import emod_api.config.default_from_schema_no_validation as dfs
import csv
import os
from . import vector_config
from emodpy_malaria.malaria_vector_species_params import species_params
#
# PUBLIC API section
#
[docs]def get_file_from_http(url):
"""
Get data files from simple http server.
"""
import urllib.request as req
import tempfile
path = tempfile.NamedTemporaryFile()
path.close()
req.urlretrieve(url, path.name)
return path.name
[docs]def set_team_defaults(config, manifest):
"""
Set configuration defaults using team-wide values, including drugs and vector species.
"""
vector_config.set_team_defaults(config, manifest)
config.parameters.Simulation_Type = "MALARIA_SIM"
# removing Infectious_Period parameteres because not allowed in MALARIA_SIM, but need in VECTOR SIM
config.parameters.pop("Infectious_Period_Constant")
config.parameters.pop("Infectious_Period_Distribution")
config.parameters.Malaria_Strain_Model = "FALCIPARUM_RANDOM_STRAIN"
config.parameters.Enable_Disease_Mortality = 0
# config.parameters.Enable_Malaria_CoTransmission = 0
# INFECTION
config.parameters.Max_MSP1_Antibody_Growthrate = 0
config.parameters.Min_Adapted_Response = 0
config.parameters.Infection_Updates_Per_Timestep = 8
config.parameters.Enable_Superinfection = 1
config.parameters.Incubation_Period_Distribution = "CONSTANT_DISTRIBUTION"
config.parameters.Incubation_Period_Constant = 7
config.parameters.Antibody_IRBC_Kill_Rate = 1.596
config.parameters.RBC_Destruction_Multiplier = 3.29
config.parameters.Parasite_Switch_Type = "RATE_PER_PARASITE_7VARS"
# 150305 calibration by JG to Burkina data + 6 of Kevin's sites
# N.B: severe disease re-calibration not done
# 'Base_Gametocyte_Production_Rate': 0.044,
# config.parameters.Gametocyte_Stage_Survival_Rate = 0.82,
# 'Antigen_Switch_Rate': 2.96e-9,
# 'Falciparum_PfEMP1_Variants': 1112,
# 'Falciparum_MSP_Variants': 7,
# 'MSP1_Merozoite_Kill_Fraction': 0.43,
# 'Falciparum_Nonspecific_Types': 90,
# 'Nonspecific_Antigenicity_Factor': 0.42,
# 'Base_Gametocyte_Mosquito_Survival_Rate': 0.00088,
# config.parameters.Max_Individual_Infections = 5,
# 180824 Prashanth parameters [description?]
import math
config.parameters.Antigen_Switch_Rate = math.pow(10, -9.116590124)
config.parameters.Base_Gametocyte_Production_Rate = 0.06150582
config.parameters.Base_Gametocyte_Mosquito_Survival_Rate = 0.002011099
config.parameters.Falciparum_MSP_Variants = 32
config.parameters.Falciparum_Nonspecific_Types = 76
config.parameters.Falciparum_PfEMP1_Variants = 1070
config.parameters.Gametocyte_Stage_Survival_Rate = 0.588569307
config.parameters.MSP1_Merozoite_Kill_Fraction = 0.511735322
config.parameters.Max_Individual_Infections = 3
config.parameters.Nonspecific_Antigenicity_Factor = 0.415111634
# IMMUNITY; these are NOT schema defaults
config.parameters.Antibody_CSP_Killing_Threshold = 20
config.parameters.Antigen_Switch_Rate = math.pow(10, -9.116590124)
