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Merge pull request #13498 from ic4f/dev_sa20_2

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More backref_cascade fixes (SQLAlchemy 2.0)
This commit is contained in:
Marius van den Beek
2022-03-09 16:40:47 +01:00
committed by GitHub
parent ff72765507 f450876804
commit cf0ff2eb89
6 changed files with 74 additions and 18 deletions
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lib/galaxy/authnz/custos_authnz.py
+3 -1
View File
@@ -22,6 +22,7 @@ from galaxy.model import (
CustosAuthnzToken,
User,
)
from galaxy.model.orm.util import add_object_to_object_session
from ..authnz import IdentityProvider
log = logging.getLogger(__name__)
@@ -186,7 +187,6 @@ class CustosAuthnz(IdentityProvider):
trans.app.user_manager.send_activation_email(trans, email, username)
custos_authnz_token = CustosAuthnzToken(
user=user,
external_user_id=user_id,
provider=self.config["provider"],
access_token=access_token,
@@ -195,6 +195,8 @@ class CustosAuthnz(IdentityProvider):
expiration_time=expiration_time,
refresh_expiration_time=refresh_expiration_time,
)
add_object_to_object_session(custos_authnz_token, user)
custos_authnz_token.user = user
trans.sa_session.add(user)
trans.sa_session.add(custos_authnz_token)
lib/galaxy/model/__init__.py
+23
View File
@@ -1721,6 +1721,7 @@ class Task(Base, JobLike, RepresentById):
self.parameters = []
self.state = Task.states.NEW
self.working_directory = working_directory
add_object_to_object_session(self, job)
self.job = job
self.prepare_input_files_cmd = prepare_files_cmd
self._init_metrics()
@@ -1980,6 +1981,7 @@ class JobToInputLibraryDatasetAssociation(Base, RepresentById):
def __init__(self, name, dataset):
self.name = name
add_object_to_object_session(self, dataset)
self.dataset = dataset
@@ -1997,6 +1999,7 @@ class JobToOutputLibraryDatasetAssociation(Base, RepresentById):
def __init__(self, name, dataset):
self.name = name
add_object_to_object_session(self, dataset)
self.dataset = dataset
@@ -2140,6 +2143,7 @@ class JobExternalOutputMetadata(Base, RepresentById):
job = relationship("Job", back_populates="external_output_metadata")
def __init__(self, job=None, dataset=None):
add_object_to_object_session(self, job)
self.job = job
if isinstance(dataset, galaxy.model.HistoryDatasetAssociation):
self.history_dataset_association = dataset
@@ -2280,6 +2284,8 @@ class JobContainerAssociation(Base, RepresentById):
job = relationship("Job", back_populates="container")
def __init__(self, **kwd):
if "job" in kwd:
add_object_to_object_session(self, kwd["job"])
super().__init__(**kwd)
self.container_info = self.container_info or {}
@@ -2371,6 +2377,7 @@ class UserGroupAssociation(Base, RepresentById):
group = relationship("Group", back_populates="users")
def __init__(self, user, group):
add_object_to_object_session(self, user)
self.user = user
self.group = group
@@ -3052,6 +3059,7 @@ class UserQuotaAssociation(Base, Dictifiable, RepresentById):
dict_element_visible_keys = ["user"]
def __init__(self, user, quota):
add_object_to_object_session(self, user)
self.user = user
self.quota = quota
@@ -3070,6 +3078,7 @@ class GroupQuotaAssociation(Base, Dictifiable, RepresentById):
dict_element_visible_keys = ["group"]
def __init__(self, group, quota):
add_object_to_object_session(self, group)
self.group = group
self.quota = quota
@@ -3257,6 +3266,7 @@ class LibraryDatasetDatasetAssociationPermissions(Base, RepresentById):
def __init__(self, action, library_item, role):
self.action = action
if isinstance(library_item, LibraryDatasetDatasetAssociation):
add_object_to_object_session(self, library_item)
self.library_dataset_dataset_association = library_item
else:
raise Exception(f"Invalid LibraryDatasetDatasetAssociation specified: {library_item.__class__.__name__}")
@@ -3291,6 +3301,7 @@ class DefaultHistoryPermissions(Base, RepresentById):
role = relationship("Role")
def __init__(self, history, action, role):
add_object_to_object_session(self, history)
self.history = history
self.action = action
self.role = role
