From 9fd726e4f1311493cbbc947de82439a741d8c194 Mon Sep 17 00:00:00 2001 From: yechen-idm Date: Tue, 15 Oct 2024 11:34:43 -0700 Subject: [PATCH] update unittest with new baseline from latest Emod --- tests/inputs/2.20.5522.0_old_campaign.json | 335 ++++++++++ .../2.20.5522.0_old_custom_reports.json | 367 +++++++++++ tests/inputs/2.20.5522.0_old_demog.json | 82 +++ tests/inputs/2.20.5522.0_old_my_config.json | 581 ++++++++++++++++++ tests/test_run_sims.py | 2 +- 5 files changed, 1366 insertions(+), 1 deletion(-) create mode 100644 tests/inputs/2.20.5522.0_old_campaign.json create mode 100644 tests/inputs/2.20.5522.0_old_custom_reports.json create mode 100644 tests/inputs/2.20.5522.0_old_demog.json create mode 100644 tests/inputs/2.20.5522.0_old_my_config.json diff --git a/tests/inputs/2.20.5522.0_old_campaign.json b/tests/inputs/2.20.5522.0_old_campaign.json new file mode 100644 index 0000000..4c3c69a --- /dev/null +++ b/tests/inputs/2.20.5522.0_old_campaign.json @@ -0,0 +1,335 @@ +{ + "Campaign_Name": "Unnamed Campaign", + "Events": [ + { + "Event_Coordinator_Config": { + "Demographic_Coverage": 1, + "Individual_Selection_Type": "DEMOGRAPHIC_COVERAGE", + "Intervention_Config": { + "Age_Dependence": "SURFACE_AREA_DEPENDENT", + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "EIR_Type": "MONTHLY", + "Intervention_Name": "InputEIR", + "Monthly_EIR": [ + 13, + 16, + 8, + 3, + 5, + 8, + 44, + 26, + 35, + 19, + 13, + 11 + ], + "New_Property_Value": "", + "Scaling_Factor": 1, + "class": "InputEIR" + }, + "Node_Property_Restrictions": [], + "Number_Repetitions": 1, + "Property_Restrictions": [], + "Property_Restrictions_Within_Node": [], + "Target_Demographic": "Everyone", + "Target_Gender": "All", + "Target_Residents_Only": 0, + "Targeting_Config": { + "HasIP": {}, + "HasIntervention": {}, + "IsPregnant": {}, + "TargetingLogic": {} + }, + "Timesteps_Between_Repetitions": 365, + "class": "StandardInterventionDistributionEventCoordinator" + }, + "Nodeset_Config": { + "class": "NodeSetAll" + }, + "Start_Day": 0, + "class": "CampaignEvent" + }, + { + "Event_Coordinator_Config": { + "Demographic_Coverage": 1, + "Individual_Selection_Type": "DEMOGRAPHIC_COVERAGE", + "Intervention_Config": { + "Actual_IndividualIntervention_Config": { + "Actual_IndividualIntervention_Configs": [ + { + "Cost_To_Consumer": 0, + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Drug_Type": "Artemether", + "Intervention_Name": "AntimalarialDrug_Artemether", + "New_Property_Value": "", + "class": "AntimalarialDrug" + }, + { + "Cost_To_Consumer": 0, + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Drug_Type": "Lumefantrine", + "Intervention_Name": "AntimalarialDrug_Lumefantrine", + "New_Property_Value": "", + "class": "AntimalarialDrug" + }, + { + "Broadcast_Event": "ReceivedTreatment", + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Intervention_Name": "BroadcastEvent", + "New_Property_Value": "", + "class": "BroadcastEvent" + } + ], + "Coverage": 1, + "Delay_Period_Distribution": "EXPONENTIAL_DISTRIBUTION", + "Delay_Period_Exponential": 3.3333333333333335, + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Intervention_Name": "DelayedIntervention", + "New_Property_Value": "", + "class": "DelayedIntervention" + }, + "Blackout_Event_Trigger": "", + "Blackout_On_First_Occurrence": 