config.parameters.Base_Gametocyte_Production_Rate = 0.06150582
config.parameters.Base_Gametocyte_Mosquito_Survival_Rate = 0.002011099
config.parameters.Pyrogenic_Threshold = 1.5e4
config.parameters.Falciparum_MSP_Variants = 32
config.parameters.Falciparum_Nonspecific_Types = 76
config.parameters.Falciparum_PfEMP1_Variants = 1070
config.parameters.Fever_IRBC_Kill_Rate = 1.4
config.parameters.Gametocyte_Stage_Survival_Rate = 0.588569307
config.parameters.Max_MSP1_Antibody_Growthrate = 0.045
config.parameters.MSP1_Merozoite_Kill_Fraction = 0.511735322
config.parameters.Max_Individual_Infections = 3
config.parameters.Nonspecific_Antigenicity_Factor = 0.415111634
config.parameters.Antibody_Capacity_Growth_Rate = 0.09
config.parameters.Antibody_Stimulation_C50 = 30
config.parameters.Antibody_Memory_Level = 0.34
config.parameters.Min_Adapted_Response = 0.05
config.parameters.Cytokine_Gametocyte_Inactivation = 0.01667
config.parameters.Enable_Maternal_Antibodies_Transmission = 1
config.parameters.Maternal_Antibodies_Type = "SIMPLE_WANING"
config.parameters.Maternal_Antibody_Protection = 0.1327
# SYMPTOMATICITY
config.parameters.Anemia_Mortality_Inverse_Width = 1
config.parameters.Anemia_Mortality_Threshold = 0.654726662830038
config.parameters.Anemia_Severe_Inverse_Width = 10
config.parameters.Anemia_Severe_Threshold = 4.50775824973078
config.parameters.Fever_Mortality_Inverse_Width = 1895.51971624351
config.parameters.Fever_Mortality_Threshold = 3.4005008555391
config.parameters.Fever_Severe_Inverse_Width = 27.5653580403806
config.parameters.Fever_Severe_Threshold = 3.98354299722192
config.parameters.Parasite_Mortality_Inverse_Width = 327.51594505874
config.parameters.Parasite_Mortality_Threshold = 10 ** 5.93
config.parameters.Parasite_Severe_Inverse_Width = 56.5754896048744
config.parameters.Parasite_Severe_Threshold = 10 ** 5.929945527
config.parameters.Clinical_Fever_Threshold_High = 1.5
config.parameters.Clinical_Fever_Threshold_Low = 0.5
config.parameters.Min_Days_Between_Clinical_Incidents = 14
# updated from mambrose Oct 11 2019, personal communication with M Plucinski
config.parameters.PfHRP2_Boost_Rate = 0.018 # original value: 0.07
config.parameters.PfHRP2_Decay_Rate = 0.167 # original value: 0.172
config.parameters.Report_Detection_Threshold_Blood_Smear_Gametocytes = 20
config.parameters.Report_Detection_Threshold_Blood_Smear_Parasites = 20
config.parameters.Report_Detection_Threshold_Fever = 1.0
config.parameters.Report_Detection_Threshold_PCR_Gametocytes = 0.05
config.parameters.Report_Detection_Threshold_PCR_Parasites = 0.05
config.parameters.Report_Detection_Threshold_PfHRP2 = 5.0
config.parameters.Report_Detection_Threshold_True_Parasite_Density = 0.0
config.parameters.Report_Gametocyte_Smear_Sensitivity = 0.1
config.parameters.Report_Parasite_Smear_Sensitivity = 0.1 # 10/uL
config = set_team_drug_params(config, manifest)
return config
[docs]def set_team_drug_params(config, manifest):
