442 lines
20 KiB
Python
442 lines
20 KiB
Python
import dataclasses
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import html
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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 numpy as np
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from caimira import models
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from caimira.store.data_registry import DataRegistry
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from .defaults import DEFAULTS, NO_DEFAULT, COFFEE_OPTIONS_INT
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LOG = logging.getLogger(__name__)
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minutes_since_midnight = typing.NewType('minutes_since_midnight', int)
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@dataclasses.dataclass
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class FormData:
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specific_breaks: dict
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exposed_coffee_break_option: str
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exposed_coffee_duration: int
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exposed_finish: minutes_since_midnight
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exposed_lunch_finish: minutes_since_midnight
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exposed_lunch_option: bool
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exposed_lunch_start: minutes_since_midnight
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exposed_start: minutes_since_midnight
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infected_coffee_break_option: str #Used if infected_dont_have_breaks_with_exposed
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infected_coffee_duration: int #Used if infected_dont_have_breaks_with_exposed
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infected_dont_have_breaks_with_exposed: bool
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infected_finish: minutes_since_midnight
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infected_lunch_finish: minutes_since_midnight #Used if infected_dont_have_breaks_with_exposed
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infected_lunch_option: bool #Used if infected_dont_have_breaks_with_exposed
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infected_lunch_start: minutes_since_midnight #Used if infected_dont_have_breaks_with_exposed
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infected_people: int
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infected_start: minutes_since_midnight
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room_volume: float
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total_people: int
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data_registry: DataRegistry
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_DEFAULTS: typing.ClassVar[typing.Dict[str, typing.Any]] = DEFAULTS
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@classmethod
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def from_dict(cls, form_data: typing.Dict, data_registry: DataRegistry):
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# Take a copy of the form data so that we can mutate it.
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form_data = form_data.copy()
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form_data.pop('_xsrf', None)
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# Don't let arbitrary unescaped HTML through the net.
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for key, value in form_data.items():
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if isinstance(value, str):
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form_data[key] = html.escape(value)
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for key, default_value in cls._DEFAULTS.items():
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if form_data.get(key, '') == '':
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if default_value is NO_DEFAULT:
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raise ValueError(f"{key} must be specified")
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form_data[key] = default_value
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for key, value in form_data.items():
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if key in _CAST_RULES_FORM_ARG_TO_NATIVE:
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form_data[key] = _CAST_RULES_FORM_ARG_TO_NATIVE[key](value)
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if key not in cls._DEFAULTS:
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raise ValueError(f'Invalid argument "{html.escape(key)}" given')
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instance = cls(**form_data, data_registry=data_registry)
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instance.validate()
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return instance
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@classmethod
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def to_dict(cls, form: "FormData", strip_defaults: bool = False) -> dict:
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form_dict = {
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field.name: getattr(form, field.name)
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for field in dataclasses.fields(form)
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}
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for attr, value in form_dict.items():
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if attr in _CAST_RULES_NATIVE_TO_FORM_ARG:
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form_dict[attr] = _CAST_RULES_NATIVE_TO_FORM_ARG[attr](value)
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if strip_defaults:
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del form_dict['calculator_version']
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for attr, value in list(form_dict.items()):
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default = cls._DEFAULTS.get(attr, NO_DEFAULT)
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if default is not NO_DEFAULT and value in [default, 'not-applicable']:
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form_dict.pop(attr)
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return form_dict
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def validate_population_parameters(self):
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# Validate number of infected <= number of total people
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if self.infected_people >= self.total_people:
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raise ValueError('Number of infected people cannot be greater or equal to the number of total people.')
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# Validate time intervals selected by user
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time_intervals = [
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['exposed_start', 'exposed_finish'],
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['infected_start', 'infected_finish'],
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]
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if self.exposed_lunch_option:
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time_intervals.append(['exposed_lunch_start', 'exposed_lunch_finish'])
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if self.infected_dont_have_breaks_with_exposed and self.infected_lunch_option:
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time_intervals.append(['infected_lunch_start', 'infected_lunch_finish'])
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for start_name, end_name in time_intervals:
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start = getattr(self, start_name)
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end = getattr(self, end_name)
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if start > end:
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raise ValueError(
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f"{start_name} must be less than {end_name}. Got {start} and {end}.")
