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Add missing members to ABM serialization #1408

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Merged
merged 1 commit into from
Nov 4, 2025
Merged

Add missing members to ABM serialization #1408

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1 change: 1 addition & 0 deletions cpp/models/abm/infection.h
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Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,7 @@ class Infection
.add("viral_load", m_viral_load)
.add("log_norm_alpha", m_log_norm_alpha)
.add("log_norm_beta", m_log_norm_beta)
.add("individual_virus_shed_factor", m_individual_virus_shed_factor)
.add("detected", m_detected);
}

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28 changes: 16 additions & 12 deletions cpp/models/abm/model.h
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Expand Up @@ -130,6 +130,7 @@ class Model
// skip caches, they are rebuild by the deserialized model
obj.add_list("persons", get_persons().begin(), get_persons().end());
obj.add_list("locations", get_locations().begin(), get_locations().end());
obj.add_list("activeness_statuses", m_activeness_statuses.begin(), m_activeness_statuses.end());
obj.add_element("location_types", m_has_locations.to_ulong());
obj.add_element("testing_strategy", m_testing_strategy);
obj.add_element("trip_list", m_trip_list);
Expand All @@ -145,30 +146,33 @@ class Model
template <class IOContext>
static IOResult<Model> deserialize(IOContext& io)
{
auto obj = io.expect_object("Model");
auto params = obj.expect_element("parameters", Tag<Parameters>{});
auto persons = obj.expect_list("persons", Tag<Person>{});
auto locations = obj.expect_list("locations", Tag<Location>{});
auto location_types = obj.expect_element("location_types", Tag<unsigned long>{});
auto trip_list = obj.expect_element("trip_list", Tag<TripList>{});
auto use_mobility_rules = obj.expect_element("use_mobility_rules", Tag<bool>{});
auto cemetery_id = obj.expect_element("cemetery_id", Tag<LocationId>{});
auto rng = obj.expect_element("rng", Tag<RandomNumberGenerator>{});
auto obj = io.expect_object("Model");
auto params = obj.expect_element("parameters", Tag<Parameters>{});
auto persons = obj.expect_list("persons", Tag<Person>{});
auto locations = obj.expect_list("locations", Tag<Location>{});
auto activeness_statuses = obj.expect_list("activeness_statuses", Tag<bool>{});
auto location_types = obj.expect_element("location_types", Tag<unsigned long>{});
auto trip_list = obj.expect_element("trip_list", Tag<TripList>{});
auto use_mobility_rules = obj.expect_element("use_mobility_rules", Tag<bool>{});
auto cemetery_id = obj.expect_element("cemetery_id", Tag<LocationId>{});
auto rng = obj.expect_element("rng", Tag<RandomNumberGenerator>{});
return apply(
io,
[](auto&& params_, auto&& persons_, auto&& locations_, auto&& location_types_, auto&& trip_list_,
auto&& use_mobility_rules_, auto&& cemetery_id_, auto&& rng_) {
[](auto&& params_, auto&& persons_, auto&& locations_, auto&& activeness_statuses_, auto&& location_types_,
auto&& trip_list_, auto&& use_mobility_rules_, auto&& cemetery_id_, auto&& rng_) {
Model model{params_};
model.m_persons.assign(persons_.cbegin(), persons_.cend());
model.m_locations.assign(locations_.cbegin(), locations_.cend());
model.m_activeness_statuses.assign(activeness_statuses_.cbegin(), activeness_statuses_.cend());
model.m_has_locations = location_types_;
model.m_trip_list = trip_list_;
model.m_use_mobility_rules = use_mobility_rules_;
model.m_cemetery_id = cemetery_id_;
model.m_rng = rng_;
return model;
},
params, persons, locations, location_types, trip_list, use_mobility_rules, cemetery_id, rng);
params, persons, locations, activeness_statuses, location_types, trip_list, use_mobility_rules, cemetery_id,
rng);
}

/**
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14 changes: 8 additions & 6 deletions cpp/tests/test_abm_serialization.cpp
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Expand Up @@ -112,12 +112,13 @@ TEST(TestAbmSerialization, Infection)
viral_load["start_date"]["seconds"] = Json::Int(i++);

Json::Value reference_json;
reference_json["infection_course"] = Json::Value(Json::arrayValue);
reference_json["virus_variant"] = Json::UInt(0);
reference_json["viral_load"] = viral_load;
reference_json["log_norm_alpha"] = Json::Value((double)i++);
reference_json["log_norm_beta"] = Json::Value((double)i++);
reference_json["detected"] = Json::Value((bool)0);
reference_json["infection_course"] = Json::Value(Json::arrayValue);
reference_json["virus_variant"] = Json::UInt(0);
reference_json["viral_load"] = viral_load;
reference_json["log_norm_alpha"] = Json::Value((double)i++);
reference_json["log_norm_beta"] = Json::Value((double)i++);
reference_json["individual_virus_shed_factor"] = Json::Value((double)i++);
reference_json["detected"] = Json::Value((bool)0);

test_json_serialization<mio::abm::Infection>(reference_json);
}
Expand Down Expand Up @@ -260,6 +261,7 @@ TEST(TestAbmSerialization, Model)
reference_json["locations"] = Json::Value(Json::arrayValue);
reference_json["parameters"] = abm_parameters;
reference_json["persons"] = Json::Value(Json::arrayValue);
reference_json["activeness_statuses"] = Json::Value(Json::arrayValue);
reference_json["rng"]["counter"] = Json::UInt(i++);
reference_json["rng"]["key"] = Json::UInt(i++);
reference_json["rng"]["seeds"] = json_uint_array({i++, i++, i++, i++, i++, i++});
Expand Down