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[Hotfix] Population Table Reading #149

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Merged
MJC598 merged 1 commit into from
Nov 12, 2025
Merged

[Hotfix] Population Table Reading #149

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30 changes: 19 additions & 11 deletions extras/examples/inputs.db.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ CREATE TABLE "population" (
"hcv_link_state" INTEGER NOT NULL DEFAULT 0, -- never linked
"time_of_hcv_link_change" INTEGER NOT NULL DEFAULT -1,
"hcv_link_count" INTEGER NOT NULL DEFAULT 0,
"hiv_link_state" TEXT DEFAULT NULL, -- make foreign key
"hiv_link_state" INTEGER DEFAULT NULL,
"time_of_hiv_link_change" INTEGER DEFAULT NULL,
"hiv_link_count" INTEGER DEFAULT NULL,
"time_of_last_hcv_screening" INTEGER NOT NULL DEFAULT -1,
Expand All @@ -53,17 +53,17 @@ CREATE TABLE "population" (
"hcv_identified" INTEGER NOT NULL DEFAULT 0 CHECK (hcv_identified IN (0, 1)), -- not currently identified
"time_hcv_identified" INTEGER NOT NULL DEFAULT -1,
"num_hcv_identifications" INTEGER NOT NULL DEFAULT 0,
"hcv_screening_type" TEXT NOT NULL, -- make foreign key
"hcv_screening_type" INTEGER NOT NULL NOT NULL DEFAULT -1,
"num_hcv_false_negatives" INTEGER NOT NULL DEFAULT 0,
"identifications_cleared" INTEGER NOT NULL DEFAULT 0,
"time_of_last_hiv_screening" INTEGER DEFAULT NULL,
"num_hiv_ab_tests" INTEGER DEFAULT NULL,
"num_hiv_rna_tests" TEXT DEFAULT NULL,
"hiv_antibody_positive" TEXT DEFAULT NULL,
"num_hiv_rna_tests" INTEGER DEFAULT NULL,
"hiv_antibody_positive" INTEGER DEFAULT NULL,
"hiv_identified" INTEGER DEFAULT NULL,
"time_hiv_identified" INTEGER DEFAULT NULL,
"num_hiv_identified" INTEGER DEFAULT NULL,
"hiv_screening_type" TEXT DEFAULT NULL,
"hiv_screening_type" INTEGER DEFAULT NULL,
"initiated_hcv_treatment" INTEGER NOT NULL DEFAULT 0 CHECK (initiated_hcv_treatment IN (0, 1)), -- not started hcv treatment
"time_of_hcv_treatment_initiation" INTEGER NOT NULL DEFAULT -1,
"num_hcv_treatment_starts" INTEGER NOT NULL DEFAULT 0,
Expand Down Expand Up @@ -97,12 +97,14 @@ CREATE TABLE "population" (
FOREIGN KEY("death_reasons") REFERENCES "death_reasons"("id"),
FOREIGN KEY("drug_behavior") REFERENCES "drug_behaviors"("id"),
FOREIGN KEY("hcv") REFERENCES "hcv_states"("id"),
FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_states"("id"),
FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_diagnosis_states"("id"),
FOREIGN KEY("moud_state") REFERENCES "moud"("id"),
FOREIGN KEY("pregnancy_state") REFERENCES "pregnancy_states"("id"),
FOREIGN KEY("measured_fibrosis_state") REFERENCES "fibrosis_diagnosis_states"("id"),
FOREIGN KEY("hcv_link_state") REFERENCES "link_states"("id"),
FOREIGN KEY("link_states") REFERENCES "link_states"("id")
FOREIGN KEY ("hcv_screening_type") REFERENCES "screening_states"("id"),
FOREIGN KEY("hiv_link_states") REFERENCES "link_states"("id"),
FOREIGN KEY ("hiv_screening_type") REFERENCES "screening_states"("id")
);
DROP TABLE IF EXISTS "death_reasons";
CREATE TABLE "death_reasons" (
Expand All @@ -116,6 +118,12 @@ CREATE TABLE "link_states" (
"state" TEXT NOT NULL UNIQUE,
PRIMARY KEY ("id");
);
DROP TABLE IF EXISTS "screening_states";
CREATE TABLE "screening_states" (
"id" INTEGER NOT NULL UNIQUE,
"state" TEXT NOT NULL UNIQUE,
PRIMARY KEY ("id");
);
DROP TABLE IF EXISTS "antibody_testing";
CREATE TABLE "antibody_testing" (
"age_years" INTEGER NOT NULL,
Expand Down Expand Up @@ -192,16 +200,16 @@ CREATE TABLE "fibrosis" (
"fib4" REAL NOT NULL,
PRIMARY KEY("fibrosis_state","diagnosed_fibrosis"),
FOREIGN KEY("diagnosed_fibrosis") REFERENCES "fibrosis_diagnosis_states"("id"),
FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_states"("id")
FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_real_states"("id")
);
DROP TABLE IF EXISTS "fibrosis_diagnosis_states";