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def validate_lunch(start, finish):
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lunch_start = getattr(self, f'{population}_lunch_start')
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lunch_finish = getattr(self, f'{population}_lunch_finish')
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return (start <= lunch_start <= finish and
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start <= lunch_finish <= finish)
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def get_lunch_mins(population):
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lunch_mins = 0
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if getattr(self, f'{population}_lunch_option'):
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lunch_mins = getattr(self, f'{population}_lunch_finish') - getattr(self, f'{population}_lunch_start')
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return lunch_mins
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def get_coffee_mins(population):
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coffee_mins = 0
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if getattr(self, f'{population}_coffee_break_option') != 'coffee_break_0':
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coffee_mins = COFFEE_OPTIONS_INT[getattr(self, f'{population}_coffee_break_option')] * getattr(self, f'{population}_coffee_duration')
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return coffee_mins
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def get_activity_mins(population):
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return getattr(self, f'{population}_finish') - getattr(self, f'{population}_start')
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populations = ['exposed', 'infected'] if self.infected_dont_have_breaks_with_exposed else ['exposed']
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for population in populations:
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# Validate lunch time within the activity times.
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if (getattr(self, f'{population}_lunch_option') and
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not validate_lunch(getattr(self, f'{population}_start'), getattr(self, f'{population}_finish'))
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):
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raise ValueError(
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f"{population} lunch break must be within presence times."
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)
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# Length of breaks < length of activity
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if (get_lunch_mins(population) + get_coffee_mins(population)) >= get_activity_mins(population):
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raise ValueError(
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f"Length of breaks >= Length of {population} presence."
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)
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for attr_name, valid_set in [('exposed_coffee_break_option', COFFEE_OPTIONS_INT),
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('infected_coffee_break_option', COFFEE_OPTIONS_INT)]:
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if getattr(self, attr_name) not in valid_set:
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raise ValueError(f"{getattr(self, attr_name)} is not a valid value for {attr_name}")
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def validate(self):
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raise NotImplementedError("Subclass must implement")
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def build_model(self, sample_size=None):
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raise NotImplementedError("Subclass must implement")
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def _compute_breaks_in_interval(self, start, finish, n_breaks, duration) -> models.BoundarySequence_t:
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break_delay = ((finish - start) - (n_breaks * duration)) // (n_breaks+1)
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break_times = []
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end = start
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for n in range(n_breaks):
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begin = end + break_delay
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end = begin + duration
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break_times.append((begin, end))
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return tuple(break_times)
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def exposed_lunch_break_times(self) -> models.BoundarySequence_t:
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result = []
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if self.exposed_lunch_option:
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result.append((self.exposed_lunch_start, self.exposed_lunch_finish))
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return tuple(result)
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def infected_lunch_break_times(self) -> models.BoundarySequence_t:
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if self.infected_dont_have_breaks_with_exposed:
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result = []
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if self.infected_lunch_option:
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result.append((self.infected_lunch_start, self.infected_lunch_finish))
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return tuple(result)
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else:
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return self.exposed_lunch_break_times()
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def exposed_number_of_coffee_breaks(self) -> int:
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return COFFEE_OPTIONS_INT[self.exposed_coffee_break_option]
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def infected_number_of_coffee_breaks(self) -> int:
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return COFFEE_OPTIONS_INT[self.infected_coffee_break_option]
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def _coffee_break_times(self, activity_start, activity_finish, coffee_breaks, coffee_duration, lunch_start, lunch_finish) -> models.BoundarySequence_t:
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time_before_lunch = lunch_start - activity_start
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time_after_lunch = activity_finish - lunch_finish
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before_lunch_frac = time_before_lunch / (time_before_lunch + time_after_lunch)
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n_morning_breaks = round(coffee_breaks * before_lunch_frac)
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breaks = (
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self._compute_breaks_in_interval(
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activity_start, lunch_start, n_morning_breaks, coffee_duration
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)
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+ self._compute_breaks_in_interval(
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lunch_finish, activity_finish, coffee_breaks - n_morning_breaks, coffee_duration
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)
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)
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return breaks
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def exposed_coffee_break_times(self) -> models.BoundarySequence_t:
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exposed_coffee_breaks = self.exposed_number_of_coffee_breaks()
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if exposed_coffee_breaks == 0:
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return ()
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if self.exposed_lunch_option:
