def test_spectroscopic_table(self):
""""""
t = Table(
caption=Caption('Spectroscopic properties of Coumarins in acetonitrile at 298 K.'),
headings=[
[
Cell(''), # Blank compound heading
Cell('λmax (nm)'),
Cell('ε (M–1 cm–1)'),
Cell('λem (nm)'),
Cell('ϕ')
]
],
rows=[
[Cell('Coumarin 343'), Cell('398'), Cell('40 800'), Cell('492'), Cell('0.52')],
[Cell('C144'), Cell('429'), Cell('9500'), Cell('601'), Cell('N/A')],
[Cell('Coumarin 34'), Cell('269'), Cell('-'), Cell('435'), Cell('<0.01')],
]
)
# for record in t.caption.records:
# print(record.to_primitive())
# print(record.is_contextual)
gold = [
{'names': ['Coumarin 343'], 'quantum_yields': [{'type': '\u03d5', 'solvent': 'acetonitrile', 'value': '0.52', 'temperature': '298', 'temperature_units': 'K'}], 'uvvis_spectra': [{'temperature': '298', 'temperature_units': 'K', 'solvent': 'acetonitrile', 'peaks': [{'units': 'nm', 'value': '398'}]}, {'temperature': '298', 'temperature_units': 'K', 'solvent': 'acetonitrile', 'peaks': [{'extinction': '40800', 'extinction_units': 'M \u2013 1 cm \u2013 1'}]} ]},
{'labels': ['C144'], 'uvvis_spectra': [{'temperature': '298', 'temperature_units': 'K', 'solvent': 'acetonitrile', 'peaks': [{'units': 'nm', 'value': '429'}]}, {'temperature': '298', 'temperature_units': 'K', 'solvent': 'acetonitrile', 'peaks': [{'extinction': '9500', 'extinction_units': 'M \u2013 1 cm \u2013 1'}]}]},
{'names': ['Coumarin 34'], 'quantum_yields': [{'type': '\u03d5', 'solvent': 'acetonitrile', 'value': '<0.01', 'temperature': '298', 'temperature_units': 'K'}], 'uvvis_spectra': [{'temperature': '298', 'temperature_units': 'K', 'solvent': 'acetonitrile', 'peaks': [{'units': 'nm', 'value': '269'}]}]},
{'names': ['Coumarins']},
{'names': ['acetonitrile']}
]
# for record in t.records:
# print(record.to_primitive())
self.assertEqual(gold, [record.serialize() for record in t.records])
def test_uvvis_caption_with_multiple_compounds_is_ignored(self):
""" Checks the logic that captions are only accepted as compounds for all when they are the only chemical mentioned"""
t = Table(caption=Caption(
'Steady state spectral properties of HMBA and Carbon in different homogeneous solvents at 198 K.'
),
headings=[[Cell('Solvents'), Cell('λabs')]],
rows=[[Cell('Cyclohexane'), Cell('355')]])
gold = [{
'uvvis_spectra': [{
'peaks': [{
'value': '355'
}],
'temperature': '198',
'solvent': 'Cyclohexane',
'temperature_units': 'K'
}]
}, {
'names': ['HMBA']
}, {
'names': ['Carbon']
}]
self.assertEqual(gold, [record.serialize() for record in t.records])
def test_uvvis_caption(self):
""" Test's successful identification of compound from caption"""
t = Table(caption=Caption(
'Steady state spectral properties of HMBA in different homogeneous solvents.'
