def test_merge_all_uvvis_2(self):
uvvis1 = UvvisSpectrum(peaks=[UvvisPeak(value='345')])
uvvis2 = UvvisSpectrum(peaks=[UvvisPeak(value='123')])
comp = Compound(uvvis_spectra=[uvvis1, uvvis2])
gold = Compound(uvvis_spectra=[
UvvisSpectrum(
peaks=[UvvisPeak(value='345'),
UvvisPeak(value='123')])
])
self.assertEqual(indep.merge_all_uvvis(comp), gold)
def test_is_unidentified(self):
"""Test is_unidentified method returns expected result."""
self.assertEqual(Compound().is_unidentified, True)
self.assertEqual(
Compound(names=['Coumarin 343']).is_unidentified, False)
self.assertEqual(Compound(labels=['3a']).is_unidentified, False)
self.assertEqual(
Compound(names=['Coumarin 343'], labels=['3a']).is_unidentified,
False)
self.assertEqual(
Compound(melting_points=[MeltingPoint(
value='250')]).is_unidentified, True)
def test_is_contextual(self):
"""Test is_contextual method returns expected result."""
self.assertEqual(Compound(names=['Coumarin 343']).is_contextual, False)
self.assertEqual(
Compound(melting_points=[MeltingPoint(value='240')]).is_contextual,
False)
self.assertEqual(
Compound(melting_points=[MeltingPoint(units='K')]).is_contextual,
True)
self.assertEqual(
Compound(melting_points=[MeltingPoint(
apparatus='Some apparatus')]).is_contextual, True)
self.assertEqual(
Compound(labels=['3a'],
melting_points=[MeltingPoint(apparatus='Some apparatus')
]).is_contextual, False)
self.assertEqual(
Compound(uvvis_spectra=[UvvisSpectrum(
apparatus='Some apparatus')]).is_contextual, True)
self.assertEqual(
Compound(
uvvis_spectra=[UvvisSpectrum(peaks=[UvvisPeak(
value='378')])]).is_contextual, False)
self.assertEqual(
Compound(
uvvis_spectra=[UvvisSpectrum(peaks=[UvvisPeak(
units='nm')])]).is_contextual, True)
def interpret(self, result, start, end):
# print("inside cat cell")
# print(etree.tostring(result))
# print()
# print("test")
c = Compound(catalyst_name=[CAT(name=first(result.xpath('text()')), )])
yield c
def interpret(self, result, start, end):
context = {}
# print("footnote temp")
# print(etree.tostring(result))
# print()
c = Compound()
context = {}
tempvalue = first(result.xpath('//value/text()'))
tempunit = first(result.xpath('//units/text()'))
if tempunit and '℃' in tempunit:
tempunit = '°C'
if not tempvalue and not tempunit:
tempvalue = first(result.xpath('//tempphrase/text()'))
# print(tempvalue)
if not tempunit:
if "K" in tempvalue:
tempunit = 'K'
tempvalue = tempvalue.strip('K')
elif '°C' in tempvalue:
tempunit = '°C'
tempvalue = tempvalue.strip("°C")
else:
tempvalue = None
context["tempvalue"] = tempvalue
context["tempunits"] = tempunit
if context:
c.conv.append(Conv(**context))
yield c
def test_merge_uvvis_1(self):
"""Checks merge_peak_obj works in this context"""
uvvis = UvvisSpectrum(peaks=[
UvvisPeak(value='123'),
UvvisPeak(value='456'),
UvvisPeak(extinction='35000'),
UvvisPeak(extinction='40000')
])
comp = Compound(uvvis_spectra=[uvvis])
table_records = []
resolved_comp = indep.merge_uvvis(comp, table_records)
gold = {
'uvvis_spectra': [{
'peaks': [{
'value': '123',
'extinction': '35000'
}, {
'value': '456',
'extinction': '40000'
}]
}]
}
print(resolved_comp.serialize())
self.assertEqual(gold, resolved_comp.serialize())
def interpret(self, result, start, end):
""""""
compunits = [""]
# print("inside comp header")
# print(etree.tostring(result))
# print()
if len(result) == 1:
compunits = first(result.xpath('//unit/text()'))