# TBD: load csv with drug params and populate from that.
with open(os.path.join(os.path.dirname(__file__), 'malaria_drug_params.csv'), newline='') as csvfile:
my_reader = csv.reader(csvfile)
header = next(my_reader)
drug_name_idx = header.index("Name")
drug_pkpd_model_idx = header.index("PKPD_Model")
drug_cmax_idx = header.index("Drug_Cmax")
drug_decayt1_idx = header.index("Drug_Decay_T1")
drug_decayt2_idx = header.index("Drug_Decay_T2")
drug_vd_idx = header.index("Drug_Vd")
drug_pkpdc50_idx = header.index("Drug_PKPD_C50")
drug_ftdoses_idx = header.index("Drug_Fulltreatment_Doses")
drug_dose_interval_idx = header.index("Drug_Dose_Interval")
drug_gam02_idx = header.index("Drug_Gametocyte02_Killrate")
drug_gam34_idx = header.index("Drug_Gametocyte34_Killrate")
drug_gamM_idx = header.index("Drug_GametocyteM_Killrate")
drug_hep_idx = header.index("Drug_Hepatocyte_Killrate")
drug_maxirbc_idx = header.index("Max_Drug_IRBC_Kill")
drug_adher_idx = header.index("Drug_Adherence_Rate")
drug_bwexp_idx = header.index("Bodyweight_Exponent")
drug_fracdos_key_idx = header.index("Upper_Age_In_Years")
drug_fracdos_val_idx = header.index("Fraction_Of_Adult_Dose")
# for each
for row in my_reader:
mdp = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:MalariaDrugTypeParameters"])
mdp.parameters.Drug_Cmax = float(row[drug_cmax_idx])
mdp.parameters.Drug_Decay_T1 = float(row[drug_decayt1_idx])
mdp.parameters.Drug_Decay_T2 = float(row[drug_decayt2_idx])
mdp.parameters.Drug_Vd = float(row[drug_vd_idx])
mdp.parameters.Drug_PKPD_C50 = float(row[drug_pkpdc50_idx])
mdp.parameters.Drug_Fulltreatment_Doses = float(row[drug_ftdoses_idx])
mdp.parameters.Drug_Dose_Interval = float(row[drug_dose_interval_idx])
mdp.parameters.Drug_Gametocyte02_Killrate = float(row[drug_gam02_idx])
mdp.parameters.Drug_Gametocyte34_Killrate = float(row[drug_gam34_idx])
mdp.parameters.Drug_GametocyteM_Killrate = float(row[drug_gamM_idx])
mdp.parameters.Drug_Hepatocyte_Killrate = float(row[drug_hep_idx])
mdp.parameters.Max_Drug_IRBC_Kill = float(row[drug_maxirbc_idx])
mdp.parameters.PKPD_Model = row[drug_pkpd_model_idx]
mdp.parameters.Name = row[drug_name_idx]
# mdp.parameters.Drug_Adherence_Rate = float(row[ drug_adher_idx ])
mdp.parameters.Bodyweight_Exponent = float(row[drug_bwexp_idx])
try:
ages = [float(x) for x in row[drug_fracdos_key_idx].strip('[]').split(",")]
values = [float(x) for x in row[drug_fracdos_val_idx].strip('[]').split(",")]
except Exception as ex:
print("For drug {}, {}".format(row[0], str(ex)))
ages = []
values = []
for idx in range(len(ages)):
fdbua = dict()
# this is what we want but not ready yet
# fdbua = dfs.schema_to_config_subnode(mani.schema_file, ["idmTypes","idmType:DoseMap"] )
# fdbua.Upper_Age_In_Years = ages[idx]
# fdbua.Fraction_Of_Adult_Dose = values[idx]
fdbua["Upper_Age_In_Years"] = ages[idx]
fdbua["Fraction_Of_Adult_Dose"] = values[idx]
# fdbua.finalize()
mdp.parameters.Fractional_Dose_By_Upper_Age.append(fdbua)
config.parameters.Malaria_Drug_Params.append(mdp.parameters)
# end
return config
[docs]def set_parasite_genetics_params(config, manifest, var_gene_randomness_type: str = "ALL_RANDOM"):
"""
Sets up the default parameters for parasite genetics simulations
