void SusceptibilityVector::serialize(IArchive& ar, SusceptibilityVector* obj)
{
SusceptibilityVector& susceptibility = *obj;
Susceptibility::serialize(ar, obj);
ar.labelElement("m_relative_biting_rate") & susceptibility.m_relative_biting_rate;
ar.labelElement("m_age_dependent_biting_risk") & susceptibility.m_age_dependent_biting_risk;
}
void AbstractBednet::serialize( IArchive& ar, AbstractBednet* obj )
{
BaseIntervention::serialize( ar, obj );
AbstractBednet& bednet = *obj;
ar.labelElement( "m_pEffectBlocking" ) & bednet.m_pEffectBlocking;
ar.labelElement( "m_pEffectKilling" ) & bednet.m_pEffectKilling;
}
void serialize(IArchive& ar, IndividualHumanMalaria::gametocytes_strain_map_t& mapping)
{
size_t count = ar.IsWriter() ? mapping.size() : -1;
ar.startArray(count);
if (ar.IsWriter())
{
for (auto& entry : mapping)
{
StrainIdentity* strain = const_cast<StrainIdentity*>(&entry.first);
ar.startObject();
ar.labelElement("key"); serialize(ar, strain);
ar.labelElement("value") & entry.second;
ar.endObject();
}
}
else
{
for (size_t i = 0; i < count; i++)
{
StrainIdentity* strain;
int64_t value;
ar.startObject();
ar.labelElement("key"); serialize(ar, strain);
ar.labelElement("value") & value;
ar.endObject();
mapping[*strain] = value;
}
}
ar.endArray();
}
void BaseIntervention::serialize(IArchive& ar, BaseIntervention* obj)
{
BaseIntervention& intervention = *obj;
ar.labelElement("cost_per_unit" ) & intervention.cost_per_unit;
ar.labelElement("expired" ) & intervention.expired;
ar.labelElement("dont_allow_duplicates") & intervention.dont_allow_duplicates;
}
void HIVARTStagingByCD4Diagnostic::serialize(IArchive& ar, HIVARTStagingByCD4Diagnostic* obj)
{
HIVARTStagingAbstract::serialize( ar, obj );
HIVARTStagingByCD4Diagnostic& diag = *obj;
ar.labelElement("threshold" ) & diag.threshold;
ar.labelElement("ifActiveTB") & diag.ifActiveTB;
ar.labelElement("ifPregnant") & diag.ifPregnant;
}
void InterventionsContainer::serialize(IArchive& ar, InterventionsContainer* obj)
{
InterventionsContainer& container = *obj;
ar.labelElement("drugVaccineReducedAcquire") & container.drugVaccineReducedAcquire;
ar.labelElement("drugVaccineReducedTransmit") & container.drugVaccineReducedTransmit;
ar.labelElement("drugVaccineReducedMortality") & container.drugVaccineReducedMortality;
ar.labelElement("interventions") & container.interventions;
}
void SimpleVaccine::serialize(IArchive& ar, SimpleVaccine* obj)
{
BaseIntervention::serialize( ar, obj );
SimpleVaccine& vaccine = *obj;
ar.labelElement("vaccine_type") & vaccine.vaccine_type;
ar.labelElement("vaccine_take") & vaccine.vaccine_take;
ar.labelElement("vaccine_took") & vaccine.vaccine_took;
ar.labelElement("waning_effect") & vaccine.waning_effect;
}
void IndividualHumanVector::serialize(IArchive& ar, IndividualHumanVector* obj)
{
IndividualHumanVector& individual = *obj;
IndividualHuman::serialize(ar, obj);
ar.labelElement("m_strain_exposure");
Kernel::serialize(ar, individual.m_strain_exposure);
ar.labelElement("m_total_exposure") & individual.m_total_exposure;
}
void HIVSimpleDiagnostic::serialize(IArchive& ar, HIVSimpleDiagnostic* obj)
{
SimpleDiagnostic::serialize( ar, obj );
HIVSimpleDiagnostic& hsd = *obj;
ar.labelElement("firstUpdate" ) & hsd.firstUpdate;
ar.labelElement("result_of_positive_test" ) & hsd.result_of_positive_test;
ar.labelElement("original_days_to_diagnosis") & hsd.original_days_to_diagnosis;
ar.labelElement("absoluteDuration" ) & hsd.absoluteDuration;
ar.labelElement("negative_diagnosis_event" ) & hsd.negative_diagnosis_event;
}
void DiagnosticTreatNeg::serialize(IArchive& ar, DiagnosticTreatNeg* obj)
{
SimpleDiagnostic::serialize(ar, obj);
DiagnosticTreatNeg& diagnostic = *obj;
ar.labelElement("negative_diagnosis_config") & diagnostic.negative_diagnosis_config;
ar.labelElement("negative_diagnosis_event") & diagnostic.negative_diagnosis_event;
ar.labelElement("defaulters_config") & diagnostic.defaulters_config;
ar.labelElement("defaulters_event") & diagnostic.defaulters_event;
ar.labelElement("m_gets_positive_test_intervention") & diagnostic.m_gets_positive_test_intervention;
}
void HIVDelayedIntervention::serialize(IArchive& ar, HIVDelayedIntervention* obj)
{
DelayedIntervention::serialize( ar, obj );
