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Merge pull request #16431 from jdavcs/dev_sa20_fix13

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Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test)
This commit is contained in:
John Davis
2023-07-22 04:37:15 +10:00
committed by GitHub
parent 900bffae81 c6ec1dd12b
commit c5b499f893
27 changed files with 169 additions and 150 deletions
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test/integration/objectstore/test_selection_with_resource_parameters.py
+6 -2
View File
@@ -3,6 +3,8 @@
import os
import string
from sqlalchemy import select
from galaxy.model import Dataset
from galaxy.model.unittest_utils.store_fixtures import (
deferred_hda_model_store_dict,
@@ -87,7 +89,7 @@ class TestObjectStoreSelectionWithResourceParameterIntegration(BaseObjectStoreIn
def _assert_no_external_filename(self):
# Should maybe be its own test case ...
for external_filename_tuple in self._app.model.session.query(Dataset.external_filename).all():
for external_filename_tuple in self._app.model.session.execute(select(Dataset.external_filename)).all():
assert external_filename_tuple[0] is None
def test_objectstore_selection(self):
@@ -181,5 +183,7 @@ class TestObjectStoreSelectionWithResourceParameterIntegration(BaseObjectStoreIn
@property
def _latest_dataset(self):
latest_dataset = self._app.model.session.query(Dataset).order_by(Dataset.table.c.id.desc()).first()
latest_dataset = self._app.model.session.scalars(
select(Dataset).order_by(Dataset.table.c.id.desc()).limit(1)
).first()
return latest_dataset
test/integration/objectstore/test_selection_with_user_preferred_object_store.py
+5 -1
View File
@@ -8,6 +8,8 @@ from typing import (
Optional,
)
from sqlalchemy import select
from galaxy.model import Dataset
from galaxy_test.base.populators import WorkflowPopulator
from galaxy_test.base.workflow_fixtures import (
@@ -482,5 +484,7 @@ class TestObjectStoreSelectionWithPreferredObjectStoresIntegration(BaseObjectSto
@property
def _latest_dataset(self):
latest_dataset = self._app.model.session.query(Dataset).order_by(Dataset.table.c.id.desc()).first()
latest_dataset = self._app.model.session.scalars(
select(Dataset).order_by(Dataset.table.c.id.desc()).limit(1)
).first()
return latest_dataset
test/integration/test_celery_tasks.py
+3 -6
View File
@@ -1,6 +1,7 @@
import tarfile
from celery import shared_task
from sqlalchemy import select
from galaxy.celery import galaxy_task
from galaxy.celery.tasks import (
@@ -108,9 +109,5 @@ class TestCeleryTasksIntegration(IntegrationTestCase):
@property
def _latest_hda(self):
latest_hda = (
self._app.model.session.query(HistoryDatasetAssociation)
.order_by(HistoryDatasetAssociation.table.c.id.desc())
.first()
)
return latest_hda
stmt = select(HistoryDatasetAssociation).order_by(HistoryDatasetAssociation.table.c.id.desc()).limit(1)
return self._app.model.session.scalars(stmt).first()
test/integration/test_job_files.py
+8 -6
View File
@@ -19,6 +19,7 @@ import os
import tempfile
import requests
from sqlalchemy import select
from galaxy import model
from galaxy.model.base import transaction
@@ -50,10 +51,11 @@ class TestJobFilesIntegration(integration_util.IntegrationTestCase):
if not TestJobFilesIntegration.initialized:
history_id = self.dataset_populator.new_history()
sa_session = self.sa_session
assert len(sa_session.query(model.HistoryDatasetAssociation).all()) == 0
stmt = select(model.HistoryDatasetAssociation)
assert len(sa_session.scalars(stmt).all()) == 0
self.dataset_populator.new_dataset(history_id, content=TEST_INPUT_TEXT, wait=True)
assert len(sa_session.query(model.HistoryDatasetAssociation).all()) == 1
self.input_hda = sa_session.query(model.HistoryDatasetAssociation).all()[0]
assert len(sa_session.scalars(stmt).all()) == 1
self.input_hda = sa_session.scalars(stmt).all()[0]
TestJobFilesIntegration.initialized = True
def test_read_by_state(self):
@@ -119,11 +121,11 @@ class TestJobFilesIntegration(integration_util.IntegrationTestCase):
def create_static_job_with_state(self, state):
"""Create a job with unknown handler so its state won't change."""
