def test_load_yaml_string():
d = ConfigTree()
d._loads(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_dictionary_style_access():
d = ConfigTree()
d.test_key = 'test_value'
d['test_key2'] = 'test_value2'
assert d['test_key'] == 'test_value'
assert d.test_key2 == 'test_value2'
def test_reset_layer():
d = ConfigTree(layers=['a', 'b', 'c'])
d.set_with_metadata('test_key', 'test_value', 'a')
d.set_with_metadata('test_key', 'test_value2', 'b')
assert d.test_key == 'test_value2'
d.reset_layer('b')
assert d.test_key == 'test_value'
d.set_with_metadata('test_key', 'test_value3', 'b')
def test_exception_on_source_for_missing_key():
d = ConfigTree(layers=['inner', 'outer'])
d.read_dict({'test_key': 'test_value'},
layer='inner',
source='initial_load')
with pytest.raises(KeyError) as excinfo:
source = d.metadata('missing_key')
assert 'missing_key' in str(excinfo.value)
def test_load_yaml_file(tmpdir):
tmp_file = tmpdir.join('test_file.yaml')
tmp_file.write(TEST_YAML_ONE)
d = ConfigTree()
d._load(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_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.test_key = 'test_value'
d.test_key2 = 'test_value2'
assert d.test_key == 'test_value'
assert d.test_key2 == 'test_value2'
d.test_key2 = 'test_value3'
assert d.test_key2 == 'test_value3'
assert d.test_key == 'test_value'
def test_drop_layer():
d = ConfigTree(layers=['a', 'b', 'c'])
d.set_with_metadata('test_key', 'test_value', 'a')
d.set_with_metadata('test_key', 'test_value2', 'b')
d.set_with_metadata('test_key', 'test_value3', 'c')
assert d.test_key == 'test_value3'
d.drop_layer('c')
assert d.test_key == 'test_value2'
with pytest.raises(ValueError):
d.drop_layer('c')
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_tree_coerce_dict():
d, s = {}, 'test'
assert ConfigTree._coerce(d, s) == (d, s)
d, s = {'key': 'val'}, 'test'
assert ConfigTree._coerce(d, s) == (d, s)
d = {
'key1': {
'sub_key1': ['val', 'val', 'val'],
'sub_key2': 'val'
},
'key2': 'val'
}
s = 'test'
assert ConfigTree._coerce(d, s) == (d, s)
def test_unused_keys():
d = ConfigTree(
{'test_key': {
'test_key2': 'test_value',
'test_key3': 'test_value2'
}})
assert d.unused_keys() == {'test_key.test_key2', 'test_key.test_key3'}
_ = d.test_key.test_key2
assert d.unused_keys() == {'test_key.test_key3'}
_ = d.test_key.test_key3
assert not d.unused_keys()
def test_outer_layer_set():
d = ConfigTree(layers=['inner', 'outer'])
d.set_with_metadata('test_key', 'test_value', 'inner')
d.set_with_metadata('test_key', 'test_value2', 'outer')
d.test_key = 'test_value3'
assert d.test_key == 'test_value3'
def base_plugins():
config = {
'required': {
'data': {
'controller':
'vivarium_population_spenser.testing.mock_artifact.MockArtifactManager',
'builder_interface':
'vivarium.framework.artifact.ArtifactInterface'
}
}
}
return ConfigTree(config)
def test_tree_coerce_yaml(tmpdir):
d = '''\
key1:
sub_key1:
- val
- val
- val
sub_key2: [val, val]
key2: val'''
r = {
'key1': {
'sub_key1': ['val', 'val', 'val'],
'sub_key2': ['val', 'val']
},
'key2': 'val'
}
s = 'test'
p = tmpdir.join('model_spec.yaml')
with p.open('w') as f:
f.write(d)
assert ConfigTree._coerce(str(p), s) == (r, s)
assert ConfigTree._coerce(str(p), None) == (r, str(p))
def test_tree_coerce_str():
d = ''''''
s = 'test'
assert ConfigTree._coerce(d, s) == (None, s)
d = '''\
key: val'''
assert ConfigTree._coerce(d, s) == ({'key': 'val'}, s)
d = '''\
key1:
sub_key1:
- val
- val
- val
sub_key2: val
key2: val'''
r = {
'key1': {
'sub_key1': ['val', 'val', 'val'],
'sub_key2': 'val'
},
'key2': 'val'
}
assert ConfigTree._coerce(d, s) == (r, s)
d = '''\
key1:
sub_key1: [val, val, val]
sub_key2: val