0, + "Blackout_Period": 0, + "Demographic_Coverage": 0.1, + "Disqualifying_Properties": [], + "Distribute_On_Return_Home": 0, + "Dont_Allow_Duplicates": 0, + "Duration": -1, + "Intervention_Name": "NodeLevelHealthTriggeredIV", + "New_Property_Value": "", + "Node_Property_Restrictions": [], + "Property_Restrictions": [], + "Target_Age_Max": 5, + "Target_Age_Min": 0, + "Target_Demographic": "ExplicitAgeRanges", + "Target_Gender": "All", + "Target_Residents_Only": 0, + "Targeting_Config": { + "HasIP": {}, + "HasIntervention": {}, + "IsPregnant": {}, + "TargetingLogic": {} + }, + "Trigger_Condition_List": [ + "NewClinicalCase" + ], + "class": "NodeLevelHealthTriggeredIV" + }, + "Node_Property_Restrictions": [], + "Number_Repetitions": 1, + "Property_Restrictions": [], + "Property_Restrictions_Within_Node": [], + "Target_Demographic": "Everyone", + "Target_Gender": "All", + "Target_Residents_Only": 0, + "Targeting_Config": { + "HasIP": {}, + "HasIntervention": {}, + "IsPregnant": {}, + "TargetingLogic": {} + }, + "Timesteps_Between_Repetitions": -1, + "class": "StandardInterventionDistributionEventCoordinator" + }, + "Nodeset_Config": { + "class": "NodeSetAll" + }, + "Start_Day": 0.0, + "class": "CampaignEvent" + }, + { + "Event_Coordinator_Config": { + "Demographic_Coverage": 1, + "Individual_Selection_Type": "DEMOGRAPHIC_COVERAGE", + "Intervention_Config": { + "Actual_IndividualIntervention_Config": { + "Actual_IndividualIntervention_Configs": [ + { + "Cost_To_Consumer": 0, + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Drug_Type": "Artemether", + "Intervention_Name": "AntimalarialDrug_Artemether", + "New_Property_Value": "", + "class": "AntimalarialDrug" + }, + { + "Cost_To_Consumer": 0, + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Drug_Type": "Lumefantrine", + "Intervention_Name": "AntimalarialDrug_Lumefantrine", + "New_Property_Value": "", + "class": "AntimalarialDrug" + }, + { + "Broadcast_Event": "ReceivedTreatment", + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Intervention_Name": "BroadcastEvent", + "New_Property_Value": "", + "class": "BroadcastEvent" + } + ], + "Coverage": 1, + "Delay_Period_Distribution": "EXPONENTIAL_DISTRIBUTION", + "Delay_Period_Exponential": 3.3333333333333335, + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Intervention_Name": "DelayedIntervention", + "New_Property_Value": "", + "class": "DelayedIntervention" + }, + "Blackout_Event_Trigger": "", + "Blackout_On_First_Occurrence": 0, + "Blackout_Period": 0, + "Demographic_Coverage": 0.1, + "Disqualifying_Properties": [], + "Distribute_On_Return_Home": 0, + "Dont_Allow_Duplicates": 0, + "Duration": -1, + "Intervention_Name": "NodeLevelHealthTriggeredIV", + "New_Property_Value": "", + "Node_Property_Restrictions": [], + "Property_Restrictions": [], + "Target_Age_Max": 100, + "Target_Age_Min": 5, + "Target_Demographic": "ExplicitAgeRanges", + "Target_Gender": "All", + "Target_Residents_Only": 0, + "Targeting_Config": { + "HasIP": {}, + "HasIntervention": {}, + "IsPregnant": {}, + "TargetingLogic": {} + }, + "Trigger_Condition_List": [ + "NewClinicalCase" + ], + "class": "NodeLevelHealthTriggeredIV" + }, + "Node_Property_Restrictions": [], + "Number_Repetitions": 