elif len(result) > 1:
for item in result:
compunit = first(item.xpath('//unit/text()'))
if compunit:
compunits[0] += compunit
if compunits[0] == "":
compunits = []
# print(flowunits)
else:
compunits = []
# print("comp header")
if "/CO" in first(
result.xpath('//compphrase/text()')) or ":CO" in first(
result.xpath('//compphrase/text()')):
compunits = first(result.xpath('//compphrase/text()'))
if "CO/H2" in first(
result.xpath('//compphrase/text()')) or "CO:H2" in first(
result.xpath('//compphrase/text()')):
compunits = first(result.xpath('//compphrase/text()'))
# print(compunits)
# print(compunits)
c = Compound()
if compunits:
c.comp.append(Comp(unit=compunits))
yield c
def interpret(self, result, start, end):
""""""
context = {}
c = Compound()
no = first(result.xpath('./no/text()'))
tempunits = first(result.xpath('./tempunits/text()'))
context['tempunits'] = tempunits
tempvalues = first(result.xpath('./tempvalue/text()'))
context['tempvalue'] = tempvalues
any = first(result.xpath('//any/text()'))
context["convtype"] = any
# print("inside conv heading")
# print(etree.tostring(result))
check = result.xpath('/tempnumber')
# print("check: ", check)
# print()
if check:
# print("yes")
c.conv.append(Conv(**{'check': "True"}))
if no == None:
context['convunits'] = first(result.xpath('./convunits/text()'))
else:
context['convunits'] = first(result.xpath('./no/text()'))
if tempunits or any:
c.conv.append(Conv(**context))
yield c
def interpret(self, result, start, end):
# """"""
# print("inside bet header")
# print(etree.tostring(result))
# print()
units = first(result.xpath('//units/text()'))
# print(units)
c = Compound(bet=[BET(unit=units)])
yield c
def test_get_indices(self):
uvvis1 = UvvisSpectrum(
peaks=[UvvisPeak(
value='123'), UvvisPeak(value='456')])
uvvis2 = UvvisSpectrum(peaks=[UvvisPeak(extinction='35000')])
uvvis3 = UvvisSpectrum(peaks=[UvvisPeak(extinction='40000')])
comp = Compound(uvvis_spectra=[uvvis1, uvvis2, uvvis3])
val, ext = indep.get_indices(comp)
self.assertEqual(val, [0])
self.assertEqual(ext, [1, 2])
def interpret(self, result, start, end):
compound = Compound(
ff_pattern=[
Ff(
value=first(result.xpath('./value/text()')),
units=first(result.xpath('./units/text()'))
)
]
)
yield compound
def interpret(self, result, start, end):
compound = Compound(
melting_points=[
MeltingPoint(
value=first(result.xpath('./value/text()')),
units=first(result.xpath('./units/text()'))
)
]
)
yield compound
def interpret(self, result, start, end):
pressure = first(result.xpath('//value/text()'))
presunit = first(result.xpath('//units/text()'))
if not pressure:
pressure = first(result.xpath('//phrase/text()'))
# print("inside cell of pres")
# print(pressure)
# print(presunit)
c = Compound(conv=[Conv(pressure=pressure, pressureunit=presunit)])
yield c
def interpret(self, result, start, end):
# print("inside cell")
# print(etree.tostring(result))
# print()
tofvalue = first(result.xpath('./tofvalue/text()'))
tempvalue = first(result.xpath('./tempvalue/text()'))
tempunits = first(result.xpath('./tempunits/text()'))
c = Compound(conv=[
Conv(tofvalue=tofvalue, tempvalue=tempvalue, tempunits=tempunits)
])
yield c
def interpret(self, result, start, end):
""""""
# print("inside heading of pres")
# print(etree.tostring(result))
presunits = first(result.xpath('//units/text()'))
c = Compound()
if presunits:
c.conv.append(Conv(presunits=presunits))
yield c
