def setUp(self):
super(HistoryContentsApiTestCase, self).setUp()
self.history_id = self._new_history()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(
self.galaxy_interactor)
self.library_populator = LibraryPopulator(self.galaxy_interactor)
def test_400_on_invalid_embedded_content(self):
dataset_populator = DatasetPopulator(self.galaxy_interactor)
valid_id = dataset_populator.new_history()
page_request = self._test_page_payload(slug="invalid-id-encding")
page_request["content"] = '''<p>Page!<div class="embedded-item" id="CoolObject-%s"></div></p>''' % valid_id
page_response = self._post("pages", page_request)
self._assert_status_code_is(page_response, 400)
self._assert_error_code_is(page_response, error_codes.USER_REQUEST_INVALID_PARAMETER)
assert "embedded HTML content" in page_response.text
def test_recovery(self):
history_id = self.dataset_populator.new_history()
self.dataset_populator.run_tool(
"exit_code_oom",
{},
history_id,
assert_ok=False,
).json()
self.restart(
handle_reconfig=self.handle_reconfigure_galaxy_config_kwds)
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
def test_legacy_r_mapping(self):
"""
"""
tool_id = "legacy_R"
dataset_populator = DatasetPopulator(self.galaxy_interactor)
history_id = dataset_populator.new_history()
endpoint = "tools/%s/install_dependencies" % tool_id
data = {'id': tool_id}
create_response = self._post(endpoint, data=data, admin=True)
self._assert_status_code_is(create_response, 200)
payload = dataset_populator.run_tool_payload(
tool_id=tool_id,
inputs={},
history_id=history_id,
)
create_response = self._post("tools", data=payload)
self._assert_status_code_is(create_response, 200)
dataset_populator.wait_for_history(history_id, assert_ok=True)
def test_runs_on_mule(self):
tool_id = 'config_vars'
expect_server_name = self.expected_server_name
dataset_populator = DatasetPopulator(self.galaxy_interactor)
history_id = dataset_populator.new_history()
payload = dataset_populator.run_tool(
tool_id=tool_id,
inputs={'var': 'server_name'},
history_id=history_id,
)
dataset_id = payload['outputs'][0]['id']
dataset_populator.wait_for_dataset(history_id, dataset_id, assert_ok=True)
output = dataset_populator.get_history_dataset_content(history_id, dataset_id=dataset_id).strip()
assert output.startswith(expect_server_name), (
"Job handler's server name '{output}' does not start with expected string '{expected}'".format(
output=output,
expected=expect_server_name,
)
)
def setUp(self):
super(ObjectStoreJobsIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
with self.dataset_populator.test_history() as history_id:
hda1 = self.dataset_populator.new_dataset(
history_id, content=TEST_INPUT_FILES_CONTENT)
create_10_inputs = {
"input1": {
"src": "hda",
"id": hda1["id"]
},
"input2": {
"src": "hda",
"id": hda1["id"]
},
}
self.dataset_populator.run_tool(
"create_10",
create_10_inputs,
history_id,
assert_ok=True,
)
self.dataset_populator.wait_for_history(history_id)
def setUp(self):
super(ScriptsIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.config_dir = tempfile.mkdtemp()
def setUp(self):
super(DataManagerIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(BaseJobEnvironmentIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(JobRecoveryAfterHandledIntegerationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(ObjectStoreJobsIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(BaseWorkflowHandlerConfigurationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
def setUp(self):
super(BaseUploadContentConfigurationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.library_populator = LibraryPopulator(self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
def setUp(self):
super(DatasetCollectionApiTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(
self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
def setUp(self):
super(ToolsUploadTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(InteractiveToolsIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
def setUp(self):
super(LocalJobCancellationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(TestRepositoryInstallIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(JobRecoveryBeforeHandledIntegerationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
def setUp(self):
super(PageJsonEncodingIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(MaximumWorkflowInvocationDurationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
def setUp(self):
super(JobsApiTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
def setUp(self):
super(FailJobWhenToolUnavailableTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
def setUp(self):
super(MaximumWorkflowJobsPerSchedulingIterationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
def setUp(self):
super(HistoriesApiTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(
self.galaxy_interactor)
def setUp(self):
super(BaseEmbeddedPulsarContainerIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
def setUp(self):
super(WorkflowSyncTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
def setUp(self):
super(TestProvenance, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
