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Genotype Three Infections #71

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Merged
ddbaptiste merged 1 commit into from
Feb 28, 2025
Merged

Genotype Three Infections #71

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16 changes: 16 additions & 0 deletions src/event/Infections.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@
namespace event {
class Infections::InfectionsIMPL {
private:
double gt3_prob = 0;

using incidencemap_t =
std::unordered_map<Utils::tuple_3i, double, Utils::key_hash_3i,
Utils::key_equal_3i>;
Expand Down Expand Up @@ -101,11 +103,25 @@ namespace event {
// decide whether person is infected; if value == 0, infect
if (decider->GetDecision(prob) == 0) {
person->InfectHCV();
// decide whether hcv is genotype three
if (decider->GetDecision({gt3_prob}) == 0) {
person->SetGenotypeThree(true);
}
}
}

InfectionsIMPL(std::shared_ptr<datamanagement::DataManagerBase> dm) {
int rc = LoadIncidenceData(dm);
std::string data;
dm->GetFromConfig("infection.genotype_three_prob", data);
if (data.empty()) {
spdlog::get("main")->warn(
"[Infections] No probability of genotype three infection "
"found. Using default value of {}",
gt3_prob);
} else {
this->gt3_prob = Utils::stod_positive(data);
}
}
};
Infections::Infections(
Expand Down
99 changes: 98 additions & 1 deletion tests/src/eventtests/InfectionsTest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@ TEST_F(InfectionsTest, Infections_NewInfection) {
ON_CALL(*testPerson, GetHCV()).WillByDefault(Return(person::HCV::NONE));

// Data Setup
ON_CALL(*event_dm, GetFromConfig("infection.genotype_three_prob", _))
.WillByDefault(DoAll(SetArgReferee<1>("0.5"), Return(0)));
std::vector<double> storage = {1.0};
ON_CALL(*event_dm, SelectCustomCallback(INCIDENCE_QUERY, _, _, _))
.WillByDefault(
Expand Down Expand Up @@ -58,6 +60,9 @@ TEST_F(InfectionsTest, Infections_DoNotInfect) {
ON_CALL(*testPerson, GetHCV()).WillByDefault(Return(person::HCV::NONE));

// Data Setup
ON_CALL(*event_dm, GetFromConfig("infection.genotype_three_prob", _))
.WillByDefault(DoAll(SetArgReferee<1>("0.5"), Return(0)));

// Incidence Setup
double incidence = 0.0;
Utils::tuple_3i tup_3i = std::make_tuple(25, 0, 0);
Expand Down Expand Up @@ -89,6 +94,10 @@ TEST_F(InfectionsTest, Infections_AcuteProgression) {
ON_CALL(*testPerson, GetHCV()).WillByDefault(Return(person::HCV::ACUTE));
ON_CALL(*testPerson, GetTimeSinceHCVChanged()).WillByDefault(Return(6));

// Data Setup
ON_CALL(*event_dm, GetFromConfig("infection.genotype_three_prob", _))
.WillByDefault(DoAll(SetArgReferee<1>("0.5"), Return(0)));

// Incidence Setup
double incidence = 0.0;
Utils::tuple_3i tup_3i = std::make_tuple(25, 0, 0);
Expand Down Expand Up @@ -118,6 +127,10 @@ TEST_F(InfectionsTest, Infections_NoAcuteProgression) {
ON_CALL(*testPerson, GetHCV()).WillByDefault(Return(person::HCV::ACUTE));
ON_CALL(*testPerson, GetTimeSinceHCVChanged()).WillByDefault(Return(5));

// Data Setup
ON_CALL(*event_dm, GetFromConfig("infection.genotype_three_prob", _))
.WillByDefault(DoAll(SetArgReferee<1>("0.5"), Return(0)));

// Incidence Setup
double incidence = 0.0;
Utils::tuple_3i tup_3i = std::make_tuple(25, 0, 0);
Expand Down Expand Up @@ -150,6 +163,10 @@ TEST_F(InfectionsTest, Infections_HandleChronicHCV) {
ON_CALL(*testPerson, GetHCV()).WillByDefault(Return(person::HCV::CHRONIC));
ON_CALL(*testPerson, GetTimeSinceHCVChanged()).WillByDefault(Return(5));

// Data Setup
ON_CALL(*event_dm, GetFromConfig("infection.genotype_three_prob", _))
.WillByDefault(DoAll(SetArgReferee<1>("0.5"), Return(0)));

