def setUp(self):
"""Set up lab group."""
self.labGroup = LabGroup(title="DuplicateValues",
address='2, war drobe, Narnia',
email='*****@*****.**',
legacy_access_code='old_magic')
self.labGroup.save()
def setUp(self):
"""Test for a legacy password check set but no new password has been entered."""
self.labGroup = LabGroup(title="LegacyPassTest1",
address='1, war drobe, Narnia',
email='*****@*****.**',
legacy_access_code='old_magic')
self.labGroup.save()
formData = {'labGroup': self.labGroup.id, 'accessCode': 'old_magic'}
self.form = LabGroupJoiningForm(formData)
def setUp(self):
"""instantiate the labgroup."""
self.labGroup = LabGroup(title="LegacyPassTest2",
address='2, war drobe, Narnia',
email='*****@*****.**',
legacy_access_code='old_magic')
self.labGroup.save()
formData = {
'title': 'LegacyPasstest2',
'address': '2, war drobe',
'email': '*****@*****.**',
'accessCode': 'new_magic'
}
self.form = LabGroupForm(formData, instance=self.labGroup)
def setUp(self):
"""instantiate the labgroup."""
self.labGroup = LabGroup(title="LegacyPassTest1",
address='1, war drobe, Narnia',
email='*****@*****.**',
legacy_access_code='old_magic')
formData = {
'title': 'LegacyPasstest1',
'address': '1, war drobe',
'email': '*****@*****.**',
'users': []
}
self.form = LabGroupForm(formData, instance=self.labGroup)
self.labGroup.save()
def _joinsLabGroup(c):
_oldSetup = c.setUp
_oldTearDown = c.tearDown
labGroup = LabGroup(title=labGroupTitle,
address='War drobe',
email='*****@*****.**',
access_code='new_magic')
def setUp(self):
user = User.objects.get(username=username)
labGroup.save()
user.labgroup_set.add(labGroup)
_oldSetup(self)
def tearDown(self):
_oldTearDown(self)
labGroup.delete()
c.setUp = setUp
c.tearDown = tearDown
return c
def handle(self, *args, **kwargs):
folder = kwargs['directory']
with open(path.join(folder, 'User.tsv')) as userFile:
reader = csv.DictReader(userFile, delimiter='\t')
for r in reader:
if not User.objects.filter(username=r['username']).exists():
u = User(
username=r['username'],
first_name=r['first_name'],
last_name=r['last_name'],
email=r['email'],
is_staff=int(r['is_staff']),
is_superuser=int(r['is_superuser']),
)
u.password = r['password']
u.save()
with open(path.join(folder, 'labGroup.tsv')) as labGroups:
reader = csv.DictReader(labGroups, delimiter='\t')
for r in reader:
if not LabGroup.objects.filter(title=r['title']).exists():
l = LabGroup(**r)
l.save()
with open(path.join(folder, 'labgroup_users.tsv')) as labGroupUsers:
reader = csv.DictReader(labGroupUsers, delimiter='\t')
for r in reader:
l = LabGroup.objects.get(title=r['title'])
l.users.add(User.objects.get(username=r['username']))
if not path.isfile(path.join(folder, 'performedReactionsNoDups.tsv')):
self.stdout.write(
'Writing file with duplicate references disambiguated (arbitrarily)'
)
with open(path.join(folder,
'performedReactions.tsv')) as in_file, open(
path.join(folder,
'performedReactionsNoDups.tsv'),
'w') as out_file:
references = set()
reader = csv.DictReader(in_file, delimiter='\t')
writer = csv.DictWriter(out_file,
delimiter='\t',
fieldnames=reader.fieldnames)
writer.writeheader()
case_count = 0
valid_case_count = 0
dup_count = 0
for r in reader:
ref = r['reference'].lower()
if ref != r['reference']:
self.stderr.write(
'Reference {} was not in lowercase. Converted.'.