sa_session = self.sa_session
hda = sa_session.query(model.HistoryDatasetAssociation).all()[0]
hda = sa_session.scalars(select(model.HistoryDatasetAssociation)).all()[0]
assert hda
history = sa_session.query(model.History).all()[0]
history = sa_session.scalars(select(model.History)).all()[0]
assert history
user = sa_session.query(model.User).all()[0]
user = sa_session.scalars(select(model.User)).all()[0]
assert user
output_hda = model.HistoryDatasetAssociation(history=history, create_dataset=True, flush=False)
output_hda.hid = 2
test/integration/test_kubernetes_runner.py
+6 -6
View File
@@ -269,8 +269,8 @@ class TestKubernetesIntegration(BaseJobEnvironmentIntegrationTestCase, MulledJob
job_dict = running_response["jobs"][0]
app = self._app
sa_session = app.model.context.current
job = sa_session.query(app.model.Job).get(app.security.decode_id(job_dict["id"]))
sa_session = app.model.session
job = sa_session.get(app.model.Job, app.security.decode_id(job_dict["id"]))
self._wait_for_external_state(sa_session, job, app.model.Job.states.RUNNING)
assert not job.finished
@@ -306,8 +306,8 @@ class TestKubernetesIntegration(BaseJobEnvironmentIntegrationTestCase, MulledJob
job_dict = running_response.json()["jobs"][0]
app = self._app
sa_session = app.model.context.current
job = sa_session.query(app.model.Job).get(app.security.decode_id(job_dict["id"]))
sa_session = app.model.session
job = sa_session.get(app.model.Job, app.security.decode_id(job_dict["id"]))
self._wait_for_external_state(sa_session, job, app.model.Job.states.RUNNING)
@@ -340,8 +340,8 @@ class TestKubernetesIntegration(BaseJobEnvironmentIntegrationTestCase, MulledJob
# check that logs are also available in job logs
app = self._app
job_id = app.security.decode_id(running_response.json()["jobs"][0]["id"])
sa_session = app.model.context
job = sa_session.query(app.model.Job).get(job_id)
sa_session = app.model.session
job = sa_session.get(app.model.Job, job_id)
self._wait_for_external_state(sa_session=sa_session, job=job, expected=app.model.Job.states.RUNNING)
external_id = job.job_runner_external_id
test/integration/test_local_job_cancellation.py
+16 -12
View File
@@ -3,6 +3,7 @@
import time
import psutil
from sqlalchemy import select
from galaxy.model.base import transaction
from galaxy_test.base.populators import DatasetPopulator
@@ -43,13 +44,12 @@ class TestLocalJobCancellation(CancelsJob, integration_util.IntegrationTestCase)
with self.dataset_populator.test_history() as history_id:
job_id = self._setup_cat_data_and_sleep(history_id)
self._wait_for_job_running(job_id)
app = self._app
sa_session = app.model.context.current
Job = app.model.Job
job = sa_session.query(Job).filter_by(tool_id="cat_data_and_sleep").order_by(Job.create_time.desc()).first()
sa_session = self._app.model.session
Job = self._app.model.Job
job = self._get_job_by_tool("cat_data_and_sleep")
# This is how the admin controller code cancels a job
job.job_stderr = "admin cancelled job"
job.set_state(app.model.Job.states.DELETING)
job.set_state(Job.states.DELETING)
sa_session.add(job)
with transaction(sa_session):
sa_session.commit()
@@ -64,17 +64,16 @@ class TestLocalJobCancellation(CancelsJob, integration_util.IntegrationTestCase)
with self.dataset_populator.test_history() as history_id:
job_id = self._setup_cat_data_and_sleep(history_id)
app = self._app
sa_session = app.model.context.current
sa_session = self._app.model.session
external_id = None
state = False
Job = app.model.Job
Job = self._app.model.Job
job = sa_session.query(Job).filter_by(tool_id="cat_data_and_sleep").order_by(Job.create_time.desc()).first()
job = self._get_job_by_tool("cat_data_and_sleep")
# Not checking the state here allows the change from queued to running to overwrite
# the change from queued to deleted_new in the API thread - this is a problem because
# the job will still run. See issue https://github.com/galaxyproject/galaxy/issues/4960.
while external_id is None or state != app.model.Job.states.RUNNING:
while external_id is None or state != Job.states.RUNNING:
sa_session.refresh(job)
assert not job.finished
external_id = job.job_runner_external_id
@@ -94,7 +93,7 @@ class TestLocalJobCancellation(CancelsJob, integration_util.IntegrationTestCase)
for _ in range(100):
sa_session.refresh(job)
state = job.state
if state == app.model.Job.states.DELETED:
if state == Job.states.DELETED:
break
time.sleep(0.1)
@@ -106,5 +105,10 @@ class TestLocalJobCancellation(CancelsJob, integration_util.IntegrationTestCase)
time.sleep(0.1)
final_state = f"pid exists? {pid_exists}, final db job state {state}"
assert state == app.model.Job.states.DELETED, final_state
assert state == Job.states.DELETED, final_state
assert not pid_exists, final_state
def _get_job_by_tool(self, tool_id):
model = self._app.model
stmt = select(model.Job).filter_by(tool_id=tool_id).order_by(model.Job.create_time.desc()).limit(1)
return model.session.scalars(stmt).first()
test/integration/test_page_revision_json_encoding.py
+6 -4
View File
@@ -5,6 +5,8 @@ the security parameter to encode IDs may be changed by admins). Test case also v
exported API values are encoded though.
