Merge branch 'feature/ARIA_new_inputs' into 'master'
New precise activity and break inputs See merge request cara/caimira!404
This commit is contained in:
Andre Henriques
commit
295d975bf3
3 changed files with 224 additions and 15 deletions
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@ -5,6 +5,7 @@ import logging
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import typing
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import ast
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import json
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import re
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import numpy as np
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@ -32,6 +33,8 @@ class FormData:
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air_changes: float
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air_supply: float
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arve_sensors_option: bool
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specific_breaks: list
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precise_activity: dict
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ceiling_height: float
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exposed_coffee_break_option: str
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exposed_coffee_duration: int
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@ -97,6 +100,8 @@ class FormData:
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'air_changes': 0.,
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'air_supply': 0.,
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'arve_sensors_option': False,
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'specific_breaks': '[]',
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'precise_activity': '{}',
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'calculator_version': _NO_DEFAULT,
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'ceiling_height': 0.,
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'exposed_coffee_break_option': 'coffee_break_0',
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@ -307,6 +312,55 @@ class FormData:
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raise ValueError("mechanical_ventilation_type cannot be 'not-applicable' if "
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"ventilation_type is 'mechanical_ventilation'")
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# Validate specific inputs - breaks
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if self.specific_breaks != []:
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if type(self.specific_breaks) is not list:
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raise TypeError(f'All breaks should be in a list. Got {type(self.specific_breaks)}.')
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for input_break in self.specific_breaks:
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# Input validations.
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if type(input_break) is not dict:
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raise TypeError(f'Each break should be a dictionary. Got {type(input_break)}.')
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dict_keys = list(input_break.keys())
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if "start_time" not in input_break:
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raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys[0]}".')
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if "finish_time" not in input_break:
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raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys[1]}".')
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for time in input_break.values():
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if not re.compile("^(2[0-3]|[01]?[0-9]):([0-5]?[0-9])$").match(time):
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raise TypeError(f'Wrong time format - "HH:MM". Got "{time}".')
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# Validate specific inputs - precise activity
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if self.precise_activity != {}:
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if type(self.precise_activity) is not dict:
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raise TypeError('The precise activities should be in a dictionary.')
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dict_keys = list(self.precise_activity.keys())
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if "physical_activity" not in dict_keys:
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raise TypeError(f'Unable to fetch "physical_activity" key. Got "{dict_keys[0]}".')
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if "respiratory_activity" not in dict_keys:
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raise TypeError(f'Unable to fetch "respiratory_activity" key. Got "{dict_keys[1]}".')
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if type(self.precise_activity['physical_activity']) is not str:
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raise TypeError('The physical activities should be a single string.')
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if type(self.precise_activity['respiratory_activity']) is not list:
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raise TypeError('The respiratory activities should be in a list.')
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total_percentage = 0
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for respiratory_activity in self.precise_activity['respiratory_activity']:
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if type(respiratory_activity) is not dict:
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raise TypeError('Each respiratory activity should be defined in a dictionary.')
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dict_keys = list(respiratory_activity.keys())
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if "type" not in dict_keys:
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raise TypeError(f'Unable to fetch "type" key. Got "{dict_keys[0]}".')
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if "percentage" not in dict_keys:
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raise TypeError(f'Unable to fetch "percentage" key. Got "{dict_keys[1]}".')
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total_percentage += respiratory_activity['percentage']
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if total_percentage != 100:
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raise ValueError(f'The sum of all respiratory activities should be 100. Got {total_percentage}.')
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def build_mc_model(self) -> mc.ExposureModel:
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# Initializes room with volume either given directly or as product of area and height
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if self.volume_type == 'room_volume_explicit':
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@ -468,6 +522,15 @@ class FormData:
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mask = models.Mask.types['No mask']
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return mask
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def generate_precise_activity_expiration(self) -> typing.Tuple[typing.Any, ...]:
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if self.precise_activity == {}: # It means the precise activity is not defined by a specific input.
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return ()
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respiratory_dict = {}
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for respiratory_activity in self.precise_activity['respiratory_activity']:
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respiratory_dict[respiratory_activity['type']] = respiratory_activity['percentage']
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return (self.precise_activity['physical_activity'], respiratory_dict)
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def infected_population(self) -> mc.InfectedPopulation:
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# Initializes the virus
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virus = virus_distributions[self.virus_type]
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@ -511,8 +574,34 @@ class FormData:
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#Model 1/2 of time spent speaking in a workshop.
