def test_data_dirs():
with tempdir() as d:
mod = Mock()
mod.__name__ = "tests.bar"
cls = Mock()
cls.__name__ = "baz"
fun = Mock()
fun.__name__ = "blorf"
mod_cls_fun = d / "tests" / "bar" / "baz" / "blorf"
mod_cls_fun.mkdir(parents=True)
data_mod_cls_fun = d / "tests" / "data" / "bar" / "baz" / "blorf"
data_mod_cls_fun.mkdir(parents=True)
dd = DataDirs(d / "tests", mod, fun, cls)
assert dd.paths == [
mod_cls_fun, d / "tests" / "bar" / "baz", d / "tests" / "bar",
data_mod_cls_fun, d / "tests" / "data" / "bar" / "baz",
d / "tests" / "data" / "bar", d / "tests" / "data"
]
mod_cls_fun = d / "tests" / "bar" / "blorf"
mod_cls_fun.mkdir(parents=True)
data_mod_cls_fun = d / "tests" / "data" / "bar" / "blorf"
data_mod_cls_fun.mkdir(parents=True)
dd = DataDirs(d / "tests", mod, fun)
assert dd.paths == [
mod_cls_fun, d / "tests" / "bar", data_mod_cls_fun,
d / "tests" / "data" / "bar", d / "tests" / "data"
]
def runtest(self):
# Get/create DataManager
if self._data:
config = self._fixture_request.getfixturevalue("user_config")
data_resolver = DataResolver(self._data, config)
data_dirs = DataDirs(
ensure_path(self._fixture_request.fspath.dirpath(),
canonicalize=True),
function=self.name,
module=None, # TODO: support a top-level key for module name
cls=None, # TODO: support test groupings
)
workflow_data = DataManager(data_resolver, data_dirs)
else:
workflow_data = self._fixture_request.getfixturevalue(
"workflow_data")
# Build the arguments to workflow_runner
workflow_runner_kwargs = self._workflow_runner_kwargs
# Resolve test data requests in the inputs and outputs
if self._inputs:
workflow_runner_kwargs["inputs"] = _resolve_test_data(
self._inputs, workflow_data)
if self._expected:
workflow_runner_kwargs["expected"] = _resolve_test_data(
self._expected, workflow_data)
# Run the test
workflow_runner = self._fixture_request.getfixturevalue(
"workflow_runner")
return workflow_runner(self._wdl, **workflow_runner_kwargs)
def test_data_resolver():
with tempdir() as d:
test_data = {"foo": {"name": "foo.txt"}, "bar": 1}
foo_txt = d / "data" / "foo.txt"
foo_txt.parent.mkdir()
with open(foo_txt, "wt") as out:
out.write("bar")
mod = Mock()
mod.__name__ = ""
fun = Mock()
fun.__name__ = "test_foo"
dd = DataDirs(d, mod, fun)
resolver = DataResolver(test_data, UserConfiguration(None,
cache_dir=d))
with pytest.raises(FileNotFoundError):
resolver.resolve("bork", dd)
assert resolver.resolve("foo", dd).path == foo_txt
assert resolver.resolve("bar", dd) == 1
def test_data_resolver_create_from_datadir():
with tempdir() as d, tempdir() as d1:
mod = Mock()
mod.__name__ = "foo.bar"
cls = Mock()
cls.__name__ = "baz"
fun = Mock()
fun.__name__ = "blorf"
mod_cls_fun = d / "foo" / "bar" / "baz" / "blorf"
mod_cls_fun.mkdir(parents=True)
data_mod_cls_fun = d / "data" / "foo" / "bar" / "baz" / "blorf"
data_mod_cls_fun.mkdir(parents=True)
dd = DataDirs(d / "foo", mod, fun, cls)
resolver = DataResolver(
{
"boink": {
"name": "boink.txt",
},
"bobble": {
"name": "bobble.txt"
},
"burp": {
"name": "burp.txt",
"path": "burp.txt"
}
}, UserConfiguration(None, cache_dir=d1))
boink = d / "foo" / "bar" / "boink.txt"
with open(boink, "wt") as out:
out.write("boink")
assert boink == resolver.resolve("boink", dd).path
with pytest.raises(FileNotFoundError):
resolver.resolve("bobble", dd)
burp = d / "foo" / "bar" / "burp.txt"
with open(burp, "wt") as out:
out.write("burp")
burp_resolved = resolver.resolve("burp", dd).path
assert burp_resolved == d1 / "burp.txt"
assert burp_resolved.is_symlink()
with pytest.raises(FileNotFoundError):
resolver.resolve("bobble")
def workflow_data(request: FixtureRequest,
workflow_data_resolver: DataResolver) -> DataManager:
"""
Provides an accessor for test data files, which may be local or in a remote
repository.
Args:
request: FixtureRequest object
workflow_data_resolver: Module-level test data configuration
Examples:
def workflow_data_descriptor_file():
return "tests/test_data.json"
def test_workflow(workflow_data):
print(workflow_data["myfile"])
"""
datadirs = DataDirs(
ensure_path(request.fspath.dirpath(), canonicalize=True),
request.module, request.function, request.cls)
return DataManager(workflow_data_resolver, datadirs)