HIVDelayedIntervention& delayed = *obj;
ar.labelElement("year2DelayMap" ) & delayed.year2DelayMap;
ar.labelElement("days_remaining" ) & delayed.days_remaining;
ar.labelElement("broadcast_event" ) & delayed.broadcast_event;
ar.labelElement("broadcast_on_expiration_event" ) & delayed.broadcast_on_expiration_event;
}
void WaningEffectMapAbstract::serialize( IArchive& ar, WaningEffectMapAbstract* obj )
{
WaningEffectMapAbstract& effect = *obj;
ar.labelElement( "m_Expired" ) & effect.m_Expired;
ar.labelElement( "m_EffectOriginal" ) & effect.m_EffectOriginal;
ar.labelElement( "m_EffectCurrent" ) & effect.m_EffectCurrent;
ar.labelElement( "m_ExpireAtDurationMapEnd" ) & effect.m_ExpireAtDurationMapEnd;
ar.labelElement( "m_TimeSinceStart" ) & effect.m_TimeSinceStart;
ar.labelElement( "m_DurationMap" ) & effect.m_DurationMap;
}
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
// !!! In a scenario like 25_Madagascar that has 30000+ nodes,
// !!! we really have to minimize the data that is being shared
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
void NodeInfo::serialize( IArchive& ar, bool firstTime )
{
if( firstTime )
{
ar.labelElement("m_Suid" ) & m_Suid.data;
ar.labelElement("m_ExternalId" ) & m_ExternalId;
ar.labelElement("m_Rank" ) & m_Rank;
ar.labelElement("m_LongitudeDegrees" ) & m_LongitudeDegrees;
ar.labelElement("m_LatitudeDegrees" ) & m_LatitudeDegrees;
}
ar.labelElement("m_Population" ) & m_Population;
}
void serialize(IArchive& ar, pfemp1_antibody_t& antibodies)
{
ar.startObject();
ar.labelElement("minor") & antibodies.minor;
ar.labelElement("major") & antibodies.major;
ar.endObject();
}
void MultiEffectBoosterVaccine::serialize(IArchive& ar, MultiEffectBoosterVaccine* obj)
{
MultiEffectVaccine::serialize( ar, obj );
MultiEffectBoosterVaccine& vaccine = *obj;
ar.labelElement("prime_acquire") & vaccine.prime_acquire;
ar.labelElement("prime_transmit") & vaccine.prime_transmit;
ar.labelElement("prime_mortality") & vaccine.prime_mortality;
ar.labelElement("boost_acquire") & vaccine.boost_acquire;
ar.labelElement("boost_transmit") & vaccine.boost_transmit;
ar.labelElement("boost_mortality") & vaccine.boost_mortality;
ar.labelElement("boost_threshold_acquire") & vaccine.boost_threshold_acquire;
ar.labelElement("boost_threshold_transmit") & vaccine.boost_threshold_transmit;
ar.labelElement("boost_threshold_mortality") & vaccine.boost_threshold_mortality;
}
void PairFormationStatsImpl::serialize(IArchive& ar, PairFormationStatsImpl* obj)
{
PairFormationStatsImpl& stats = *obj;
ar.labelElement("eligible_population") & stats.eligible_population;
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
// !!! Needs to be set during serialization
//const IPairFormationParameters* parameters;
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
}
void Infection::serialize(IArchive& ar, Infection* obj)
{
Infection& infection = *obj;
ar.labelElement("suid") & infection.suid;
ar.labelElement("duration") & infection.duration;
ar.labelElement("total_duration") & infection.total_duration;
ar.labelElement("incubation_timer") & infection.incubation_timer;
ar.labelElement("infectious_timer") & infection.infectious_timer;
ar.labelElement("infectiousness") & infection.infectiousness;
ar.labelElement("infectiousnessByRoute") & infection.infectiousnessByRoute;
ar.labelElement("StateChange") & (uint32_t&)infection.StateChange;
ar.labelElement( "infection_strain" ); StrainIdentity::serialize( ar, infection.infection_strain );
}
void VectorCohortIndividual::serialize(IArchive& ar, VectorCohortIndividual* obj)
{
VectorCohortAbstract::serialize(ar, obj);
VectorCohortIndividual& cohort = *obj;
//ar.labelElement("m_ID" ) & cohort.m_ID;
ar.labelElement("additional_mortality" ) & cohort.additional_mortality;
ar.labelElement("oviposition_timer" ) & cohort.oviposition_timer;
ar.labelElement("parity" ) & cohort.parity;
ar.labelElement("neweggs" ) & cohort.neweggs;
/* TODO - this 'has_strain' stuff is left over from when m_strain could be a nullptr. */
bool has_strain = true;
ar.labelElement("__has_strain__");
ar & has_strain;
// clorton TODO - perhaps the cohort should always have a non-null m_strain, just use a dummy StrainIdentity when there's no infection.