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{'Speaking': 1, 'Breathing': 1}),
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'gym':('Heavy exercise', 'Breathing'),
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# Other activity types
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'household-day': (
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'Light activity',
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{'Breathing': 5, 'Speaking': 5}
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),
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'household-night': (
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'Seated',
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{'Breathing': 7, 'Speaking': 3}
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),
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'primary-school': (
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'Light activity',
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{'Breathing': 5, 'Speaking': 5}
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),
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'secondary-school': (
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'Light activity',
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{'Breathing': 7, 'Speaking': 3}
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),
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'university': (
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'Seated',
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{'Breathing': 9, 'Speaking': 1}
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),
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'restaurant': (
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'Seated',
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{'Breathing': 1, 'Speaking': 9}
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),
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'precise': self.generate_precise_activity_expiration(),
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}
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[activity_defn, expiration_defn] = scenario_activity_and_expiration[self.activity_type]
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activity = activity_distributions[activity_defn]
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expiration = build_expiration(expiration_defn)
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@ -544,6 +633,13 @@ class FormData:
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'workshop': 'Moderate activity',
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'lab':'Light activity',
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'gym':'Heavy exercise',
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'household-day': 'Light activity',
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'household-night': 'Seated',
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'primary-school': 'Light activity',
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'secondary-school': 'Light activity',
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'university': 'Seated',
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'restaurant': 'Seated',
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'precise': 'Seated',
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}
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activity_defn = scenario_activity[self.activity_type]
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@ -642,6 +738,20 @@ class FormData:
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else:
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return self.exposed_coffee_break_times()
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def generate_specific_break_times(self) -> models.BoundarySequence_t:
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break_times = []
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for n in self.specific_breaks:
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# Parse break times.
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begin = time_string_to_minutes(n["start_time"])
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end = time_string_to_minutes(n["finish_time"])
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for time in [begin, end]:
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# For a specific break, the infected and exposed presence is the same.
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if not getattr(self, 'infected_start') < time < getattr(self, 'infected_finish'):
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raise ValueError(f'All breaks should be within the simulation time. Got {time_minutes_to_string(time)}.')
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break_times.append((begin, end))
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return tuple(break_times)
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def present_interval(
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self,
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start: int,
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@ -735,9 +845,13 @@ class FormData:
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return models.SpecificInterval(tuple(present_intervals))
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def infected_present_interval(self) -> models.Interval:
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if self.specific_breaks != []: # It means the breaks are specific and not predefined
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breaks = self.generate_specific_break_times()
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else:
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breaks = self.infected_lunch_break_times() + self.infected_coffee_break_times()
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return self.present_interval(
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self.infected_start, self.infected_finish,
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breaks=self.infected_lunch_break_times() + self.infected_coffee_break_times(),
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breaks=breaks,
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)
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def short_range_interval(self, interaction) -> models.SpecificInterval:
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@ -746,9 +860,13 @@ class FormData:
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return models.SpecificInterval(present_times=((start_time/60, (start_time + duration)/60),))
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def exposed_present_interval(self) -> models.Interval:
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if self.specific_breaks != []: # It means the breaks are specific and not predefined
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breaks = self.generate_specific_break_times()
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else:
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breaks = self.exposed_lunch_break_times() + self.exposed_coffee_break_times()
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return self.present_interval(
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self.exposed_start, self.exposed_finish,
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breaks=self.exposed_lunch_break_times() + self.exposed_coffee_break_times(),
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breaks=breaks,
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)
