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)