def interpret(self, result, start, end):
context = {}
# print("footnote")
# print(etree.tostring(result))
# print()
c = Compound()
catname = first(result.xpath('./cat_phrase/name/text()'))
# print(catname)
context["captioncatname"] = catname
if context:
c.conv.append(Conv(**context))
yield c
def interpret(self, result, start, end):
# print("inside cell selectivity")
# print(etree.tostring(result))
# print()
value = result.xpath('./value/text()')
sel = Selectivity(value=value)
c = Compound()
if value:
c.conv.append(Conv(selectivity=[sel]))
yield c
def test_merge_all_uvvis_1(self):
peak1 = UvvisPeak(value='123', extinction='35000')
peak2 = UvvisPeak(value='456', extinction='40000')
comp = Compound(uvvis_spectra=[
UvvisSpectrum(peaks=[peak1]),
UvvisSpectrum(peaks=[peak2])
])
comp = indep.merge_all_uvvis(comp)
gold = {
'uvvis_spectra': [{
'peaks': [{
'value': '123',
'extinction': '35000'
}, {
'value': '456',
'extinction': '40000'
}]
}]
}
self.assertEqual(gold, comp.serialize())
def interpret(self, result, start, end):
""""""
# print("inside temp")
# print(etree.tostring(result))
# print()
# print(lollol)
tempunits = first(result.xpath('./units/text()'))
c = Compound()
if tempunits:
c.temp.append(Temp(unit=tempunits))
yield c
def interpret(self, result, start, end):
# print("inside flow cell")
# print(etree.tostring(result))
# print()
c = Compound(flow=[
Flow(
value=first(result.xpath('./value/text()')),
unit=first(result.xpath('./units/text()')),
)
])
yield c
def test_merge_uvvis_3(self):
"""Checks check_prev works in this context"""
uvvis_prev_1 = UvvisSpectrum(peaks=[UvvisPeak(value='123')])
uvvis_prev_2 = UvvisSpectrum(peaks=[UvvisPeak(value='456')])
uvvis_current_1 = UvvisSpectrum(peaks=[UvvisPeak(extinction='35000')])
uvvis_current_2 = UvvisSpectrum(peaks=[UvvisPeak(extinction='40000')])
comp_prev = Compound(uvvis_spectra=[uvvis_prev_1, uvvis_prev_2])
comp_current = Compound(
uvvis_spectra=[uvvis_current_1, uvvis_current_2])
table_records = [comp_prev]
comp_current = indep.merge_uvvis(comp_current, table_records)
gold_prev = {
'uvvis_spectra': [{
'peaks': [{
'value': '123',
'extinction': '35000'
}]
}, {
'peaks': [{
'value': '456',
'extinction': '40000'
}]
}]
}
gold_current = {}
self.assertEqual(gold_prev, comp_prev.serialize())
self.assertEqual(gold_current, comp_current.serialize())
def test_check_prev(self):
uvvis_prev_1 = UvvisSpectrum(peaks=[UvvisPeak(value='123')])
uvvis_prev_2 = UvvisSpectrum(peaks=[UvvisPeak(value='456')])
uvvis_current_1 = UvvisSpectrum(peaks=[UvvisPeak(extinction='35000')])
uvvis_current_2 = UvvisSpectrum(peaks=[UvvisPeak(extinction='40000')])
comp_prev = Compound(uvvis_spectra=[uvvis_prev_1, uvvis_prev_2])
comp_current = Compound(
uvvis_spectra=[uvvis_current_1, uvvis_current_2])
table_records = [comp_prev]
comp_current = indep.check_prev(comp_current, [], [0, 1],
table_records)
gold_prev = {
'uvvis_spectra': [{
'peaks': [{
'value': '123',
'extinction': '35000'
}]
}, {
'peaks': [{
'value': '456',
'extinction': '40000'
}]
}]
}
gold_current = {}
self.assertEqual(gold_prev, comp_prev.serialize())
self.assertEqual(gold_current, comp_current.serialize())
def interpret(self, result, start, end):
# print("inside betcell")
# print(etree.tostring(result))
# print()
value = result.xpath('//betvalue/text()')
if len(value) < 1:
value = result.xpath("//betcell/text()")
units = first(result.xpath('//units/text()'))
