Merge branch 'feature/global_store' into 'master'

Global Store and Configuration Implementation

See merge request caimira/caimira!466

caimira/apps/calculator/__init__.py

@@ -28,7 +28,6 @@
 from . import markdown_tools
 from . import model_generator
 from .report_generator import ReportGenerator, calculate_report_data
-from .data_service import DataService
 from .user import AuthenticatedUser, AnonymousUser
 
 # The calculator version is based on a combination of the model version and the
@@ -38,7 +37,7 @@
 # calculator version. If the calculator needs to make breaking changes (e.g. change
 # form attributes) then it can also increase its MAJOR version without needing to
 # increase the overall CAiMIRA version (found at ``caimira.__version__``).
-__version__ = "4.12.1"
+__version__ = "4.13.0"
 
 LOG = logging.getLogger(__name__)
 
@@ -105,17 +104,6 @@ async def post(self) -> None:
             from pprint import pprint
             pprint(requested_model_config)
             start = datetime.datetime.now()
-
-        # Data Service API Integration
-        fetched_service_data = None
-        data_service: DataService = self.settings["data_service"]
-        if self.settings["data_service"]:
-            try:
-                fetched_service_data = await data_service.fetch()
-            except Exception as err:
-                error_message = f"Something went wrong with the data service: {str(err)}"
-                LOG.error(error_message, exc_info=True)
-                self.send_error(500, reason=error_message)
 
         try:
             form = model_generator.FormData.from_dict(requested_model_config)
@@ -429,15 +417,6 @@ def make_app(
     )
     template_environment.globals['get_url']=get_root_url
     template_environment.globals['get_calculator_url']=get_root_calculator_url
-
-    data_service_credentials = {
-        'data_service_client_email': os.environ.get('DATA_SERVICE_CLIENT_EMAIL', None),
-        'data_service_client_password': os.environ.get('DATA_SERVICE_CLIENT_PASSWORD', None),
-    }
-    data_service = None
-    data_service_enabled = os.environ.get('DATA_SERVICE_ENABLED', 'False').lower() == 'true'
-    if data_service_enabled:
-        data_service = DataService(data_service_credentials)
 
     if debug:
         tornado.log.enable_pretty_logging()
@@ -456,9 +435,6 @@ def make_app(
         arve_client_secret=os.environ.get('ARVE_CLIENT_SECRET', None),
         arve_api_key=os.environ.get('ARVE_API_KEY', None),
 
-        # Data Service Integration
-        data_service=data_service,
-
         # Process parallelism controls. There is a balance between serving a single report
         # requests quickly or serving multiple requests concurrently.
         # The defaults are: handle one report at a time, and allow parallelism

caimira/apps/calculator/defaults.py

@@ -1,11 +1,13 @@
 import typing
 
+from caimira.store.configuration import config
+
 # ------------------ Default form values ----------------------
 
 # Used to declare when an attribute of a class must have a value provided, and
 # there should be no default value used.
 NO_DEFAULT = object()
-DEFAULT_MC_SAMPLE_SIZE = 250_000
+DEFAULT_MC_SAMPLE_SIZE = config.monte_carlo_sample_size
 
 #: The default values for undefined fields. Note that the defaults here
 #: and the defaults in the html form must not be contradictory.
@@ -79,57 +81,17 @@
 
 # ------------------ Activities ----------------------
 
-ACTIVITIES: typing.List[typing.Dict[str, typing.Any]] = [
-    # Mostly silent in the office, but 1/3rd of time speaking.
-    {'name': 'office', 'activity': 'Seated',
-        'expiration': {'Speaking': 1, 'Breathing': 2}},
-    {'name': 'smallmeeting', 'activity': 'Seated',
-        'expiration': {'Speaking': 1, 'Breathing': None}},
-    # Each infected person spends 1/3 of time speaking.
-    {'name': 'largemeeting', 'activity': 'Standing',
-        'expiration': {'Speaking': 1, 'Breathing': 2}},
-    {'name': 'callcentre', 'activity': 'Seated', 'expiration': 'Speaking'},
-    # Daytime control room shift, 50% speaking.
-    {'name': 'controlroom-day', 'activity': 'Seated',
-        'expiration': {'Speaking': 1, 'Breathing': 1}},
-    # Nightshift control room, 10% speaking.
-    {'name': 'controlroom-night', 'activity': 'Seated',
-        'expiration': {'Speaking': 1, 'Breathing': 9}},
-    {'name': 'library', 'activity': 'Seated', 'expiration': 'Breathing'},
-    # Model 1/2 of time spent speaking in a lab.
-    {'name': 'lab', 'activity': 'Light activity',
-        'expiration': {'Speaking': 1, 'Breathing': 1}},
-    # Model 1/2 of time spent speaking in a workshop.
-    {'name': 'workshop', 'activity': 'Moderate activity',
-        'expiration': {'Speaking': 1, 'Breathing': 1}},
-    {'name': 'training', 'activity': 'Standing', 'expiration': 'Speaking'},
-    {'name': 'training_attendee', 'activity': 'Seated', 'expiration': 'Breathing'},
-    {'name': 'gym', 'activity': 'Heavy exercise', 'expiration': 'Breathing'},
-    {'name': 'household-day', 'activity': 'Light activity',
-        'expiration': {'Breathing': 5, 'Speaking': 5}},
-    {'name': 'household-night', 'activity': 'Seated',
-        'expiration': {'Breathing': 7, 'Speaking': 3}},
-    {'name': 'primary-school', 'activity': 'Light activity',
-        'expiration': {'Breathing': 5, 'Speaking': 5}},
-    {'name': 'secondary-school', 'activity': 'Light activity',
-        'expiration': {'Breathing': 7, 'Speaking': 3}},
-    {'name': 'university', 'activity': 'Seated',
-        'expiration': {'Breathing': 9, 'Speaking': 1}},
-    {'name': 'restaurant', 'activity': 'Seated',
-        'expiration': {'Breathing': 1, 'Speaking': 9}},
-    {'name': 'precise', 'activity': None, 'expiration': None},
-]
+ACTIVITIES: typing.Dict[str, typing.Dict] = config.population_scenario_activity
 
