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galaxy_test.driver package

Submodules

galaxy_test.driver.driver_util module

Scripts for drivers of Galaxy functional tests.

galaxy_test.driver.driver_util.copy_database_template(source, db_path)

Copy a ‘clean’ sqlite template database.

From file or URL to specified path for sqlite database.

galaxy_test.driver.driver_util.build_logger()

Build a logger for test driver script.

galaxy_test.driver.driver_util.drive_test(test_driver_class)

Instantiate driver class, run, and exit appropriately.

galaxy_test.driver.driver_util.database_conf(db_path, prefix='GALAXY', prefer_template_database=False)

Find (and populate if needed) Galaxy database connection.

galaxy_test.driver.driver_util.get_webapp_global_conf()

Get the global_conf dictionary sent to app_factory.

galaxy_test.driver.driver_util.setup_galaxy_config(tmpdir, use_test_file_dir=False, default_install_db_merged=True, default_tool_data_table_config_path=None, default_shed_tool_data_table_config=None, default_job_config_file=None, enable_tool_shed_check=False, default_tool_conf=None, shed_tool_conf=None, datatypes_conf=None, update_integrated_tool_panel=False, prefer_template_database=False, log_format=None, conda_auto_init=False, conda_auto_install=False, use_shared_connection_for_amqp=False, allow_tool_conf_override: bool = True, allow_path_paste=False)

Setup environment and build config for test Galaxy instance.

class galaxy_test.driver.driver_util.TestDriver

Bases: object

Responsible for the life-cycle of a Galaxy-style functional test.

Sets up servers, configures tests, and tears things down. This is somewhat like a Python TestCase - but different because it is meant to provide a main() endpoint.

__init__()

Setup tracked resources.

setup() → None

Called before tests are built.

tear_down() → None

Cleanup resources tracked by this object.

stop_servers() → None

mkdtemp() → str

Return a temp directory that is properly cleaned up or not based on the config.

galaxy_test.driver.driver_util.wait_for_http_server(host, port, prefix=None, sleep_amount=0.1, sleep_tries=150)

Wait for an HTTP server to boot up.

galaxy_test.driver.integration_setup module

Test classes that should be shared between test scenarios.

galaxy_test.driver.integration_setup.get_posix_file_source_config(root_dir: str, roles: str, groups: str, include_test_data_dir: bool, prefer_links: bool = False) → str

galaxy_test.driver.integration_setup.create_file_source_config_file_on(temp_dir: str, root_dir: str, include_test_data_dir: bool, required_role_expression: str, required_group_expression: str, prefer_links: bool = False)

class galaxy_test.driver.integration_setup.PosixFileSourceSetup

Bases: object

root_dir: str

include_test_data_dir: ClassVar[bool] = False

required_role_expression: str = 'user@bx.psu.edu'

required_group_expression: str = ''

prefer_links: bool = False

classmethod handle_galaxy_config_kwds(config)

class galaxy_test.driver.integration_setup.CuratedWorkflowsNetworkGuard

Bases: object

Keeps curated workflow tests offline.

The feature’s one outbound request is the IWC manifest download. Both it and the refresh that would trigger it are replaced with functions that raise, and every test asserts the download was never attempted.

download_mock: MagicMock

refresh_mock: MagicMock

setUp()

tearDown()

galaxy_test.driver.integration_setup.store_raw_annotation(app: UniverseApplication, workflow_id: str, annotation: str) → None

Annotate a stored workflow straight in the database.

Bypasses the API write path on purpose, so a test can store exactly the text it means to - including text a write would sanitize.

galaxy_test.driver.integration_util module

Utilities for constructing Galaxy integration tests.

Tests that start an actual Galaxy server with a particular configuration in order to test something that cannot be tested with the default functional/api testing configuration.

class galaxy_test.driver.integration_util.CachedToolBoxIntegrationMixin

Bases: object

Run an existing integration-test configuration with lazy tools.

classmethod handle_galaxy_config_kwds(config)

galaxy_test.driver.integration_util.docker_run(image, name, *args, detach=True, remove=True, ports=None, env_vars: dict[str, str] | None = None)

galaxy_test.driver.integration_util.docker_exec(container_name, *args, output=True)

galaxy_test.driver.integration_util.docker_ip_address(container_name)

galaxy_test.driver.integration_util.docker_rm(container_name)

galaxy_test.driver.integration_util.skip_if_jenkins(cls)

galaxy_test.driver.integration_util.skip_unless_amqp()

galaxy_test.driver.integration_util.skip_unless_postgres()

galaxy_test.driver.integration_util.skip_unless_docker()

galaxy_test.driver.integration_util.skip_unless_kubernetes()

galaxy_test.driver.integration_util.k8s_config_path()

galaxy_test.driver.integration_util.skip_unless_fixed_port()

galaxy_test.driver.integration_util.skip_for_older_python(min_python_version)

galaxy_test.driver.integration_util.skip_if_github_workflow()

class galaxy_test.driver.integration_util.IntegrationInstance

Bases: UsesApiTestCaseMixin, UsesCeleryTasks

Unit test case with utilities for spinning up Galaxy.

prefer_template_database = True

isolate_galaxy_config = True

dataset_populator: BaseDatasetPopulator | None

classmethod setUpClass()

Configure and start Galaxy for a test.

classmethod tearDownClass()

Shutdown Galaxy server and cleanup temp directory.

tearDown()

setUp()

restart(handle_reconfig=None)

classmethod temp_config_dir(name)

history_id() → Iterator[str]

class galaxy_test.driver.integration_util.IntegrationTestCase

Bases: IntegrationInstance, TestCase

Unit TestCase with utilities for spinning up Galaxy.

galaxy_test.driver.integration_util.integration_module_instance(clazz: type[IntegrationInstance])

galaxy_test.driver.integration_util.integration_tool_runner(tool_ids)

class galaxy_test.driver.integration_util.ConfiguresObjectStores

Bases: object

object_stores_parent: ClassVar[str]

classmethod write_object_store_config_file(filename: str, contents: str) → str

class galaxy_test.driver.integration_util.ConfiguresFileSourceTemplates

Bases: object

class galaxy_test.driver.integration_util.ConfiguresObjectStoreTemplates

Bases: object

class galaxy_test.driver.integration_util.ConfiguresDatabaseVault

Bases: object

class galaxy_test.driver.integration_util.ConfiguresWorkflowScheduling

Bases: object

class galaxy_test.driver.integration_util.ConfigureAllowedUrlHeaders

Bases: object

galaxy_test.driver.test_logging module

galaxy_test.driver.testcase module

class galaxy_test.driver.testcase.DrivenFunctionalTestCase

Bases: FunctionalTestCase

Variant of FunctionalTestCase that can launch Galaxy instances.

galaxy_driver_class

alias of TestDriver