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vioscreen.py
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vioscreen.py
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import pandas as pd
from microsetta_private_api.model.model_base import ModelBase
def normalize_timestamp(timestamp, timezone, normalize_to='US/Pacific'):
"""Normalize a timestamp to a specific timezone
Vioscreen timezone information is not encoded directly within the
timestamp, but separately.
Parameters
----------
timestamp : str
The timestamp to normalize
timezone : str
The timezone information as provided by vioscreen
normalize_to : str
What timezone to normalize too, using Pandas timezone conventions
Returns
-------
pd.Timestamp
A normalized timestamp
"""
timezone_lookup = {'Eastern Standard Time': 'US/Eastern',
'Central Standard Time': 'US/Central',
'Pacific Standard Time': 'US/Pacific'}
if timezone not in timezone_lookup:
raise KeyError(f"Unexpected timezone '{timezone}' observed")
if timestamp is None:
return None
timestamp = pd.to_datetime(timestamp)
timestamp_tz = timestamp.tz_localize(timezone_lookup[timezone])
return timestamp_tz.tz_convert(normalize_to)
class VioscreenSession(ModelBase):
def __init__(self, sessionId, username, protocolId, status, startDate,
endDate, cultureCode, created, modified):
self.sessionId = sessionId
self.username = username
self.protocolId = protocolId
self.status = status
self.startDate = startDate
self.endDate = endDate
self.cultureCode = cultureCode
self.created = created
self.modified = modified
def update_from_vioscreen(self, update):
self.startDate = update.startDate
self.endDate = update.endDate
self.modified = update.modified
self.status = update.status
self.protocolId = update.protocolId
self.cultureCode = update.cultureCode
self.created = update.created
return self
@property
def is_complete(self):
return (self.endDate is not None) and (self.status == 'Finished')
@classmethod
def from_registry(cls, username):
# Support the special case of a username existing in the
# vioscreen_registry but not yet existing in the vioscreen_sessions
# table
return cls(sessionId=None, username=username, protocolId=None,
status=None, startDate=None, endDate=None, cultureCode=None,
created=None, modified=None)
@classmethod
def from_vioscreen(cls, sessions_data, users_data):
timeZone = users_data['timeZone']
startDate = normalize_timestamp(sessions_data['startDate'], timeZone)
endDate = normalize_timestamp(sessions_data['endDate'], timeZone)
created = normalize_timestamp(sessions_data['created'], timeZone)
modified = normalize_timestamp(sessions_data['modified'], timeZone)
return cls(sessions_data['sessionId'], sessions_data['username'],
sessions_data['protocolId'], sessions_data['status'],
startDate, endDate, sessions_data['cultureCode'],
created, modified)
def to_api(self):
return {
'sessionId': self.sessionId,
'username': self.username,
'protocolId': self.protocolId,
'status': self.status,
'startDate': self.startDate,
'endDate': self.endDate,
'cultureCode': self.cultureCode,
'created': self.created,
'modified': self.modified
}
def __repr__(self):
args = ", ".join([f"{key}={str(value)}"
for key, value in self.__dict__.items()])
return f"VioscreenSession({args})"
class VioscreenPercentEnergyComponent(ModelBase):
def __init__(self, code, description, short_description, units, amount):
self.code = code
self.description = description
self.short_description = short_description
self.units = units
self.amount = amount
@classmethod
def from_vioscreen(cls, component):
return cls(component['code'], component['description'],
component['shortDescription'], component['units'],
component['amount'])
def to_api(self):
return {
'code': self.code,
'description': self.description,
'shortDescription': self.short_description,
'units': self.units,
'amount': self.amount
}
def __lt__(self, other):
return self.code < other.code
class VioscreenPercentEnergy(ModelBase):
def __init__(self, sessionId, energy_components):
self.sessionId = sessionId
self.energy_components = energy_components
@classmethod
def from_vioscreen(cls, pe_data):
sessionId = pe_data['sessionId']
energy_components = [
VioscreenPercentEnergyComponent.from_vioscreen(component)
for component in pe_data['calculations']
]
return cls(sessionId, energy_components)
def to_api(self):
return {
'sessionId': self.sessionId,
'calculations': [component.to_api()
for component in self.energy_components]
}
def __eq__(self, other):
if self.sessionId != other.sessionId:
return False
a = sorted(self.energy_components)
b = sorted(other.energy_components)
return a == b
class VioscreenDietaryScoreComponent(ModelBase):
def __init__(self, code, name, score, lowerLimit, upperLimit):
self.code = code
self.name = name
self.score = score
self.lowerLimit = lowerLimit
self.upperLimit = upperLimit
@classmethod
def from_vioscreen(cls, component):