@@ -5392,6 +5403,7 @@ class ImplicitlyConvertedDatasetAssociation(Base, RepresentById):
self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True
):
self.id = id
add_object_to_object_session(self, dataset)
if isinstance(dataset, HistoryDatasetAssociation):
self.dataset = dataset
elif isinstance(dataset, LibraryDatasetDatasetAssociation):
@@ -6471,6 +6483,7 @@ class GalaxySessionToHistoryAssociation(Base, RepresentById):
def __init__(self, galaxy_session, history):
self.galaxy_session = galaxy_session
add_object_to_object_session(self, history)
self.history = history
@@ -6573,6 +6586,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
workflow=None,
hidden=False,
):
add_object_to_object_session(self, user)
self.user = user
self.name = name
self.slug = slug
@@ -6891,6 +6905,7 @@ class WorkflowStep(Base, RepresentById):
conn = WorkflowStepConnection()
conn.input_step_input = step_input
conn.output_name = output_name
add_object_to_object_session(conn, output_step)
conn.output_step = output_step
if input_subworkflow_step_index is not None:
input_subworkflow_step = self.subworkflow.step_by_index(input_subworkflow_step_index)
@@ -7059,6 +7074,7 @@ class WorkflowStepInput(Base, RepresentById):
)
def __init__(self, workflow_step):
add_object_to_object_session(self, workflow_step)
self.workflow_step = workflow_step
self.default_value_set = False
@@ -7247,6 +7263,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
assoc = WorkflowInvocationToSubworkflowInvocationAssociation()
assoc.workflow_invocation = self
assoc.workflow_step = step
add_object_to_object_session(subworkflow_invocation, self.history)
subworkflow_invocation.history = self.history
subworkflow_invocation.workflow = step.subworkflow
assoc.subworkflow_invocation = subworkflow_invocation
@@ -9026,6 +9043,7 @@ class HistoryDatasetAssociationRatingAssociation(ItemRatingAssociation, Represen
user = relationship("User")
def _set_item(self, history_dataset_association):
add_object_to_object_session(self, history_dataset_association)
self.history_dataset_association = history_dataset_association
@@ -9040,6 +9058,7 @@ class StoredWorkflowRatingAssociation(ItemRatingAssociation, RepresentById):
user = relationship("User")
def _set_item(self, stored_workflow):
add_object_to_object_session(self, stored_workflow)
self.stored_workflow = stored_workflow
@@ -9054,6 +9073,7 @@ class PageRatingAssociation(ItemRatingAssociation, RepresentById):
user = relationship("User")
def _set_item(self, page):
add_object_to_object_session(self, page)
self.page = page
@@ -9068,6 +9088,7 @@ class VisualizationRatingAssociation(ItemRatingAssociation, RepresentById):
user = relationship("User")
def _set_item(self, visualization):
add_object_to_object_session(self, visualization)
self.visualization = visualization
@@ -9082,6 +9103,7 @@ class HistoryDatasetCollectionRatingAssociation(ItemRatingAssociation, Represent
user = relationship("User")
def _set_item(self, dataset_collection):
add_object_to_object_session(self, dataset_collection)
self.dataset_collection = dataset_collection
@@ -9096,6 +9118,7 @@ class LibraryDatasetCollectionRatingAssociation(ItemRatingAssociation, Represent
user = relationship("User")
def _set_item(self, dataset_collection):
add_object_to_object_session(self, dataset_collection)
self.dataset_collection = dataset_collection
lib/tool_shed/webapp/model/__init__.py
+6
View File
@@ -39,6 +39,7 @@ from galaxy.model.custom_types import (
TrimmedString,
)
from galaxy.model.orm.now import now
from galaxy.model.orm.util import add_object_to_object_session
from galaxy.security.validate_user_input import validate_password_str
from galaxy.util import unique_id
from galaxy.util.bunch import Bunch
@@ -182,6 +183,7 @@ class PasswordResetToken(Base, _HasTable):
self.token = token
else:
self.token = unique_id()
add_object_to_object_session(self, user)
self.user = user
self.expiration_time = now() + timedelta(hours=24)
@@ -252,6 +254,7 @@ class UserGroupAssociation(Base, _HasTable):
group = relationship("Group", back_populates="users")