"""
from sqlalchemy import select
from galaxy import model
from galaxy_test.base import api_asserts
from galaxy_test.base.populators import DatasetPopulator
@@ -26,8 +28,8 @@ class TestPageJsonEncodingIntegration(integration_util.IntegrationTestCase):
)
page_response = self._post("pages", request, json=True)
api_asserts.assert_status_code_is_ok(page_response)
sa_session = self._app.model.context
page_revision = sa_session.query(model.PageRevision).filter_by(content_format="html").all()[0]
sa_session = self._app.model.session
page_revision = sa_session.scalars(select(model.PageRevision).filter_by(content_format="html")).all()[0]
assert '''id="History-1"''' in page_revision.content, page_revision.content
assert f'''id="History-{history_id}"''' not in page_revision.content, page_revision.content
@@ -52,8 +54,8 @@ history_dataset_display(history_dataset_id={})
)
page_response = self._post("pages", request, json=True)
api_asserts.assert_status_code_is_ok(page_response)
sa_session = self._app.model.context
page_revision = sa_session.query(model.PageRevision).filter_by(content_format="markdown").all()[0]
sa_session = self._app.model.session
page_revision = sa_session.scalars(select(model.PageRevision).filter_by(content_format="markdown")).all()[0]
assert (
"""```galaxy
history_dataset_display(history_dataset_id=1)
test/integration/test_repository_operations.py
+3 -1
View File
@@ -1,6 +1,8 @@
import os
from collections import namedtuple
from sqlalchemy import select
from galaxy.model.base import transaction
from galaxy_test.base.populators import DatasetPopulator
from galaxy_test.driver import integration_util
@@ -86,7 +88,7 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
hg_util.update_repository(repository_path, ctx_rev="3")
# change repo to revision 3 in database
model = self._app.install_model
tsr = model.context.query(model.ToolShedRepository).first()
tsr = model.session.scalars(select(model.ToolShedRepository).limit(1)).first()
assert tsr.name == REPO.name
assert tsr.changeset_revision == latest_revision
assert int(tsr.ctx_rev) >= 4
test/integration/test_save_job_id_on_datasets.py
+3 -2
View File
@@ -8,6 +8,7 @@ Here we test the creation of this reference in various contexts:
"""
import pytest
from sqlalchemy import select
from galaxy import model
from galaxy_test.driver.driver_util import GalaxyTestDriver
@@ -39,8 +40,8 @@ def test_driver():
def test_tool_datasets(tool_id, test_driver):
test_driver.run_tool_test(tool_id)
session = test_driver.app.model.context.current
job = session.query(model.Job).order_by(model.Job.id.desc()).first()
datasets = session.query(model.Dataset).filter(model.Dataset.job_id == job.id).all()
job = session.scalars(select(model.Job).order_by(model.Job.id.desc()).limit(1)).first()
datasets = session.scalars(select(model.Dataset).filter(model.Dataset.job_id == job.id)).all()
if tool_id == "boolean_conditional":
assert len(datasets) == 1
test/integration/test_user_preferences.py
+3 -1
View File
@@ -7,6 +7,7 @@ from requests import (
get,
put,
)
from sqlalchemy import select
from galaxy_test.driver import integration_util
@@ -18,7 +19,8 @@ class TestUserPreferences(integration_util.IntegrationTestCase):
user = self._setup_user(TEST_USER_EMAIL)
url = self._api_url(f"users/{user['id']}/theme/test_theme", params=dict(key=self.master_api_key))
app = cast(Any, self._test_driver.app if self._test_driver else None)
db_user = app.model.context.query(app.model.User).filter(app.model.User.email == user["email"]).first()
stmt = select(app.model.User).filter(app.model.User.email == user["email"]).limit(1)
db_user = app.model.session.scalars(stmt).first()
# create some initial data
put(url)
test/integration/test_vault_extra_prefs.py
+7 -2
View File
@@ -9,6 +9,7 @@ from requests import (
get,
put,
)
from sqlalchemy import select
from galaxy_test.driver import integration_util
@@ -28,7 +29,7 @@ class TestExtraUserPreferences(integration_util.IntegrationTestCase, integration
user = self._setup_user(TEST_USER_EMAIL)
url = self.__url("information/inputs", user)
app = cast(Any, self._test_driver.app if self._test_driver else None)
db_user = app.model.context.query(app.model.User).filter(app.model.User.email == user["email"]).first()
db_user = self._get_dbuser(app, user)
# create some initial data
put(
@@ -84,7 +85,7 @@ class TestExtraUserPreferences(integration_util.IntegrationTestCase, integration
user = self._setup_user(TEST_USER_EMAIL)
url = self.__url("information/inputs", user)
app = cast(Any, self._test_driver.app if self._test_driver else None)
db_user = app.model.context.query(app.model.User).filter(app.model.User.email == user["email"]).first()
db_user = self._get_dbuser(app, user)
# write the initial secret value
put(
@@ -130,3 +131,7 @@ class TestExtraUserPreferences(integration_util.IntegrationTestCase, integration
def __url(self, action, user):
return self._api_url(f"users/{user['id']}/{action}", params=dict(key=self.master_api_key))
def _get_dbuser(self, app, user):
stmt = select(app.model.User).filter(app.model.User.email == user["email"]).limit(1)
return app.model.session.scalars(stmt).first()
test/integration/test_vault_file_source.py
+18 -32
View File
@@ -1,6 +1,8 @@
import os
import tempfile
from sqlalchemy import select
from galaxy.security.vault import UserVaultWrapper
from galaxy_test.base import api_asserts
from galaxy_test.base.populators import DatasetPopulator
@@ -31,14 +33,11 @@ class TestVaultFileSourceIntegration(integration_util.IntegrationTestCase, integ
This file source performs a user vault lookup. The secret stored for the first user is a
valid path and should succeed, while the second user's stored secret should fail.
