Fix unit tests

test/unit/app/jobs/test_job_context.py

@@ -46,7 +46,7 @@ def test_job_context_discover_outputs_flushes_once(mocker):
     sa_session = app.model.context
     # mocker is a pytest-mock fixture
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
     h = model.History(name="Test History", user=u)
 
     tool = Tool(app)

test/unit/app/jobs/test_rule_helper.py

@@ -64,9 +64,9 @@ def __setup_fixtures(app):
     # user1 has 3 jobs queued and 2 jobs running on cluster1 and one queued and
     # on running job on local. user2 has a queued and running job on the cluster.
     # user3 has no jobs.
-    user1 = model.User(email=USER_EMAIL_1, password="pass1")
-    user2 = model.User(email=USER_EMAIL_2, password="pass2")
-    user3 = model.User(email=USER_EMAIL_2, password="pass2")
+    user1 = model.User(email=USER_EMAIL_1, password="pass1", username="u1")
+    user2 = model.User(email=USER_EMAIL_2, password="pass2", username="u2")
+    user3 = model.User(email=USER_EMAIL_2, password="pass2", username="u3")
 
     app.add(user1, user2, user3)
 

test/unit/app/managers/test_JobConnectionsManager.py

@@ -3,6 +3,8 @@
 
 from galaxy.managers.job_connections import JobConnectionsManager
 from galaxy.model import (
+    DatasetCollection,
+    History,
     HistoryDatasetAssociation,
     HistoryDatasetCollectionAssociation,
     Job,
@@ -25,11 +27,19 @@ def job_connections_manager(sa_session) -> JobConnectionsManager:
 
 # =============================================================================
 def setup_connected_dataset(sa_session: galaxy_scoped_session):
+    history = History()
+    sa_session.add(history)
     center_hda = HistoryDatasetAssociation(sa_session=sa_session, create_dataset=True)
     input_hda = HistoryDatasetAssociation(sa_session=sa_session, create_dataset=True)
+    input_dc = DatasetCollection(collection_type="list")
     input_hdca = HistoryDatasetCollectionAssociation()
+    input_hdca.collection = input_dc
     output_hda = HistoryDatasetAssociation(sa_session=sa_session, create_dataset=True)
+    output_dc = DatasetCollection(collection_type="list")
     output_hdca = HistoryDatasetCollectionAssociation()
+    output_hdca.collection = output_dc
+    history.stage_addition([center_hda, input_hda, input_hdca, output_hda, output_hdca])
+    history.add_pending_items()
     input_job = Job()
     output_job = Job()
     input_job.add_output_dataset("output_hda", center_hda)
@@ -55,12 +65,22 @@ def setup_connected_dataset(sa_session: galaxy_scoped_session):
 
 
 def setup_connected_dataset_collection(sa_session: galaxy_scoped_session):
+    history = History()
+    sa_session.add(history)
+    center_dc = DatasetCollection(collection_type="list")
     center_hdca = HistoryDatasetCollectionAssociation()
+    center_hdca.collection = center_dc
     input_hda1 = HistoryDatasetAssociation(sa_session=sa_session, create_dataset=True)
     input_hda2 = HistoryDatasetAssociation(sa_session=sa_session, create_dataset=True)
+    input_dc = DatasetCollection(collection_type="list")
     input_hdca = HistoryDatasetCollectionAssociation()
+    input_hdca.collection = input_dc
     output_hda = HistoryDatasetAssociation(sa_session=sa_session, create_dataset=True)
+    output_dc = DatasetCollection(collection_type="list")
     output_hdca = HistoryDatasetCollectionAssociation()
+    output_hdca.collection = output_dc
+    history.stage_addition([center_hdca, input_hda1, input_hda2, input_hdca, output_hda, output_hdca])
+    history.add_pending_items()
     input_job = Job()
     output_job = Job()
     input_job.add_output_dataset_collection("output_hdca", center_hdca)

test/unit/app/tools/test_error_reporting.py

@@ -57,7 +57,7 @@ def test_hda_security(self, tmp_path):
         permissions = {access_action: [private_role], manage_action: [private_role]}
         security_agent.set_all_dataset_permissions(hda.dataset, permissions)
 
