def test_two_concats():
config, paths, concats, extras = config_from_toml(
DIR / 'two_concats.toml',
path_guess='{0.stem}.csv',
)
assert config == {
'well': {
'A1': {
'x': 2
},
}
}
assert row(concats[0], 'well == "A1"') == dict(
path=DIR / 'one_well_xy.csv',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
)
assert row(concats[1], 'well == "A1"') == dict(
path=DIR / 'one_well_xyz.csv',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=0,
y=0,
z=1,
)
def test_two_plates():
df = bio96.load(
DIR / 'two_plates.toml',
data_loader=pd.read_csv,
merge_cols={'well': 'Well'},
)
assert row(df, 'plate == "a"') == dict(
path=DIR / 'two_plates_a.csv',
plate='a',
well='A1',
Well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
Data=0,
)
assert row(df, 'plate == "b"') == dict(
path=DIR / 'two_plates_b.csv',
plate='b',
well='A1',
Well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=2,
Data=1,
)
def test_named_plates_with_defaults():
config = {
'expt': {
'z': 1,
},
'well': {
'A1': {
'x': 1,
'y': 1
},
},
'plate': {
'Q': {
'well': {
'A1': {
'x': 2
},
},
},
'R': {
'well': {
'A1': {
'y': 2
},
},
},
},
}
df = table_from_config(config, DummyPathManager())
assert row(df, 'plate == "Q"') == dict(
plate='Q',
path='/path/to/q',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=2,
y=1,
z=1,
)
assert row(df, 'plate == "R"') == dict(
plate='R',
path='/path/to/r',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=2,
z=1,
)
def test_top_level():
config = {
'plate': {
'Q': {
'y': 3,
'well': {
'A1': {
'x': 1
},
},
},
'R': {
'y': 4,
'well': {
'A1': {
'x': 2
},
},
},
},
}
df = table_from_config(config, DummyPathManager())
assert row(df, 'plate == "Q"') == dict(
plate='Q',
path='/path/to/q',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=3,
)
assert row(df, 'plate == "R"') == dict(
plate='R',
path='/path/to/r',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=2,
y=4,
)
def test_one_plate():
labels = bio96.load(DIR / 'one_plate.toml')
assert row(labels, 'well == "A1"') == dict(
path=DIR / 'one_plate.csv',
plate='a',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
)
def test_only_plate():
config = {
'expt': {
'y': 2,
},
'well': {
'A1': {
'x': 1
},
},
}
df = table_from_config(config, DummyPathManager())
assert row(df, 'well == "A1"') == dict(
path='/path/to/data',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=2,
)
def test_one_well():
labels = bio96.load(DIR / 'one_well_xy.toml')
assert row(labels, 'well == "A1"') == dict(
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
)
labels = bio96.load(DIR / 'one_well_xy.toml', path_guess='{0.stem}.csv')
assert row(labels, 'well == "A1"') == dict(
path=DIR / 'one_well_xy.csv',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
)
with raises(ConfigError, match='one_well_xy.toml'):
bio96.load(DIR / 'one_well_xy.toml', path_required=True)
with raises(ConfigError, match='one_well_xy.toml'):
bio96.load(DIR / 'one_well_xy.toml', data_loader=pd.read_csv)
labels, data = bio96.load(
DIR / 'one_well_xy.toml',
data_loader=pd.read_csv,
path_guess='{0.stem}.csv',
)
assert row(labels, 'well == "A1"') == dict(
path=DIR / 'one_well_xy.csv',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
)
assert row(data, 'Well == "A1"') == dict(
Well='A1',
path=DIR / 'one_well_xy.csv',
Data='xy',
)
df = bio96.load(
DIR / 'one_well_xy.toml',
data_loader=pd.read_csv,
merge_cols={'well': 'Well'},
path_guess='{0.stem}.csv',
)
assert row(df, 'well == "A1"') == dict(
path=DIR / 'one_well_xy.csv',
well='A1',
Well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
Data='xy',
)
df = bio96.load(
DIR / 'one_well_xy.toml',
data_loader=read_csv_and_rename,
merge_cols=True,
path_guess='{0.stem}.csv',
)
assert row(df, 'well == "A1"') == dict(
path=DIR / 'one_well_xy.csv',
well='A1',
Well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
Data='xy',
)
def test_one_well_with_extras(extras_arg, expected):
labels, extras = bio96.load(
DIR / 'one_well_xy_extras.toml',
extras=extras_arg,
)
assert extras == expected
assert row(labels, 'well == "A1"') == dict(
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
)
labels, data, extras = bio96.load(
DIR / 'one_well_xy_extras.toml',
data_loader=pd.read_csv,
path_guess='{0.stem}.csv',
extras=extras_arg,
)
assert extras == expected
assert row(labels, 'well == "A1"') == dict(
path=DIR / 'one_well_xy_extras.csv',
well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
)
assert row(data, 'Well == "A1"') == dict(
Well='A1',
path=DIR / 'one_well_xy_extras.csv',
Data='xy',
)
# Merged data
a1_expected = dict(
path=DIR / 'one_well_xy_extras.csv',
well='A1',
Well='A1',
well0='A01',
row='A',
col='1',
row_i=0,
col_j=0,
x=1,
y=1,
Data='xy',
)
df, extras = bio96.load(
DIR / 'one_well_xy_extras.toml',
data_loader=pd.read_csv,
merge_cols={'well': 'Well'},
path_guess='{0.stem}.csv',
extras=extras_arg,
)
assert extras == expected
assert row(df, 'well == "A1"') == a1_expected
df, extras = bio96.load(
DIR / 'one_well_xy_extras.toml',
data_loader=read_csv_and_rename,
merge_cols=True,
path_guess='{0.stem}.csv',
extras=extras_arg,
)
assert extras == expected
assert row(df, 'well == "A1"') == a1_expected