format(r['reference']))
case_count += 1
if r['valid'] == '1':
valid_case_count += 1
if ref in references:
r['notes'] += ' Duplicated reference'
r['valid'] = 0
dup_count += 1
i = 1
new_ref = ref
while new_ref in references:
new_ref = '{}_dup{}'.format(ref, i)
i += 1
self.stderr.write(
'Reference {} duplicated {} times. Renamed and invalidated'
.format(ref, i))
ref = new_ref
references.add(ref)
r['reference'] = ref
writer.writerow(r)
self.stderr.write(
'{} references converted to lowercase. {} were valid'.format(
case_count, valid_case_count))
self.stderr.write(
'{} references with _dupX appended to remove duplicate reference'
.format(dup_count))
with open(path.join(folder,
'performedReactionsNoDups.tsv')) as reactions:
reader = csv.DictReader(reactions, delimiter='\t')
for r in reader:
if not PerformedReaction.objects.filter(
reference=r['reference'].lower()).exists():
p = PerformedReaction(
reference=r['reference'],
labGroup=LabGroup.objects.get(
title=r['labGroup.title']),
notes=r['notes'],
user=User.objects.get(username=r['user.username']),
valid=int(r['valid']),
legacyRecommendedFlag=r['legacyRecommendedFlag'] ==
'Yes',
insertedDateTime=r['insertedDateTime'],
public=int(r['public']))
self.stdout.write(
'Creating reaction with reference {}'.format(
p.reference))
p.validate_unique()
p.save(calcDescriptors=False)
with open(path.join(folder,
'performedReactionsNoDups.tsv')) as reactions:
reader = csv.DictReader(reactions, delimiter='\t')
outValues = []
outBoolValues = []
purityValues = []
temperatureValues = []
timeValues = []
pHValues = []
preHeatStandingValues = []
teflonValues = []
for r in reader:
self.stdout.write(
'Reiterating for reaction with reference {}'.format(
r['reference'].lower()))
ps = PerformedReaction.objects.filter(
reference=r['reference'].lower())
if ps.count() > 1:
ps = ps.filter(valid=True)
if ps.exists():
if ps.count() > 1:
raise RuntimeError(
'{} has more than one reaction'.format(
r['reference'].lower()))
p = ps[0]
try:
p.duplicateOf = PerformedReaction.objects.get(
reference=r['duplicateOf.reference'].lower())
p.save()
except PerformedReaction.DoesNotExist:
pass
#outValue = OrdRxnDescriptorValue.objects.get_or_create(descriptor=outcomeDescriptor, reaction=p)[0]
outcomeValue = int(r['outcome']) if (r['outcome'] in (
str(x) for x in range(1, 5))) else None
try:
v = OrdRxnDescriptorValue.objects.get(
descriptor=outcomeDescriptor, reaction=p)
if v.value != outcomeValue:
v.value = outcomeValue
v.save()
except OrdRxnDescriptorValue.DoesNotExist:
outValue = outcomeDescriptor.createValue(
p, outcomeValue)
# outValue.save()
outValues.append(outValue)
#outBoolValue = BoolRxnDescriptorValue.objects.get_or_create(descriptor=outcomeBooleanDescriptor, reaction=p)[0]
value = True if (outcomeValue > 2) else False
try:
v = BoolRxnDescriptorValue.objects.get(
descriptor=outcomeBooleanDescriptor, reaction=p)
if v.value != value:
v.value = value
v.save()
except BoolRxnDescriptorValue.DoesNotExist:
# outBoolValue.save()
outBoolValue = outcomeBooleanDescriptor.createValue(
p, value)
outBoolValues.append(outBoolValue)
#purityValue = OrdRxnDescriptorValue.objects.get_or_create(descriptor=purityDescriptor, reaction=p)[0]
value = int(r['purity']) if (r['purity']
in ('1', '2')) else None
try:
v = OrdRxnDescriptorValue.objects.get(
descriptor=purityDescriptor, reaction=p)
if v.value != value:
v.value = value
v.save()
except OrdRxnDescriptorValue.DoesNotExist:
# purityValue.save()
purityValue = purityDescriptor.createValue(p, value)
purityValues.append(purityValue)
#temperatureDescriptorValue = NumRxnDescriptorValue.objects.get_or_create(descriptor=temperatureDescriptor, reaction=p)[0]
