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()