key2: val'''
r = {
'key1': {
'sub_key1': ['val', 'val', 'val'],
'sub_key2': 'val'
},
'key2': 'val'
}
assert ConfigTree._coerce(d, s) == (r, s)
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 test_read_dict():
d = ConfigTree(layers=['inner', 'outer'])
d.read_dict({
'test_key': 'test_value',
'test_key2': 'test_value2'
},
layer='inner')
d.read_dict({'test_key': 'test_value3'}, layer='outer')
assert d.test_key == 'test_value3'
assert d.test_key2 == 'test_value2'
def test_read_dict_nested():
d = ConfigTree(layers=['inner', 'outer'])
d.read_dict(
{
'test_container': {
'test_key': 'test_value',
'test_key2': 'test_value2'
}
},
layer='inner')
d.read_dict({'test_container': {'test_key': 'test_value3'}}, layer='inner')
assert d.test_container.test_key == 'test_value3'
assert d.test_container.test_key2 == 'test_value2'
d.read_dict({'test_container': {
'test_key2': 'test_value4'
}},
layer='outer')
assert d.test_container.test_key2 == 'test_value4'
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_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_reset_layer_with_preserved_keys_at_depth():
d = ConfigTree(layers=['a', 'b', 'c'])
d.read_dict(
{
'test_key': {
'test_key2': 'test_value',
'test_key3': {
'test_key4': 'test_value2'
}
},
'test_key5': {
'test_key6': 'test_value3',
'test_key7': 'test_value4'
}
},
layer='a')
d.read_dict(
{
'test_key': {
'test_key2': 'test_value5',
'test_key3': {
'test_key4': 'test_value6'
}
},
'test_key5': {
'test_key6': 'test_value7',
'test_key7': 'test_value8'
}
},
layer='b')
d.reset_layer(
'b',
preserve_keys=['test_key.test_key3', 'test_key.test_key5.test_key6'])
d.test_key.test_key2 == 'test_value'
d.test_key.test_key3.test_key4 == 'test_value6'
d.test_key5.test_key6 == 'test_value7'
d.test_key5.test_key7 == 'test_value4'
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_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')
def test_to_dict_dict():
test_dict = {'configuration': {'time': {'start': {'year': 2000}}}}
config = ConfigTree(test_dict)
assert config.to_dict() == test_dict
def test_to_dict_yaml(test_spec):
config = ConfigTree(str(test_spec))
with test_spec.open() as f:
yaml_config = yaml.full_load(f)
assert yaml_config == config.to_dict()
def test_multiple_layer_get():
d = ConfigTree(layers=['first', 'second', 'third'])
d.set_with_metadata('test_key', 'test_value', 'first')
d.set_with_metadata('test_key', 'test_value2', 'second')
d.set_with_metadata('test_key', 'test_value3', 'third')
d.set_with_metadata('test_key2', 'test_value4', 'first')
d.set_with_metadata('test_key2', 'test_value5', 'second')
d.set_with_metadata('test_key3', 'test_value6', 'first')
assert d.test_key == 'test_value3'
assert d.test_key2 == 'test_value5'
assert d.test_key3 == 'test_value6'
def test_get_missing():
d = ConfigTree()
d.test_key = 'test_value'
# Missing keys should be empty containers
assert len(d.missing_key) == 0
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_reset_layer_with_preserved_keys():
d = ConfigTree(layers=['a', 'b', 'c'])
d.set_with_metadata('test_key', 'test_value', 'a')
d.set_with_metadata('test_key2', 'test_value2', 'a')
d.set_with_metadata('test_key3', 'test_value3', 'a')
d.set_with_metadata('test_key4', 'test_value4', 'a')
d.set_with_metadata('test_key', 'test_value5', 'b')
d.set_with_metadata('test_key2', 'test_value6', 'b')
d.set_with_metadata('test_key3', 'test_value7', 'b')
d.set_with_metadata('test_key4', 'test_value8', 'b')
d.reset_layer('b', preserve_keys=['test_key2', 'test_key3'])
assert d.test_key == 'test_value'
assert d.test_key2 == 'test_value6'
assert d.test_key3 == 'test_value7'
assert d.test_key4 == 'test_value4'