return cls(component['type'], component['name'], component['score'],
component['lowerLimit'], component['upperLimit'])
def to_api(self):
return {
'type': self.code,
'name': self.name,
'score': self.score,
'lowerLimit': self.lowerLimit,
'upperLimit': self.upperLimit
}
def __lt__(self, other):
return self.code < other.code
class VioscreenDietaryScore(ModelBase):
def __init__(self, sessionId, scoresType, scores):
self.sessionId = sessionId
self.scoresType = scoresType
self.scores = scores
@classmethod
def from_vioscreen(cls, ds_data):
sessionId = ds_data['sessionId']
scoresType = ds_data['dietaryScore']['type']
scores = [
VioscreenDietaryScoreComponent.from_vioscreen(component)
for component in ds_data['dietaryScore']['scores']
]
return cls(sessionId, scoresType, scores)
def to_api(self):
return {
'sessionId': self.sessionId,
'type': self.scoresType,
'scores': [component.to_api()
for component in self.scores]
}
def __eq__(self, other):
if self.sessionId != other.sessionId:
return False
if self.scoresType != other.scoresType:
return False
a = sorted(self.scores)
b = sorted(other.scores)
return a == b
class VioscreenSupplementsComponent(ModelBase):
def __init__(self, supplement, frequency, amount, average):
self.supplement = supplement
self.frequency = frequency
self.amount = amount
self.average = average
@classmethod
def from_vioscreen(cls, component):
return cls(component['supplement'], component['frequency'],
component['amount'], component['average'])
def to_api(self):
return {
'supplement': self.supplement,
'frequency': self.frequency,
'amount': self.amount,
'average': self.average
}
def __lt__(self, other):
return self.supplement < other.supplement
class VioscreenSupplements(ModelBase):
def __init__(self, sessionId, supplements_components):
self.sessionId = sessionId
self.supplements_components = supplements_components
@classmethod
def from_vioscreen(cls, supplements_data):
sessionId = supplements_data['sessionId']
supplements_components = [
VioscreenSupplementsComponent.from_vioscreen(component)
for component in supplements_data['data']
]
return cls(sessionId, supplements_components)
def to_api(self):
return {
'sessionId': self.sessionId,
'data': [component.to_api()
for component in self.supplements_components]
}
def __eq__(self, other):
if self.sessionId != other.sessionId:
return False
a = sorted(self.supplements_components)
b = sorted(other.supplements_components)
return a == b
class VioscreenFoodComponentsComponent(ModelBase):
def __init__(self, code, description, units, amount, valueType):
self.code = code
self.description = description
self.units = units
self.amount = amount
self.valueType = valueType
@classmethod
def from_vioscreen(cls, component):
return cls(component['code'], component['description'],
component['units'], component['amount'],
component['valueType'])
def to_api(self):
return {
'code': self.code,
'description': self.description,
'units': self.units,
'amount': self.amount,
'valueType': self.valueType
}
def __lt__(self, other):
return self.code < other.code
class VioscreenFoodComponents(ModelBase):
def __init__(self, sessionId, components):
self.sessionId = sessionId
self.components = components
@classmethod
def from_vioscreen(cls, fc_data):
sessionId = fc_data['sessionId']
food_components = [
VioscreenFoodComponentsComponent.from_vioscreen(component)
for component in fc_data['data']
]
return cls(sessionId, food_components)
def to_api(self):
return {
'sessionId': self.sessionId,
'data': [component.to_api()
for component in self.components]
}
def __eq__(self, other):
if self.sessionId != other.sessionId:
return False
a = sorted(self.components)
b = sorted(other.components)
return a == b
class VioscreenEatingPatternsComponent(ModelBase):
def __init__(self, code, description, units, amount, valueType):
self.code = code
self.description = description
self.units = units
self.amount = amount
self.valueType = valueType
@classmethod
def from_vioscreen(cls, component):
return cls(component['code'], component['description'],
component['units'], component['amount'],
component['valueType'])
def to_api(self):
return {
'code': self.code,
'description': self.description,
'units': self.units,
'amount': self.amount,
'valueType': self.valueType
}
def __lt__(self, other):
return self.code < other.code
class VioscreenEatingPatterns(ModelBase):
def __init__(self, sessionId, components):
self.sessionId = sessionId
self.components = components
@classmethod
def from_vioscreen(cls, ep_data):
sessionId = ep_data['sessionId']
ep_components = [
VioscreenEatingPatternsComponent.from_vioscreen(component)
for component in ep_data['data']
]
return cls(sessionId, ep_components)
def to_api(self):
return {
'sessionId': self.sessionId,
'data': [component.to_api()
for component in self.components]
}
def __eq__(self, other):
if self.sessionId != other.sessionId:
return False
a = sorted(self.components)
