import abc import os import shutil import string import tempfile from typing import ClassVar from unittest import SkipTest from galaxy.app import UniverseApplication from galaxy.util.tool_shed.tool_shed_registry import DEFAULT_TOOL_SHED_URL from galaxy.util.unittest_utils import is_site_up from galaxy_test.base.populators import DEFAULT_TIMEOUT from galaxy_test.base.uses_shed_api import UsesShedApi from galaxy_test.driver.driver_util import ( FRAMEWORK_UPLOAD_TOOL_CONF, GalaxyTestDriver, ) # Needs a longer timeout because of the conda_auto_install. CONDA_AUTO_INSTALL_JOB_TIMEOUT = DEFAULT_TIMEOUT * 3 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__)) TOOL_SHEDS_CONF = os.path.join(SCRIPT_DIRECTORY, "tool_sheds_conf.xml") SHED_TOOL_CONF = string.Template(""" """) SHED_DATA_MANAGER_CONF = """ """ SHED_DATA_TABLES = """ """ class UsesShed(UsesShedApi): @property @abc.abstractmethod def _app(self) -> UniverseApplication: ... shed_tools_dir: ClassVar[str] shed_tool_data_dir: ClassVar[str] conda_tmp_prefix: ClassVar[str] _test_driver: GalaxyTestDriver @classmethod def configure_shed(cls, config): if not is_site_up(DEFAULT_TOOL_SHED_URL): raise SkipTest(f"Test depends on [{DEFAULT_TOOL_SHED_URL}] being up and it appears to be down.") cls.shed_tools_dir = tempfile.mkdtemp() cls.shed_tool_data_dir = tempfile.mkdtemp() cls._test_driver.temp_directories.extend([cls.shed_tool_data_dir, cls.shed_tools_dir]) shed_tool_config = os.path.join(cls.shed_tools_dir, "shed_tool_conf.xml") config["tool_sheds_config_file"] = TOOL_SHEDS_CONF config["tool_config_file"] = FRAMEWORK_UPLOAD_TOOL_CONF config["shed_tool_config_file"] = shed_tool_config config["shed_data_manager_config_file"] = os.path.join(cls.shed_tool_data_dir, "shed_data_manager_config_file") config["shed_tool_data_table_config"] = os.path.join(cls.shed_tool_data_dir, "shed_data_table_conf.xml") config["shed_tool_data_path"] = cls.shed_tool_data_dir with open(shed_tool_config, "w") as tool_conf_file: tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=cls.shed_tools_dir)) with open(config["shed_data_manager_config_file"], "w") as shed_data_config: shed_data_config.write(SHED_DATA_MANAGER_CONF) with open(config["shed_tool_data_table_config"], "w") as shed_data_table_config: shed_data_table_config.write(SHED_DATA_TABLES) @classmethod def configure_shed_and_conda(cls, config): cls.configure_shed(config) cls.conda_tmp_prefix = cls._test_driver.mkdtemp() config["conda_auto_init"] = True config["conda_auto_install"] = True config["conda_prefix"] = os.environ.get("GALAXY_TEST_CONDA_PREFIX") or os.path.join( cls.conda_tmp_prefix, "conda" ) def setup_shed_config(self): shutil.rmtree(self._app.config.shed_tools_dir, ignore_errors=True) os.makedirs(self._app.config.shed_tools_dir) self._app.config.shed_tools_dir = self.shed_tools_dir with open(self._app.config.shed_tool_config_file, "w") as tool_conf_file: tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=self._app.config.shed_tools_dir)) # deleting the containing folder doesn't trigger a toolbox reload, so signal it now and wait until it's done self._app.queue_worker.send_control_task("reload_toolbox", get_response=True) def reset_shed_tools(self): self.setup_shed_config() model = self._app.install_model models_to_delete = [ model.RepositoryRepositoryDependencyAssociation, model.RepositoryDependency, model.ToolVersion, model.ToolVersionAssociation, model.ToolDependency, model.ToolShedRepository, ] for item in models_to_delete: model.context.query(item).delete() model.context.commit()