value = (float(r['temp']) +
273.15) if (r['temp'] not in ('', '?')) else None
try:
v = NumRxnDescriptorValue.objects.get(
descriptor=temperatureDescriptor, reaction=p)
if v.value != value:
v.value = value
v.save()
except NumRxnDescriptorValue.DoesNotExist:
# temperatureDescriptorValue.save()
temperatureDescriptorValue = temperatureDescriptor.createValue(
p, value)
temperatureValues.append(temperatureDescriptorValue)
#timeDescriptorValue = NumRxnDescriptorValue.objects.get_or_create(descriptor=timeDescriptor, reaction=p)[0]
value = float(r['time']) * 60 if (
r['time'] not in ['', '?']) else None
try:
v = NumRxnDescriptorValue.objects.get(
descriptor=timeDescriptor, reaction=p)
if v.value != value:
v.value = value
v.save()
except NumRxnDescriptorValue.DoesNotExist:
# timeDescriptorValue.save()
timeDescriptorValue = timeDescriptor.createValue(
p, value)
timeValues.append(timeDescriptorValue)
#pHDescriptorValue = NumRxnDescriptorValue.objects.get_or_create(descriptor=pHDescriptor, reaction=p)[0]
value = float(r['pH']) if (r['pH'] not in ('',
'?')) else None
try:
v = NumRxnDescriptorValue.objects.get(
descriptor=pHDescriptor, reaction=p)
if v.value != value:
v.value = value
v.save()
except NumRxnDescriptorValue.DoesNotExist:
# pHDescriptorValue.save()
pHDescriptorValue = pHDescriptor.createValue(p, value)
pHValues.append(pHDescriptorValue)
#preHeatStandingDescriptorValue = NumRxnDescriptorValue.objects.get_or_create(descriptor=preHeatStandingDescriptor, reaction=p)[0]
value = bool(r['pre_heat standing']) if (
r.get('pre_heat standing') not in ('', None)) else None
try:
v = NumRxnDescriptorValue.objects.get(
descriptor=preHeatStandingDescriptor, reaction=p)
if v.value != value:
v.value = value
v.save()
except NumRxnDescriptorValue.DoesNotExist:
# preHeatStandingDescriptorValue.save()
preHeatStandingDescriptorValue = preHeatStandingDescriptor.createValue(
p, value)
preHeatStandingValues.append(
preHeatStandingDescriptorValue)
#teflonDescriptorValue = BoolRxnDescriptorValue.objects.get_or_create(descriptor=teflonDescriptor, reaction=p)[0]
value = bool(int(r['teflon_pouch'])) if (
r.get('teflon_pouch') not in (None, '')) else None
try:
v = BoolRxnDescriptorValue.objects.get(
descriptor=teflonDescriptor, reaction=p)
if v.value != value:
v.value = value
v.save()
except BoolRxnDescriptorValue.DoesNotExist:
# teflonDescriptorValue.save()
teflonDescriptorValue = teflonDescriptor.createValue(
p, value)
teflonValues.append(teflonDescriptorValue)
if len(outValues) > 500:
self.stdout.write("Saving...")
OrdRxnDescriptorValue.objects.bulk_create(outValues)
BoolRxnDescriptorValue.objects.bulk_create(
outBoolValues)
OrdRxnDescriptorValue.objects.bulk_create(purityValues)
NumRxnDescriptorValue.objects.bulk_create(
temperatureValues)
NumRxnDescriptorValue.objects.bulk_create(timeValues)
NumRxnDescriptorValue.objects.bulk_create(pHValues)
NumRxnDescriptorValue.objects.bulk_create(
preHeatStandingValues)
BoolRxnDescriptorValue.objects.bulk_create(
teflonValues)
outValues = []
outBoolValues = []
purityValues = []
temperatureValues = []
timeValues = []
pHValues = []
preHeatStandingValues = []
teflonValues = []
self.stdout.write("...saved")
with open(path.join(folder, 'compound_labs.tsv')) as compounds:
reader = csv.DictReader(compounds, delimiter='\t')
cs = ChemSpider(settings.CHEMSPIDER_TOKEN)
for r in reader:
l = LabGroup.objects.get(title=r['labGroup.title'])
if not Compound.objects.filter(abbrev=r['abbrev']).exists():
self.stdout.write(
'Importing compound with abbreviation {} and name {}'.