-        other_user = model.User(email="[email protected]", password="mockpass2")
+        other_user = model.User(email="[email protected]", password="mockpass2", username="otheruser")
         self._commit_objects([other_user])
         security_agent = self.app.security_agent
         email_path = self.email_path
@@ -125,7 +125,7 @@ def test_no_redact_user_details_in_bugreport(self, tmp_path):
         )
 
     def _setup_model_objects(self):
-        user = model.User(email=TEST_USER_EMAIL, password="mockpass")
+        user = model.User(email=TEST_USER_EMAIL, password="mockpass", username=TEST_USER_EMAIL.split("@")[0])
         job = model.Job()
         job.tool_id = "cat1"
         job.history = model.History()

test/unit/app/tools/test_history_imp_exp.py

@@ -36,7 +36,7 @@ def t_data_path(name):
 def _run_jihaw_cleanup(archive_dir, app=None):
     app = app or _mock_app()
     job = model.Job()
-    job.user = model.User(email="[email protected]", password="test")
+    job.user = model.User(email="[email protected]", password="test", username="test")
     job.tool_stderr = ""
     jiha = model.JobImportHistoryArchive(job=job, archive_dir=archive_dir)
     app.model.context.current.add_all([job, jiha])
@@ -661,7 +661,7 @@ def _setup_history_for_export(history_name):
     sa_session = app.model.context
 
     email = history_name.replace(" ", "-") + "[email protected]"
-    u = model.User(email=email, password="password")
+    u = model.User(email=email, password="password", username=email.split("@")[0])
     h = model.History(name=history_name, user=u)
 
     return app, sa_session, h

test/unit/app/tools/test_toolbox.py

@@ -356,9 +356,7 @@ def __test_workflow(self):
         workflow = model.Workflow()
         workflow.stored_workflow = stored_workflow
         stored_workflow.latest_workflow = workflow
-        user = model.User()
-        user.email = "[email protected]"
-        user.password = "passw0rD1"
+        user = model.User(email="[email protected]", password="passw0rD1", username="test")
         stored_workflow.user = user
         self.app.model.context.add(workflow)
         self.app.model.context.add(stored_workflow)

test/unit/data/model/test_model_discovery.py

@@ -225,7 +225,7 @@ def _import_library_target(target, work_directory):
     with store.DirectoryModelExportStore(temp_directory, app=app, serialize_dataset_objects=True) as export_store:
         persist_target_to_export_store(target, export_store, app.object_store, work_directory)
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="library")
 
     import_options = store.ImportOptions(allow_dataset_object_edit=True, allow_library_creation=True)
     import_model_store = store.get_import_model_store_for_directory(
@@ -240,7 +240,7 @@ def _import_library_target(target, work_directory):
 def _import_directory_to_history(app, target, work_directory):
     sa_session = app.model.context
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
     import_history = model.History(name="Test History for Import", user=u)
 
     sa_session = app.model.context

test/unit/data/model/test_model_store.py

@@ -312,7 +312,7 @@ def test_import_library_require_permissions():
     app = _mock_app()
     sa_session = app.model.context
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
 
     library = model.Library(name="my library 1", description="my library description", synopsis="my synopsis")
     root_folder = model.LibraryFolder(name="my library 1", description="folder description")
@@ -340,7 +340,7 @@ def test_import_export_library():
     app = _mock_app()
     sa_session = app.model.context
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
 
     library = model.Library(name="my library 1", description="my library description", synopsis="my synopsis")
     root_folder = model.LibraryFolder(name="my library 1", description="folder description")
@@ -684,7 +684,7 @@ def test_import_export_edit_collection():
     app = _mock_app()
     sa_session = app.model.context
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
     h = model.History(name="Test History", user=u)
 
     c1 = model.DatasetCollection(collection_type="list", populated=False)
@@ -761,7 +761,7 @@ def test_import_export_composite_datasets():
     app = _mock_app()
     sa_session = app.model.context
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
     h = model.History(name="Test History", user=u)
 
     d1 = _create_datasets(sa_session, h, 1, extension="html")[0]
@@ -804,7 +804,7 @@ def test_edit_metadata_files():
     app = _mock_app(store_by="uuid")
     sa_session = app.model.context
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
     h = model.History(name="Test History", user=u)
 
     d1 = _create_datasets(sa_session, h, 1, extension="bam")[0]
@@ -910,7 +910,7 @@ def _assert_simple_cat_job_imported(imported_history, state="ok"):
 def _setup_simple_cat_job(app, state="ok"):
     sa_session = app.model.context
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
     h = model.History(name="Test History", user=u)
 
     d1, d2 = _create_datasets(sa_session, h, 2)
@@ -966,7 +966,7 @@ def _setup_invocation(app):
 def _setup_simple_collection_job(app, state="ok"):
     sa_session = app.model.context
 
-    u = model.User(email="[email protected]", password="password")
+    u = model.User(email="[email protected]", password="password", username="collection")
     h = model.History(name="Test History", user=u)
 
     d1, d2, d3, d4 = _create_datasets(sa_session, h, 4)
@@ -1170,7 +1170,7 @@ def setup_fixture_context_with_user(
 ) -> StoreFixtureContextWithUser:
     app = _mock_app(store_by=store_by)
     sa_session = app.model.context
-    user = model.User(email=user_email, password="password")
+    user = model.User(email=user_email, password="password", username=user_email.split("@")[0])
     return StoreFixtureContextWithUser(app=app, sa_session=sa_session, user=user)