1, + "Property_Restrictions": [], + "Property_Restrictions_Within_Node": [], + "Target_Demographic": "Everyone", + "Target_Gender": "All", + "Target_Residents_Only": 0, + "Targeting_Config": { + "HasIP": {}, + "HasIntervention": {}, + "IsPregnant": {}, + "TargetingLogic": {} + }, + "Timesteps_Between_Repetitions": -1, + "class": "StandardInterventionDistributionEventCoordinator" + }, + "Nodeset_Config": { + "class": "NodeSetAll" + }, + "Start_Day": 0.0, + "class": "CampaignEvent" + }, + { + "Event_Coordinator_Config": { + "Demographic_Coverage": 1, + "Individual_Selection_Type": "DEMOGRAPHIC_COVERAGE", + "Intervention_Config": { + "Actual_IndividualIntervention_Config": { + "Actual_IndividualIntervention_Configs": [ + { + "Cost_To_Consumer": 0, + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Drug_Type": "Artemether", + "Intervention_Name": "AntimalarialDrug_Artemether", + "New_Property_Value": "", + "class": "AntimalarialDrug" + }, + { + "Cost_To_Consumer": 0, + "Disqualifying_Properties": [], + "Dont_Allow_Duplicates": 0, + "Drug_Type": "Lumefantrine", + "Intervention_Name": "AntimalarialDrug_Lumefantrine", + "New_Property_Value": "", + "class": "AntimalarialDrug" + }, + { + "Broadcast_Event": "ReceivedTreatment", + "Disqualifying_Properties": 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{}, + "HasIntervention": {}, + "IsPregnant": {}, + "TargetingLogic": {} + }, + "Trigger_Condition_List": [ + "NewSevereCase" + ], + "class": "NodeLevelHealthTriggeredIV" + }, + "Node_Property_Restrictions": [], + "Number_Repetitions": 1, + "Property_Restrictions": [], + "Property_Restrictions_Within_Node": [], + "Target_Demographic": "Everyone", + "Target_Gender": "All", + "Target_Residents_Only": 0, + "Targeting_Config": { + "HasIP": {}, + "HasIntervention": {}, + "IsPregnant": {}, + "TargetingLogic": {} + }, + "Timesteps_Between_Repetitions": -1, + "class": "StandardInterventionDistributionEventCoordinator" + }, + "Nodeset_Config": { + "class": "NodeSetAll" + }, + "Start_Day": 0.0, + "class": "CampaignEvent" + } + ], + "Use_Defaults": 1 +} \ No newline at end of file diff --git a/tests/inputs/2.20.5522.0_old_custom_reports.json b/tests/inputs/2.20.5522.0_old_custom_reports.json new file mode 100644 index 0000000..10ad60e --- /dev/null +++ b/tests/inputs/2.20.5522.0_old_custom_reports.json @@ -0,0 +1,367 @@ +{ + "Custom_Reports": { + "Use_Explicit_Dlls": 1 + }, + "Reports": [ + { + "Age_Bins": [ + 5.0, + 15.0, + 80.0 + ], + "Enabled": 1, + "End_Day": 365, + "Filename_Suffix": "Monthly_Report_0", + "Infectiousness_Bins": [ + 0, + 100 + ], + "Max_Number_Reports": 1000, + "Must_Have_IP_Key_Value": "", + "Must_Have_Intervention": "", + "Node_IDs_Of_Interest": [], + "Parasitemia_Bins": [ + 0, + 50, + 500, + 4000, + 6000, + 8000, + 10000, + 50000, + 500000, + 5000000 + ], + "Pretty_Format": 0, + "Reporting_Interval": 30, + "Start_Day": 0, + "class": "MalariaSummaryReport" + }, + { + "Age_Bins": [ + 5.0, + 15.0, + 80.0 + ], + "Enabled": 1, + "End_Day": 730, + "Filename_Suffix": "Monthly_Report_1", + "Infectiousness_Bins": [ + 0, + 100 + ], + "Max_Number_Reports": 1000, + "Must_Have_IP_Key_Value": "", + "Must_Have_Intervention": "", + "Node_IDs_Of_Interest": [], + "Parasitemia_Bins": [ + 0, + 50, + 500, + 4000, + 6000, + 8000, + 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"Infectiousness_Bins": [ + 0, + 5, + 20, + 50, + 80, + 100 + ], + "Max_Number_Reports": 1000, + "Must_Have_IP_Key_Value": "", + "Must_Have_Intervention": "", + "Node_IDs_Of_Interest": [], + "Parasitemia_Bins": [ + 0, + 50, + 500, + 4000, + 6000, + 8000, + 10000, + 50000, + 500000, + 5000000 + ], + "Pretty_Format": 0, + "Reporting_Interval": 30, + "Start_Day": 1460, + "class": "MalariaSummaryReport" + } + ] +} \ No newline at end of file diff --git a/tests/inputs/2.20.5522.0_old_demog.json b/tests/inputs/2.20.5522.0_old_demog.json new file mode 100644 index 0000000..b54051f --- /dev/null +++ b/tests/inputs/2.20.5522.0_old_demog.json @@ -0,0 +1,82 @@ +{ + "Metadata": { + "DateCreated": "Fri Aug 8 18:30:00 2021", + "Tool": "", + "Author": "pselvaraj", + "IdReference": "", + "Resolution": 150, + "NodeCount": 1 + }, + "Nodes": [ + { + "IndividualAttributes": { + "AgeDistribution1": 0, + "AgeDistribution2": 0, + "AgeDistributionFlag": 0, + "ImmunityDistribution1": 1, + "ImmunityDistribution2": 0, + "ImmunityDistributionFlag": 0, + "MigrationHeterogeneityDistribution1": 1, + "MigrationHeterogeneityDistribution2": 0, + "MigrationHeterogeneityDistributionFlag": 0, + "MortalityDistribution": { + "AxisNames": [ + "gender", + "age" + ], + "AxisScaleFactors": [ + 1, + 365 + ], + "AxisUnits": [ + "male=0,female=1", + "years" + ], + "NumDistributionAxes": 2, + "NumPopulationGroups": [ + 2, + 1 + ], + "PopulationGroups": [ + [ + 0, + 1 + ], + [ + 0 + ] + ], + "ResultScaleFactor": 2.74e-06, + "ResultUnits": "annual deaths per 1000 individuals", + "ResultValues": [ + [ + 45 + ], + [ + 45 + ] + ] + }, + "PrevalenceDistribution1": 0, + "PrevalenceDistribution2": 0, + "PrevalenceDistributionFlag": 0, + "RiskDistribution1": 1, + "RiskDistribution2": 0, + "RiskDistributionFlag": 0 + }, + "NodeAttributes": { + "AbovePoverty": 0.5, + "Airport": 0, + "Altitude": 0, + "BirthRate": 0.0274, + "InitialPopulation": 1000, + "Latitude": -8.5, + "Longitude": 36.5, + "Region": 1, + "Seaport": 0, + "Urban": 0 + }, + "NodeID": 340461476 + } + ] +} \ No newline at end of file diff --git a/tests/inputs/2.20.5522.0_old_my_config.json b/tests/inputs/2.20.5522.0_old_my_config.json new file mode 100644 index 0000000..de52756 --- /dev/null +++ b/tests/inputs/2.20.5522.0_old_my_config.json @@ -0,0 +1,581 @@ +{ + "parameters": { + "Age_Dependent_Biting_Risk_Type": "SURFACE_AREA_DEPENDENT", + "Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE", + "Anemia_Mortality_Inverse_Width": 1, + "Anemia_Mortality_Threshold": 0.654726662830038, + "Anemia_Severe_Inverse_Width": 10, + "Anemia_Severe_Threshold": 4.50775824973078, + "Antibody_CSP_Decay_Days": 90, + "Antibody_CSP_Killing_Inverse_Width": 1.5, + "Antibody_CSP_Killing_Threshold": 20, + "Antibody_Capacity_Growth_Rate": 0.09, + "Antibody_IRBC_Kill_Rate": 1.596, + "Antibody_Memory_Level": 0.34, + "Antibody_Stimulation_C50": 30, + "Antigen_Switch_Rate": 7.645570124964182e-10, + "Base_Air_Temperature": 27, + 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"Infectious_Period_Proportion_1": 