b = sorted(other.components)
return a == b
class VioscreenMPedsComponent(ModelBase):
def __init__(self, code, description, units, amount, valueType):
self.code = code
self.description = description
self.units = units
self.amount = amount
self.valueType = valueType
@classmethod
def from_vioscreen(cls, component):
return cls(component['code'], component['description'],
component['units'], component['amount'],
component['valueType'])
def to_api(self):
return {
'code': self.code,
'description': self.description,
'units': self.units,
'amount': self.amount,
'valueType': self.valueType
}
def __lt__(self, other):
return self.code < other.code
class VioscreenMPeds(ModelBase):
def __init__(self, sessionId, components):
self.sessionId = sessionId
self.components = components
@classmethod
def from_vioscreen(cls, mp_data):
sessionId = mp_data['sessionId']
mp_components = [
VioscreenMPedsComponent.from_vioscreen(component)
for component in mp_data['data']
]
return cls(sessionId, mp_components)
def to_api(self):
return {
'sessionId': self.sessionId,
'data': [component.to_api()
for component in self.components]
}
def __eq__(self, other):
if self.sessionId != other.sessionId:
return False
a = sorted(self.components)
b = sorted(other.components)
return a == b
class VioscreenFoodConsumptionComponent(ModelBase):
def __init__(self, foodCode, description, foodGroup, amount, frequency,
consumptionAdjustment, servingSizeText, servingFrequencyText,
created, data):
self.foodCode = foodCode
self.description = description
self.foodGroup = foodGroup
self.amount = amount
self.frequency = frequency
self.consumptionAdjustment = consumptionAdjustment
self.servingSizeText = servingSizeText
self.servingFrequencyText = servingFrequencyText
self.created = created
# data is a list of individual VioscreenFoodComponentsComponent objects
self.data = data
def __repr__(self):
parts = ', '.join([f"{k}={v}"
for k, v in sorted(self.__dict__.items())
if k != 'data'])
return "<%s>" % parts
@classmethod
def from_vioscreen(cls, component):
data = [
VioscreenFoodComponentsComponent.from_vioscreen(component2)
for component2 in component['data']
]
return cls(component['foodCode'], component['description'],
component['foodGroup'], component['amount'],
component['frequency'], component['consumptionAdjustment'],
component['servingSizeText'],
component['servingFrequencyText'], component['created'],
data)
def to_api(self):
return {
'foodCode': self.foodCode,
'description': self.description,
'foodGroup': self.foodGroup,
'amount': self.amount,
'frequency': self.frequency,
'consumptionAdjustment': self.consumptionAdjustment,
'servingSizeText': self.servingSizeText,
'servingFrequencyText': self.servingFrequencyText,
'created': self.created,
'data': [component.to_api()
for component in self.data]
}
def __lt__(self, other):
return self.description < other.description
def __eq__(self, other):
for k in self.__dict__:
if k == 'data':
continue
if self.__dict__[k] != other.__dict__[k]:
return False
self_data = sorted(self.data)
other_data = sorted(other.data)
return self_data == other_data
class VioscreenFoodConsumption(ModelBase):
def __init__(self, sessionId, components):
self.sessionId = sessionId
self.components = components
@classmethod
def from_vioscreen(cls, cons_data):
sessionId = cons_data['sessionId']
cons_components = [
VioscreenFoodConsumptionComponent.from_vioscreen(component)
for component in cons_data['foodConsumption']
]
return cls(sessionId, cons_components)
def to_api(self):
return {
'sessionId': self.sessionId,
'foodConsumption': [component.to_api()
for component in self.components]
}
def __eq__(self, other):
if self.sessionId != other.sessionId:
return False
a = sorted(self.components)
b = sorted(other.components)
return a == b
class VioscreenComposite(ModelBase):
def __init__(self, session, percent_energy, dietary_scores, supplements,
food_components, eating_patterns, mpeds, food_consumption):
self.session = session
self.percent_energy = percent_energy
self.dietary_scores = dietary_scores
self.supplements = supplements
self.food_components = food_components
self.eating_patterns = eating_patterns
self.mpeds = mpeds
self.food_consumption = food_consumption
# make first class as the vioscreen username is our internal
# survey identifier
self.vio_id = session.username
def __eq__(self, other):
return self.__dict__ == other.__dict__
class VioscreenRegistryEntry(ModelBase):
def __init__(self, survey_id, vioscreen_status, creation_time, sample_id,
registration_code):
self.survey_id = survey_id
self.vioscreen_status = vioscreen_status
self.creation_time = creation_time
self.sample_id = sample_id
self.registration_code = registration_code
def to_api(self):
return {
'survey_id': self.survey_id,
'vioscreen_status': self.vioscreen_status,
'creation_time': self.creation_time,
'sample_id': self.sample_id,
'registration_code': self.registration_code
}