def test_load_from_dict_invalid_property(write_yaml):
dict_ = {
"properties": {"dummy": 300},
"policy": {"properties": {"C": 1.9}},
"finder": {"properties": {"time_limit": 300}},
}
with pytest.raises(AttributeError):
Configuration.from_dict(dict_)
def __init__(self,
configfile: str = None,
configdict: StrDict = None) -> None:
self._logger = logger()
if configfile:
self.config = Configuration.from_file(configfile)
elif configdict:
self.config = Configuration.from_dict(configdict)
else:
self.config = Configuration()
self.expansion_policy = self.config.expansion_policy
self.filter_policy = self.config.filter_policy
def test_load_stock(write_yaml, create_dummy_stock1):
stock_filename = create_dummy_stock1("hdf5")
filename = write_yaml({"stock": {"files": {"test": stock_filename}}})
config = Configuration.from_file(filename)
assert config.stock.items == ["test"]
def test_load_stock(write_yaml, shared_datadir):
stock_filename = str(shared_datadir / "stock1.h5")
filename = write_yaml({"stock": {"files": {"test": stock_filename}}})
config = Configuration.from_file(filename)
assert config.stock.items == ["test"]
def test_load_scorer_from_module_spec(write_yaml):
filename = write_yaml(
{"scorer": {"aizynthfinder.context.scoring.PriceSumScorer": None}}
)
config = Configuration.from_file(filename)
assert "sum of prices" in config.scorers.items
def test_load_default_mongodb(write_yaml, mocker):
mocked_client = mocker.patch("aizynthfinder.context.stock.MongoClient")
filename = write_yaml({"stock": {"mongodb": {}}})
config = Configuration.from_file(filename)
mocked_client.assert_called_with(None)
assert config.stock.items == ["mongodb_stock"]
def test_load_policy(write_yaml, create_dummy_templates, mock_keras_model):
templates_filename = create_dummy_templates(3)
filename = write_yaml(
{"policy": {"files": {"test": ["dummy", templates_filename]}}}
)
config = Configuration.from_file(filename)
assert config.expansion_policy.items == ["test"]
def test_load_filter_policy(write_yaml, shared_datadir, mock_policy_model):
templates_filename = str(shared_datadir / "templates.hdf5")
filename = write_yaml(
{"filter": {"files": {"test": ["dummy", templates_filename]}}}
)
config = Configuration.from_file(filename)
assert config.filter_policy.items == ["test"]
def __init__(self, configfile=None, configdict=None):
self._logger = logger()
if configfile:
self.config = Configuration.from_file(configfile)
elif configdict:
self.config = Configuration.from_dict(configdict)
else:
self.config = Configuration()
self.expansion_policy = self.config.expansion_policy
self.filter_policy = self.config.filter_policy
self.stock = self.config.stock
self.scorers = self.config.scorers
self.tree = None
self._target_mol = None
self.search_stats = {}
self.routes = None
self.analysis = None
def __init__(self, configfile: str = None, configdict: StrDict = None) -> None:
self._logger = logger()
if configfile:
self.config = Configuration.from_file(configfile)
elif configdict:
self.config = Configuration.from_dict(configdict)
else:
self.config = Configuration()
self.expansion_policy = self.config.expansion_policy
self.filter_policy = self.config.filter_policy
self.stock = self.config.stock
self.scorers = self.config.scorers
self.tree: Optional[SearchTree] = None
self._target_mol: Optional[Molecule] = None
self.search_stats: StrDict = dict()
self.routes = RouteCollection([])
self.analysis: Optional[TreeAnalysis] = None
def test_load_stop_criteria(write_yaml):
filename = write_yaml(
{"stock": {"stop_criteria": {"price": 100, "counts": {"C": 10}}}}
)
config = Configuration.from_file(filename)
set_keys = [key for key, item in config.stock.stop_criteria.items() if item]
assert set_keys == ["price", "counts"]
assert list(config.stock.stop_criteria["counts"].keys()) == ["C"]
assert config.stock.stop_criteria["counts"]["C"] == 10
def test_load_external_stock_incorrect_class(write_yaml, shared_datadir):
stock_filename = str(shared_datadir / "stock1.h5")
filename = write_yaml({
"stock": {
"aizynthfinder.context.stock.InnMemoryInchiKeyQuery": {
"filename": stock_filename
}
}
})
config = Configuration.from_file(filename)
assert config.stock.items == []
def test_load_from_file(write_yaml):
filename = write_yaml(
{
"properties": {"cutoff_number": 300},
"policy": {"properties": {"C": 1.9}},
"finder": {"properties": {"time_limit": 300}},
}
)
config = Configuration.from_file(filename)
assert config.cutoff_number == 300
assert config.C == 1.9
assert config.time_limit == 300
def test_load_external_stock_incorrect_class(write_yaml, create_dummy_stock1):
stock_filename = create_dummy_stock1("hdf5")
filename = write_yaml(
{
"stock": {
"aizynthfinder.context.stock.InnMemoryInchiKeyQuery": {
"filename": stock_filename
}
}
}
)
config = Configuration.from_file(filename)
assert config.stock.items == []
def test_load_specific_mongodb(write_yaml, mocker):
mocked_client = mocker.patch(
"aizynthfinder.context.stock.get_mongo_client")
filename = write_yaml({
"stock": {
"mongodb": {
"host": "myhost",
"database": "mydatabase",
"collection": "mycollection",
}
}
})
config = Configuration.from_file(filename)
mocked_client.assert_called_with("myhost")
assert config.stock.items == ["mongodb_stock"]
config.stock["mongodb_stock"].client.__getitem__.assert_called_with(
"mydatabase")
config.stock["mongodb_stock"].database.__getitem__.assert_called_with(
"mycollection")
def default_config():
return Configuration()
def test_load_empty_dict(default_config):
config = Configuration.from_dict({})
assert config == default_config
def test_load_scorer_from_context_module(write_yaml):
filename = write_yaml({"scorer": {"PriceSumScorer": None}})
config = Configuration.from_file(filename)
assert "sum of prices" in config.scorers.items
def test_load_empty_file(default_config, write_yaml):
filename = write_yaml({})
config = Configuration.from_file(filename)
assert config == default_config
def test_load_filter_policy(write_yaml, mock_keras_model):
filename = write_yaml({"filter": {"files": {"test": "dummy"}}})
config = Configuration.from_file(filename)
assert config.filter_policy.items == ["test"]