Malaria_Model = "MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS"
Args:
config: schema-backed config smart dict
manifest: schema path container
var_gene_randomness_type: possible values are "FIXED_NEIGHBORHOOD", "FIXED_MSP", "ALL_RANDOM" (default)
Returns:
configured config
"""
set_team_defaults(config, manifest)
config.parameters.pop("Malaria_Strain_Model") # removing incompatible Malaria_Strain_Model parameter
# config.parameters.pop("Enable_Initial_Prevalence") # popping it here doesn't work
config.parameters.Malaria_Model = "MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS"
config.parameters.Falciparum_MSP_Variants = 100
config.parameters.Falciparum_Nonspecific_Types = 20
config.parameters.Falciparum_PfEMP1_Variants = 1000
config.parameters.Vector_Sampling_Type = "TRACK_ALL_VECTORS"
config.parameters.Max_Individual_Infections = 10
# setting up Parasite_Genetics parameteres
fpg = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:ParasiteGenetics"])
fpg.parameters.Var_Gene_Randomness_Type = var_gene_randomness_type
fpg.parameters.Sporozoite_Life_Expectancy = 25
fpg.parameters.Num_Sporozoites_In_Bite_Fail = 12
fpg.parameters.Probability_Sporozoite_In_Bite_Fails = 0.5
fpg.parameters.Num_Oocyst_From_Bite_Fail = 3
fpg.parameters.Probability_Oocyst_From_Bite_Fails = 0.5
fpg.parameters.Sporozoites_Per_Oocyst_Distribution = "GAUSSIAN_DISTRIBUTION"
fpg.parameters.Sporozoites_Per_Oocyst_Gaussian_Mean = 10000
fpg.parameters.Sporozoites_Per_Oocyst_Gaussian_Std_Dev = 1000
fpg.parameters.Crossover_Gamma_K = 2
fpg.parameters.Crossover_Gamma_Theta = 0.38
fpg.parameters.Drug_Resistant_Genome_Locations = []
fpg.parameters.Barcode_Genome_Locations = [
311500,
1116500,
2140000,
3290000,
4323333,
4756667,
5656667,
6123333,
7056667,
7523333,
8423333,
8856667,
9790000,
10290000,
11356667,
11923333,
13156667,
13823333,
15256667,
16023333,
17690000,
18590000,
20590000,
21690000
]
if var_gene_randomness_type == "FIXED_NEIGHBORHOOD" or var_gene_randomness_type == "FIXED_MSP":
fpg.parameters.MSP_Genome_Location = 200000
fpg.parameters.Neighborhood_Size_MSP = 4
if var_gene_randomness_type == "FIXED_NEIGHBORHOOD":
fpg.parameters.PfEMP1_Variants_Genome_Locations = [
214333,
428667,
958667,
1274333,
1864900,
2139900,
2414900,
2989900,
3289900,
3589900,
4150000,
4410000,
4670000,
4930000,
5470000,
5750000,
6030000,
6310000,
6870000,
7150000,
7430000,
7710000,
8250000,
8510000,
8770000,
9030000,
9590000,
9890000,
10190000,
10490000,
11130000,
11470000,
11810000,
12150000,
12890000,
13290000,
13690000,
14090000,
14950000,
15410000,
15870000,
16330000,
17330000,
17870000,
18410000,
18950000,
20150000,
20810000,
21470000,
22130000
]
fpg.parameters.Neighborhood_Size_PfEMP1 = 10
config.parameters.Parasite_Genetics = fpg.parameters
# setting up gambiae parameters for parasite genetics
fpg_gambiae_params = species_params(manifest, "fpg_gambiae")
config.parameters.Vector_Species_Params = [fpg_gambiae_params]
# end vector species
return config
[docs]def get_drug_params(cb, drug_name):
for idx, drug_params in enumerate(cb.parameters.Malaria_Drug_Params):
if drug_params.Name == drug_name:
return cb.parameters.Malaria_Drug_Params[idx]
raise ValueError(f"{drug_name} not found.")