def __init__(self, user, group):
add_object_to_object_session(self, user)
self.user = user
self.group = group
@@ -268,7 +271,9 @@ class UserRoleAssociation(Base, _HasTable):
role = relationship("Role", back_populates="users")
def __init__(self, user, role):
add_object_to_object_session(self, user)
self.user = user
add_object_to_object_session(self, role)
self.role = role
@@ -300,6 +305,7 @@ class RepositoryRoleAssociation(Base, _HasTable):
role = relationship("Role", back_populates="repositories")
def __init__(self, repository, role):
add_object_to_object_session(self, repository)
self.repository = repository
self.role = role
test/unit/app/tools/test_execution.py
+2
View File
@@ -7,6 +7,7 @@ import webob.exc
import galaxy.model
from galaxy.app_unittest_utils import tools_support
from galaxy.model.orm.util import add_object_to_object_session
from galaxy.util.bunch import Bunch
BASE_REPEAT_TOOL_CONTENTS = """<tool id="test_tool" name="Test Tool">
@@ -126,6 +127,7 @@ class ToolExecutionTestCase(TestCase, tools_support.UsesTools):
hda.dataset.state = "ok"
self.trans.sa_session.add(hda)
add_object_to_object_session(self.history, hda)
self.history.datasets.append(hda)
self.trans.sa_session.flush()
return hda
test/unit/data/model/mapping/test_model_mapping.py
+18 -17
View File
@@ -74,6 +74,7 @@ from sqlalchemy import (
from galaxy import model
from galaxy.model.orm.now import now
from galaxy.model.orm.util import add_object_to_object_session
from .common import (
AbstractBaseTest,
collection_consists_of_objects,
@@ -1375,8 +1376,7 @@ class TestHistory(BaseTest):
workflow_invocation,
job,
):
obj = cls_()
obj.user = user
obj = cls_(user=user)
obj.datasets.append(history_dataset_association)
obj.dataset_collections.append(history_dataset_collection_association)
obj.exports.append(job_export_history_archive)
@@ -1580,9 +1580,8 @@ class TestHistoryDatasetAssociation(BaseTest):
icpda,
]
obj = cls_()
obj = cls_(dataset=dataset)
obj.history = history
obj.dataset = dataset
obj.copied_from_history_dataset_association = copied_from_hda
obj.copied_from_library_dataset_dataset_association = copied_from_ldda
obj.extended_metadata = extended_metadata
@@ -1902,6 +1901,7 @@ class TestHistoryDatasetCollectionAssociation(BaseTest):
obj = cls_()
obj.collection = dataset_collection
obj.history = history
add_object_to_object_session(obj, history_dataset_collection_association)
obj.copied_from_history_dataset_collection_association = history_dataset_collection_association
obj.copied_to_history_dataset_collection_association.append(copied_to_hdca)
obj.job = job
@@ -2146,7 +2146,6 @@ class TestImplicitCollectionJobsJobAssociation(BaseTest):
order_index = 1
obj = cls_()
obj.implicit_collection_jobs = implicit_collection_jobs
session.add(job) # must be bound to a session for lazy load of attributes
obj.job = job
obj.order_index = order_index
@@ -2160,7 +2159,6 @@ class TestImplicitCollectionJobsJobAssociation(BaseTest):
def test_relationships(self, session, cls_, implicit_collection_jobs, job):
obj = cls_()
obj.implicit_collection_jobs = implicit_collection_jobs
session.add(job) # must be bound to a session for lazy load of attributes
obj.job = job
obj.order_index = 1
@@ -2502,6 +2500,7 @@ class TestJob(BaseTest):
obj.implicit_collection_jobs_association = implicit_collection_jobs_job_association
obj.container = job_container_association
obj.data_manager_association = data_manager_job_association
add_object_to_object_session(obj, history_dataset_collection_association)
obj.history_dataset_collection_associations.append(history_dataset_collection_association)
obj.workflow_invocation_step = workflow_invocation_step
@@ -2566,9 +2565,7 @@ class TestJobContainerAssociation(BaseTest):
created_time = now()
modified_time = created_time + timedelta(hours=1)
session.add(job) # must be bound to a session for lazy load of attributes
obj = cls_()
obj.job = job
obj = cls_(job=job)
obj.container_type = container_type
obj.container_name = container_name
obj.container_info = container_info
