def test_cache_remove_all():
config = Config("""{
"a": {
"b": {
"c": true
}
}
}""")
config.lookup(("a", "b", "c"), {}, remove=True)
assert not config.data
def test_cache_config():
config = Config("""{
"caching": {
"enabled": true,
"size_limit": 5e9,
"directory": "/tmp"
}
}""")
cache_config = config.lookup(("caching", ), {})
assert cache_config["enabled"]
assert cache_config["size_limit"] == 5 * 10**9
def test_lookup_deep():
config = Config(deep_str)
assert config.lookup(["a"]) == {"b": {"c": [1, 2, 3]}}
assert config.lookup(["a", "b"]) == {"c": [1, 2, 3]}
assert config.lookup(["a", "b", "c"]) == [1, 2, 3]
with raises(AttributeError):
config.lookup(["a", "b", "c", "d"])
assert config.lookup(["a", "b", "c", "d"], "x") == "x"
def __init__(self) -> None:
"""
Loads the configuration specified by the STARFISH_CONFIG environment variable.
Parameters
----------
STARISH_CONFIG :
This parameter is read from the environment to permit setting configuration
values either directly or via a file. Keys read include:
- ["slicedimage"]["caching"]["directory"] (default: ~/.starfish/cache)
- ["slicedimage"]["caching"]["size_limit"] (default: None; 0 disables caching)
- ["validation"]["strict"] (default: False)
- ["verbose"] (default: True)
Note: all keys can also be set by and environment variable constructed from the
key parts and prefixed with STARFISH, e.g. STARFISH_VALIDATION_STRICT.
"""
config = os.environ.get("STARFISH_CONFIG", "@~/.starfish/config")
self._config_obj = Config(config)
self._env_keys = [
x for x in os.environ.keys()
if special_prefix(x) and x != "STARFISH_CONFIG"
]
# If no directory is set, then force the default
self._slicedimage = self._config_obj.lookup(("slicedimage", ),
NestedDict(),
remove=True)
if not self._slicedimage["caching"]["directory"]:
self._slicedimage["caching"]["directory"] = "~/.starfish/cache"
self._slicedimage_update(('caching', 'directory'))
self._slicedimage_update(('caching', 'size_limit'), int)
env_val = self.flag("STARFISH_VALIDATION_STRICT", None)
config_val = self._config_obj.lookup(("validation", "strict"),
False,
remove=True)
self._strict = env_val if env_val is not None else config_val
env_val = self.flag("STARFISH_VERBOSE", None)
config_val = self._config_obj.lookup(("verbose", ), True, remove=True)
self._verbose = env_val if env_val is not None else config_val
if self._config_obj.data:
warnings.warn(f"unknown configuration: {self._config_obj.data}")
if self._env_keys:
warnings.warn(f"unknown environment variables: {self._env_keys}")
def test_simple_config_false():
# config says the value is False. Do we return False?
config = Config("{\"a\": false}")
assert config.lookup(("a", ), None) is False
# config says the value is not known. Do we return the default valueS?
config = Config("{}")
assert config.lookup(("a", ), None) is None
assert config.lookup(("a", ), False) is False
def test_cache_remove_step_wise():
config = Config("""{
"a": {
"b": {
"c": true,
"d": true
},
"e": 1
},
"f": 2
}""")
config.lookup(("a", "b", "c"), {}, remove=True)
assert "c" not in config.data["a"]["b"]
config.lookup(("a", "b"), {}, remove=True)
assert "b" not in config.data["a"]
config.lookup(("a", ), {}, remove=True)
assert "a" not in config.data
class StarfishConfig(object):
"""
Application specific configuration settings which can be loaded throughout
the starfish codebase.