if (has_strain)
{
ar.labelElement("m_strain");
StrainIdentity::serialize(ar, cohort.m_strain);
}
}
void PropertyValueChanger::serialize(IArchive& ar, PropertyValueChanger* obj)
{
BaseIntervention::serialize( ar, obj );
PropertyValueChanger& changer = *obj;
ar.labelElement("target_property_key" ) & changer.target_property_key;
ar.labelElement("target_property_value") & changer.target_property_value;
ar.labelElement("probability" ) & changer.probability;
ar.labelElement("revert" ) & changer.revert;
ar.labelElement("max_duration" ) & changer.max_duration;
ar.labelElement("action_timer" ) & changer.action_timer;
ar.labelElement("reversion_timer" ) & changer.reversion_timer;
if( !ar.IsWriter() )
{
changer.target_property_key.constraints = IPKey::GetConstrainedStringConstraintKey();
changer.target_property_value.constraints = IPKey::GetConstrainedStringConstraintValue();
//TODO - Need to actual use the constrained string
}
}
void PropertyValueChanger::serialize(IArchive& ar, PropertyValueChanger* obj)
{
BaseIntervention::serialize( ar, obj );
PropertyValueChanger& changer = *obj;
ar.labelElement("target_property_key" ) & changer.target_property_key;
ar.labelElement("target_property_value") & changer.target_property_value;
ar.labelElement("probability" ) & changer.probability;
ar.labelElement("revert" ) & changer.revert;
ar.labelElement("max_duration" ) & changer.max_duration;
ar.labelElement("action_timer" ) & changer.action_timer;
ar.labelElement("reversion_timer" ) & changer.reversion_timer;
if( !ar.IsWriter() )
{
changer.target_property_key.constraints = "<demographics>::Defaults.Individual_Properties.*.Property.<keys>";
changer.target_property_value.constraints = "<demographics>::Defaults.Individual_Properties.*.Value.<keys>";
//TODO - Need to actual use the constrained string
}
}
void IndividualHumanMalaria::serialize(IArchive& ar, IndividualHumanMalaria* obj)
{
IndividualHumanVector::serialize(ar, obj);
IndividualHumanMalaria& individual = *obj;
ar.labelElement("m_inv_microliters_blood") & individual.m_inv_microliters_blood;
ar.labelElement("m_male_gametocytes") & individual.m_male_gametocytes;
ar.labelElement("m_female_gametocytes") & individual.m_female_gametocytes;
ar.labelElement("m_male_gametocytes_by_strain"); Kernel::serialize(ar, individual.m_male_gametocytes_by_strain);
ar.labelElement("m_female_gametocytes_by_strain"); Kernel::serialize(ar, individual.m_female_gametocytes_by_strain);
ar.labelElement("m_parasites_detected_by_blood_smear") & individual.m_parasites_detected_by_blood_smear;
ar.labelElement("m_parasites_detected_by_new_diagnostic") & individual.m_parasites_detected_by_new_diagnostic;
ar.labelElement("m_gametocytes_detected") & individual.m_gametocytes_detected;
ar.labelElement("m_clinical_symptoms"); ar.serialize( individual.m_clinical_symptoms, ClinicalSymptomsEnum::CLINICAL_SYMPTOMS_COUNT);
ar.labelElement("m_initial_infected_hepatocytes") & individual.m_initial_infected_hepatocytes;
// ----------------------------------------------------------------------
// --- This is a pointer to an object held in the Susceptibility object.