"""
app = self._app
with self._different_user(email=self.USER_1_APP_VAULT_ENTRY):
app = self._app
user = (
app.model.context.query(app.model.User)
.filter(app.model.User.email == self.USER_1_APP_VAULT_ENTRY)
.first()
)
user_vault = UserVaultWrapper(self._app.vault, user)
user = self._get_user_by_email(self.USER_1_APP_VAULT_ENTRY)
user_vault = UserVaultWrapper(app.vault, user)
# use a valid symlink path so the posix list succeeds
user_vault.write_secret("posix/root_path", app.config.user_library_import_symlink_allowlist[0])
@@ -49,13 +48,8 @@ class TestVaultFileSourceIntegration(integration_util.IntegrationTestCase, integ
print(remote_files)
with self._different_user(email=self.USER_2_APP_VAULT_ENTRY):
app = self._app
user = (
app.model.context.query(app.model.User)
.filter(app.model.User.email == self.USER_2_APP_VAULT_ENTRY)
.first()
)
user_vault = UserVaultWrapper(self._app.vault, user)
user = self._get_user_by_email(self.USER_2_APP_VAULT_ENTRY)
user_vault = UserVaultWrapper(app.vault, user)
# use an invalid symlink path so the posix list fails
user_vault.write_secret("posix/root_path", "/invalid/root")
@@ -75,12 +69,8 @@ class TestVaultFileSourceIntegration(integration_util.IntegrationTestCase, integ
app.vault.write_secret("posix/root_path", app.config.user_library_import_symlink_allowlist[0])
with self._different_user(email=self.USER_1_APP_VAULT_ENTRY):
user = (
app.model.context.query(app.model.User)
.filter(app.model.User.email == self.USER_1_APP_VAULT_ENTRY)
.first()
)
user_vault = UserVaultWrapper(self._app.vault, user)
user = self._get_user_by_email(self.USER_1_APP_VAULT_ENTRY)
user_vault = UserVaultWrapper(app.vault, user)
# use a valid symlink path so the posix list succeeds
user_vault.write_secret("posix/root_path", app.config.user_library_import_symlink_allowlist[0])
@@ -91,12 +81,8 @@ class TestVaultFileSourceIntegration(integration_util.IntegrationTestCase, integ
print(remote_files)
with self._different_user(email=self.USER_2_APP_VAULT_ENTRY):
user = (
app.model.context.query(app.model.User)
.filter(app.model.User.email == self.USER_2_APP_VAULT_ENTRY)
.first()
)
user_vault = UserVaultWrapper(self._app.vault, user)
user = self._get_user_by_email(self.USER_2_APP_VAULT_ENTRY)
user_vault = UserVaultWrapper(app.vault, user)
# use an invalid symlink path so the posix list would fail if used
user_vault.write_secret("posix/root_path", "/invalid/root")
@@ -109,12 +95,8 @@ class TestVaultFileSourceIntegration(integration_util.IntegrationTestCase, integ
def test_upload_file_from_remote_source(self):
with self._different_user(email=self.USER_1_APP_VAULT_ENTRY):
app = self._app
user = (
app.model.context.query(app.model.User)
.filter(app.model.User.email == self.USER_1_APP_VAULT_ENTRY)
.first()
)
user_vault = UserVaultWrapper(self._app.vault, user)
user = self._get_user_by_email(self.USER_1_APP_VAULT_ENTRY)
user_vault = UserVaultWrapper(app.vault, user)
# use a valid symlink path so the posix list succeeds
user_vault.write_secret("posix/root_path", app.config.user_library_import_symlink_allowlist[0])
data = {"target": "gxfiles://test_user_vault"}
@@ -138,3 +120,7 @@ class TestVaultFileSourceIntegration(integration_util.IntegrationTestCase, integ
new_dataset = self.dataset_populator.fetch(payload, assert_ok=True).json()["outputs"][0]
content = self.dataset_populator.get_history_dataset_content(history_id, dataset=new_dataset)
assert content == "I require access to the vault", content
def _get_user_by_email(self, email):
stmt = select(self._app.model.User).filter(self._app.model.User.email == email).limit(1)
return self._app.model.session.scalars(stmt).first()
test/integration/test_workflow_handler_configuration.py
+1 -2
View File
@@ -127,8 +127,7 @@ class BaseWorkflowHandlerConfigurationTestCase(integration_util.IntegrationTestC