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breaks = self._coffee_break_times(self.exposed_start, self.exposed_finish, exposed_coffee_breaks, self.exposed_coffee_duration, self.exposed_lunch_start, self.exposed_lunch_finish)
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else:
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breaks = self._compute_breaks_in_interval(self.exposed_start, self.exposed_finish, exposed_coffee_breaks, self.exposed_coffee_duration)
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return breaks
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def infected_coffee_break_times(self) -> models.BoundarySequence_t:
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if self.infected_dont_have_breaks_with_exposed:
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infected_coffee_breaks = self.infected_number_of_coffee_breaks()
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if infected_coffee_breaks == 0:
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return ()
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if self.infected_lunch_option:
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breaks = self._coffee_break_times(self.infected_start, self.infected_finish, infected_coffee_breaks, self.infected_coffee_duration, self.infected_lunch_start, self.infected_lunch_finish)
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else:
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breaks = self._compute_breaks_in_interval(self.infected_start, self.infected_finish, infected_coffee_breaks, self.infected_coffee_duration)
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return breaks
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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, breaks_dict: dict, target: str) -> models.BoundarySequence_t:
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break_times = []
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for n in breaks_dict[f'{target}_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, f'{target}_start') < time < getattr(self, f'{target}_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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finish: int,
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breaks: typing.Optional[models.BoundarySequence_t] = None,
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) -> models.Interval:
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"""
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Calculate the presence interval given the start and end times (in minutes), and
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a number of monotonic, non-overlapping, but potentially unsorted, breaks (also in minutes).
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"""
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if not breaks:
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# If there are no breaks, the interval is the start and end.
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return models.SpecificInterval(((start/60, finish/60),))
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# Order the breaks by their start-time, and ensure that they are monotonic
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# and that the start of one break happens after the end of another.
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break_boundaries: models.BoundarySequence_t = tuple(sorted(breaks, key=lambda break_pair: break_pair[0]))
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for break_start, break_end in break_boundaries:
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if break_start >= break_end:
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raise ValueError("Break ends before it begins.")
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prev_break_end = break_boundaries[0][1]
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for break_start, break_end in break_boundaries[1:]:
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if prev_break_end >= break_start:
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raise ValueError(f"A break starts before another ends ({break_start}, {break_end}, {prev_break_end}).")
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prev_break_end = break_end
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present_intervals = []
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current_time = start
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LOG.debug(f"starting time march at {_hours2timestring(current_time/60)} to {_hours2timestring(finish/60)}")
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# As we step through the breaks. For each break there are 6 important cases
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# we must cover. Let S=start; E=end; Bs=Break start; Be=Break end:
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# 1. The interval is entirely before the break. S < E <= Bs < Be
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# 2. The interval straddles the start of the break. S < Bs < E <= Be
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# 3. The break is entirely inside the interval. S < Bs < Be <= E
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# 4. The interval is entirely inside the break. Bs <= S < E <= Be
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# 5. The interval straddles the end of the break. Bs <= S < Be <= E
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# 6. The interval is entirely after the break. Bs < Be <= S < E
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for current_break in break_boundaries:
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if current_time >= finish:
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break
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LOG.debug(f"handling break {_hours2timestring(current_break[0]/60)}-{_hours2timestring(current_break[1]/60)} "
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f" (current time: {_hours2timestring(current_time/60)})")
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break_s, break_e = current_break
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case1 = finish <= break_s
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case2 = current_time < break_s < finish < break_e
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case3 = current_time < break_s < break_e <= finish
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case4 = break_s <= current_time < finish <= break_e
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case5 = break_s <= current_time < break_e < finish
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case6 = break_e <= current_time
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if case1:
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LOG.debug(f"case 1: interval entirely before break")
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present_intervals.append((current_time / 60, finish / 60))
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LOG.debug(f" + added interval {_hours2timestring(present_intervals[-1][0])} "
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f"- {_hours2timestring(present_intervals[-1][1])}")
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current_time = finish
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elif case2:
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LOG.debug(f"case 2: interval straddles start of break")
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present_intervals.append((current_time / 60, break_s / 60))
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LOG.debug(f" + added interval {_hours2timestring(present_intervals[-1][0])} "
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f"- {_hours2timestring(present_intervals[-1][1])}")
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current_time = break_e
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elif case3:
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LOG.debug(f"case 3: break entirely inside interval")
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# We add the bit before the break, but not the bit afterwards,
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# as it may hit another break.
