orm import (
-    joinedload,
-    object_session,
-)
+from sqlalchemy.orm import joinedload
 from sqlalchemy.orm.scoping import scoped_session
 from sqlalchemy.sql import expression
 from typing_extensions import Protocol
@@ -60,6 +57,7 @@
 )
 from galaxy.files.uris import stream_url_to_file
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.model.metadata import MetadataCollection
 from galaxy.model.orm.util import (
@@ -1027,9 +1025,7 @@ def _import_workflow_invocations(
             imported_invocation = model.WorkflowInvocation()
             imported_invocation.user = self.user
             imported_invocation.history = history
-            # Safeguard: imported_invocation was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if history and object_session(history):
-                object_session(history).add(imported_invocation)
+            ensure_object_added_to_session(imported_invocation, object_in_session=history)
             workflow_key = invocation_attrs["workflow"]
             if workflow_key not in object_import_tracker.workflows_by_key:
                 raise Exception(f"Failed to find key {workflow_key} in {object_import_tracker.workflows_by_key.keys()}")
@@ -1051,8 +1047,7 @@ def attach_workflow_step(imported_object, attrs):
             for step_attrs in invocation_attrs["steps"]:
                 imported_invocation_step = model.WorkflowInvocationStep()
                 imported_invocation_step.workflow_invocation = imported_invocation
-                # Safeguard: imported_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(imported_invocation_step)
+                ensure_object_added_to_session(imported_invocation, session=self.sa_session)
                 attach_workflow_step(imported_invocation_step, step_attrs)
                 restore_times(imported_invocation_step, step_attrs)
                 imported_invocation_step.action = step_attrs["action"]
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index d9766abf3fea..59c3adda8a22 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -24,7 +24,6 @@
     select,
     true,
 )
-from sqlalchemy.orm import object_session
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import util
@@ -39,6 +38,7 @@
 from galaxy.managers.session import GalaxySessionManager
 from galaxy.managers.users import UserManager
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.structured_app import (
     BasicSharedApp,
     MinimalApp,
@@ -1120,9 +1120,7 @@ def create_new_session(trans, prev_galaxy_session=None, user_for_new_session=Non
     if user_for_new_session:
         # The new session should be associated with the user
         galaxy_session.user = user_for_new_session
-        # Safeguard: galaxy_session was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if user_for_new_session and object_session(user_for_new_session):
-            object_session(user_for_new_session).add(galaxy_session)
+        ensure_object_added_to_session(galaxy_session, object_in_session=user_for_new_session)
     return galaxy_session
 
 
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 064b15f7efd9..ad196a82d28e 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -9,6 +9,7 @@
     model,
 )
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.tool_util.parser import ToolOutputCollectionPart
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
@@ -71,8 +72,7 @@ def extract_workflow(
     workflow.stored_workflow = stored
     stored.latest_workflow = workflow
     trans.sa_session.add(stored)
-    # Safeguard: workflow was implicitly merged into this Session prior to SQLAlchemy 2.0.
-    trans.sa_session.add(workflow)
+    ensure_object_added_to_session(workflow, session=trans.sa_session)
     with transaction(trans.sa_session):
         trans.sa_session.commit()
     return stored
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 9a2240b2dd67..cf6d0ebcce30 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -18,7 +18,6 @@
 )
 
 from cwl_utils.expression import do_eval
-from sqlalchemy.orm import object_session
 from typing_extensions import TypedDict
 
 from galaxy import (
@@ -36,6 +35,7 @@
     WorkflowStep,
     WorkflowStepConnection,
 )
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.model.dataset_collections import matching
 from galaxy.schema.invocation import (
     CancelReason,
@@ -645,9 +645,7 @@ def from_workflow_step(Class, trans, step, **kwds):
     def save_to_step(self, step, **kwd):
         step.type = self.type
         step.subworkflow = self.subworkflow
-        # Safeguard: step was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if self.subworkflow and object_session(self.subworkflow):
-            object_session(self.subworkflow).add(step)
+        ensure_object_added_to_session(step, object_in_session=self.subworkflow)
 
     def get_name(self):
         if hasattr(self.subworkflow, "name"):
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index e50962b8a27f..de89a6a40329 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -10,7 +10,6 @@
     Union,
 )
 
