def test_overwrite_prohibited(envvars):
""" Prohibition of overwrite causes ValueError in case of collision. """
check_unset(envvars)
with TmpEnv(**envvars), pytest.raises(ValueError):
TmpEnv(overwrite=False,
**{k: v + "_EXTRA"
for k, v in envvars.items()})
check_unset(envvars)
def test_overwrite_allowed(envvars):
""" Verify that overwriting existing value with different one works if permitted. """
check_unset(envvars)
with TmpEnv(**envvars):
modified = {k: v + "_EXTRA" for k, v in envvars.items()}
with TmpEnv(overwrite=True, **modified):
for k, v in modified.items():
assert v == os.getenv(k)
check_unset(envvars)
def test_non_PathExAttMap_preserves_all_variables(path, fetch, env):
""" Only a PathExAttMap eagerly attempts expansion of text as a path. """
m = AttMap()
k = random.choice(string.ascii_letters)
with TmpEnv(**env):
m[k] = path
assert path == fetch(m, k)
def test_select_local_config_file(tmpdir, setup, expect):
"""Selection of local filepath hinges on its existence as a file"""
with TmpEnv(overwrite=True, **{ev: "" for ev in CFG_ENV_VARS}):
_check_no_env_vars()
path = setup(tmpdir)
print("Path: {}".format(path))
with ExpectContext(expect(path), select_genome_config) as ctx:
ctx(path)
def test_select_via_env_var_implicit(env_var, tmpdir):
"""Config file selection can leverage default environmanent variables."""
conf_file = tmpdir.join("test-refgenconf-conf.yaml").strpath
assert not os.path.exists(conf_file)
with open(conf_file, "w"):
pass
assert os.path.isfile(conf_file)
with TmpEnv(overwrite=True, **{env_var: conf_file}):
assert conf_file == select_genome_config(None)
def test_PathExAttMap_substitution_is_selective(path, pres, repl, env, pam,
fetch):
""" Values that are environment variables are replaced; others aren't. """
k = random.choice(string.ascii_lowercase)
with TmpEnv(**env):
pam[k] = path
res = fetch(pam, k)
print("Inserted path: {}".format(path))
print("Retrieved path: {}".format(res))
assert all(map(lambda s: s in res, pres))
assert all(map(lambda s: s not in res, repl))
def test_multiple_syntax_path_expansion(varname, path_parts, var_idx, tmpdir,
store, fetch):
""" Test the different combinations of setting and retrieving an env var path. """
key = "arbitrary"
parts = copy.copy(path_parts)
env_var = "$" + varname
env_var_val = "set-via-env-var"
parts.insert(var_idx, env_var)
final_parts = [tmpdir.strpath] + parts
print("FINAL PARTS: {}".format(final_parts))
path = os.path.join(*final_parts)
m = PathExAttMap()
store(m, key, path)
with TmpEnv(**{varname: env_var_val}):
assert env_var_val == os.getenv(varname)
assert path != expandpath(path)
assert expandpath(path) == fetch(m, key)
def test_select_null():
"""Test prioritized selection of genome configuration file."""
with TmpEnv(overwrite=True, **{ev: "" for ev in CFG_ENV_VARS}):
_check_no_env_vars()
assert select_genome_config(None) is None
def test_PathExAttMap_expands_available_variables(pam, path, env, fetch):
""" Insertion of text encoding environment variables should expand. """
k = random.choice(string.ascii_lowercase)
with TmpEnv(**env):
pam[k] = path
assert expandpath(path) == fetch(pam, k)
def test_no_intersection(overwrite, envvars):
""" Verify that overwrite permission is irrelevant if no variable name collision occurs. """
check_unset(envvars)
with TmpEnv(overwrite=overwrite, **envvars):
for k, v in envvars.items():
assert v == os.getenv(k)