1, + "Infectivity_Scale_Type": "CONSTANT_INFECTIVITY", + "Innate_Immune_Variation_Type": "NONE", + "Insecticides": [], + "Inset_Chart_Has_IP": [], + "Inset_Chart_Has_Interventions": [], + "Inset_Chart_Include_Pregnancies": 0, + "Inset_Chart_Reporting_Include_30Day_Avg_Infection_Duration": 1, + "Larval_Density_Dependence": "UNIFORM_WHEN_OVERPOPULATION", + "Load_Balance_Filename": "", + "MSP1_Merozoite_Kill_Fraction": 0.511735322, + "Malaria_Drug_Params": [ + { + "Bodyweight_Exponent": 1.0, + "Drug_Cmax": 114.0, + "Drug_Decay_T1": 0.12, + "Drug_Decay_T2": 0.12, + "Drug_Dose_Interval": 0.5, + "Drug_Fulltreatment_Doses": 6.0, + "Drug_Gametocyte02_Killrate": 2.5, + "Drug_Gametocyte34_Killrate": 1.5, + "Drug_GametocyteM_Killrate": 0.7, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 0.6, + "Drug_Vd": 1.0, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.25, + "Upper_Age_In_Years": 3.0 + }, + { + "Fraction_Of_Adult_Dose": 0.5, + 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"Drug_Hepatocyte_Killrate": 0.1, + "Drug_PKPD_C50": 15.0, + "Drug_Vd": 1.0, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.17, + "Upper_Age_In_Years": 5.0 + }, + { + "Fraction_Of_Adult_Dose": 0.33, + "Upper_Age_In_Years": 9.0 + }, + { + "Fraction_Of_Adult_Dose": 0.67, + "Upper_Age_In_Years": 14.0 + } + ], + "Max_Drug_IRBC_Kill": 0.0, + "Name": "Primaquine", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + }, + { + "Bodyweight_Exponent": 1.0, + "Drug_Cmax": 150.0, + "Drug_Decay_T1": 8.9, + "Drug_Decay_T2": 244.0, + "Drug_Dose_Interval": 1, + "Drug_Fulltreatment_Doses": 3, + "Drug_Gametocyte02_Killrate": 0, + "Drug_Gametocyte34_Killrate": 0, + "Drug_GametocyteM_Killrate": 0, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 150.0, + "Drug_Vd": 3.9, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.17, + "Upper_Age_In_Years": 5.0 + }, + { + "Fraction_Of_Adult_Dose": 0.33, + "Upper_Age_In_Years": 9.0 + }, + { + "Fraction_Of_Adult_Dose": 0.67, + "Upper_Age_In_Years": 14.0 + } + ], + "Max_Drug_IRBC_Kill": 4.8, + "Name": "Chloroquine", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + }, + { + "Bodyweight_Exponent": 1.0, + "Drug_Cmax": 200.0, + "Drug_Decay_T1": 0.12, + "Drug_Decay_T2": 0.12, + "Drug_Dose_Interval": 1, + "Drug_Fulltreatment_Doses": 3, + "Drug_Gametocyte02_Killrate": 2.5, + "Drug_Gametocyte34_Killrate": 1.5, + "Drug_GametocyteM_Killrate": 0.7, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 0.03, + "Drug_Vd": 1.0, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.167, + "Upper_Age_In_Years": 2.0 + }, + { + "Fraction_Of_Adult_Dose": 0.33, + "Upper_Age_In_Years": 5.0 + } + ], + "Max_Drug_IRBC_Kill": 4.2, + "Name": "Artesunate", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + }, + { + "Bodyweight_Exponent": 1.0, + "Drug_Cmax": 105.8, + "Drug_Decay_T1": 8.55, + "Drug_Decay_T2": 8.55, + "Drug_Dose_Interval": 1, + "Drug_Fulltreatment_Doses": 1.0, + "Drug_Gametocyte02_Killrate": 0, + "Drug_Gametocyte34_Killrate": 0, + "Drug_GametocyteM_Killrate": 0, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 0.2, + "Drug_Vd": 1.0, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.167, + "Upper_Age_In_Years": 2.0 + }, + { + "Fraction_Of_Adult_Dose": 0.33, + "Upper_Age_In_Years": 5.0 + } + ], + "Max_Drug_IRBC_Kill": 