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@ -828,7 +946,10 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]:
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}
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ACTIVITY_TYPES = {'office', 'smallmeeting', 'largemeeting', 'training', 'training_attendee', 'callcentre', 'controlroom-day', 'controlroom-night', 'library', 'workshop', 'lab', 'gym'}
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ACTIVITY_TYPES = {
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'office', 'smallmeeting', 'largemeeting', 'training', 'callcentre', 'controlroom-day', 'controlroom-night', 'library', 'workshop', 'lab', 'gym',
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'household-day', 'household-night', 'primary-school', 'secondary-school', 'university', 'restaurant', 'precise',
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}
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MECHANICAL_VENTILATION_TYPES = {'mech_type_air_changes', 'mech_type_air_supply', 'not-applicable'}
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MASK_TYPES = {'Type I', 'FFP2', 'Cloth'}
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MASK_WEARING_OPTIONS = {'mask_on', 'mask_off'}
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@ -873,12 +994,20 @@ def time_minutes_to_string(time: int) -> str:
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return "{0:0=2d}".format(int(time/60)) + ":" + "{0:0=2d}".format(time%60)
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def string_to_list(l: str) -> list:
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return list(ast.literal_eval(l.replace(""", "\"")))
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def string_to_list(s: str) -> list:
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return list(ast.literal_eval(s.replace(""", "\"")))
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def list_to_string(s: list) -> str:
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return json.dumps(s)
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def list_to_string(l: list) -> str:
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return json.dumps(l)
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def string_to_dict(s: str) -> dict:
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return dict(ast.literal_eval(s.replace(""", "\"")))
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def dict_to_string(d: dict) -> str:
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return json.dumps(d)
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def _safe_int_cast(value) -> int:
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@ -915,3 +1044,6 @@ for _field in dataclasses.fields(FormData):
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elif _field.type is list:
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_CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = string_to_list
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_CAST_RULES_NATIVE_TO_FORM_ARG[_field.name] = list_to_string
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elif _field.type is dict:
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_CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = string_to_dict
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_CAST_RULES_NATIVE_TO_FORM_ARG[_field.name] = dict_to_string
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@ -18,6 +18,13 @@
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{% block main %}
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{% if DEBUG %}
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<form id="covid_calculator" name="covid_calculator" onsubmit="return debug_submit(this)" class="form-inline">
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{% else %}
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<form id="covid_calculator" name="covid_calculator" action="{{ calculator_prefix }}/report" onsubmit="return validate_form(this)" method="POST">
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{% endif %}
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{{ xsrf_form_html }}
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<span class="caimira_version">v{{ calculator_version }}</span>
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<span class="feedback">Please send feedback to <a href="mailto:CAiMIRA-dev@cern.ch">CAiMIRA-dev@cern.ch</a></span>
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<header class= "bg-light">
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@ -29,13 +36,6 @@
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</div>
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</header>
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{% if DEBUG %}
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<form id="covid_calculator" name="covid_calculator" onsubmit="return debug_submit(this)" class="form-inline">
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{% else %}
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<form id="covid_calculator" name="covid_calculator" action="{{ calculator_prefix }}/report" onsubmit="return validate_form(this)" method="POST">
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{% endif %}
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{{ xsrf_form_html }}
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<input type="hidden" name="calculator_version" value="{{ calculator_version }}">
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<section>
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@ -424,6 +424,8 @@
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</select>
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</div>
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</div>
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<input type="text" class="form-control d-none" name="precise_activity" value='{}'>
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<div style=" margin-right:2rem;">
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<div class="boxMargin pb-0">
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@ -529,6 +531,7 @@
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<div data-tooltip="Input breaks that, by default, are the same for infected/exposed person(s) unless specified otherwise.">
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<span class="tooltip_text">?</span>
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</div>
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<input type="text" class="form-control d-none" name="specific_breaks" value='[]'>
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</span><br>
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<!-- Lunch Options -->
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@ -728,4 +731,7 @@
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</form>
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{% block external_dependencies %}
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{% endblock external_dependencies %}
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{% endblock main %}
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@ -0,0 +1,71 @@
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from typing import Type
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import numpy as np
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import pytest
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from caimira.apps.calculator import model_generator
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@pytest.mark.parametrize(
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["break_input", "error"],