CREATE TABLE "fibrosis_diagnosis_states" (
"id" INTEGER NOT NULL UNIQUE,
"state" TEXT NOT NULL,
PRIMARY KEY("id")
);
DROP TABLE IF EXISTS "fibrosis_states";
CREATE TABLE "fibrosis_states" (
DROP TABLE IF EXISTS "fibrosis_real_states";
CREATE TABLE "fibrosis_real_states" (
"id" INTEGER NOT NULL UNIQUE,
"state" TEXT NOT NULL,
PRIMARY KEY("id")
Expand All @@ -213,7 +221,7 @@ CREATE TABLE "hcv_impacts" (
"cost" REAL NOT NULL DEFAULT 0.0,
"utility" REAL NOT NULL,
PRIMARY KEY("hcv_status","fibrosis_state"),
FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_states"("id"),
FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_real_states"("id"),
FOREIGN KEY("hcv_status") REFERENCES "bool_lookup"("id")
);
DROP TABLE IF EXISTS "hcv_states";
Expand Down
14 changes: 7 additions & 7 deletions include/hepce/data/types.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
// Created Date: 2025-04-17 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2025-10-14 //
// Last Modified: 2025-11-12 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2025 Syndemics Lab at Boston Medical Center //
Expand Down Expand Up @@ -33,10 +33,10 @@ POPULATION_HEADERS(bool pregnancy = false, bool hcc = false,
"acute_cleared,svrs,";
// HIVDetails
std::string hiv_details =
hiv ? "hiv,time_hiv_changed,low_cd4_months_count," : "none,-1,0,";
hiv ? "hiv,time_hiv_changed,low_cd4_months_count," : "NULL,-1,0,";
headers << hiv_details;
// HCCDetails
std::string hcc_details = hcc ? "hcc_state,hcc_diagnosed," : "none,false,";
std::string hcc_details = hcc ? "hcc_state,hcc_diagnosed," : "NULL,false,";
headers << hcc_details;
// overdose characteristics
std::string overdoses =
Expand All @@ -46,14 +46,14 @@ POPULATION_HEADERS(bool pregnancy = false, bool hcc = false,
std::string moud_details =
moud ? "moud_state,time_started_moud,current_moud_state_concurrent_"
"months,total_moud_months,"
: "none,-1,0,0,";
: "0,-1,0,0,";
headers << moud_details;
// PregnancyDetails
std::string pregnancy_details =
pregnancy ? "pregnancy_state,time_of_pregnancy_change,pregnancy_count,"
"num_infants,num_stillbirths,num_infant_hcv_exposures,num_"
"infant_hcv_infections,num_infant_hcv_tests,"
: "na,-1,0,0,0,0,0,0,";
: "-1,-1,0,0,0,0,0,0,";
headers << pregnancy_details;
// StagingDetails
headers << "measured_fibrosis_state,had_second_test,time_of_last_staging,";
Expand All @@ -62,7 +62,7 @@ POPULATION_HEADERS(bool pregnancy = false, bool hcc = false,
if (hiv) {
headers << "hiv_link_state,time_of_hiv_link_change,hiv_link_count,";
} else {
headers << "never,-1,0,";
headers << "0,-1,0,";
}
// ScreeningDetails
headers << "time_of_last_hcv_screening,num_hcv_ab_tests,num_hcv_rna_tests,"
Expand All @@ -75,7 +75,7 @@ POPULATION_HEADERS(bool pregnancy = false, bool hcc = false,
"hiv_antibody_positive,hiv_identified,time_hiv_identified,num_"
"hiv_identified,hiv_screening_type,";
} else {
headers << "-1,0,0,false,false,-1,0,na";
headers << "-1,0,0,false,false,-1,0,NULL,";
}
// TreatmentDetails
headers << "initiated_hcv_treatment,time_of_hcv_treatment_initiation,num_"
Expand Down
4 changes: 2 additions & 2 deletions src/model/simulation.cpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2025-04-22 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2025-10-31 //
// Last Modified: 2025-11-12 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2025 Syndemics Lab at Boston Medical Center //
Expand Down Expand Up @@ -138,7 +138,7 @@ HepceImpl::ReadPopPopulation(const int population_size,
// TODO: Add string santization (i.e. verify no extra special characters/numbers/phrases/etc.)
query << "SELECT "
<< data::POPULATION_HEADERS(pregnancy, hcc, overdose, hiv, moud);
query << "FROM population ";
query << " FROM population ";
query << "ORDER BY id ";
query << "LIMIT " << std::to_string(population_size) << ";";

Expand Down
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