0.506, + "Name": "Sulfadoxine", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + }, + { + "Bodyweight_Exponent": 1.0, + "Drug_Cmax": 354.1, + "Drug_Decay_T1": 5.411, + "Drug_Decay_T2": 5.411, + "Drug_Dose_Interval": 1, + "Drug_Fulltreatment_Doses": 1.0, + "Drug_Gametocyte02_Killrate": 0, + "Drug_Gametocyte34_Killrate": 0, + "Drug_GametocyteM_Killrate": 0, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 2.0, + "Drug_Vd": 1.0, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.167, + "Upper_Age_In_Years": 2.0 + }, + { + "Fraction_Of_Adult_Dose": 0.33, + "Upper_Age_In_Years": 5.0 + } + ], + "Max_Drug_IRBC_Kill": 0.6, + "Name": "Pyrimethamine", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + }, + { + "Bodyweight_Exponent": 1.0, + "Drug_Cmax": 1185.0, + "Drug_Decay_T1": 0.12, + "Drug_Decay_T2": 6.25, + "Drug_Dose_Interval": 1, + "Drug_Fulltreatment_Doses": 3, + "Drug_Gametocyte02_Killrate": 0, + "Drug_Gametocyte34_Killrate": 0, + "Drug_GametocyteM_Killrate": 0, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 35.5, + "Drug_Vd": 2.51, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.22, + "Upper_Age_In_Years": 1.0 + }, + { + "Fraction_Of_Adult_Dose": 0.44, + "Upper_Age_In_Years": 5.0 + } + ], + "Max_Drug_IRBC_Kill": 0.67089, + "Name": "Amodiaquine", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + }, + { + "Bodyweight_Exponent": 1.0, + "Drug_Cmax": 537.0, + "Drug_Decay_T1": 0.12, + "Drug_Decay_T2": 6.25, + "Drug_Dose_Interval": 1, + "Drug_Fulltreatment_Doses": 3, + "Drug_Gametocyte02_Killrate": 0, + "Drug_Gametocyte34_Killrate": 0, + "Drug_GametocyteM_Killrate": 0, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 80.0, + "Drug_Vd": 2.51, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.22, + "Upper_Age_In_Years": 1.0 + }, + { + "Fraction_Of_Adult_Dose": 0.44, + "Upper_Age_In_Years": 5.0 + } + ], + "Max_Drug_IRBC_Kill": 0.7089, + "Name": "Amodiaquine_for_AS_combination", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + }, + { + "Bodyweight_Exponent": 1.0, + "Drug_Cmax": 100.0, + "Drug_Decay_T1": 10.0, + "Drug_Decay_T2": 10.0, + "Drug_Dose_Interval": 1, + "Drug_Fulltreatment_Doses": 3, + "Drug_Gametocyte02_Killrate": 0, + "Drug_Gametocyte34_Killrate": 0, + "Drug_GametocyteM_Killrate": 0, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 10.0, + "Drug_Vd": 1.0, + "Fractional_Dose_By_Upper_Age": [ + { + "Fraction_Of_Adult_Dose": 0.25, + "Upper_Age_In_Years": 3.0 + }, + { + "Fraction_Of_Adult_Dose": 0.5, + "Upper_Age_In_Years": 6.0 + }, + { + "Fraction_Of_Adult_Dose": 0.75, + "Upper_Age_In_Years": 10.0 + } + ], + "Max_Drug_IRBC_Kill": 4.0, + "Name": "Abstract", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + }, + { + "Bodyweight_Exponent": 0, + "Drug_Cmax": 10.0, + "Drug_Decay_T1": 1, + "Drug_Decay_T2": 1, + "Drug_Dose_Interval": 1, + "Drug_Fulltreatment_Doses": 1.0, + "Drug_Gametocyte02_Killrate": 0, + "Drug_Gametocyte34_Killrate": 0, + "Drug_GametocyteM_Killrate": 0, + "Drug_Hepatocyte_Killrate": 0, + "Drug_PKPD_C50": 5.0, + "Drug_Vd": 10, + "Fractional_Dose_By_Upper_Age": [], + "Max_Drug_IRBC_Kill": 0.0, + "Name": "Vehicle", + "PKPD_Model": "CONCENTRATION_VERSUS_TIME", + "Resistances": [] + } + ], + "Malaria_Model": "MALARIA_MECHANISTIC_MODEL", + "Malaria_Strain_Model": "FALCIPARUM_RANDOM_STRAIN", + "Maternal_Antibodies_Type": "SIMPLE_WANING", + "Maternal_Antibody_Decay_Rate": 