[docs]def set_drug_param(config, drug_name: str = None, parameter: str = None, value: any = None):
"""
Set a drug parameter, by passing in drug name, parameter and the parameter value.
Added to facilitate adding drug Resistances,
**Example**::
artemether_drug_resistance = [{
"Drug_Resistant_String": "A",
"PKPD_C50_Modifier": 2.0,
"Max_IRBC_Kill_Modifier": 0.9}]
set_drug_param(cb, drug_name='Artemether', parameter="Resistances", value=artemether_drug_resistance)
Args:
config: schema-backed config smart dict
drug_name: The drug that has a parameter to set
parameter: The parameter to set
value: The new value to set
Returns:
Nothing or error if drug name is not found
"""
if not drug_name or not parameter or not value:
raise Exception("Please pass in all: drug_name, parameter, and value.\n")
for drug in config.parameters.Malaria_Drug_Params:
if drug.Name == drug_name:
drug[parameter] = value
return # should I return anything here?
raise ValueError(f"{drug_name} not found.\n")
[docs]def add_drug_resistance(config, manifest, drugname: str = None, drug_resistant_string: str = None,
pkpd_c50_modifier: float = 1.0, max_irbc_kill_modifier: float = 1.0):
"""
Adds drug resistances by drug name and parameters
Args:
config: schema-backed config smart dict
manifest: manifest file containing the schema path
drugname: name of the drug for which to assign resistances
drug_resistant_string: A series of nucleotide base letters (A, C, G, T) that represent the drug resistant
values at locations in the genome
pkpd_c50_modifier: If the parasite has this genome marker, this value will be multiplied times the
'Drug_PKPD_C50' value of the drug. Genomes with multiple markers will be simply multiplied together
max_irbc_kill_modifier: If the parasite has this genome marker, this value will be multiplied times the
'Max_Drug_IRBC_Kill' value of the drug. Genomes with multiple markers will be simply multiplied together
Returns:
configured config
"""
drugmod = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:DrugModifier"])
drugmod.parameters.Drug_Resistant_String = drug_resistant_string
drugmod.parameters.Max_IRBC_Kill_Modifier = max_irbc_kill_modifier
drugmod.parameters.PKPD_C50_Modifier = pkpd_c50_modifier
for drug_param in config.parameters.Malaria_Drug_Params:
if drug_param.Name == drugname:
drug_param.Resistances.append(drugmod.parameters)
return config
raise ValueError(f"Drug name {drugname} not found.\n")
[docs]def set_species_param(config, species, parameter, value, overwrite=False):
"""
Pass through for vector version of function.
"""
return vector_config.set_species_param(config, species, parameter, value, overwrite=overwrite)
[docs]def add_species(config, manifest, species_to_select):
"""
Pass through for vector version of function.
"""
vector_config.add_species(config, manifest, species_to_select)
[docs]def add_insecticide_resistance(config, manifest, insecticide_name: str = "", species: str = "",
allele_combo: list = None, blocking: float = 1.0, killing: float = 1.0,
repelling: float = 1.0, larval_killing: float = 1.0):
"""
Pass through for vector version of function.
"""
vector_config.add_insecticide_resistance(config, manifest, insecticide_name, species,
allele_combo, blocking, killing,
repelling, larval_killing)
[docs]def get_species_params(config, species: str = None):
"""
Pass through for vector version of function.
"""
return vector_config.get_species_params(config, species)
[docs]def set_max_larval_capacity(config, species_name: str, habitat_type: str, max_larval_capacity: int):
"""
Set the Max_Larval_Capacity for a given species and habitat. Effectively doing something like:
simulation.task.config.parameters.Vector_Species_Params[i]["Habitats"][j]["Max_Larval_Capacity"] = max_larval_capacity
where i is index of species_name and j is index of habitat_type.
Args:
config: schema-backed config smart dict
species_name: string. Species_Name to target.
habitat_type: enum. Habitat_Type to target.
max_larval_capacity: integer. New value of Max_Larval_Capacity.