# into Galaxy's internal state.
app = self._app
history_id = app.security.decode_id(history_id)
sa_session = app.model.context.current
history = sa_session.query(app.model.History).get(history_id)
history = app.model.session.get(app.model.History, history_id)
workflow_invocations = history.workflow_invocations
return workflow_invocations
test/integration/test_workflow_refactoring.py
+10 -4
View File
@@ -6,6 +6,8 @@ from typing import (
List,
)
from sqlalchemy import select
from galaxy.managers.context import ProvidesAppContext
from galaxy.managers.workflows import RefactorRequest
from galaxy.model import (
@@ -767,7 +769,8 @@ steps:
yield workflow_object
def _refactor(self, actions: List[Dict[str, Any]], stored_workflow=None, dry_run=False, style="ga"):
user = self._app.model.session.query(User).order_by(User.id.desc()).limit(1).one()
stmt = select(User).order_by(User.id.desc()).limit(1)
user = self._app.model.session.execute(stmt).scalar_one()
mock_trans = MockTrans(self._app, user)
app = self._app
@@ -818,11 +821,13 @@ steps:
return response
def _model_last_time(self, clazz):
obj = self._app.model.session.query(clazz).order_by(clazz.update_time.desc()).limit(1).one()
stmt = select(clazz).order_by(clazz.update_time.desc()).limit(1)
obj = self._app.model.session.execute(stmt).unique().scalar_one()
return obj.update_time
def _model_last_id(self, clazz):
obj = self._app.model.session.query(clazz).order_by(clazz.id.desc()).limit(1).one_or_none()
stmt = select(clazz).order_by(clazz.id.desc()).limit(1)
obj = self._app.model.session.execute(stmt).scalar_one_or_none()
return obj.id if obj else None
@property
@@ -835,7 +840,8 @@ steps:
def _recent_stored_workflow(self, n=1):
app = self._app
return app.model.session.query(StoredWorkflow).order_by(StoredWorkflow.id.desc()).limit(n).all()[-1]
stmt = select(StoredWorkflow).order_by(StoredWorkflow.id.desc()).limit(n)
return app.model.session.scalars(stmt).unique().all()[-1]
@property
def _latest_workflow(self):
test/unit/app/managers/test_DatasetManager.py
+3 -14
View File
@@ -3,6 +3,7 @@
from unittest import mock
import sqlalchemy
from sqlalchemy import select
from galaxy import (
exceptions,
@@ -32,14 +33,14 @@ class TestDatasetManager(BaseTestCase):
self.log("should be able to create a new Dataset")
dataset1 = self.dataset_manager.create()
assert isinstance(dataset1, model.Dataset)
assert dataset1 == self.trans.sa_session.query(model.Dataset).get(dataset1.id)
assert dataset1 == self.trans.sa_session.get(model.Dataset, dataset1.id)
def test_base(self):
dataset1 = self.dataset_manager.create()
dataset2 = self.dataset_manager.create()
self.log("should be able to query")
datasets = self.trans.sa_session.query(model.Dataset).all()
datasets = self.trans.sa_session.scalars(select(model.Dataset)).all()
assert self.dataset_manager.list() == datasets
assert self.dataset_manager.one(filters=(model.Dataset.id == dataset1.id)) == dataset1
assert self.dataset_manager.by_id(dataset1.id) == dataset1
@@ -187,18 +188,6 @@ class TestDatasetManager(BaseTestCase):
assert not self.dataset_manager.permissions.access.is_permitted(dataset, None)
# class TestDatasetRBACPermissions(BaseTestCase):
# def set_up_managers(self):
# super().set_up_managers()
# self.dataset_manager = DatasetManager(self.app)
#
# def test_manage( self ):
# self.log("should be able to create a new Dataset")
# dataset1 = self.dataset_manager.create()
# assert isinstance(dataset1, model.Dataset)
# assert dataset1 == self.app.model.context.query(model.Dataset).get(dataset1.id)
# web.url_for doesn't work well in the framework
def testable_url_for(*a, **k):
return f"(fake url): {a}, {k}"
test/unit/app/managers/test_HDAManager.py
+4 -3
View File
@@ -1,6 +1,7 @@
from unittest import mock
import sqlalchemy
from sqlalchemy import select
from galaxy import (
exceptions,
@@ -44,7 +45,7 @@ class TestHDAManager(HDATestCase):
hda3 = self.hda_manager.create(history=history1, hid=3)
self.log("should be able to query")
hdas = self.trans.sa_session.query(hda_model).all()
hdas = self.trans.sa_session.scalars(select(hda_model)).all()
assert self.hda_manager.list() == hdas
assert self.hda_manager.one(filters=(hda_model.id == hda1.id)) == hda1
assert self.hda_manager.by_id(hda1.id) == hda1
@@ -70,7 +71,7 @@ class TestHDAManager(HDATestCase):
self.log("should be able to create a new HDA with a specified history and dataset")
hda1 = self.hda_manager.create(history=history1, dataset=dataset1)
assert isinstance(hda1, model.HistoryDatasetAssociation)
assert hda1 == self.trans.sa_session.query(model.HistoryDatasetAssociation).get(hda1.id)
assert hda1 == self.trans.sa_session.get(model.HistoryDatasetAssociation, hda1.id)
assert hda1.history == history1
assert hda1.dataset == dataset1
assert hda1.hid == 1
@@ -121,7 +122,7 @@ class TestHDAManager(HDATestCase):
self.log("should be able to copy an HDA")
hda2 = self.hda_manager.copy(hda1, history=history1)
assert isinstance(hda2, model.HistoryDatasetAssociation)
assert hda2 == self.trans.sa_session.query(model.HistoryDatasetAssociation).get(hda2.id)
assert hda2 == self.trans.sa_session.get(model.HistoryDatasetAssociation, hda2.id)
assert hda2.name == hda1.name
assert hda2.history == hda1.history