 # ------------------ Validation ----------------------
-
-ACTIVITY_TYPES = [activity['name'] for activity in ACTIVITIES]
+ACTIVITY_TYPES: typing.List[str] = list(ACTIVITIES.keys())
 COFFEE_OPTIONS_INT = {'coffee_break_0': 0, 'coffee_break_1': 1,
                       'coffee_break_2': 2, 'coffee_break_4': 4}
 CONFIDENCE_LEVEL_OPTIONS = {'confidence_low': 10,
                             'confidence_medium': 5, 'confidence_high': 2}
 MECHANICAL_VENTILATION_TYPES = {
     'mech_type_air_changes', 'mech_type_air_supply', 'not-applicable'}
-MASK_TYPES = {'Type I', 'FFP2', 'Cloth'}
+MASK_TYPES: typing.List[str] = list(config.mask_distributions.keys())
 MASK_WEARING_OPTIONS = {'mask_on', 'mask_off'}
 MONTH_NAMES = [
     'January', 'February', 'March', 'April', 'May', 'June', 'July',
@@ -143,8 +105,7 @@
                 'mRNA-1273_(Moderna)', 'Sputnik_V_(Gamaleya)', 'CoronaVac_(Sinovac)_and_BNT162b2_(Pfizer)']
 VENTILATION_TYPES = {'natural_ventilation',
                      'mechanical_ventilation', 'no_ventilation'}
-VIRUS_TYPES = {'SARS_CoV_2', 'SARS_CoV_2_ALPHA', 'SARS_CoV_2_BETA',
-               'SARS_CoV_2_GAMMA', 'SARS_CoV_2_DELTA', 'SARS_CoV_2_OMICRON'}
+VIRUS_TYPES: typing.List[str] = list(config.virus_distributions)
 VOLUME_TYPES = {'room_volume_explicit', 'room_volume_from_dimensions'}
 WINDOWS_OPENING_REGIMES = {'windows_open_permanently',
                            'windows_open_periodically', 'not-applicable'}

caimira/apps/calculator/model_generator.py

@@ -19,6 +19,7 @@
 from .defaults import (NO_DEFAULT, DEFAULT_MC_SAMPLE_SIZE, DEFAULTS, ACTIVITIES, ACTIVITY_TYPES, COFFEE_OPTIONS_INT, CONFIDENCE_LEVEL_OPTIONS, 
                        MECHANICAL_VENTILATION_TYPES, MASK_TYPES, MASK_WEARING_OPTIONS, MONTH_NAMES, VACCINE_BOOSTER_TYPE, VACCINE_TYPE, 
                        VENTILATION_TYPES, VIRUS_TYPES, VOLUME_TYPES, WINDOWS_OPENING_REGIMES, WINDOWS_TYPES)
+from caimira.store.configuration import config
 
 LOG = logging.getLogger(__name__)
 
@@ -314,10 +315,10 @@ def initialize_room(self) -> models.Room:
 
         if self.arve_sensors_option == False:
             if self.room_heating_option:
-                humidity = 0.3
+                humidity = config.room['defaults']['humidity_with_heating']
             else:
-                humidity = 0.5
-            inside_temp = 293.
+                humidity = config.room['defaults']['humidity_without_heating']
+            inside_temp = config.room['defaults']['inside_temp']
         else:
             humidity = float(self.humidity)
             inside_temp = self.inside_temp
@@ -373,7 +374,7 @@ def build_CO2_model(self, sample_size=DEFAULT_MC_SAMPLE_SIZE) -> models.CO2Conce
         if (self.activity_type == 'precise'):
             activity_defn, _ = self.generate_precise_activity_expiration()
         else:
-            activity_defn = ACTIVITIES[ACTIVITY_TYPES.index(self.activity_type)]['activity']
+            activity_defn = activity_defn = ACTIVITIES[self.activity_type]['activity']
 