),
headings=[[Cell('Solvents'), Cell('λabs')]],
rows=[[Cell('Cyclohexane'), Cell('355')]])
gold = [{
'names': ['HMBA'],
'uvvis_spectra': [{
'peaks': [{
'value': '355'
}],
'solvent': 'Cyclohexane'
}]
}]
self.assertEqual(gold, [record.serialize() for record in t.records])
def test_uvvis_heading_units_different_cell(self):
""" Tests the specific case where the uvvis units are on a different row to the statement"""
t = Table(caption=Caption(''),
headings=[[Cell('Compound'), Cell('λmax')],
[Cell(''), Cell('(cm-1)')]],
rows=[[Cell('Coumarin 343'),
Cell('398')]])
gold = [{
'names': ['Coumarin 343'],
'uvvis_spectra': [{
'peaks': [{
'units': 'cm-1',
'value': '398'
}]
}]
}]
self.assertEqual(gold, [record.serialize() for record in t.records])
def test_uvvis_table(self):
""""""
t = Table(
caption=Caption(
'Selected photophysical properties of biarylsubstituted pyrazoles 5–8 and 1-methyl-3,5-diphenylpyrazole (9) at room temperature'
),
headings=[[
Cell('Compound'),
Cell('Absorption maxima λmax,abs (ε) [nm] (L cm−1 mol−1)'),
Cell('Emission maxima λmax,em (Φf) [nm] (a.u.)'),
Cell('Stokes-shift Δṽ [cm−1]')
]],
rows=[
[
Cell(' 5a '),
Cell('273.5 (40 100)'),
Cell('357.0 (0.77)'),
Cell('9400')
],
[
Cell(' 5b '),
Cell('268.5 (36 700)'),
Cell('359.0 (0.77)'),
Cell('8600')
],
[
Cell('Coumarin 343'),
Cell('263.0 (38 400)'),
Cell('344.5 (0.67)'),
Cell('9000')
],
[
Cell(' 5d '),
Cell('281.0 (34 200)'),
Cell('351.5 (0.97)'),
Cell('7100')
],
[
Cell(' 5e '),
Cell('285.0 (44 000)'),
Cell('382.0 (0.35)'),
Cell('8900')
],
[
Cell(' 5f '),
Cell('289.0 (43 300)'),
Cell('363.0 (0.80)'),
Cell('7100')
],
[
Cell(' 5g '),
Cell('285.0 (42 000)'),
Cell('343.5 (0.86)'),
Cell('6000')
],
[
Cell(' 6a '),
Cell('283.5 (35 600)'),
Cell('344.5 (0.49)'),
Cell('6300')
],
[
Cell(' 6b '),
Cell('267.5 (35 800)'),
Cell('338.5 (0.83)'),
Cell('7800')
],
[
Cell(' 6c '),
Cell('286.0 (33 000)'),
Cell('347.0 (0.27)'),
Cell('6200')
],
[
Cell(' 6d '),
Cell('306.5 (36 600)'),
Cell('384.0 (0.10)'),
Cell('6600')
],
[
Cell(' 7 '),
Cell('288.5 (62 500)'),
Cell('367.0 (0.07)'),
Cell('7400')
],
[
Cell('Compound 8a '),
Cell('257.0 (36 300), 293.0 sh (25 000)'),
Cell('385.0 (0.41)'),
Cell('8200')
],
[
Cell(' 8b '),
Cell('257.0 (32 000), 296.0 sh (23000)'),
Cell('388.0 (0.33)'),
Cell('8000')
],
[
Cell(' 8c '),
Cell('257.0 (27 400), 307.5 (18900)'),
Cell('387.0 (0.12)'),
Cell('6700')
],
[
Cell(' 8d '),
Cell('268.5 (29 500)'),
Cell('385.0 (0.29)'),
Cell('11 300')
],
[
Cell('Dye 8e '),
Cell('261.5 (39 900), 288.0 sh (29 600), 311.0 sh (20 500)'
),
Cell('386.5 (0.37)'),
Cell('6300')
],
[
Cell(' 8f '),
Cell('256.5 (27 260), 296.0 (28404)'),
Cell('388.5 (0.35)'),
Cell('8000')
],
[
Cell(' 8g '),
Cell('272.5 (39 600)'),
Cell('394.0 (0.30)'),
Cell('11 300')
],
[
Cell(' 8h '),
Cell('286.0 (22 900)'),
Cell('382.5 (0.33)'),
Cell('8800')
],
[
Cell(' 9 '),
Cell('254.0 (28 800)'),
Cell('338.5 (0.40)'),
Cell('9800')
]
])
gold = [
{
'labels': [u'5a'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'40100',
'value': u'273.5'
}]
}],
'quantum_yields': [{
'value': u'0.77'
}]
},
{
'labels': [u'5b'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'36700',
'value': u'268.5'
}]
}],
'quantum_yields': [{
'value': u'0.77'
}]
},
{
'names': [u'Coumarin 343'],
'quantum_yields': [{
'value': u'0.67'
}],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'38400',
'value': u'263.0'
}]
}]
},
{
'labels': [u'5d'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'34200',
