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Source code for galaxy_test.driver.integration_setup

Test classes that should be shared between test scenarios.
import os
import shutil
from tempfile import mkdtemp
from typing import ClassVar

from galaxy_test.driver.driver_util import GalaxyTestDriver

REQUIRED_ROLE_EXPRESSION = "user@bx.psu.edu"
GROUP_A = "fs_test_group"
GROUP_B = "group name with spaces"

[docs]def get_posix_file_source_config(root_dir: str, roles: str, groups: str, include_test_data_dir: bool) -> str: rval = f""" - type: posix id: posix_test label: Posix doc: Files from local path root: {root_dir} writable: true requires_roles: {roles} requires_groups: {groups} """ if include_test_data_dir: rval += """ - type: posix id: testdatafiles label: Galaxy Stock Test Data doc: Galaxy's test-data directory. root: test-data writable: false """ return rval
[docs]def create_file_source_config_file_on(temp_dir, root_dir, include_test_data_dir): file_contents = get_posix_file_source_config( root_dir, REQUIRED_ROLE_EXPRESSION, REQUIRED_GROUP_EXPRESSION, include_test_data_dir ) file_path = os.path.join(temp_dir, "file_sources_conf_posix.yml") with open(file_path, "w") as f: f.write(file_contents) return file_path
[docs]class PosixFileSourceSetup: _test_driver: GalaxyTestDriver root_dir: str include_test_data_dir: ClassVar[bool] = False
[docs] @classmethod def handle_galaxy_config_kwds(cls, config, clazz_=None): temp_dir = os.path.realpath(mkdtemp()) clazz_ = clazz_ or cls clazz_._test_driver.temp_directories.append(temp_dir) clazz_.root_dir = os.path.join(temp_dir, "root") file_sources_config_file = create_file_source_config_file_on( temp_dir, clazz_.root_dir, clazz_.include_test_data_dir ) config["file_sources_config_file"] = file_sources_config_file # Disable all stock plugins config["ftp_upload_dir"] = None config["library_import_dir"] = None config["user_library_import_dir"] = None
def _write_file_fixtures(self): root = self.root_dir if os.path.exists(root): shutil.rmtree(root) os.mkdir(root) with open(os.path.join(root, "a"), "w") as f: f.write("a\n") subdir1 = os.path.join(root, "subdir1") os.mkdir(subdir1) with open(os.path.join(subdir1, "b"), "w") as f: f.write("b\n") return root