assert hda2.dataset == hda1.dataset
test/unit/app/managers/test_HistoryManager.py
+14 -5
View File
@@ -4,6 +4,7 @@ import pytest
import sqlalchemy
from sqlalchemy import (
false,
select,
true,
)
@@ -51,14 +52,22 @@ class TestHistoryManager(BaseTestCase):
assert isinstance(history1, model.History)
assert history1.name == "history1"
assert history1.user == user2
assert history1 == self.trans.sa_session.query(model.History).get(history1.id)
assert history1 == self.trans.sa_session.query(model.History).filter(model.History.name == "history1").one()
assert history1 == self.trans.sa_session.query(model.History).filter(model.History.user == user2).one()
assert history1 == self.trans.sa_session.get(model.History, history1.id)
assert (
history1
== self.trans.sa_session.execute(
select(model.History).filter(model.History.name == "history1")
).scalar_one()
)
assert (
history1
== self.trans.sa_session.execute(select(model.History).filter(model.History.user == user2)).scalar_one()
)
history2 = self.history_manager.copy(history1, user=user3)
self.log("should be able to query")
histories = self.trans.sa_session.query(model.History).all()
histories = self.trans.sa_session.scalars(select(model.History)).all()
assert self.history_manager.one(filters=(model.History.id == history1.id)) == history1
assert self.history_manager.list() == histories
assert self.history_manager.by_id(history1.id) == history1
@@ -97,7 +106,7 @@ class TestHistoryManager(BaseTestCase):
history2 = self.history_manager.copy(history1, user=user3)
assert isinstance(history2, model.History)
assert history2.user == user3
assert history2 == self.trans.sa_session.query(model.History).get(history2.id)
assert history2 == self.trans.sa_session.get(model.History, history2.id)
assert history2.name == history1.name
assert history2 != history1
test/unit/app/managers/test_UserManager.py
+5 -2
View File
@@ -6,7 +6,10 @@ Executable directly using: python -m test.unit.managers.test_UserManager
from datetime import datetime
from unittest.mock import patch
from sqlalchemy import desc
from sqlalchemy import (
desc,
select,
)
from galaxy import (
exceptions,
@@ -47,7 +50,7 @@ class TestUserManager(BaseTestCase):
user3 = self.user_manager.create(**user3_data)
self.log("should be able to query")
users = self.trans.sa_session.query(model.User).all()
users = self.trans.sa_session.scalars(select(model.User)).all()
assert self.user_manager.list() == users
assert self.user_manager.by_id(user2.id) == user2
test/unit/app/tools/test_execution.py
+2 -1
View File
@@ -4,6 +4,7 @@ from collections import OrderedDict
from typing import cast
import webob.exc
from sqlalchemy import select
import galaxy.model
from galaxy.app_unittest_utils import tools_support
@@ -198,7 +199,7 @@ class MockTrans:
self.user = None
self.history._active_datasets_and_roles = [
hda
for hda in self.app.model.context.query(galaxy.model.HistoryDatasetAssociation).all()
for hda in self.app.model.session.scalars(select(galaxy.model.HistoryDatasetAssociation)).all()
if hda.active and hda.history == history
]
self.workflow_building_mode = False
test/unit/app/tools/test_history_imp_exp.py
+4 -1
View File
@@ -5,6 +5,8 @@ import tempfile
from shutil import rmtree
from unittest.mock import Mock
from sqlalchemy import select
from galaxy import model
from galaxy.app_unittest_utils.galaxy_mock import MockApp
from galaxy.exceptions import MalformedContents
@@ -704,7 +706,8 @@ def test_import_1901_default():
# There was a deleted dataset so skip to 3
assert dataset1.hid == 3, dataset1.hid
jobs = app.model.context.query(model.Job).filter_by(history_id=new_history.id).order_by(model.Job.table.c.id).all()
stmt = select(model.Job).filter_by(history_id=new_history.id).order_by(model.Job.id)
jobs = app.model.session.scalars(stmt).all()
assert len(jobs) == 2
assert jobs[0].tool_id == "upload1"
assert jobs[1].tool_id == "cat"
test/unit/data/model/test_model_discovery.py
+3 -1
View File
@@ -1,6 +1,8 @@
import os
from tempfile import mkdtemp
from sqlalchemy import select
from galaxy import model
from galaxy.model import store
from galaxy.model.base import transaction
@@ -211,7 +213,7 @@ def test_persist_target_hdca():
def _assert_one_library_created(sa_session):
all_libraries = sa_session.query(model.Library).all()
all_libraries = sa_session.scalars(select(model.Library)).all()
assert len(all_libraries) == 1, len(all_libraries)
new_library = all_libraries[0]
return new_library
test/unit/data/model/test_model_store.py
+5 -4
View File
@@ -16,6 +16,7 @@ from typing import (
import pytest
from rocrate.rocrate import ROCrate
from sqlalchemy import select
from sqlalchemy.orm.scoping import scoped_session
from galaxy import model
@@ -195,9 +196,9 @@ def test_import_library_from_dict():
perform_import_from_store_dict(fixture_context, import_dict, import_options=import_options)
sa_session = fixture_context.sa_session
all_libraries = sa_session.query(model.Library).all()
all_libraries = sa_session.scalars(select(model.Library)).all()
assert len(all_libraries) == 1, len(all_libraries)
all_lddas = sa_session.query(model.LibraryDatasetDatasetAssociation).all()
all_lddas = sa_session.scalars(select(model.LibraryDatasetDatasetAssociation)).all()
assert len(all_lddas) == 1, len(all_lddas)