0.01, + "Maternal_Antibody_Protection": 0.12113742216538194, + "Max_Individual_Infections": 3, + "Max_MSP1_Antibody_Growthrate": 0.045, + "Mean_Egg_Hatch_Delay": 0, + "Mean_Sporozoites_Per_Bite": 11, + "Memory_Usage_Halting_Threshold_Working_Set_MB": 8000, + "Memory_Usage_Warning_Threshold_Working_Set_MB": 7000, + "Merozoites_Per_Hepatocyte": 15000, + "Merozoites_Per_Schizont": 16, + "Migration_Model": "NO_MIGRATION", + "Min_Adapted_Response": 0.05, + "Min_Days_Between_Clinical_Incidents": 14, + "Node_Grid_Size": 0.042, + "Nonspecific_Antibody_Growth_Rate_Factor": 0.5, + "Nonspecific_Antigenicity_Factor": 0.415111634, + "Number_Basestrains": 1, + "Number_Of_Asexual_Cycles_Without_Gametocytes": 1, + "Parasite_Mortality_Inverse_Width": 327.51594505874, + "Parasite_Mortality_Threshold": 851138.0382023759, + "Parasite_Severe_Inverse_Width": 56.5754896048744, + "Parasite_Severe_Threshold": 851031.2877445256, + "Parasite_Switch_Type": "RATE_PER_PARASITE_7VARS", + "PfHRP2_Boost_Rate": 0.018, + "PfHRP2_Decay_Rate": 0.167, + "Population_Density_Infectivity_Correction": "CONSTANT_INFECTIVITY", + "Population_Scale_Type": "FIXED_SCALING", + "Pyrogenic_Threshold": 15000.0, + "RBC_Destruction_Multiplier": 3.29, + "Rainfall_In_mm_To_Fill_Swamp": 1000, + "Random_Number_Generator_Policy": "ONE_PER_CORE", + "Random_Number_Generator_Type": "USE_PSEUDO_DES", + "Report_Coordinator_Event_Recorder": 0, + "Report_Detection_Threshold_Blood_Smear_Gametocytes": 0, + "Report_Detection_Threshold_Blood_Smear_Parasites": 0, + "Report_Detection_Threshold_Fever": 1, + "Report_Detection_Threshold_PCR_Gametocytes": 0.05, + "Report_Detection_Threshold_PCR_Parasites": 0.05, + "Report_Detection_Threshold_PfHRP2": 5, + "Report_Detection_Threshold_True_Parasite_Density": 0, + "Report_Event_Recorder": 0, + "Report_Event_Recorder_PropertyChange_IP_Key_Of_Interest": "", + "Report_Gametocyte_Smear_Sensitivity": 0.01, + "Report_Node_Event_Recorder": 0, + "Report_Parasite_Smear_Sensitivity": 0.01, + "Report_Surveillance_Event_Recorder": 0, + "Run_Number": 1, + "Semipermanent_Habitat_Decay_Rate": 0.01, + "Serialized_Population_Reading_Type": "NONE", + "Serialized_Population_Writing_Type": "NONE", + "Simulation_Duration": 1825, + "Simulation_Timestep": 1, + "Simulation_Type": "MALARIA_SIM", + "Start_Time": 0, + "Temporary_Habitat_Decay_Factor": 0.05, + "Vector_Larval_Rainfall_Mortality": "NONE", + "Vector_Migration_Food_Modifier": 0, + "Vector_Migration_Habitat_Modifier": 0, + "Vector_Migration_Modifier_Equation": "LINEAR", + "Vector_Migration_Stay_Put_Modifier": 0, + "Vector_Sampling_Type": "VECTOR_COMPARTMENTS_NUMBER", + "Vector_Species_Params": [], + "Wolbachia_Infection_Modification": 1, + "Wolbachia_Mortality_Modification": 1, + "x_Base_Population": 1, + "x_Temporary_Larval_Habitat": 1, + "x_Vector_Migration_Local": 1 + } +} \ No newline at end of file diff --git a/tests/test_run_sims.py b/tests/test_run_sims.py index 37e6941..865f1b6 100644 --- a/tests/test_run_sims.py +++ b/tests/test_run_sims.py @@ -8,7 +8,7 @@ import pathlib import json -latest_version = '2.20.5347.0' +latest_version = '2.20.5522.0' class RunSimsTest(BaseTest):