def test_load_yaml_string():
d = ConfigTree()
d.update(TEST_YAML_ONE, source='inline_test')
assert d.test_section.test_key == 'test_value'
assert d.test_section.test_key2 == 'test_value2'
assert d.test_section2.test_key == 'test_value3'
def test_load_yaml_file(tmpdir):
tmp_file = tmpdir.join('test_file.yaml')
tmp_file.write(TEST_YAML_ONE)
d = ConfigTree()
d.update(str(tmp_file))
assert d.test_section.test_key == 'test_value'
assert d.test_section.test_key2 == 'test_value2'
assert d.test_section2.test_key == 'test_value3'
def test_update_dict():
d = ConfigTree(layers=['inner', 'outer'])
d.update({
'test_key': 'test_value',
'test_key2': 'test_value2'
},
layer='inner')
d.update({'test_key': 'test_value3'}, layer='outer')
assert d.test_key == 'test_value3'
assert d.test_key2 == 'test_value2'
def test_dictionary_style_access():
d = ConfigTree()
d.update({'test_key': 'test_value', 'test_key2': 'test_value2'})
assert d['test_key'] == 'test_value'
assert d['test_key2'] == 'test_value2'
with pytest.raises(DuplicatedConfigurationError):
d['test_key2'] = 'test_value3'
assert d['test_key2'] == 'test_value2'
assert d['test_key'] == 'test_value'
def test_single_layer():
d = ConfigTree()
d.update({'test_key': 'test_value', 'test_key2': 'test_value2'})
assert d.test_key == 'test_value'
assert d.test_key2 == 'test_value2'
with pytest.raises(DuplicatedConfigurationError):
d.test_key2 = 'test_value3'
assert d.test_key2 == 'test_value2'
assert d.test_key == 'test_value'
def test_source_metadata():
d = ConfigTree(layers=['inner', 'outer'])
d.update({'test_key': 'test_value'}, layer='inner', source='initial_load')
d.update({'test_key': 'test_value2'}, layer='outer', source='update')
assert d.metadata('test_key') == [{
'layer': 'inner',
'source': 'initial_load',
'value': 'test_value'
}, {
'layer': 'outer',
'source': 'update',
'value': 'test_value2'
}]
def _get_default_specification():
default_config_layers = [
'base', 'component_configs', 'model_override', 'override'
]
default_metadata = {'layer': 'base', 'source': 'vivarium_defaults'}
model_specification = ConfigTree(layers=default_config_layers)
model_specification.update(DEFAULT_PLUGINS, **default_metadata)
model_specification.update({'components': None})
user_config_path = os.path.expanduser('~/vivarium.yaml')
if os.path.exists(user_config_path):
model_specification.configuration.update(user_config_path,
layer='component_configs')
return model_specification
def test_freeze():
config = ConfigTree(
data={'configuration': {
'time': {
'start': {
'year': 2000
}
}
}})
config.freeze()
with pytest.raises(ConfigurationError):
config.update(
data={'configuration': {
'time': {
'end': {
'year': 2001
}
}
}})
def test_retrieval_behavior():
layer_inner = 'inner'
layer_middle = 'middle'
layer_outer = 'outer'
default_cfg_value = 'value_a'
layer_list = [layer_inner, layer_middle, layer_outer]
# update the ConfigTree layers in different order and verify that has no effect on
# the values retrieved ("outer" is retrieved when no layer is specified regardless of
# the initialization order
for scenario in [layer_list, reversed(layer_list)]:
cfg = ConfigTree(layers=layer_list)
for layer in scenario:
cfg.update({default_cfg_value: layer}, layer=layer)
assert cfg.get_from_layer(default_cfg_value) == layer_outer
assert cfg.get_from_layer(default_cfg_value,
layer=layer_outer) == layer_outer
assert cfg.get_from_layer(default_cfg_value,
layer=layer_middle) == layer_middle
assert cfg.get_from_layer(default_cfg_value,
layer=layer_inner) == layer_inner
def test_repr_display():
expected_repr = '''\
Key1:
override_2: value_ov_2
source: ov2_src
override_1: value_ov_1
source: ov1_src
base: value_base
source: base_src'''
