mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
89 lines
3.8 KiB
Python
89 lines
3.8 KiB
Python
from contextlib import contextmanager
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from os.path import join
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from galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
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from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
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from galaxy.util import parse_xml_string
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TEST_DEPENDENCIES_DIR = "/opt/galaxy/dependencies"
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TEST_INSTALL_DIR = "%s/test_install_dir" % TEST_DEPENDENCIES_DIR
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class MockApp:
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def __init__(self):
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pass
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def test_create_or_update_env_shell_file():
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test_path = "/usr/share/R/libs"
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env_file_builder = EnvFileBuilder(test_path)
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line, path = env_file_builder.create_or_update_env_shell_file(TEST_INSTALL_DIR, dict(action="append_to", name="R_LIBS", value=test_path))
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assert path == join(TEST_INSTALL_DIR, "env.sh")
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assert line == "R_LIBS=$R_LIBS:/usr/share/R/libs; export R_LIBS"
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line, path = env_file_builder.create_or_update_env_shell_file(TEST_INSTALL_DIR, dict(action="prepend_to", name="R_LIBS", value=test_path))
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assert path == join(TEST_INSTALL_DIR, "env.sh")
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assert line == "R_LIBS=/usr/share/R/libs:$R_LIBS; export R_LIBS"
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line, path = env_file_builder.create_or_update_env_shell_file(TEST_INSTALL_DIR, dict(action="set_to", name="R_LIBS", value=test_path))
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assert path == join(TEST_INSTALL_DIR, "env.sh")
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assert line == "R_LIBS=/usr/share/R/libs; export R_LIBS"
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line, path = env_file_builder.create_or_update_env_shell_file(TEST_INSTALL_DIR, dict(action="source", value=test_path))
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assert path == join(TEST_INSTALL_DIR, "env.sh")
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assert line == "if [ -f /usr/share/R/libs ] ; then . /usr/share/R/libs ; fi"
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def test_get_env_shell_file_paths_from_setup_environment_elem():
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xml = """<action name="setup_r_environment">
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<repository name="package_r_3_0_1" owner="bgruening" toolshed="toolshed.g2.bx.psu.edu" changeset_revision="1234567">
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<package name="R" version="3.0.1" />
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</repository>
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<repository name="package_zlib_1_2_8" owner="iuc" toolshed="toolshed.g2.bx.psu.edu" changeset_revision="7654321">
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<package name="zlib" version="1.2.8" />
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</repository>
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</action>
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"""
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mock_app = MockApp()
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action_elem = parse_xml_string(xml)
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required_for_install_env_sh = '/path/to/existing.sh'
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all_env_paths = [required_for_install_env_sh]
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action_dict = {}
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env_manager = EnvManager(mock_app)
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r_env_sh = '/path/to/go/env.sh'
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def mock_get_env_shell_file_paths(elem):
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assert elem.get('name') in ["package_r_3_0_1", "package_zlib_1_2_8"]
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return [r_env_sh]
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with __mock_common_util_method(env_manager, "get_env_shell_file_paths", mock_get_env_shell_file_paths):
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env_manager.get_env_shell_file_paths_from_setup_environment_elem(all_env_paths, action_elem, action_dict)
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# Verify old env files weren't deleted.
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assert required_for_install_env_sh in all_env_paths
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# Verify new ones added.
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assert r_env_sh in all_env_paths
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# env_shell_file_paths includes everything
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assert all([env in action_dict['env_shell_file_paths'] for env in all_env_paths])
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# for every given repository there should be one env
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# file + the required_for_install_env_sh file
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assert len(action_dict['env_shell_file_paths']) == 3
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# action_shell_file_paths includes only env files defined
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# inside the setup_ action element.
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assert required_for_install_env_sh in action_dict['action_shell_file_paths']
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assert r_env_sh in action_dict['action_shell_file_paths']
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# Poor man's mocking. Need to get a real mocking library as real Galaxy development
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# dependnecy.
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@contextmanager
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def __mock_common_util_method(env_manager, name, mock_method):
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real_method = getattr(env_manager, name)
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try:
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setattr(env_manager, name, mock_method)
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yield
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finally:
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setattr(env_manager, name, real_method)
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