-from sqlalchemy.orm import object_session
 from typing_extensions import Protocol
 
 from galaxy import model
@@ -20,6 +19,7 @@
     WorkflowInvocationStep,
 )
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.schema.invocation import (
     CancelReason,
     FailureReason,
@@ -226,9 +226,7 @@ def invoke(self) -> Dict[int, Any]:
                     workflow_invocation_step = WorkflowInvocationStep()
                     assert workflow_invocation_step
                     workflow_invocation_step.workflow_invocation = workflow_invocation
-                    # Safeguard: workflow_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                    if workflow_invocation and object_session(workflow_invocation):
-                        object_session(workflow_invocation).add(workflow_invocation_step)
+                    ensure_object_added_to_session(workflow_invocation_step, object_in_session=workflow_invocation)
                     workflow_invocation_step.workflow_step = step
                     workflow_invocation_step.state = "new"
 
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index b6ce3070e549..2ba9c4e82599 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -9,8 +9,6 @@
     TYPE_CHECKING,
 )
 
-from sqlalchemy.orm import object_session
-
 from galaxy import exceptions
 from galaxy.model import (
     EffectiveOutput,
@@ -24,6 +22,7 @@
     WorkflowRequestStepState,
 )
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.tools.parameters.meta import expand_workflow_inputs
 from galaxy.workflow.resources import get_resource_mapper_function
 
@@ -488,9 +487,7 @@ def workflow_run_config_to_request(
     workflow_invocation = WorkflowInvocation()
     workflow_invocation.uuid = uuid.uuid1()
     workflow_invocation.history = run_config.target_history
-    # Safeguard: workflow_invocation was implicitly merged into this Session prior to SQLAlchemy 2.0.
-    if run_config.target_history and object_session(run_config.target_history):
-        object_session(run_config.target_history).add(workflow_invocation)
+    ensure_object_added_to_session(workflow_invocation, object_in_session=run_config.target_history)
 
     def add_parameter(name: str, value: str, type: WorkflowRequestInputParameter.types) -> None:
         parameter = WorkflowRequestInputParameter(
diff --git a/test/integration/test_job_files.py b/test/integration/test_job_files.py
index f9f6cfaae540..8d0d4422c732 100644
--- a/test/integration/test_job_files.py
+++ b/test/integration/test_job_files.py
@@ -20,10 +20,10 @@
 
 import requests
 from sqlalchemy import select
-from sqlalchemy.orm import object_session
 
 from galaxy import model
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
@@ -139,8 +139,7 @@ def create_static_job_with_state(self, state):
             sa_session.commit()
         job = model.Job()
         job.history = history
-        # Safeguard: job was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        object_session(history).add(job)
+        ensure_object_added_to_session(job, object_in_session=history)
         job.user = user
         job.handler = "unknown-handler"
         job.state = state

From 631e84dd82e960e27a13cc20e50638810d9b8bfe Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 5 Dec 2023 15:31:39 -0500
Subject: [PATCH 43/43] Move function to model.base to avoid circular import

---
 lib/galaxy/managers/workflows.py   |  6 ++++--
 lib/galaxy/model/__init__.py       |  6 ++++--
 lib/galaxy/model/base.py           | 20 ++++++++++++++++++++
 lib/galaxy/model/store/__init__.py |  6 ++++--
 lib/galaxy/webapps/base/webapp.py  |  6 ++++--
 lib/galaxy/workflow/extract.py     |  6 ++++--
 lib/galaxy/workflow/modules.py     |  2 +-
 lib/galaxy/workflow/run.py         |  6 ++++--
 lib/galaxy/workflow/run_request.py |  6 ++++--
 test/integration/test_job_files.py |  6 ++++--
 10 files changed, 53 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 5c1a1481e6e7..4d542abd23b5 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -65,8 +65,10 @@
     WorkflowInvocation,
     WorkflowInvocationStep,
 )
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.model.index_filter_util import (
     append_user_filter,
     raw_text_column_filter,
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 02f1e4985f52..2bf193dd334a 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -119,7 +119,10 @@
 import galaxy.model.tags
 import galaxy.security.passwords
 import galaxy.util
-from galaxy.model.base import transaction
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.model.custom_types import (
     DoubleEncodedJsonType,
     JSONType,
@@ -129,7 +132,6 @@
     UUIDType,
 )
 from galaxy.model.database_object_names import NAMING_CONVENTION
-from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.model.item_attrs import (
     get_item_annotation_str,
     UsesAnnotations,
diff --git a/lib/galaxy/model/base.py b/lib/galaxy/model/base.py
index 2aade3f4ff36..2e4d248afeb4 100644
--- a/lib/galaxy/model/base.py
+++ b/lib/galaxy/model/base.py
@@ -20,6 +20,7 @@
 
