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Source code for galaxy_test.driver.integration_util

"""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.
"""

import os
import re
import sys
from typing import (
    ClassVar,
    Iterator,
    Optional,
    Type,
    TYPE_CHECKING,
)
from unittest import (
    skip,
    SkipTest,
)

import pytest

from galaxy.app import UniverseApplication
from galaxy.tool_util.verify.test_data import TestDataResolver
from galaxy.util import safe_makedirs
from galaxy.util.unittest import TestCase
from galaxy.util.unittest_utils import (
    _identity,
    skip_unless_executable,
)
from galaxy_test.base.api import (
    UsesApiTestCaseMixin,
    UsesCeleryTasks,
)
from .driver_util import GalaxyTestDriver

if TYPE_CHECKING:
    from galaxy_test.base.populators import BaseDatasetPopulator

NO_APP_MESSAGE = "test_case._app called though no Galaxy has been configured."
# Following should be for Homebrew Rabbitmq and Docker on Mac "amqp://guest:guest@localhost:5672//"
AMQP_URL = os.environ.get("GALAXY_TEST_AMQP_URL", None)
POSTGRES_CONFIGURED = "postgres" in os.environ.get("GALAXY_TEST_DBURI", "")
SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
VAULT_CONF = os.path.join(SCRIPT_DIRECTORY, "vault_conf.yml")