         population = mc.SimplePopulation(
             number=models.IntPiecewiseConstant(transition_times=tuple(transition_times), values=tuple(total_people)),
@@ -476,7 +477,8 @@ def ventilation(self) -> models._VentilationBase:
         # This is a minimal, always present source of ventilation, due
         # to the air infiltration from the outside.
         # See CERN-OPEN-2021-004, p. 12.
-        infiltration_ventilation = models.AirChange(active=always_on, air_exch=0.25)
+        residual_vent: float = config.ventilation['infiltration_ventilation'] # type: ignore
+        infiltration_ventilation = models.AirChange(active=always_on, air_exch=residual_vent)
         if self.hepa_option:
             hepa = models.HEPAFilter(active=always_on, q_air_mech=self.hepa_amount)
             return models.MultipleVentilation((ventilation, hepa, infiltration_ventilation))
@@ -511,9 +513,8 @@ def infected_population(self) -> mc.InfectedPopulation:
         # Initializes the virus
         virus = virus_distributions[self.virus_type]
 
-        activity_index = ACTIVITY_TYPES.index(self.activity_type)
-        activity_defn = ACTIVITIES[activity_index]['activity']
-        expiration_defn = ACTIVITIES[activity_index]['expiration']
+        activity_defn = ACTIVITIES[self.activity_type]['activity']
+        expiration_defn = ACTIVITIES[self.activity_type]['expiration']
 
         if (self.activity_type == 'smallmeeting'):
             # Conversation of N people is approximately 1/N% of the time speaking.
@@ -538,29 +539,9 @@ def infected_population(self) -> mc.InfectedPopulation:
         return infected
 
     def exposed_population(self) -> mc.Population:
-        scenario_activity = {
-            'office': 'Seated',
-            'controlroom-day': 'Seated',
-            'controlroom-night': 'Seated',
-            'smallmeeting': 'Seated',
-            'largemeeting': 'Standing',
-            'callcentre': 'Seated',
-            'library': 'Seated',
-            'training': 'Standing',
-            'training_attendee': 'Seated',
-            'lab':'Light activity',
-            'workshop': 'Moderate activity',
-            'gym':'Heavy exercise',
-            'household-day': 'Light activity',
-            'household-night': 'Seated', 
-            'primary-school': 'Light activity', 
-            'secondary-school': 'Light activity', 
-            'university': 'Seated', 
-            'restaurant': 'Seated',
-            'precise': self.precise_activity['physical_activity'] if self.activity_type == 'precise' else None,
-        }
-
-        activity_defn = scenario_activity[self.activity_type]
+        activity_defn = (self.precise_activity['physical_activity'] 
+                         if self.activity_type == 'precise' 
+                         else str(config.population_scenario_activity[self.activity_type]['activity']))
         activity = activity_distributions[activity_defn]
 
         infected_occupants = self.infected_people

caimira/apps/calculator/report_generator.py

@@ -17,6 +17,7 @@
 from ... import monte_carlo as mc
 from .model_generator import FormData, DEFAULT_MC_SAMPLE_SIZE
 from ... import dataclass_utils
+from caimira.store.configuration import config
 
 
 def model_start_end(model: models.ExposureModel):
@@ -201,16 +202,18 @@ def conditional_prob_inf_given_vl_dist(infection_probability: models._Vectorised
     for vl_log in viral_loads:
         specific_prob = infection_probability[np.where((vl_log-step/2-specific_vl)*(vl_log+step/2-specific_vl)<0)[0]] #type: ignore
         pi_means.append(specific_prob.mean())
-        lower_percentiles.append(np.quantile(specific_prob, 0.05))
-        upper_percentiles.append(np.quantile(specific_prob, 0.95))
+        lower_percentiles.append(np.quantile(specific_prob, config.conditional_prob_inf_given_viral_load['lower_percentile']))
+        upper_percentiles.append(np.quantile(specific_prob, config.conditional_prob_inf_given_viral_load['upper_percentile']))
 
     return pi_means, lower_percentiles, upper_percentiles
 
 
 def manufacture_conditional_probability_data(exposure_model: models.ExposureModel, 
                                              infection_probability: models._VectorisedFloat):
 
-    min_vl, max_vl, step = 2, 10, 8/100
+    min_vl = config.conditional_prob_inf_given_viral_load['min_vl']
+    max_vl = config.conditional_prob_inf_given_viral_load['max_vl']
+    step = (max_vl - min_vl)/100
     viral_loads = np.arange(min_vl, max_vl, step)   
     specific_vl = np.log10(exposure_model.concentration_model.virus.viral_load_in_sputum)
     pi_means, lower_percentiles, upper_percentiles = conditional_prob_inf_given_vl_dist(infection_probability, viral_loads,