@@ -2586,7 +2583,6 @@ class TestJobContainerAssociation(BaseTest):
assert stored_obj.modified_time == modified_time
def test_relationships(self, session, cls_, job):
session.add(job) # must be bound to a session for lazy load of attributes
obj = cls_(job=job)
with dbcleanup(session, obj) as obj_id:
@@ -3293,6 +3289,7 @@ class TestLibraryDatasetDatasetAssociation(BaseTest):
obj = cls_()
obj.library_dataset = library_dataset
add_object_to_object_session(obj, dataset)
obj.dataset = dataset
obj.create_time = create_time
obj.copied_from_history_dataset_association = history_dataset_association
@@ -3381,6 +3378,7 @@ class TestLibraryDatasetDatasetAssociation(BaseTest):
obj = cls_()
obj.library_dataset = library_dataset
add_object_to_object_session(obj, dataset)
obj.dataset = dataset
obj.copied_from_history_dataset_association = history_dataset_association
obj.copied_from_library_dataset_dataset_association = copied_from_ldda
@@ -3607,6 +3605,7 @@ class TestLibraryFolder(BaseTest):
library_folder_factory,
):
obj = cls_()
add_object_to_object_session(obj, library_folder)
obj.parent = library_folder
folder1 = library_folder_factory()
obj.folders.append(folder1)
@@ -4401,6 +4400,7 @@ class TestStoredWorkflowMenuEntry(BaseTest):
order_index = 1
obj = cls_()
obj.stored_workflow = stored_workflow
add_object_to_object_session(obj, user)
obj.user = user
obj.order_index = order_index
@@ -4414,6 +4414,7 @@ class TestStoredWorkflowMenuEntry(BaseTest):
def test_relationships(self, session, cls_, stored_workflow, user):
obj = cls_()
obj.stored_workflow = stored_workflow
add_object_to_object_session(obj, user)
obj.user = user
with dbcleanup(session, obj) as obj_id:
@@ -5646,6 +5647,7 @@ class TestWorkflowInvocationOutputValue(BaseTest):
persist(session, workflow_invocation_step)
obj = cls_()
add_object_to_object_session(obj, workflow_invocation)
obj.workflow_invocation = workflow_invocation
obj.workflow_step = workflow_step
obj.workflow_output = workflow_output
@@ -5677,9 +5679,6 @@ class TestWorkflowInvocationStep(BaseTest):
update_time = create_time + timedelta(hours=1)
state, action = "a", "b"
session.add(job) # must be bound to a session for lazy load of attributes
session.add(implicit_collection_jobs) # must be bound to a session for lazy load of attributes
obj = cls_()
obj.create_time = create_time
obj.update_time = update_time
@@ -5714,9 +5713,6 @@ class TestWorkflowInvocationStep(BaseTest):
workflow_invocation_step_output_dataset_association,
workflow_invocation_output_value,
):
session.add(job) # must be bound to a session for lazy load of attributes
session.add(implicit_collection_jobs) # must be bound to a session for lazy load of attributes
# setup workflow_invocation_output_value to test the output_value attribute
output_value = workflow_invocation_output_value
output_value.workflow_invocation = workflow_invocation
@@ -5724,6 +5720,7 @@ class TestWorkflowInvocationStep(BaseTest):
persist(session, output_value)
obj = cls_()
add_object_to_object_session(obj, workflow_invocation)
obj.workflow_invocation = workflow_invocation
obj.workflow_step = workflow_step
obj.job = job
@@ -6952,6 +6949,7 @@ def role(session):
@pytest.fixture
def stored_workflow(session, user):
instance = model.StoredWorkflow()
add_object_to_object_session(instance, user)
instance.user = user
yield from dbcleanup_wrapper(session, instance)
@@ -7185,6 +7183,7 @@ def workflow_request_to_input_dataset_collection_association(session):
@pytest.fixture
def workflow_step(session, workflow):
instance = model.WorkflowStep()
add_object_to_object_session(instance, workflow)
instance.workflow = workflow
yield from dbcleanup_wrapper(session, instance)
@@ -7392,7 +7391,9 @@ def workflow_step_connection_factory():
def workflow_step_factory(workflow):
def make_instance(*args, **kwds):
instance = model.WorkflowStep()
instance.workflow = kwds.get("workflow", workflow)
workflow2 = kwds.get("workflow", workflow) # rename workflow not to confuse pytest
add_object_to_object_session(instance, workflow2)
instance.workflow = workflow2