// Incidence Setup
double incidence = 0.0;
Utils::tuple_3i tup_3i = std::make_tuple(25, 0, 0);
Expand All @@ -168,4 +185,84 @@ TEST_F(InfectionsTest, Infections_HandleChronicHCV) {
std::shared_ptr<event::Event> event =
efactory.create("Infections", event_dm);
event->Execute(testPerson, event_dm, decider);
}
}

TEST_F(InfectionsTest, Infections_NewInfectionGenotype3) {
// Person Setup
ON_CALL(*testPerson, GetAge()).WillByDefault(Return(300));
ON_CALL(*testPerson, GetSex()).WillByDefault(Return(person::Sex::MALE));
ON_CALL(*testPerson, GetBehavior())
.WillByDefault(Return(person::Behavior::NEVER));
ON_CALL(*testPerson, GetHCV()).WillByDefault(Return(person::HCV::NONE));

// Data Setup
ON_CALL(*event_dm, GetFromConfig("infection.genotype_three_prob", _))
.WillByDefault(DoAll(SetArgReferee<1>("0.5"), Return(0)));
std::vector<double> storage = {1.0};
ON_CALL(*event_dm, SelectCustomCallback(INCIDENCE_QUERY, _, _, _))
.WillByDefault(
DoAll(SetArg2ToDoubleCallbackValue(&storage), Return(0)));

// Incidence Setup
double incidence = 1.0;
Utils::tuple_3i tup_3i = std::make_tuple(25, 0, 0);
std::unordered_map<Utils::tuple_3i, double, Utils::key_hash_3i,
Utils::key_equal_3i>
istorage;
istorage[tup_3i] = incidence;
ON_CALL(*event_dm, SelectCustomCallback(INCIDENCE_QUERY, _, _, _))
.WillByDefault(DoAll(SetArg2ToUM_T3I_Double(&istorage), Return(0)));

// Decider Setup
ON_CALL(*decider, GetDecision(_)).WillByDefault(Return(0)); // Infect

// Expectations
EXPECT_CALL(*testPerson, InfectHCV()).Times(1);
EXPECT_CALL(*testPerson, SetGenotypeThree(true)).Times(1);

// Running Test
std::shared_ptr<event::Event> event =
efactory.create("Infections", event_dm);
event->Execute(testPerson, event_dm, decider);
}

TEST_F(InfectionsTest, Infections_NewInfectionNotGenotype3) {
// Person Setup
ON_CALL(*testPerson, GetAge()).WillByDefault(Return(300));
ON_CALL(*testPerson, GetSex()).WillByDefault(Return(person::Sex::MALE));
ON_CALL(*testPerson, GetBehavior())
.WillByDefault(Return(person::Behavior::NEVER));
ON_CALL(*testPerson, GetHCV()).WillByDefault(Return(person::HCV::NONE));

// Data Setup
ON_CALL(*event_dm, GetFromConfig("infection.genotype_three_prob", _))
.WillByDefault(DoAll(SetArgReferee<1>("0.5"), Return(0)));
std::vector<double> storage = {1.0};
ON_CALL(*event_dm, SelectCustomCallback(INCIDENCE_QUERY, _, _, _))
.WillByDefault(
DoAll(SetArg2ToDoubleCallbackValue(&storage), Return(0)));

// Incidence Setup
double incidence = 1.0;
Utils::tuple_3i tup_3i = std::make_tuple(25, 0, 0);
std::unordered_map<Utils::tuple_3i, double, Utils::key_hash_3i,
Utils::key_equal_3i>
istorage;
istorage[tup_3i] = incidence;
ON_CALL(*event_dm, SelectCustomCallback(INCIDENCE_QUERY, _, _, _))
.WillByDefault(DoAll(SetArg2ToUM_T3I_Double(&istorage), Return(0)));

// Decider Setup
EXPECT_CALL(*decider, GetDecision(_))
.WillOnce(Return(0)) // Infect
.WillRepeatedly(Return(1));

// Expectations
EXPECT_CALL(*testPerson, InfectHCV()).Times(1);
EXPECT_CALL(*testPerson, SetGenotypeThree(_)).Times(0);

// Running Test
std::shared_ptr<event::Event> event =
efactory.create("Infections", event_dm);
event->Execute(testPerson, event_dm, decider);
}