format(r['abbrev'], r['name']))
if r.get('custom') != '1':
try:
if r.get('CSID') not in ('', None):
c = Compound(CSID=r['CSID'],
labGroup=l,
abbrev=r['abbrev'])
c.csConsistencyCheck()
c.save()
else:
if r.get('CAS_ID') not in (None, ''):
CASResults = cs.simple_search(r['CAS_ID'])
else:
CASResults = []
if len(CASResults) != 1:
nameResults = cs.simple_search(
r.get('name'))
if len(nameResults) != 1:
raise RuntimeError(
'Could not get unambiguous chemspider entry for CAS ID {} with name{}'
.format(r['CAS_ID'], r['name']))
else:
c = Compound(CSID=nameResults[0].csid,
labGroup=l,
abbrev=r['abbrev'])
c.csConsistencyCheck()
c.save()
else:
c = Compound(CSID=CASResults[0].csid,
labGroup=l,
abbrev=r['abbrev'])
c.csConsistencyCheck()
c.save()
except ValidationError as e:
c.delete()
raise e
else:
if r.get('INCHI') is None:
r['INCHI'] = ''
if r.get('smiles') is None:
r['smiles'] = ''
c = Compound.objects.get_or_create(
labGroup=l,
custom=True,
name=r['name'],
abbrev=r['abbrev'],
formula=r['formula'],
smiles=r['smiles'],
INCHI=r['INCHI'])[0]
self.stdout.write(c.name.encode('utf-8'))
c.save()
with open(path.join(
folder, 'compound_chemicalClasses.tsv')) as chemicalClasses:
reader = csv.DictReader(chemicalClasses, delimiter='\t')
for r in reader:
self.stdout.write('working with class {}'.format(
r['chemicalClass.label']))
cs = Compound.objects.filter(abbrev=r['compound.abbrev'])
if cs.count() > 0:
c1 = ChemicalClass.objects.get_or_create(
label=r['chemicalClass.label'])[0]
for c2 in cs:
if c1 not in c2.chemicalClasses.all():
c2.chemicalClasses.add(c1)
c2.save()
with open(path.join(folder, 'compoundquantities.tsv')) as cqs:
reader = csv.DictReader(cqs, delimiter='\t')
for r in reader:
try:
reaction = PerformedReaction.objects.get(
reference=r['reaction.reference'].lower())
compound = Compound.objects.get(
abbrev=r['compound.abbrev'],
labGroup=reaction.labGroup)
if r['compound.abbrev'] in ('water', 'H2O'):
r['density'] = 1
mw = NumMolDescriptorValue.objects.get(
compound=compound, descriptor__heading='mw').value
if r['compoundrole.name'] != 'pH':
self.stdout.write('adding {} to {}'.format(
compound.abbrev, reaction.reference))
compoundrole = CompoundRole.objects.get_or_create(
label=r['compoundrole.name'])[0]
if r['amount'] in ('', '?'):
amount = None
elif r['unit'] == 'g':
amount = float(r['amount']) / mw
elif r['unit'] == 'd':
amount = float(r['amount']) * \
0.0375 * float(r['density']) / mw
elif r['unit'] == 'mL':
amount = float(r['amount']) * \
float(r['density']) / mw
else:
raise RuntimeError('invalid unit entered')
if amount is not None:
amount = (amount * 1000)
cqq = CompoundQuantity.objects.filter(
role=compoundrole,
compound=compound,
reaction=reaction)
if cqq.count() > 1:
cqq.delete()
quantity = CompoundQuantity.objects.get_or_create(
role=compoundrole,
compound=compound,
reaction=reaction)[0]
quantity.amount = amount
quantity.save()
else:
reaction.notes += ' pH adjusting reagent used: {}, {}{}'.format(
r['compound.abbrev'], r['amount'], r['unit'])
reaction.save(calcDescriptors=False)
except Compound.DoesNotExist as e:
self.stderr.write(
'Unknown Reactant {} with amount {} {} in reaction {}'.
format(r['compound.abbrev'], r['amount'], r['unit'],
r['reaction.reference']))
raw_input("Continue?")
reaction.notes += ' Unknown Reactant {} with amount {} {}'.format(
r['compound.abbrev'], r['amount'], r['unit'])
reaction.valid = False
reaction.save(calcDescriptors=False)
except PerformedReaction.DoesNotExist as e:
raise e