Source code for emodpy_generic.interventions.emergence

from emod_api import schema_to_class as s2c
from emod_api.interventions.utils import *

schema_path =  None

def basicEmergenceEvent(camp, genome=0, clade=0, start_day=1, nods=[]): 
    """
    Seed infection at a particular time by importing a new infected individual.

    Note that this function imports 20 individuals age 5. This could be made configurable but is not 
    yet because this was created with a particular use case in mind. All other values are set to
    schema defaults.

    :param genome: Genome of new infection.
    :param clade: Clade of new infection.  
    :param start_day: WHEN: Day to start campaign event.
    :param nods: WHERE: List of nodes at which infections will be seeded.

    Returns:
        Campaign event that can be added to campaign.

    """
    if camp is not None:
        schema_path = camp.schema_path

    event = s2c.get_class_with_defaults( "CampaignEvent", schema_path )
    coordinator = s2c.get_class_with_defaults( "StandardInterventionDistributionEventCoordinator", schema_path )
    if coordinator is None:
        print( "s2c.get_class_with_defaults returned None. Maybe no schema.json was provided." )
        return ""
    try:
        coordinator.Max_Distributions_Per_Node = cases
    except Exception as ex:
        # This can be fine because this is a new parameter only in some branches.
        # Obviously this question is more general and needs a better general solution
        # if at all possible. Max_Distributions_Per_Node is an event coordinator optional param.
        print( str( ex ) ) 
    
    event.Event_Coordinator_Config = coordinator
    # The intervention itself should be reused from another module
    intervention = s2c.get_class_with_defaults( "Outbreak", schema_path )
    intervention.Genome=genome
    intervention.Clade=clade
    intervention.Import_Age=5*365
    intervention.Number_Cases_Per_Node=20

    coordinator.Intervention_Config = intervention
    event.Start_Day = float(start_day)

    if len(nods) > 0:
        nodelist = s2c.get_class_with_defaults( "NodeSetNodeList", schema_path )
        nodelist.Node_List = nods
        event.Nodeset_Config = nodelist

    #event["Event_Name"] = Event_Name

    return event

def basicSIAEvent(camp, cov=1.0, genome=0, clade=0, start_day=1, nods=[]):
    """
    Seed infection at a particular time by infected existing individuals (or agents really) in the simulation.

    Note that the targeted ages are 0-5 years, not configurable without code change. 

    :param clade: Clade of new infection.
    :param genome: Genome of new infection.
    :param cov: WHO. Percentage of population to infect (given other targeting constrants).
    :param start_day: WHEN: Day to start campaign event.
    :param nods: WHERE: List of nodes at which infections will be seeded.

    Returns:
        Campaign event that can be added to campaign.

    """
    if camp is not None:
        schema_path = camp.schema_path
    event = s2c.get_class_with_defaults( "CampaignEvent", schema_path )
    coordinator = s2c.get_class_with_defaults( "StandardInterventionDistributionEventCoordinator", schema_path )
    if coordinator is None:
        print( "s2c.get_class_with_defaults returned None. Maybe no schema.json was provided." )
        return ""
    try:
        coordinator.Max_Distributions_Per_Node = cases
    except Exception as ex:
        # This can be fine because this is a new parameter only in some branches.
        # Obviously this question is more general and needs a better general solution
        # if at all possible. Max_Distributions_Per_Node is an event coordinator optional param.
        print( str( ex ) ) 
    coordinator.Target_Age_Max=5
    coordinator.Target_Age_Min=0
    coordinator.Demographic_Coverage = cov

    event.Event_Coordinator_Config = coordinator
    # The intervention itself should be reused from another module
    # intervention = emodpy-generic.interventions.standard_generic_vaccine
    intervention = s2c.get_class_with_defaults( "OutbreakIndividual", schema_path )
    intervention.Ignore_Immunity=0
    intervention.Incubation_Period_Override=1
    intervention.Genome=genome
    intervention.Clade=clade

    coordinator.Intervention_Config = intervention
    event.Start_Day = float(start_day)

    if len(nods) > 0:
        nodelist = do_nodes( camp, nods )
 
    #event["Event_Name"] = Event_Name

    return event

def new_intervention_as_file( timestep, filename=None ):
    """
        This function mostly exists for testing so one can exercise the functionality in a single function call.
    """
    camp.add( basicEmergenceEvent( timestep, vaccine_type, iv_name ) )
    if filename is None:
        filename = "emergence.json"
    camp.save( filename )
    return filename