# codifies the notion that repr() displays values from most to least overridden
# regardless of initialization order
layers = ['base', 'override_1', 'override_2']
cfg = ConfigTree(layers=layers)
cfg.update({'Key1': 'value_ov_2'}, layer='override_2', source='ov2_src')
cfg.update({'Key1': 'value_ov_1'}, layer='override_1', source='ov1_src')
cfg.update({'Key1': 'value_base'}, layer='base', source='base_src')
assert repr(cfg) == textwrap.dedent(expected_repr)
cfg = ConfigTree(layers=layers)
cfg.update({'Key1': 'value_base'}, layer='base', source='base_src')
cfg.update({'Key1': 'value_ov_1'}, layer='override_1', source='ov1_src')
cfg.update({'Key1': 'value_ov_2'}, layer='override_2', source='ov2_src')
assert repr(cfg) == textwrap.dedent(expected_repr)
def test_update_dict_nested():
d = ConfigTree(layers=['inner', 'outer'])
d.update(
{
'test_container': {
'test_key': 'test_value',
'test_key2': 'test_value2'
}
},
layer='inner')
with pytest.raises(DuplicatedConfigurationError):
d.update({'test_container': {
'test_key': 'test_value3'
}},
layer='inner')
assert d.test_container.test_key == 'test_value'
assert d.test_container.test_key2 == 'test_value2'
d.update({'test_container': {'test_key2': 'test_value4'}}, layer='outer')
assert d.test_container.test_key2 == 'test_value4'
def test_exception_on_source_for_missing_key():
d = ConfigTree(layers=['inner', 'outer'])
d.update({'test_key': 'test_value'}, layer='inner', source='initial_load')
with pytest.raises(ConfigurationKeyError):
d.metadata('missing_key')
class PluginManager:
def __init__(self, plugin_configuration=None):
self._plugin_configuration = ConfigTree(DEFAULT_PLUGINS['plugins'],
layers=['base', 'override'])
self._plugin_configuration.update(plugin_configuration,
source='initialization_args')
self._plugins = {}
def get_plugin(self, name):
if name not in self._plugins:
self._plugins[name] = self._get(name)
return self._plugins[name]['controller']
def get_plugin_interface(self, name):
if name not in self._plugins:
self._plugins[name] = self._get(name)
return self._plugins[name]['builder_interface']
def get_core_controllers(self):
core_components = [
name for name in self._plugin_configuration['required'].keys()
] + list(_MANAGERS.keys())
return {name: self.get_plugin(name) for name in core_components}
def get_core_interfaces(self):
core_components = [
name for name in self._plugin_configuration['required'].keys()
] + list(_MANAGERS.keys())
return {
name: self.get_plugin_interface(name)
for name in core_components
}
def get_optional_controllers(self):
return {
name: self.get_plugin(name)
for name in self._plugin_configuration['optional'].keys()
}
def get_optional_interfaces(self):
return {
name: self.get_plugin_interface(name)
for name in self._plugin_configuration['optional'].keys()
}
def _get(self, name):
if name not in self._plugins:
self._plugins[name] = self._build_plugin(name)
return self._plugins[name]
def _build_plugin(self, name):
plugin = self._lookup(name)
try:
controller = import_by_path(plugin['controller'])()
except ValueError:
raise PluginConfigurationError(
f'Invalid plugin specification {plugin["controller"]}')
if plugin['builder_interface'] is not None:
try:
interface = import_by_path(
plugin['builder_interface'])(controller)
except ValueError:
raise PluginConfigurationError(
f'Invalid plugin specification {plugin["builder_interface"]}'
)
else:
interface = None
return {'controller': controller, 'builder_interface': interface}
def _lookup(self, name):
if name in self._plugin_configuration['required']:
return self._plugin_configuration['required'][name]
elif name in self._plugin_configuration['optional']:
return self._plugin_configuration['optional'][name]
elif name in _MANAGERS:
return _MANAGERS[name]
else:
raise PluginConfigurationError(f'Plugin {name} not found.')
def __repr__(self):
return "PluginManager()"