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)