'value': u'281.0'
}]
}],
'quantum_yields': [{
'value': u'0.97'
}]
},
{
'labels': [u'5e'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'44000',
'value': u'285.0'
}]
}],
'quantum_yields': [{
'value': u'0.35'
}]
},
{
'labels': [u'5f'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'43300',
'value': u'289.0'
}]
}],
'quantum_yields': [{
'value': u'0.80'
}]
},
{
'labels': [u'5g'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'42000',
'value': u'285.0'
}]
}],
'quantum_yields': [{
'value': u'0.86'
}]
},
{
'labels': [u'6a'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'35600',
'value': u'283.5'
}]
}],
'quantum_yields': [{
'value': u'0.49'
}]
},
{
'labels': [u'6b'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'35800',
'value': u'267.5'
}]
}],
'quantum_yields': [{
'value': u'0.83'
}]
},
{
'labels': [u'6c'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'33000',
'value': u'286.0'
}]
}],
'quantum_yields': [{
'value': u'0.27'
}]
},
{
'labels': [u'6d'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'36600',
'value': u'306.5'
}]
}],
'quantum_yields': [{
'value': u'0.10'
}]
},
{
'labels': [u'7'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'62500',
'value': u'288.5'
}]
}],
'quantum_yields': [{
'value': u'0.07'
}]
},
{
'labels': [u'8a'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'36300',
'value': u'257.0'
}, {
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'shape': u'sh',
'extinction': u'25000',
'value': u'293.0'
}]
}],
'quantum_yields': [{
'value': u'0.41'
}]
},
{
'labels': [u'8b'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'32000',
'value': u'257.0'
}, {
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'shape': u'sh',
'extinction': u'23000',
'value': u'296.0'
}]
}],
'quantum_yields': [{
'value': u'0.33'
}]
},
{
'labels': [u'8c'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'27400',
'value': u'257.0'
}, {
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'18900',
'value': u'307.5'
}]
}],
'quantum_yields': [{
'value': u'0.12'
}]
},
{
'labels': [u'8d'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'29500',
'value': u'268.5'
}]
}],
'quantum_yields': [{
'value': u'0.29'
}]
},
{
'labels': [u'8e'],
'quantum_yields': [{
'value': u'0.37'
}],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'39900',
'value': u'261.5'
}, {
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'shape': u'sh',
'extinction': u'29600',
'value': u'288.0'
}, {
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'shape': u'sh',
'extinction': u'20500',
'value': u'311.0'
}]
}]
},
{
'labels': [u'8f'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'27260',
'value': u'256.5'
}, {
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'28404',
'value': u'296.0'
}]
}],
'quantum_yields': [{
'value': u'0.35'
}]
},
{
'labels': [u'8g'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'39600',
'value': u'272.5'
}]
}],
'quantum_yields': [{
'value': u'0.30'
}]
},
{
'labels': [u'8h'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'22900',
'value': u'286.0'
}]
}],
'quantum_yields': [{
'value': u'0.33'
}]
},
{
'labels': [u'9'],
'uvvis_spectra': [{
'peaks': [{
'units': u'nm',
'extinction_units': u'L cm \u2212 1 mol \u2212 1',
'extinction': u'28800',
'value': u'254.0'
}]
}],
'quantum_yields': [{
'value': u'0.40'
}]
},
]
for record in t.records:
print(record.to_primitive())
self.assertEqual(gold, [record.to_primitive() for record in t.records])