// --- It will be re-set after de-serialization. See SetContextTo()
// ----------------------------------------------------------------------
//ar.labelElement("m_CSP_antibody") & individual.m_CSP_antibody;
// ----------------------------------------------------------------------
}
void DiagnosticTreatNeg::serialize(IArchive& ar, DiagnosticTreatNeg* obj)
{
SimpleDiagnostic::serialize(ar, obj);
DiagnosticTreatNeg& diagnostic = *obj;
ar.labelElement("negative_diagnosis_config") & diagnostic.negative_diagnosis_config;
// Remove after testing (implemented above)
// clorton if ( ar.IsWriter() )
// clorton {
// clorton std::ostringstream string_stream;
// clorton json::Writer::Write( diagnostic.negative_diagnosis_config._json, string_stream );
// clorton ar & string_stream.str();
// clorton }
// clorton else
// clorton {
// clorton std::string json;
// clorton ar & json;
// clorton std::istringstream string_stream( json );
// clorton json::Reader::Read( diagnostic.negative_diagnosis_config._json, string_stream );
// clorton }
ar.labelElement("negative_diagnosis_event") & diagnostic.negative_diagnosis_event;
ar.labelElement("defaulters_config") & diagnostic.defaulters_config;
// Remove after testing (implemented above)
// clorton if ( ar.IsWriter() )
// clorton {
// clorton std::ostringstream string_stream;
// clorton json::Writer::Write( diagnostic.defaulters_config._json, string_stream );
// clorton ar & string_stream.str();
// clorton }
// clorton else
// clorton {
// clorton std::string json;
// clorton ar & json;
// clorton std::istringstream string_stream( json );
// clorton json::Reader::Read( diagnostic.defaulters_config._json, string_stream );
// clorton }
ar.labelElement("defaulters_event") & diagnostic.defaulters_event;
ar.labelElement("m_gets_positive_test_intervention") & diagnostic.m_gets_positive_test_intervention;
}
void FlowControllerImpl::serialize(IArchive& ar, FlowControllerImpl* obj)
{
FlowControllerImpl& flow = *obj;
ar.labelElement("rate_ratio" ); ar.serialize( flow.rate_ratio, Gender::COUNT );
ar.labelElement("desired_flow" ) & flow.desired_flow;
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
// !!! Needs to be set during serialization
//IPairFormationAgent* pair_formation_agent;
//IPairFormationStats* pair_formation_stats;
//IPairFormationRateTable* rate_table;
//const IPairFormationParameters* parameters;
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
}
void PairFormationParametersImpl::serialize(IArchive& ar, PairFormationParametersImpl* obj)
{
PairFormationParametersImpl& parameters = *obj;
ar.labelElement("rel_type" ) & (uint32_t&)parameters.rel_type;
ar.labelElement("male_age_bin_count" ) & parameters.male_age_bin_count;
ar.labelElement("initial_male_age" ) & parameters.initial_male_age;
ar.labelElement("male_age_increment" ) & parameters.male_age_increment;
ar.labelElement("female_age_bin_count" ) & parameters.female_age_bin_count;
ar.labelElement("initial_female_age" ) & parameters.initial_female_age;
ar.labelElement("female_age_increment" ) & parameters.female_age_increment;
ar.labelElement("rate_ratio" ); ar.serialize( parameters.rate_ratio, Gender::COUNT );
ar.labelElement("age_bins" ) & parameters.age_bins;
ar.labelElement("joint_probabilities" ) & parameters.joint_probabilities;
ar.labelElement("cumulative_joint_probabilities") & parameters.cumulative_joint_probabilities;
ar.labelElement("marginal_values" ) & parameters.marginal_values;
ar.labelElement("update_period" ) & parameters.update_period;
ar.labelElement("formation_rate_type" ) & (uint32_t&)parameters.formation_rate_type;
ar.labelElement("formation_rate_constant" ) & parameters.formation_rate_constant;
ar.labelElement("formation_rate_sigmoid" ) & parameters.formation_rate_sigmoid;
ar.labelElement("formation_rate_value_map" ) & (std::map<float,float>&)parameters.formation_rate_value_map;
}
void MalariaAntibody::serialize(IArchive& ar, MalariaAntibody* obj)
{
MalariaAntibody& antibody = *obj;
ar.labelElement("m_antibody_capacity") & antibody.m_antibody_capacity;