#
# print(value)
# print(units)
c = Compound(bet=[BET(value=value, unit=units)])
yield c
def test_merge_uvvis_4(self):
"""Checks merge_all_uvvis works in this context"""
peak1 = UvvisPeak(value='123', extinction='35000')
peak2 = UvvisPeak(value='456', extinction='40000')
comp = Compound(uvvis_spectra=[
UvvisSpectrum(peaks=[peak1]),
UvvisSpectrum(peaks=[peak2])
])
row_compound = []
comp = indep.merge_uvvis(comp, row_compound)
gold = {
'uvvis_spectra': [{
'peaks': [{
'value': '123',
'extinction': '35000'
}, {
'value': '456',
'extinction': '40000'
}]
}]
}
self.assertEqual(gold, comp.serialize())
def interpret(self, result, start, end):
""""""
# print("inside heading selectivity")
# print(etree.tostring(result))
# print()
selectivityunits = first(result.xpath('//units/text()'))
# print(selectivityunits)
# print()
c = Compound()
if selectivityunits:
sel = Selectivity(unit=selectivityunits)
c.conv.append(Conv(selectivity=[sel]))
# print(c.serialize())
yield c
def interpret(self, result, start, end):
# for item in result:
# print("inside cell")
# print(etree.tostring(item))
# print()
convvalue = first(result.xpath('//convvalue/text()'))
convunits = first(result.xpath('//convunits/text()'))
tempvalue = first(result.xpath('//tempvalue/text()'))
tempunits = first(result.xpath('//tempunits/text()'))
c = Compound(conv=[
Conv(convvalue=convvalue,
convunits=convunits,
tempvalue=tempvalue,
tempunits=tempunits)
])
yield c
def interpret(self, result, start, end):
""""""
# print("inside flow header")
# print(etree.tostring(result))
# print()
if type(result) == type([]):
for i in result:
flowunits = first(i.xpath('//unit/text()'))
if flowunits != None:
break
else:
flowunits = first(result.xpath('//unit/text()'))
c = Compound()
if flowunits:
c.flow.append(Flow(unit=flowunits))
yield c
def interpret(self, result, start, end):
c = Compound()
s = Anneal()
tempunits = first(result.xpath('./tempunits/text()'))
timeunits = first(result.xpath('./timeunits/text()'))
for temp in result.xpath('./temps/temp'):
anneal_temp = AnnealTemp(tempvalue=first(
temp.xpath('./tempvalue/text()')),
tempunits=tempunits)
s.temps.append(anneal_temp)
for time in result.xpath('./times/time'):
anneal_time = AnnealTime(timevalue=first(
time.xpath('./timevalue/text()')),
timeunits=timeunits)
s.times.append(anneal_time)
c.anneal.append(s)
yield c
def interpret(self, result, start, end):
# print("inside heading of tof")
# print(etree.tostring(result))
context = {}
no = first(result.xpath('./no/text()'))
context['tempunits'] = first(result.xpath('./tempunits/text()'))
context['tempvalue'] = first(result.xpath('./tempvalue/text()'))
if no == None:
context['convunits'] = first(result.xpath('./convunits/text()'))
else:
context['convunits'] = first(result.xpath('./no/text()'))
c = Compound()
if tempunits:
c.conv.append(Conv(**context))
yield c
def interpret(self, result, start, end):
c = Compound()
s = SpinCoat(
# solvent=first(result.xpath('./solvent/text()'))
)
spdunits = first(result.xpath('./spdunits/text()'))
timeunits = first(result.xpath('./timeunits/text()'))
for spd in result.xpath('./spds/spd'):
spin_spd = SpinSpd(spdvalue=first(spd.xpath('./spdvalue/text()')),
spdunits=spdunits)
s.spds.append(spin_spd)
for time in result.xpath('./times/time'):
spin_time = SpinTime(timevalue=first(
time.xpath('./timevalue/text()')),
timeunits=timeunits)
s.times.append(spin_time)
c.spin_coat.append(s)
yield c