@@ -308,9 +309,9 @@ def test_import_export_library():
)
import_model_store.perform_import()
all_libraries = sa_session.query(model.Library).all()
all_libraries = sa_session.scalars(select(model.Library)).all()
assert len(all_libraries) == 2, len(all_libraries)
all_lddas = sa_session.query(model.LibraryDatasetDatasetAssociation).all()
all_lddas = sa_session.scalars(select(model.LibraryDatasetDatasetAssociation)).all()
assert len(all_lddas) == 2, len(all_lddas)
new_library = [lib for lib in all_libraries if lib.id != library.id][0]
test/unit/data/test_dataset_materialization.py
+2 -1
View File
@@ -1,4 +1,5 @@
from pkg_resources import resource_string
from sqlalchemy import select
from galaxy.files.unittest_utils import TestPosixConfiguredFileSources
from galaxy.model import (
@@ -154,7 +155,7 @@ def test_deferred_ldda_basic_attached():
fixture_context = setup_fixture_context_with_history()
store_dict = one_ld_library_deferred_model_store_dict()
perform_import_from_store_dict(fixture_context, store_dict, import_options=import_options)
deferred_ldda = fixture_context.sa_session.query(LibraryDatasetDatasetAssociation).all()[0]
deferred_ldda = fixture_context.sa_session.scalars(select(LibraryDatasetDatasetAssociation)).all()[0]
assert deferred_ldda
assert deferred_ldda.dataset.state == "deferred"
test/unit/data/test_galaxy_mapping.py
+23 -29
View File
@@ -53,10 +53,6 @@ class BaseModelTestCase(TestCase):
cls.model = mapping.init("/tmp", cls._db_uri(), create_tables=True, object_store=MockObjectStore())
assert cls.model.engine is not None
@classmethod
def query(cls, type):
return cls.model.session.query(type)
@classmethod
def persist(cls, *args, **kwargs):
session = cls.session()
@@ -90,7 +86,7 @@ class TestMappings(BaseModelTestCase):
rating_association = rating_class(u, item, rating)
self.persist(rating_association)
self.expunge()
stored_rating = self.query(rating_class).all()[0]
stored_rating = self.model.session.scalars(select(rating_class)).all()[0]
assert stored_rating.rating == rating
assert stored_rating.user.email == user_email
@@ -329,12 +325,12 @@ class TestMappings(BaseModelTestCase):
self.persist(u, h1, d1, d2, c1, hc1, dce1, dce2)
loaded_dataset_collection = (
self.query(model.HistoryDatasetCollectionAssociation)
stmt = (
select(model.HistoryDatasetCollectionAssociation)
.filter(model.HistoryDatasetCollectionAssociation.name == "HistoryCollectionTest1")
.first()
.collection
.limit(1)
)
loaded_dataset_collection = self.model.session.scalars(stmt).first().collection
assert len(loaded_dataset_collection.elements) == 2
assert loaded_dataset_collection.collection_type == "pair"
assert loaded_dataset_collection["left"] == dce1
@@ -502,11 +498,11 @@ class TestMappings(BaseModelTestCase):
u.adjust_total_disk_usage(1, None)
u_id = u.id
self.expunge()
user_reload = self.model.session.query(model.User).get(u_id)
user_reload = self.model.session.get(model.User, u_id)
assert user_reload.disk_usage == 1
def test_basic(self):
original_user_count = len(self.model.session.query(model.User).all())
original_user_count = len(self.model.session.scalars(select(model.User)).all())
# Make some changes and commit them
u = model.User(email="james@foo.bar.baz", password="password")
@@ -520,14 +516,14 @@ class TestMappings(BaseModelTestCase):
self.persist(d1)
# Check
users = self.model.session.query(model.User).all()
users = self.model.session.scalars(select(model.User)).all()
assert len(users) == original_user_count + 1
user = [user for user in users if user.email == "james@foo.bar.baz"][0]
assert user.email == "james@foo.bar.baz"
assert user.password == "password"
assert len(user.histories) == 1
assert user.histories[0].name == "History 1"
hists = self.model.session.query(model.History).all()
hists = self.model.session.scalars(select(model.History)).all()
hist0 = [history for history in hists if history.id == h1.id][0]
hist1 = [history for history in hists if history.id == h2.id][0]
assert hist0.name == "History 1"
@@ -541,7 +537,7 @@ class TestMappings(BaseModelTestCase):
# Do an update and check
hist1.name = "History 2b"
self.expunge()
hists = self.model.session.query(model.History).all()
hists = self.model.session.scalars(select(model.History)).all()
hist0 = [history for history in hists if history.name == "History 1"][0]
hist1 = [history for history in hists if history.name == "History 2b"][0]
assert hist0.name == "History 1"
@@ -560,7 +556,9 @@ class TestMappings(BaseModelTestCase):
job = model.Job()
dataset.job = job
self.persist(job, dataset)
loaded_dataset = self.model.session.query(model.Dataset).filter(model.Dataset.id == dataset.id).one()
loaded_dataset = self.model.session.execute(
select(model.Dataset).filter(model.Dataset.id == dataset.id)
).scalar_one()
assert loaded_dataset.job_id == job.id
def test_jobs(self):
@@ -571,7 +569,7 @@ class TestMappings(BaseModelTestCase):
self.persist(u, job)
loaded_job = self.model.session.query(model.Job).filter(model.Job.user == u).first()
loaded_job = self.model.session.scalars(select(model.Job).filter(model.Job.user == u).limit(1)).first()
assert loaded_job.tool_id == "cat1"
def test_job_metrics(self):
@@ -602,7 +600,7 @@ class TestMappings(BaseModelTestCase):
job.user = u