[docs]def skip_if_jenkins(cls): if os.environ.get("BUILD_NUMBER", ""): return skip return cls
[docs]def skip_unless_amqp(): if AMQP_URL is not None: return _identity return pytest.mark.skip("AMQP_URL is not set, required for this test.")
[docs]def skip_unless_postgres(): if POSTGRES_CONFIGURED: return _identity return pytest.mark.skip("GALAXY_TEST_DBURI does not point to postgres database, required for this test.")
[docs]def skip_unless_docker(): return skip_unless_executable("docker")
[docs]def skip_unless_kubernetes(): return skip_unless_executable("kubectl")
[docs]def k8s_config_path(): return os.environ.get("GALAXY_TEST_KUBE_CONFIG_PATH", "~/.kube/config")
[docs]def skip_unless_fixed_port(): if os.environ.get("GALAXY_TEST_PORT_RANDOM") != "1": return _identity return pytest.mark.skip("GALAXY_TEST_PORT must be set for this test.")
[docs]def skip_for_older_python(min_python_version): if min_python_version is None: return _identity if sys.version_info < min_python_version: return pytest.mark.skip(f"Skipping tests for Python version less than {min_python_version}") return _identity
[docs]def skip_if_github_workflow(): if os.environ.get("GITHUB_ACTIONS", None) is None: return _identity return pytest.mark.skip("This test is skipped for Github actions.")
[docs]def skip_unless_environ(env_var): if os.environ.get(env_var): return _identity return pytest.mark.skip(f"{env_var} must be set for this test")
[docs]class IntegrationInstance(UsesApiTestCaseMixin, UsesCeleryTasks): """Unit test case with utilities for spinning up Galaxy.""" _test_driver: GalaxyTestDriver # Optional in parent class, but required for integration tests. _app_available: ClassVar[bool] prefer_template_database = True # Don't pull in default configs for un-configured things from Galaxy's # config directory and such. isolate_galaxy_config = True dataset_populator: Optional["BaseDatasetPopulator"]
[docs] @classmethod def setUpClass(cls): """Configure and start Galaxy for a test.""" cls._app_available = False cls._test_driver = GalaxyTestDriver() cls._prepare_galaxy() cls._test_driver.setup(config_object=cls) cls._app_available = True cls._configure_app()
[docs] @classmethod def tearDownClass(cls): """Shutdown Galaxy server and cleanup temp directory.""" cls._test_driver.tear_down() cls._app_available = False
[docs] def tearDown(self): if logs := self._test_driver.get_logs(): print(logs) return super().tearDown()
[docs] def setUp(self): self.test_data_resolver = TestDataResolver() self._configure_interactor()
def _configure_interactor(self): # Setup attributes needed for API testing... server_wrapper = self._test_driver.server_wrappers[0] host = server_wrapper.host port = server_wrapper.port prefix = server_wrapper.prefix or "" self.url = f"http://{host}:{port}{prefix.rstrip('/')}/" self._setup_interactor()
[docs] def restart(self, handle_reconfig=None): self._test_driver.restart(config_object=self.__class__, handle_config=handle_reconfig) self._configure_app() self._configure_interactor()
@property def _app(self) -> UniverseApplication: assert self._app_available, NO_APP_MESSAGE app = self._test_driver.app assert app, NO_APP_MESSAGE return app @property def _tempdir(self): return self._test_driver.galaxy_test_tmp_dir @classmethod def _prepare_galaxy(cls): """Extension point for subclasses called before Galaxy is launched.""" @classmethod def _configure_app(cls): """Extension point for subclasses called after Galaxy is launched. ```self._app``` can be used to access Galaxy core app. """ def _skip_unless_postgres(self): if not self._app.config.database_connection.startswith("post"): raise SkipTest("Test only valid for postgres") def _run_tool_test(self, *args, **kwargs): return self._test_driver.run_tool_test(*args, **kwargs)
[docs] @classmethod def temp_config_dir(cls, name): # realpath here to get around problems with symlinks being blocked. return os.path.realpath(os.path.join(cls._test_driver.galaxy_test_tmp_dir, name))
[docs] @pytest.fixture def history_id(self) -> Iterator[str]: assert self.dataset_populator with self.dataset_populator.test_history() as history_id: yield history_id
[docs]class IntegrationTestCase(IntegrationInstance, TestCase): """Unit TestCase with utilities for spinning up Galaxy."""
[docs]def integration_module_instance(clazz: Type[IntegrationInstance]): def _instance() -> Iterator[IntegrationInstance]: instance = clazz() instance.setUpClass() instance.setUp() try: yield instance finally: instance.tearDown() instance.tearDownClass() return pytest.fixture(scope="module")(_instance)
[docs]def integration_tool_runner(tool_ids): def test_tools(instance, tool_id): instance._run_tool_test(tool_id) return pytest.mark.parametrize("tool_id", tool_ids)(test_tools)
[docs]class ConfiguresObjectStores: object_stores_parent: ClassVar[str] _test_driver: GalaxyTestDriver
[docs] @classmethod def write_object_store_config_file(cls, filename: str, contents: str) -> str: temp_directory = cls.object_stores_parent config_path = os.path.join(temp_directory, filename) with open(config_path, "w") as f: f.write(contents) return config_path
@classmethod def _configure_object_store(cls, template, config): temp_directory = cls._test_driver.mkdtemp() cls.object_stores_parent = temp_directory xml = template.safe_substitute({"temp_directory": temp_directory}) config_path = cls.write_object_store_config_file("object_store_conf.xml", xml) config["object_store_config_file"] = config_path for path in re.findall(r'files_dir path="([^"]*)"', xml): assert path.startswith(temp_directory) dir_name = os.path.basename(path) os.path.join(temp_directory, dir_name) safe_makedirs(path) setattr(cls, f"{dir_name}_path", path) @classmethod def _configure_object_store_template_catalog(cls, catalog, config): template = catalog.replace("/data", cls.object_stores_parent) template_config_path = cls.write_object_store_config_file("templates.yml", template) config["object_store_templates_config_file"] = template_config_path
[docs]class ConfiguresFileSourceTemplates: _test_driver: GalaxyTestDriver @classmethod def _configure_file_source_template_catalog(cls, catalog: str, config): temp_directory = cls._test_driver.mkdtemp() template_config_path = os.path.join(temp_directory, "file_source_templates.yml") with open(template_config_path, "w") as f: f.write(catalog) config["file_source_templates_config_file"] = template_config_path
[docs]class ConfiguresObjectStoreTemplates: _test_driver: GalaxyTestDriver @classmethod def _configure_object_Store_template_catalog(cls, catalog: str, config): temp_directory = cls._test_driver.mkdtemp() template_config_path = os.path.join(temp_directory, "object_store_templates.yml") with open(template_config_path, "w") as f: f.write(catalog) config["object_store_templates_config_file"] = template_config_path
[docs]class ConfiguresDatabaseVault: @classmethod def _configure_database_vault(cls, config): config["vault_config_file"] = VAULT_CONF
[docs]class ConfiguresWorkflowScheduling: _test_driver: GalaxyTestDriver @classmethod def _configure_workflow_schedulers(cls, schedulers_conf: str, config): temp_directory = cls._test_driver.mkdtemp() template_config_path = os.path.join(temp_directory, "workflow_schedulers.xml") with open(template_config_path, "w") as f: f.write(schedulers_conf) config["workflow_schedulers_config_file"] = template_config_path @classmethod def _disable_workflow_scheduling(cls, config): noop_schedulers_conf = """<?xml version="1.0"?> <workflow_schedulers default="core"> <core id="core" /> <handlers> <handler id="a_fake_handler_should_prevent_the_real_process_from_scheduling" /> </handlers> </workflow_schedulers> """ cls._configure_workflow_schedulers(noop_schedulers_conf, config)