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Use utility function for safeguards

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This commit is contained in:
John Davis
2023-12-05 15:21:06 -05:00
parent 3ef86ebcc8
commit ab2f76c94d
9 changed files with 36 additions and 86 deletions
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lib/galaxy/managers/workflows.py
+2 -3
View File
@@ -35,7 +35,6 @@ from sqlalchemy import (
from sqlalchemy.orm import (
aliased,
joinedload,
object_session,
Query,
subqueryload,
)
@@ -67,6 +66,7 @@ from galaxy.model import (
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 @@ class WorkflowContentsManager(UsesAnnotations):
# 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] = []
lib/galaxy/model/__init__.py
+18 -52
View File
@@ -129,6 +129,7 @@ from galaxy.model.custom_types import (
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 @@ class PostJobAction(Base, RepresentById):
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 @@ class DefaultQuotaAssociation(Base, Dictifiable, RepresentById):
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 @@ class LibraryPermissions(Base, RepresentById):
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 @@ class LibraryFolderPermissions(Base, RepresentById):
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 @@ class LibraryDatasetPermissions(Base, RepresentById):
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 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
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 @@ class WorkflowStep(Base, RepresentById):
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 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
# 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 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
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 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
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 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
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)
lib/galaxy/model/store/__init__.py
+4 -9
View File
@@ -40,10 +40,7 @@ from rocrate.model.computationalworkflow import (
)
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 import (
)
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 @@ class ModelImportStore(metaclass=abc.ABCMeta):
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 @@ class ModelImportStore(metaclass=abc.ABCMeta):
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"]
lib/galaxy/webapps/base/webapp.py
+2 -4
View File
@@ -24,7 +24,6 @@ from sqlalchemy import (
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 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.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
lib/galaxy/workflow/extract.py
+2 -2
View File
@@ -9,6 +9,7 @@ from galaxy import (
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
lib/galaxy/workflow/modules.py
+2 -4
View File
@@ -18,7 +18,6 @@ from typing import (
)
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 @@ from galaxy.model import (
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 @@ class SubWorkflowModule(WorkflowModule):
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"):
lib/galaxy/workflow/run.py
+2 -4
View File
@@ -10,7 +10,6 @@ from typing import (
Union,
)
from sqlalchemy.orm import object_session
from typing_extensions import Protocol
from galaxy import model
@@ -20,6 +19,7 @@ from galaxy.model import (
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 @@ class WorkflowInvoker:
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"
lib/galaxy/workflow/run_request.py
+2 -5
View File
@@ -9,8 +9,6 @@ from typing import (
TYPE_CHECKING,
)
from sqlalchemy.orm import object_session
from galaxy import exceptions
from galaxy.model import (
EffectiveOutput,
@@ -24,6 +22,7 @@ from galaxy.model import (
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(
test/integration/test_job_files.py
+2 -3
View File
@@ -20,10 +20,10 @@ import tempfile
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 @@ class TestJobFilesIntegration(integration_util.IntegrationTestCase):
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