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)[source]

Copy a ‘clean’ sqlite template database.

From file or URL to specified path for sqlite database.

galaxy_test.driver.driver_util.build_logger()[source]: Build a logger for test driver script.

galaxy_test.driver.driver_util.drive_test(test_driver_class)[source]: Instantiate driver class, run, and exit appropriately.

galaxy_test.driver.driver_util.database_conf(db_path, prefix='GALAXY', prefer_template_database=False)[source]: Find (and populate if needed) Galaxy database connection.

galaxy_test.driver.driver_util.get_webapp_global_conf()[source]: 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)[source]: Setup environment and build config for test Galaxy instance.

class galaxy_test.driver.driver_util.TestDriver[source]

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__()[source]: Setup tracked resources.

setup(config_object=None) → None[source]: Called before tests are built.

tear_down() → None[source]: Cleanup resources tracked by this object.

stop_servers() → None[source]

mkdtemp() → str[source]: 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)[source]: 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) → str[source]

galaxy_test.driver.integration_setup.create_file_source_config_file_on(temp_dir, root_dir, include_test_data_dir, required_role_expression, required_group_expression)[source]

class galaxy_test.driver.integration_setup.PosixFileSourceSetup[source]

Bases: object

root_dir: str

include_test_data_dir: ClassVar[bool] = False

classmethod handle_galaxy_config_kwds(config, clazz_=None, required_role_expression='user@bx.psu.edu', required_group_expression='')[source]

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.

galaxy_test.driver.integration_util.skip_if_jenkins(cls)[source]

galaxy_test.driver.integration_util.skip_unless_amqp()[source]

galaxy_test.driver.integration_util.skip_unless_postgres()[source]

galaxy_test.driver.integration_util.skip_unless_docker()[source]

galaxy_test.driver.integration_util.skip_unless_kubernetes()[source]

galaxy_test.driver.integration_util.k8s_config_path()[source]

galaxy_test.driver.integration_util.skip_unless_fixed_port()[source]

galaxy_test.driver.integration_util.skip_for_older_python(min_python_version)[source]

galaxy_test.driver.integration_util.skip_if_github_workflow()[source]

galaxy_test.driver.integration_util.skip_unless_environ(env_var)[source]

class galaxy_test.driver.integration_util.IntegrationInstance[source]

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()[source]: Configure and start Galaxy for a test.

classmethod tearDownClass()[source]: Shutdown Galaxy server and cleanup temp directory.

tearDown()[source]

setUp()[source]

restart(handle_reconfig=None)[source]

classmethod temp_config_dir(name)[source]

history_id() → Iterator[str][source]

class galaxy_test.driver.integration_util.IntegrationTestCase[source]

Bases: IntegrationInstance, TestCase

Unit TestCase with utilities for spinning up Galaxy.

dataset_populator: BaseDatasetPopulator | None

url: str

galaxy_test.driver.integration_util.integration_module_instance(clazz: Type[IntegrationInstance])[source]

galaxy_test.driver.integration_util.integration_tool_runner(tool_ids)[source]

class galaxy_test.driver.integration_util.ConfiguresObjectStores[source]

Bases: object

object_stores_parent: ClassVar[str]

classmethod write_object_store_config_file(filename: str, contents: str) → str[source]

class galaxy_test.driver.integration_util.ConfiguresFileSourceTemplates[source]: Bases: object

class galaxy_test.driver.integration_util.ConfiguresObjectStoreTemplates[source]: Bases: object

class galaxy_test.driver.integration_util.ConfiguresDatabaseVault[source]: Bases: object

class galaxy_test.driver.integration_util.ConfiguresWorkflowScheduling[source]: Bases: object

galaxy_test.driver.test_logging module

galaxy_test.driver.testcase module

class galaxy_test.driver.testcase.DrivenFunctionalTestCase[source]

Bases: FunctionalTestCase

Variant of FunctionalTestCase that can launch Galaxy instances.

galaxy_driver_class: alias of TestDriver

host: str

port: str | None

url: str

keepOutdir: str

test_data_resolver: TestDataResolver