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[
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[{"start_time": "10:00", "finish_time": "11:00"}, "All breaks should be in a list. Got <class 'dict'>."],
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[[["start_time", "10:00", "finish_time", "11:00"]], "Each break should be a dictionary. Got <class 'list'>."],
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[[{"art_time": "10:00", "finish_time": "11:00"}], 'Unable to fetch "start_time" key. Got "art_time".'],
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[[{"start_time": "10:00", "ish_time": "11:00"}], 'Unable to fetch "finish_time" key. Got "ish_time".'],
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[[{"start_time": "10", "finish_time": "11:00"}], 'Wrong time format - "HH:MM". Got "10".'],
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[[{"start_time": "10:00", "finish_time": "11"}], 'Wrong time format - "HH:MM". Got "11".'],
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]
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)
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def test_specific_break_data_structure(break_input, error, baseline_form: model_generator.FormData):
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baseline_form.specific_breaks = break_input
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with pytest.raises(TypeError, match=error):
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baseline_form.validate()
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@pytest.mark.parametrize(
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["break_input", "error"],
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[
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[[{"start_time": "07:00", "finish_time": "11:00"}, ], "All breaks should be within the simulation time. Got 07:00."],
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[[{"start_time": "17:00", "finish_time": "18:00"}, ], "All breaks should be within the simulation time. Got 18:00."],
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[[{"start_time": "10:00", "finish_time": "11:00"}, {"start_time": "17:00", "finish_time": "20:00"}, ], "All breaks should be within the simulation time. Got 20:00."],
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[[{"start_time": "08:00", "finish_time": "11:00"}, {"start_time": "14:00", "finish_time": "15:00"}, ], "All breaks should be within the simulation time. Got 08:00."],
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]
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)
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def test_specific_break_time(break_input, error, baseline_form: model_generator.FormData):
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baseline_form.specific_breaks = break_input
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with pytest.raises(ValueError, match=error):
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baseline_form.generate_specific_break_times()
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@pytest.mark.parametrize(
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["precise_activity_input", "error"],
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[
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[["physical_activity", "Light activity", "respiratory_activity", [{"type": "Breathing", "percentage": 50}, {"type": "Speaking", "percentage": 50}]], "The precise activities should be in a dictionary."],
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[{"pysical_activity": "Light activity", "respiratory_activity": [{"type": "Breathing", "percentage": 50}, {"type": "Speaking", "percentage": 50}]}, 'Unable to fetch "physical_activity" key. Got "pysical_activity".'],
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[{"physical_activity": "Light activity", "rspiratory_activity": [{"type": "Breathing", "percentage": 50}, {"type": "Speaking", "percentage": 50}]}, 'Unable to fetch "respiratory_activity" key. Got "rspiratory_activity".'],
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[{"physical_activity": ["Light activity"], "respiratory_activity": [{"type": "Breathing", "percentage": 50}, {"type": "Speaking", "percentage": 50}]}, "The physical activities should be a single string."],
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[{"physical_activity": "Light activity", "respiratory_activity": {"type": "Breathing", "percentage": 100}}, 'The respiratory activities should be in a list.'],
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[{"physical_activity": "Light activity", "respiratory_activity": [["type", "Speaking", "percentage", 100]]}, 'Each respiratory activity should be defined in a dictionary.'],
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[{"physical_activity": "Light activity", "respiratory_activity": [{"tpe": "Breathing", "percentage": 50}, {"type": "Speaking", "percentage": 50}]}, 'Unable to fetch "type" key. Got "tpe".'],
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[{"physical_activity": "Light activity", "respiratory_activity": [{"type": "Breathing", "percentag": 50}, {"type": "Speaking", "percentage": 50}]}, 'Unable to fetch "percentage" key. Got "percentag".'],
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]
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)
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def test_precise_activity_structure(precise_activity_input, error, baseline_form: model_generator.FormData):
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baseline_form.precise_activity = precise_activity_input
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with pytest.raises(TypeError, match=error):
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baseline_form.validate()
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@pytest.mark.parametrize(
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["precise_activity_input", "error"],
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[
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[{"physical_activity": "Light activity", "respiratory_activity": [{"type": "Breathing", "percentage": 10}, {"type": "Speaking", "percentage": 50}]}, 'The sum of all respiratory activities should be 100. Got 60.'],
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[{"physical_activity": "Light activity", "respiratory_activity": [{"type": "Breathing", "percentage": 50}, {"type": "Speaking", "percentage": 10}]}, 'The sum of all respiratory activities should be 100. Got 60.'],
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[{"physical_activity": "Light activity", "respiratory_activity": [{"type": "Breathing", "percentage": 10}, {"type": "Speaking", "percentage": 50}, {"type": "Shouting", "percentage": 50}]}, 'The sum of all respiratory activities should be 100. Got 110.'],
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[{"physical_activity": "Light activity", "respiratory_activity": [{"type": "Breathing", "percentage": 50}]}, 'The sum of all respiratory activities should be 100. Got 50.'],
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]
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)
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def test_sum_precise_activity(precise_activity_input, error, baseline_form: model_generator.FormData):
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baseline_form.precise_activity = precise_activity_input
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with pytest.raises(ValueError, match=error):
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baseline_form.validate()
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