self.persist(u, job, task)
loaded_task = self.model.session.query(model.Task).filter(model.Task.job == job).first()
loaded_task = self.model.session.scalars(select(model.Task).filter(model.Task.job == job).limit(1)).first()
assert loaded_task.prepare_input_files_cmd == "split.sh"
def test_history_contents(self):
@@ -620,9 +618,9 @@ class TestMappings(BaseModelTestCase):
self.session().flush()
def contents_iter_names(**kwds):
history = (
self.model.context.query(model.History).filter(model.History.name == "HistoryContentsHistory1").first()
)
history = self.model.session.scalars(
select(model.History).filter(model.History.name == "HistoryContentsHistory1").limit(1)
).first()
return list(map(lambda hda: hda.name, history.contents_iter(**kwds)))
assert contents_iter_names() == ["1", "2", "3", "4"]
@@ -645,12 +643,8 @@ class TestMappings(BaseModelTestCase):
h2 = model.History(name="HistoryAuditHistory", user=u)
def get_audit_table_entries(history):
return (
self.session()
.query(model.HistoryAudit.table)
.filter(model.HistoryAudit.table.c.history_id == history.id)
.all()
)
stmt = select(model.HistoryAudit.table).filter(model.HistoryAudit.table.c.history_id == history.id)
return self.session().execute(stmt).all()
def get_latest_entry(entries):
# key ensures result is correct if new columns are added
@@ -713,7 +707,7 @@ class TestMappings(BaseModelTestCase):
self.expunge()
session = self.session()
galaxy_model_object = self.query(model.GalaxySession).get(galaxy_session_id)
galaxy_model_object = self.model.session.get(model.GalaxySession, galaxy_session_id)
expected_id = galaxy_model_object.id
# id loaded as part of the object query, could be any non-deferred attribute.
@@ -841,7 +835,7 @@ class TestMappings(BaseModelTestCase):
history_id = h1.id
self.expunge()
loaded_invocation = self.query(model.WorkflowInvocation).get(workflow_invocation.id)
loaded_invocation = self.model.session.get(model.WorkflowInvocation, workflow_invocation.id)
assert loaded_invocation.uuid == invocation_uuid, f"{loaded_invocation.uuid} != {invocation_uuid}"
assert loaded_invocation
assert loaded_invocation.history.id == history_id
@@ -859,7 +853,7 @@ class TestMappings(BaseModelTestCase):
assert subworkflow_invocation_assoc.subworkflow_invocation.history.id == history_id
loaded_workflow = self.query(model.Workflow).get(workflow_id)
loaded_workflow = self.model.session.get(model.Workflow, workflow_id)
assert len(loaded_workflow.steps[0].annotations) == 1
copied_workflow = loaded_workflow.copy(user=user)
annotations = copied_workflow.steps[0].annotations
test/unit/data/test_mutable_json_column.py
+1 -1
View File
@@ -12,7 +12,7 @@ class TestMutableColumn(BaseModelTestCase):
with transaction(session):
session.commit()
self.model.session.expunge_all()
return self.model.session.query(model.DynamicTool).get(item_id)
return self.model.session.get(model.DynamicTool, item_id)
def test_metadata_mutable_column(self):
w = model.DynamicTool()
test/unit/test_galaxy_transactions.py
+7 -6
View File
@@ -1,4 +1,5 @@
import pytest
from sqlalchemy import select
from galaxy import model
from galaxy.managers import context
@@ -36,26 +37,26 @@ def transaction():
def test_logging_events_off(transaction):
transaction.log_event("test event 123")
assert len(transaction.sa_session.query(model.Event).all()) == 0
assert len(transaction.sa_session.scalars(select(model.Event)).all()) == 0
def test_logging_events_on(transaction):
transaction.app.config.log_events = True
transaction.log_event("test event 123")
events = transaction.sa_session.query(model.Event).all()
events = transaction.sa_session.scalars(select(model.Event)).all()
assert len(events) == 1
assert events[0].message == "test event 123"
def test_logging_actions_off(transaction):
transaction.log_action("test action 123")
assert len(transaction.sa_session.query(model.Event).all()) == 0
assert len(transaction.sa_session.scalars(select(model.Event)).all()) == 0
def test_logging_actions_on(transaction):
transaction.app.config.log_actions = True
transaction.log_action(None, "test action 123", context="the context", params=dict(foo="bar"))
actions = transaction.sa_session.query(model.UserAction).all()
actions = transaction.sa_session.scalars(select(model.UserAction)).all()
assert len(actions) == 1
assert actions[0].action == "test action 123"
@@ -69,7 +70,7 @@ def test_expunge_all(transaction):
with db_transaction(session):
session.commit()
assert transaction.sa_session.query(model.User).first().password == "bar2"
assert transaction.sa_session.scalars(select(model.User).limit(1)).first().password == "bar2"
transaction.sa_session.expunge_all()
@@ -79,4 +80,4 @@ def test_expunge_all(transaction):
session.commit()
# Password unchange because not attached to session/context.
assert transaction.sa_session.query(model.User).first().password == "bar2"
assert transaction.sa_session.scalars(select(model.User).limit(1)).first().password == "bar2"
test/unit/workflows/test_run_parameters.py
+1 -1
View File
@@ -124,4 +124,4 @@ def __workflow_fixure(trans):
workflow_id = workflow.id
trans.app.model.context.expunge_all()
return trans.app.model.context.query(model.Workflow).get(workflow_id)
return trans.app.model.session.get(model.Workflow, workflow_id)