instance.subworkflow = kwds.get("subworkflow")
return instance
test/unit/data/test_galaxy_mapping.py
+22
View File
@@ -18,6 +18,10 @@ import galaxy.model.mapping as mapping
from galaxy import model
from galaxy.model.database_utils import create_database
from galaxy.model.metadata import MetadataTempFile
from galaxy.model.orm.util import (
add_object_to_object_session,
get_object_session,
)
from galaxy.model.security import GalaxyRBACAgent
datatypes_registry = galaxy.datatypes.registry.Registry()
@@ -82,6 +86,7 @@ class MappingTests(BaseModelTestCase):
annotated_association.annotation = "Test Annotation"
annotated_association.user = u
for key, value in kwds.items():
add_object_to_object_session(annotated_association, value)
setattr(annotated_association, key, value)
self.persist(annotated_association)
self.expunge()
@@ -90,6 +95,7 @@ class MappingTests(BaseModelTestCase):
assert stored_annotation.user.email == "annotator@example.com"
sw = model.StoredWorkflow()
add_object_to_object_session(sw, u)
sw.user = u
self.persist(sw)
persist_and_check_annotation(model.StoredWorkflowAnnotationAssociation, stored_workflow=sw)
@@ -99,6 +105,7 @@ class MappingTests(BaseModelTestCase):
self.persist(workflow)
ws = model.WorkflowStep()
add_object_to_object_session(ws, workflow)
ws.workflow = workflow
self.persist(ws)
persist_and_check_annotation(model.WorkflowStepAnnotationAssociation, workflow_step=ws)
@@ -152,6 +159,7 @@ class MappingTests(BaseModelTestCase):
assert stored_rating.user.email == user_email
sw = model.StoredWorkflow()
add_object_to_object_session(sw, u)
sw.user = u
self.persist(sw)
persist_and_check_rating(model.StoredWorkflowRatingAssociation, sw)
@@ -801,8 +809,16 @@ class MappingTests(BaseModelTestCase):
def workflow_from_steps(steps):
stored_workflow = model.StoredWorkflow()
add_object_to_object_session(stored_workflow, user)
stored_workflow.user = user
workflow = model.Workflow()
if steps:
for step in steps:
if get_object_session(step):
add_object_to_object_session(workflow, step)
break
workflow.steps = steps
workflow.stored_workflow = stored_workflow
return workflow
@@ -816,6 +832,7 @@ class MappingTests(BaseModelTestCase):
workflow_step_2 = model.WorkflowStep()
workflow_step_2.order_index = 1
workflow_step_2.type = "subworkflow"
add_object_to_object_session(workflow_step_2, child_workflow)
workflow_step_2.subworkflow = child_workflow
workflow_step_1.get_or_add_input("moo1")
@@ -830,6 +847,7 @@ class MappingTests(BaseModelTestCase):
annotation = model.WorkflowStepAnnotationAssociation()
annotation.annotation = "Test Step Annotation"
annotation.user = user
add_object_to_object_session(annotation, workflow_step_1)
annotation.workflow_step = workflow_step_1
self.persist(annotation)
@@ -840,9 +858,11 @@ class MappingTests(BaseModelTestCase):
workflow_invocation = model.WorkflowInvocation()
workflow_invocation.uuid = invocation_uuid
add_object_to_object_session(workflow_invocation, h1)
workflow_invocation.history = h1
workflow_invocation_step1 = model.WorkflowInvocationStep()
add_object_to_object_session(workflow_invocation_step1, workflow_invocation)
workflow_invocation_step1.workflow_invocation = workflow_invocation
workflow_invocation_step1.workflow_step = workflow_step_1
@@ -850,6 +870,7 @@ class MappingTests(BaseModelTestCase):
workflow_invocation.attach_subworkflow_invocation_for_step(workflow_step_2, subworkflow_invocation)
workflow_invocation_step2 = model.WorkflowInvocationStep()
add_object_to_object_session(workflow_invocation_step2, workflow_invocation)
workflow_invocation_step2.workflow_invocation = workflow_invocation
workflow_invocation_step2.workflow_step = workflow_step_2
@@ -857,6 +878,7 @@ class MappingTests(BaseModelTestCase):
d1 = self.new_hda(h1, name="1")
workflow_request_dataset = model.WorkflowRequestToInputDatasetAssociation()
add_object_to_object_session(workflow_request_dataset, workflow_invocation)
workflow_request_dataset.workflow_invocation = workflow_invocation
workflow_request_dataset.workflow_step = workflow_step_1
workflow_request_dataset.dataset = d1