Merge pull request #9 from CDCgov/gce_pop_loader_fix_tract

Cargo.toml

@@ -9,3 +9,5 @@ csv = "1.3.1"
 ixa = { git = "https://github.com/cdcgov/ixa", version = "0.0.1" }
 ixa-derive = { git = "https://github.com/cdcgov/ixa", version = "0.0.0" }
 serde = "1.0.215"
+serde_derive = "1.0.215"
+tempfile = "3.14.0"

src/parameters_loader.rs

@@ -9,7 +9,6 @@ use serde::{Deserialize, Serialize};
 
 #[derive(Serialize, Deserialize, Debug, Clone)]
 pub struct ParametersValues {
-    pub population: usize,
     pub max_time: f64,
     pub seed: u64,
     pub r_0: f64,

src/population_loader.rs

@@ -1,112 +1,110 @@
 use crate::parameters_loader::Parameters;
 use ixa::{
     context::Context,
-    define_derived_property, define_person_property, define_person_property_with_default,
+    define_person_property, define_person_property_with_default,
     error::IxaError,
     global_properties::ContextGlobalPropertiesExt,
     people::{ContextPeopleExt, PersonId},
 };
 
 use serde::Deserialize;
+use std::path::PathBuf;
 
 #[derive(Deserialize, Debug)]
 #[allow(non_snake_case)]
-pub struct PeopleRecord {
+pub struct PeopleRecord<'a> {
     age: u8,
-    homeId: usize,
+    homeId: &'a [u8],
 }
 
 define_person_property!(Age, u8);
 define_person_property!(HomeId, usize);
 define_person_property_with_default!(Alive, bool, true);
 
-#[allow(clippy::cast_possible_truncation)]
-#[allow(clippy::cast_sign_loss)]
-const CENSUS_MAX: usize = 1e15 as usize;
-
-#[allow(clippy::cast_possible_truncation)]
-#[allow(clippy::cast_sign_loss)]
-const CENSUS_MIN: usize = 1e14 as usize;
-
-define_derived_property!(CensusTract, usize, [HomeId], |home_id| {
-    if (CENSUS_MIN..CENSUS_MAX).contains(&home_id) {
-        home_id / 10_000
-    } else {
-        0 //Err(IxaError::IxaError(String::from("Census tract invalid from homeId")))
-    }
-});
+define_person_property!(CensusTract, usize);
 
 fn create_person_from_record(
     context: &mut Context,
     person_record: &PeopleRecord,
 ) -> Result<PersonId, IxaError> {
-    let person_id =
-        context.add_person(((Age, person_record.age), (HomeId, person_record.homeId)))?;
+    let tract: usize = String::from_utf8(person_record.homeId[..11].to_owned())
+        .expect("Home id should have 11 digits for tract + home id")
+        .parse()
+        .expect("Could not parse census tract");
+    let home_id: usize = String::from_utf8(person_record.homeId.to_owned())
+        .expect("Could not read home id")
+        .parse()
+        .expect("Could not read home id");
+
+    let person_id = context.add_person((
+        (Age, person_record.age),
+        (HomeId, home_id),
+        (CensusTract, tract),
+    ))?;
     Ok(person_id)
 }
 
+fn load_synth_population(context: &mut Context, synth_input_file: PathBuf) -> Result<(), IxaError> {
+    let mut reader =
+        csv::Reader::from_path(synth_input_file).expect("Failed to open file. No headers found.");
+    let mut raw_record = csv::ByteRecord::new();
+    let headers = reader.byte_headers().unwrap().clone();
+
+    while reader.read_byte_record(&mut raw_record).unwrap() {
+        let record: PeopleRecord = raw_record
+            .deserialize(Some(&headers))
+            .expect("Failed to parse record.");
+        create_person_from_record(context, &record)?;
+    }
+    Ok(())
+}
+
 pub fn init(context: &mut Context) -> Result<(), IxaError> {
     let parameters = context
         .get_global_property_value(Parameters)
         .unwrap()
         .clone();
 
-    let mut reader =
-        csv::Reader::from_path(parameters.synth_population_file).expect("Failed to open file.");
-
-    for result in reader.deserialize() {
-        let record: PeopleRecord = result.expect("Failed to parse record.");
-        create_person_from_record(context, &record)?;
-    }
+    load_synth_population(context, PathBuf::from(parameters.synth_population_file))?;
     context.index_property(Age);
     context.index_property(CensusTract);
     Ok(())
 }
 
 #[cfg(test)]
-
-mod tests {
+mod test {
     use super::*;
-    use ixa::{context::Context, people::ContextPeopleExt, random::ContextRandomExt};
+    use std::fs::File;
+    use std::io::Write;
+    use std::path::PathBuf;
+    use tempfile::tempdir;
 
     #[test]
-    #[allow(clippy::inconsistent_digit_grouping)]
-    fn test_create_person_from_record() {
+    fn check_synth_file_tract() {
         let mut context = Context::new();
-        context.init_random(0);
-        let record = PeopleRecord {
-            age: 42,
-            homeId: 36_09_30_33102_0005,
-        };
-        let person_id = create_person_from_record(&mut context, &record).unwrap();
-        assert_eq!(context.get_person_property(person_id, Age), 42);
-        assert_eq!(
-            context.get_person_property(person_id, HomeId),
-            36_09_30_33102_0005
-        );
-        assert!(context.get_person_property(person_id, Alive));
+        let temp_dir = tempdir().unwrap();
+        let path = PathBuf::from(&temp_dir.path());
+        let persisted_file = path.join("synth_pop_test.csv");
+        let mut file = File::create(persisted_file).unwrap();
+        file.write_all(
+            b"
+age,homeId
+43,360930331020001
+42,360930331020002",
+        )
+        .unwrap();
+        let synth_file = path.join("synth_pop_test.csv");
+        load_synth_population(&mut context, synth_file).unwrap();
+        let age: u8 = 43;
+        let tract: usize = 36_093_033_102;
+
         assert_eq!(
-            context.get_person_property(person_id, CensusTract),
-            36_09_30_33102
+            age,
+            context.get_person_property(context.get_person_id(0), Age)
         );
-    }
-
-    #[test]
-    #[allow(clippy::inconsistent_digit_grouping)]
-    fn test_create_person_from_record_invalid_census_tract() {
-        let mut context = Context::new();
-        context.init_random(0);
-        let record = PeopleRecord {
-            age: 42,
-            homeId: 36_09_30_33102_0005_0005,
-        };
-        let person_id = create_person_from_record(&mut context, &record).unwrap();
-        assert_eq!(context.get_person_property(person_id, Age), 42);
         assert_eq!(
-            context.get_person_property(person_id, HomeId),
-            36_09_30_33102_0005_0005
+            tract,
+            context.get_person_property(context.get_person_id(0), CensusTract)
         );
-        assert!(context.get_person_property(person_id, Alive));
-        assert_eq!(context.get_person_property(person_id, CensusTract), 0);
     }
 }