def test_read_precision(precision_path):
gc = GC()
precision, precision_series = gc.read_precision(precision_path)
prec_test = [
"NF3", "CF4", "PFC-116", "PFC-218", "PFC-318", "C4F10", "C6F14", "SF6"
]
end_prec_test = [
"ethene",
"ethane",
"propane",
"c-propane",
"benzene",
"toluene",
"COS",
"desflurane",
]
assert precision_series[:8] == prec_test
assert precision_series[-8:] == end_prec_test
precision_head = precision.head(1)
assert precision_head.iloc[0, 0] == 0.02531
assert precision_head.iloc[0, 2] == 0.08338
assert precision_head.iloc[0, 5] == 10
assert precision_head.iloc[0, 7] == 10
assert precision_head.iloc[0, 10] == 0.00565
def clear_datasources(args):
from HUGS.Modules import CRDS, GC
gc = GC.load()
crds = CRDS.load()
crds.clear_datasources()
gc.clear_datasources()
crds.save()
gc.save()
def test_read_invalid_instrument_raises(data_path_no_instrument,
precision_path_no_instrument):
gc = GC()
with pytest.raises(ValueError):
gc.read_file(
data_filepath=data_path_no_instrument,
precision_filepath=precision_path_no_instrument,
source_name="capegrim_medusa",
site="CGO",
instrument_name="fish",
)
def test_read_valid_instrument_passed(data_path_no_instrument,
precision_path_no_instrument):
gc = GC()
data = gc.read_file(
data_filepath=data_path_no_instrument,
precision_filepath=precision_path_no_instrument,
source_name="capegrim_medusa",
site="CGO",
instrument_name="medusa",
)
assert sorted(list(data.keys())) == sorted([
'CH4', 'CFC-12', 'N2O', 'CFC-11', 'CFC-113', 'CHCl3', 'CH3CCl3', 'CCl4'
])
def test_read_file_incorrect_inlet_raises(precision_path):
data_path = Path(__file__).resolve().parent.joinpath(
"../data/proc_test_data/GC/capegrim-incorrect-inlet.18.C")
gc = GC()
with pytest.raises(ValueError):
gc.read_file(
data_filepath=data_path,
precision_filepath=precision_path,
source_name="capegrim_medusa",
site="CGO",
instrument_name="medusa",
)
def test_read_data(data_path, precision_path):
# Capegrim
site = "CGO"
instrument = "GCMD"
gc = GC()
data = gc.read_data(
data_filepath=data_path,
precision_filepath=precision_path,
site=site,
instrument=instrument,
)
propane_data = data["propane"]["data"]
head_data = propane_data.head(1)
tail_data = propane_data.tail(1)
assert head_data.time[0] == pd.Timestamp("2018-01-01 02:33:22.500")
assert head_data["propane"][0] == pytest.approx(5.458)
assert head_data["propane repeatability"][0] == 0.22325
assert tail_data.time[0] == pd.Timestamp("2018-01-31 23:42:22.500")
assert tail_data["propane"][0] == 4.136
assert tail_data["propane repeatability"][0] == 0.16027
species = list(data.keys())
assert species[:8] == [
"NF3",
"CF4",
"PFC-116",
"PFC-218",
"PFC-318",
"C4F10",
"C6F14",
"SF6",
]
attributes = {
"data_owner": "Paul Krummel",
"data_owner_email": "*****@*****.**",
"inlet_height_magl": "75m_4",
"comment": "Gas chromatograph measurements. Output from GCWerks.",
}
assert data["NF3"]["attributes"] == attributes
def test_read_file(data_path, precision_path):
gc = GC()
gas_data = gc.read_file(
data_filepath=data_path,
precision_filepath=precision_path,
source_name="capegrim_medusa",
site="CGO",
instrument_name="medusa",
)
expected_eight = [
'C4F10', 'C6F14', 'CCl4', 'CF4', 'CFC-11', 'CFC-112', 'CFC-113',
'CFC-114'
]
sorted_keys = sorted(list(gas_data.keys()))
assert sorted_keys[:8] == expected_eight
assert len(sorted_keys) == 56
def test_split(data_path, precision_path):
site = "CGO"
instrument = "GCMD"
data_path = (Path(__file__).resolve().parent.joinpath(
"../data/proc_test_data/GC/test_split_data.pkl"))
# Load in the test data
# TODO - investigate error here
# df = pd.read_hdf(data_path)
# Use pickle due to error in CI with hdf verion
df = pd.read_pickle(data_path)
species = [
"NF3",
"CF4",
"PFC-116",
"PFC-218",
"PFC-318",
"C4F10",
"C6F14",
"SF6",
"SO2F2",
"SF5CF3",
"HFC-23",
"HFC-32",
"HFC-125",
"HFC-134a",
"HFC-143a",
"HFC-152a",
"HFC-227ea",
"HFC-236fa",
"HFC-245fa",
"HFC-365mfc",
"HFC-4310mee",
"HCFC-22",
"HCFC-123",
"HCFC-124",
"HCFC-132b",
"HCFC-133a",
"HCFC-141b",
"HCFC-142b",
"CFC-11",
"CFC-12",
"CFC-13",
"CFC-112",
"CFC-113",
"CFC-114",
"CFC-115",
"H-1211",
"H-1301",
"H-2402",
"CH3Cl",
"CH3Br",
"CH3I",
"CH2Cl2",
"CHCl3",
"CCl4",
"CH2Br2",
"CHBr3",
"CH3CCl3",
"TCE",
"PCE",
"ethyne",
"ethene",
"ethane",
"propane",
"c-propane",
"benzene",
"toluene",
"COS",
"desflurane",
]
metadata = {"foo": "bar"}
gc = GC()
units = {}
scale = {}
for s in species:
units[s] = "test_units"
scale[s] = "test_scale"
data = gc.split_species(
data=df,
site=site,
instrument=instrument,
species=species,
metadata=metadata,
units=units,
scale=scale,
)
sorted_species = [
"C4F10",
"C6F14",
"CCl4",
"CF4",
"CFC-11",
"CFC-112",
"CFC-113",
"CFC-114",
"CFC-115",
"CFC-12",
]
assert len(data) == 56
assert sorted(list(data.keys()))[:10] == sorted_species