 from sqlalchemy import event
 from sqlalchemy.orm import (
+    object_session,
     scoped_session,
     Session,
     sessionmaker,
@@ -167,3 +168,22 @@ def before_flush(session, flush_context, instances):
             obj.__create_version__(session)
         for obj in versioned_objects(session.deleted):
             obj.__create_version__(session, deleted=True)
+
+
+def ensure_object_added_to_session(object_to_add, *, object_in_session=None, session=None) -> bool:
+    """
+    This function is intended as a safeguard to mimic pre-SQLAlchemy 2.0 behavior.
+    `object_to_add` was implicitly merged into a Session prior to SQLAlchemy 2.0, which was indicated
+    by `RemovedIn20Warning` warnings logged while running Galaxy's tests. (See https://github.com/galaxyproject/galaxy/issues/12541)
+    As part of the upgrade to 2.0, the `cascade_backrefs=False` argument was added to the relevant relationships that turned off this behavior.
+    This function is called from the code that triggered these warnings, thus emulating the cascading behavior.
+    The intention is to remove all such calls, as well as this function definition, after the move to SQLAlchemy 2.0.
+    # Ref: https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#cascade-backrefs-behavior-deprecated-for-removal-in-2-0
+    """
+    if session:
+        session.add(object_to_add)
+        return True
+    if object_in_session and object_session(object_in_session):
+        object_session(object_in_session).add(object_to_add)
+        return True
+    return False
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 27dbaa6ffa34..eb30696b1e34 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -56,8 +56,10 @@
     ProvidesUserFileSourcesUserContext,
 )
 from galaxy.files.uris import stream_url_to_file
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.model.metadata import MetadataCollection
 from galaxy.model.orm.util import (
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 59c3adda8a22..92633b3188ed 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -37,8 +37,10 @@
 from galaxy.managers import context
 from galaxy.managers.session import GalaxySessionManager
 from galaxy.managers.users import UserManager
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.structured_app import (
     BasicSharedApp,
     MinimalApp,
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index ad196a82d28e..bfa74d404d17 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -8,8 +8,10 @@
     exceptions,
     model,
 )
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.tool_util.parser import ToolOutputCollectionPart
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index cf6d0ebcce30..2ff8fe290e0b 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -35,7 +35,7 @@
     WorkflowStep,
     WorkflowStepConnection,
 )
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import ensure_object_added_to_session
 from galaxy.model.dataset_collections import matching
 from galaxy.schema.invocation import (
     CancelReason,
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index de89a6a40329..c7eab00a7a1d 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -18,8 +18,10 @@
     WorkflowInvocation,
     WorkflowInvocationStep,
 )
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.schema.invocation import (
     CancelReason,
     FailureReason,
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index 2ba9c4e82599..029b1e7630c6 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -21,8 +21,10 @@
     WorkflowRequestInputParameter,
     WorkflowRequestStepState,
 )
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.tools.parameters.meta import expand_workflow_inputs
 from galaxy.workflow.resources import get_resource_mapper_function
 
diff --git a/test/integration/test_job_files.py b/test/integration/test_job_files.py
index 8d0d4422c732..4ed02b350dd3 100644
--- a/test/integration/test_job_files.py
+++ b/test/integration/test_job_files.py
@@ -22,8 +22,10 @@
 from sqlalchemy import select
 
 from galaxy import model
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util