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present_intervals.append((current_time / 60, break_s / 60))
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LOG.debug(f" + added interval {_hours2timestring(present_intervals[-1][0])} "
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f"- {_hours2timestring(present_intervals[-1][1])}")
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current_time = break_e
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elif case4:
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LOG.debug(f"case 4: interval entirely inside break")
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current_time = finish
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elif case5:
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LOG.debug(f"case 5: interval straddles end of break")
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current_time = break_e
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elif case6:
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LOG.debug(f"case 6: interval entirely after the break")
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if current_time < finish:
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LOG.debug("trailing interval")
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present_intervals.append((current_time / 60, finish / 60))
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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(breaks_dict=self.specific_breaks, target='exposed')
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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=breaks,
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)
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def population_present_interval(self) -> models.Interval:
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state_change_times = set(self.infected_present_interval().transition_times())
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state_change_times.update(self.exposed_present_interval().transition_times())
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all_state_changes = sorted(state_change_times)
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return models.SpecificInterval(tuple(zip(all_state_changes[:-1], all_state_changes[1:])))
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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(breaks_dict=self.specific_breaks, target='exposed')
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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=breaks,
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)
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def _hours2timestring(hours: float):
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# Convert times like 14.5 to strings, like "14:30"
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return f"{int(np.floor(hours)):02d}:{int(np.round((hours % 1) * 60)):02d}"
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def time_string_to_minutes(time: str) -> minutes_since_midnight:
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"""
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Converts time from string-format to an integer number of minutes after 00:00
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:param time: A string of the form "HH:MM" representing a time of day
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:return: The number of minutes between 'time' and 00:00
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"""
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return minutes_since_midnight(60 * int(time[:2]) + int(time[3:]))
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def time_minutes_to_string(time: int) -> str:
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"""
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Converts time from an integer number of minutes after 00:00 to string-format
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:param time: The number of minutes between 'time' and 00:00
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:return: A string of the form "HH:MM" representing a time of day
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"""
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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(s: str) -> list:
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return list(ast.literal_eval(s.replace(""", "\"")))
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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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if isinstance(value, int):
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return value
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elif isinstance(value, float) and int(value) == value:
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return int(value)
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elif isinstance(value, str) and value.isdecimal():
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return int(value)
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else:
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raise TypeError(f"Unable to safely cast {value} ({type(value)} type) to int")
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#: Mapping of field name to a callable which can convert values from form
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#: input (URL encoded arguments / string) into the correct type.
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_CAST_RULES_FORM_ARG_TO_NATIVE: typing.Dict[str, typing.Callable] = {}
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#: Mapping of field name to callable which can convert native type to values
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#: that can be encoded to URL arguments.
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_CAST_RULES_NATIVE_TO_FORM_ARG: typing.Dict[str, typing.Callable] = {}
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def cast_class_fields(cls):
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for _field in dataclasses.fields(cls):
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if _field.type is minutes_since_midnight:
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_CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = time_string_to_minutes
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_CAST_RULES_NATIVE_TO_FORM_ARG[_field.name] = time_minutes_to_string
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elif _field.type is int:
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_CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = _safe_int_cast
|
|
elif _field.type is float:
|
|
_CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = float
|
|
elif _field.type is bool:
|
|
_CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = lambda v: v == '1'
|
|
_CAST_RULES_NATIVE_TO_FORM_ARG[_field.name] = int
|
|
elif _field.type is list:
|
|
_CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = string_to_list
|
|
_CAST_RULES_NATIVE_TO_FORM_ARG[_field.name] = list_to_string
|
|
elif _field.type is dict:
|
|
_CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = string_to_dict
|
|
_CAST_RULES_NATIVE_TO_FORM_ARG[_field.name] = dict_to_string
|
|
|
|
cast_class_fields(FormData)
|