Attributes
----------
slicedimage : dictionary
Subdictionary that can be passed to slicedimage.io methods.
strict : bool
Whether or not loaded json should be validated.
verbose : bool
Controls output like from tqdm
Examples
--------
Check strict property
>>> from starfish.core.config import StarfishConfig
>>> config = StarfishConfig()
>>> if config.strict:
>>> validate(json)
Default starfish configuration equivalent:
>>> {
>>> "slicedimage": {
>>> "caching": {
>>> "debug": false,
>>> "directory": "~/.starfish/cache",
>>> "size_limit": 5e9
>>> },
>>> },
>>> "validation": {
>>> "strict": false
>>> },
>>> "verbose": true
>>> }
Example of a ~/.starfish.config file to disable caching:
>>> {
>>> "slicedimage": {
>>> "caching": {
>>> "size_limit": 0
>>> }
>>> }
>>> }
"""
def __init__(self) -> None:
"""
Loads the configuration specified by the STARFISH_CONFIG environment variable.
Parameters
----------
STARISH_CONFIG :
This parameter is read from the environment to permit setting configuration
values either directly or via a file. Keys read include:
- ["slicedimage"]["caching"]["directory"] (default: ~/.starfish/cache)
- ["slicedimage"]["caching"]["size_limit"] (default: None; 0 disables caching)
- ["validation"]["strict"] (default: False)
- ["verbose"] (default: True)
Note: all keys can also be set by and environment variable constructed from the
key parts and prefixed with STARFISH, e.g. STARFISH_VALIDATION_STRICT.
"""
config = os.environ.get("STARFISH_CONFIG", "@~/.starfish/config")
self._config_obj = Config(config)
self._env_keys = [
x for x in os.environ.keys()
if special_prefix(x) and x != "STARFISH_CONFIG"]
# If no directory is set, then force the default
self._slicedimage = self._config_obj.lookup(("slicedimage",), NestedDict(), remove=True)
if not self._slicedimage["caching"]["directory"]:
self._slicedimage["caching"]["directory"] = "~/.starfish/cache"
self._slicedimage_update(('caching', 'directory'))
self._slicedimage_update(('caching', 'size_limit'), int)
self._strict = self._config_obj.lookup(
("validation", "strict"), self.flag("STARFISH_VALIDATION_STRICT", "false"), remove=True)
self._verbose = self._config_obj.lookup(
("verbose",), self.flag("STARFISH_VERBOSE", "true"), remove=True)
if self._config_obj.data:
warnings.warn(f"unknown configuration: {self._config_obj.data}")
if self._env_keys:
warnings.warn(f"unknown environment variables: {self._env_keys}")
def _slicedimage_update(self, lookup, parse=lambda x: x):
""" accept STARFISH_SLICEDIMAGE_ or SLICEDIMAGE_ prefixes"""
value = None
name1 = "SLICEDIMAGE_" + "_".join([x.upper() for x in lookup])
if name1 in os.environ:
self._env_keys.remove(name1)
value = parse(os.environ[name1])
name2 = "STARFISH_" + name1
if name2 in os.environ:
if value:
warnings.warn(f"duplicate variable: (STARFISH_){name1}")
self._env_keys.remove(name2)
value = parse(os.environ[name2])
if value is None:
return # Nothing found
v = self._slicedimage
for k in lookup[:-1]:
v = v[k]
v[lookup[-1]] = value
def flag(self, name, default_value=""):
if name in os.environ:
value = os.environ[name]
self._env_keys.remove(name)
else:
value = default_value
if isinstance(value, str):
value = value.lower()
return value in ("true", "1", "yes", "y", "on", "active", "enabled")
@property
def slicedimage(self):
return dict(self._slicedimage)
@property
def strict(self):
return self._strict
@property
def verbose(self):
return self._verbose
def test_lookup_dne():
config = Config(simple_str)
with raises(KeyError):
config.lookup(["foo"])
assert config.lookup(["foo"], 1) == 1
assert config.lookup(["foo", "bar"], 2) == 2
def test_simple_config_value_file(tmpdir):
f = tmpdir.join("config.json")
f.write(simple_str)
config = Config(f"@{f}")
assert config.data["a"] == 1
def test_simple_config_value_map():
config = Config(simple_map)
assert config.data["a"] == 1