Returns:
Nothing.
"""
return vector_config.set_max_larval_capacity(config, species_name, habitat_type, max_larval_capacity)
[docs]def add_microsporidia(config, manifest, species_name: str = None,
strain_name: str = "Strain_A",
female_to_male_probability: float = 0,
female_to_egg_probability: float = 0,
male_to_female_probability: float = 0,
male_to_egg_probability: float = 0,
duration_to_disease_acquisition_modification: dict = None,
duration_to_disease_transmission_modification: dict = None,
larval_growth_modifier: float = 1,
female_mortality_modifier: float = 1,
male_mortality_modifier: float = 1):
"""
Adds microsporidia parameters to the named species' parameters.
Args:
config: schema-backed config dictionary, written to config.json
manifest: file that contains path to the schema file
species_name: Species to target, **Name** parameter
strain_name: **Strain_Name** The name/identifier of the collection of transmission parameters.
Cannot be empty string
female_to_male_probability: **Microsporidia_Female_to_Male_Transmission_Probability** The probability
an infected female will infect an uninfected male.
female_to_egg_probability: **Microsporidia_Female_To_Egg_Transmission_Probability** The probability
an infected female will infect her eggs when laying them.
male_to_female_probability: **Microsporidia_Male_To_Female_Transmission_Probability** The probability
an infected male will infect an uninfected female
male_to_egg_probability: **Microsporidia_Male_To_Egg_Transmission_Probability** The probability a female that
mated with an infected male will infect her eggs when laying them, independent of her being infected and
transmitting to her offspring.
duration_to_disease_acquisition_modification: **Microsporidia_Duration_To_Disease_Acquisition_Modification**,
A dictionary for "Times" and "Values" as an age-based modification that the female will acquire malaria.
**Times** is an array of days in ascending order that represent the number of days since the vector became
infected. **Values** is an array of probabilities with values from 0 to 1 where each probability is the
probability that the vector will acquire malaria due to Microsporidia.
**Example**::
{
"Times": [ 0, 3, 6, 9 ],
"Values": [ 1.0, 1.0, 0.5, 0.0 ]
}
duration_to_disease_transmission_modification: **Microsporidia_Duration_To_Disease_Transmission_Modification**,
A dictionary for "Times" and "Values" as an age-based modification that the female will transmit malaria.
**Times** is an array of days in ascending order that represent the number of days since the vector became
infected. **Values** is an array of probabilities with values from 0 to 1 where each probability is the
probability that the vector will acquire malaria due to Microsporidia.
**Example**::
{
"Times": [ 0, 3, 6, 9 ],
"Values": [ 1.0, 1.0, 0.75, 0.5]
}
larval_growth_modifier: **Microsporidia_Larval_Growth_Modifier** A multiplier modifier to the daily, temperature
dependent, larval growth progress.
female_mortality_modifier: **Microsporidia_Female_Mortality_Modifier** A multiplier modifier on the death
rate for female vectors due to general life expectancy, age, and dry heat
male_mortality_modifier: **Microsporidia_Male_Mortality_Modifier** A multiplier modifier on the death rate for
male vectors due to general life expectancy, age, and dry heat
Returns:
Nothing
"""
vector_config.add_microsporidia(config, manifest,
species_name=species_name,
strain_name=strain_name,
female_to_male_probability=female_to_male_probability,
female_to_egg_probability=female_to_egg_probability,
male_to_female_probability=male_to_female_probability,
male_to_egg_probability=male_to_egg_probability,
duration_to_disease_acquisition_modification=duration_to_disease_acquisition_modification,
duration_to_disease_transmission_modification=duration_to_disease_transmission_modification,
larval_growth_modifier=larval_growth_modifier,
female_mortality_modifier=female_mortality_modifier,
male_mortality_modifier=male_mortality_modifier)