ar.labelElement("m_antibody_concentration") & antibody.m_antibody_concentration;
ar.labelElement("m_antigen_count") & antibody.m_antigen_count;
ar.labelElement("m_antigen_present") & antibody.m_antigen_present;
ar.labelElement("m_antibody_type") & (uint32_t&)antibody.m_antibody_type;
ar.labelElement("m_antibody_variant") & antibody.m_antibody_variant;
}
void Susceptibility::serialize(IArchive& ar, Susceptibility* obj)
{
Susceptibility& susceptibility = *obj;
ar.labelElement("age") & susceptibility.age;
ar.labelElement("mod_acquire") & susceptibility.mod_acquire;
ar.labelElement("mod_transmit") & susceptibility.mod_transmit;
ar.labelElement("mod_mortality") & susceptibility.mod_mortality;
ar.labelElement("acqdecayoffset") & susceptibility.acqdecayoffset;
ar.labelElement("trandecayoffset") & susceptibility.trandecayoffset;
ar.labelElement("mortdecayoffset") & susceptibility.mortdecayoffset;
ar.labelElement("immune_failage") & susceptibility.immune_failage;
}
void SusceptibilityAirborne::serialize(IArchive& ar, SusceptibilityAirborne* obj)
{
Susceptibility::serialize(ar, obj);
SusceptibilityAirborne& susceptibility = *obj;
ar.labelElement("demographic_risk") & susceptibility.demographic_risk;
}
void WaningEffectExponential::serialize(IArchive& ar, WaningEffectExponential* obj)
{
WaningEffectExponential& effect = *obj;
ar.labelElement("currentEffect") & effect.currentEffect;
ar.labelElement("decayTimeConstant") & effect.decayTimeConstant;
}
void SimpleBednet::serialize(IArchive& ar, SimpleBednet* obj)
{
AbstractBednet::serialize( ar, obj );
SimpleBednet& bednet = *obj;
ar.labelElement("m_pEffectUsage") & bednet.m_pEffectUsage;
}
void HIVInterventionsContainer::serialize(IArchive& ar, HIVInterventionsContainer* obj)
{
STIInterventionsContainer::serialize( ar, obj );
HIVInterventionsContainer& container = *obj;
ar.labelElement("HIV_drug_inactivation_rate" ) & container.HIV_drug_inactivation_rate;
ar.labelElement("HIV_drug_clearance_rate" ) & container.HIV_drug_clearance_rate;
ar.labelElement("ART_status" ) & (uint32_t&)container.ART_status;
ar.labelElement("full_suppression_timer" ) & container.full_suppression_timer;
ar.labelElement("days_to_achieve_suppression" ) & container.days_to_achieve_suppression;
ar.labelElement("days_since_most_recent_ART_start" ) & container.days_since_most_recent_ART_start;
ar.labelElement("m_suppression_failure_timer" ) & container.m_suppression_failure_timer;
ar.labelElement("maternal_transmission_suppression") & container.maternal_transmission_suppression;
ar.labelElement("campaign_semaphores" ) & container.campaign_semaphores;
ar.labelElement("on_PreART" ) & container.on_PreART;
ar.labelElement("ever_tested_HIV_positive" ) & container.ever_tested_HIV_positive;
ar.labelElement("ever_tested" ) & container.ever_tested;
ar.labelElement("ever_received_CD4" ) & container.ever_received_CD4;
ar.labelElement("ever_staged_for_ART" ) & container.ever_staged_for_ART;
ar.labelElement("ever_staged" ) & container.ever_staged;
ar.labelElement("ever_been_on_PreART" ) & container.ever_been_on_PreART;
ar.labelElement("ever_been_on_ART" ) & container.ever_been_on_ART;
ar.labelElement("time_of_most_recent_test" ) & container.time_of_most_recent_test;
ar.labelElement("time_of_most_recent_CD4" ) & container.time_of_most_recent_CD4;
ar.labelElement("time_last_seen_by_healthcare" ) & container.time_last_seen_by_healthcare;
ar.labelElement("time_first_started_ART" ) & container.time_first_started_ART;
ar.labelElement("time_last_started_ART" ) & container.time_last_started_ART;
ar.labelElement("total_time_on_ART" ) & container.total_time_on_ART;
ar.labelElement("last_recorded_WHO_stage" ) & container.last_recorded_WHO_stage;
ar.labelElement("lowest_recorded_CD4" ) & container.lowest_recorded_CD4;
ar.labelElement("first_recorded_CD4" ) & container.first_recorded_CD4;
ar.labelElement("last_recorded_CD4" ) & container.last_recorded_CD4;
ar.labelElement("num_times_started_ART" ) & container.num_times_started_ART;
ar.labelElement("received_HIV_test_results" ) & (uint32_t&)container.received_HIV_test_results;
//hiv_parent set in SetContextTo
}