updates for entity gender/birthsex/race

synthetichealth · Aug 17, 2023 · 07a7b55 · 07a7b55
1 parent b7e5edc
commit 07a7b55
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Showing 6 changed files with 103 additions and 9 deletions.
diff --git a/src/main/java/org/mitre/synthea/engine/Generator.java b/src/main/java/org/mitre/synthea/engine/Generator.java
@@ -844,6 +844,7 @@ private Map<String, Object> pickDemographics(RandomNumberGenerator random, Demog
         gender = "F";
       }
     }
+    demographicsOutput.put(Person.BIRTH_SEX, gender);
     demographicsOutput.put(Person.GENDER, gender);
 
     // Pick the person's socioeconomic variables of education/income/occupation based on location.

diff --git a/src/main/java/org/mitre/synthea/export/FhirR4.java b/src/main/java/org/mitre/synthea/export/FhirR4.java
@@ -560,19 +560,26 @@ private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long
 
     Extension birthSexExtension = new Extension(
         "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
-    if (person.attributes.get(Person.GENDER).equals("M")) {
-      patientResource.setGender(AdministrativeGender.MALE);
+    if (person.attributes.get(Person.BIRTH_SEX).equals("M")) {
       birthSexExtension.setValue(new CodeType("M"));
-    } else if (person.attributes.get(Person.GENDER).equals("F")) {
-      patientResource.setGender(AdministrativeGender.FEMALE);
+    } else if (person.attributes.get(Person.BIRTH_SEX).equals("F")) {
       birthSexExtension.setValue(new CodeType("F"));
-    } else if (person.attributes.get(Person.GENDER).equals("UNK")) {
+    } else if (person.attributes.get(Person.BIRTH_SEX).equals("UNK")) {
       patientResource.setGender(AdministrativeGender.UNKNOWN);
     }
     if (USE_US_CORE_IG) {
       patientResource.addExtension(birthSexExtension);
     }
 
+    if (person.attributes.get(Person.GENDER).equals("M")) {
+      patientResource.setGender(AdministrativeGender.MALE);
+    } else if (person.attributes.get(Person.GENDER).equals("F")) {
+      patientResource.setGender(AdministrativeGender.FEMALE);
+    } else if (person.attributes.get(Person.GENDER).equals("UNK")) {
+      patientResource.setGender(AdministrativeGender.UNKNOWN);
+    }
+
+
     String state = (String) person.attributes.get(Person.STATE);
     if (USE_US_CORE_IG) {
       if (state.length() > 2) {

diff --git a/src/main/java/org/mitre/synthea/identity/Entity.java b/src/main/java/org/mitre/synthea/identity/Entity.java
@@ -12,6 +12,9 @@ public class Entity implements Serializable {
   private List<Seed> seeds;
   private LocalDate dateOfBirth;
   private String gender;
+  private String sexAtBirth;
+  private String ombRaceCategory;
+  private String socioeconomicLevel;
   private String individualId;
   private String housingStatus;
 
@@ -102,4 +105,62 @@ public String getHousingStatus() {
   public void setHousingStatus(String housingStatus) {
     this.housingStatus = housingStatus;
   }
+
+  public String getSexAtBirth() {
+    return sexAtBirth;
+  }
+
+  public void setSexAtBirth(String sexAtBirth) {
+    this.sexAtBirth = sexAtBirth;
+  }
+
+  public String getOmbRaceCategory() {
+    return ombRaceCategory;
+  }
+
+  public String getSyntheaRace() {
+    if (ombRaceCategory == null || ombRaceCategory.trim().isEmpty()) {
+      return null;
+    }
+    switch (ombRaceCategory) {
+    case "American Indian/Alaska Native":
+      return "native";
+    case "Asian":
+      return "asian";
+    case "Black/African American":
+      return "black";
+    case "Hispanic/Latino":
+      // TODO
+      return "white";
+    case "Multiple races":
+      return "other";
+    case "White":
+      return "white";
+    default:
+      throw new IllegalArgumentException("Unexpected ombRaceCategory: " + ombRaceCategory);
+    }
+
+  }
+
+  public String getSyntheaEthnicity() {
+    if (ombRaceCategory == null) {
+      return null;
+    } else if (ombRaceCategory.equals("Hispanic/Latino")) {
+      return "hispanic";
+    } else {
+      return "nonhispanic";
+    }
+  }
+
+  public void setOmbRaceCategory(String ombRaceCategory) {
+    this.ombRaceCategory = ombRaceCategory;
+  }
+
+  public String getSocioeconomicLevel() {
+    return socioeconomicLevel;
+  }
+
+  public void setSocioeconomicLevel(String socioeconomicLevel) {
+    this.socioeconomicLevel = socioeconomicLevel;
+  }
 }
diff --git a/src/main/java/org/mitre/synthea/identity/EntityDeserializer.java b/src/main/java/org/mitre/synthea/identity/EntityDeserializer.java
@@ -11,17 +11,26 @@
 import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.function.Function;
 
 public class EntityDeserializer implements JsonDeserializer<Entity> {
   @Override
   public Entity deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context)
       throws JsonParseException {
     Entity entity = new Entity();
     JsonObject entityObject = json.getAsJsonObject();
-    entity.setIndividualId(entityObject.getAsJsonPrimitive("individualId").getAsString());
-    entity.setGender(entityObject.getAsJsonPrimitive("gender").getAsString());
+
+    Function<String, String> getString = (fieldName) -> {
+      if (!entityObject.has(fieldName)) return null;
+      return entityObject.getAsJsonPrimitive(fieldName).getAsString();
+    };
+    entity.setIndividualId(getString.apply("individualId"));
+    entity.setGender(getString.apply("gender"));
+    entity.setSexAtBirth(getString.apply("sexAtBirth"));
+    entity.setOmbRaceCategory(getString.apply("ombRaceCategory"));
+    entity.setSocioeconomicLevel(getString.apply("socioeconomicLevel"));
     entity.setDateOfBirth(LocalDate.parse(
-        entityObject.getAsJsonPrimitive("dateOfBirth").getAsString(),
+        getString.apply("dateOfBirth"),
         DateTimeFormatter.ISO_LOCAL_DATE));
     List<Seed> seeds = new ArrayList<>();
     entityObject.getAsJsonArray("seeds").forEach(seedElement -> {

diff --git a/src/main/java/org/mitre/synthea/identity/Seed.java b/src/main/java/org/mitre/synthea/identity/Seed.java
@@ -20,6 +20,7 @@ public class Seed implements IdentityRecord, Serializable {
   private Period period;
   private String givenName;
   private String familyName;
+  private String gender;
   private String phone;
   private List<String> addressLines;
   private String city;
@@ -59,6 +60,10 @@ public void setGivenName(String givenName) {
   public void setFamilyName(String familyName) {
     this.familyName = familyName;
   }
+
+  public void setGender(String gender) {
+    this.gender = gender;
+  }
 
   public void setPhone(String phone) {
     this.phone = phone;
@@ -108,7 +113,7 @@ public LocalDate getDateOfBirth() {
 
   @Override
   public String getGender() {
-    return entity.getGender();
+    return gender;
   }
 
   @Override
@@ -177,6 +182,15 @@ public Map<String, Object> demographicAttributesForPerson() {
     attributes.put(Person.NAME, this.givenName + " " + this.familyName);
     attributes.put(Person.TELECOM, this.getPhone());
     attributes.put(Person.GENDER, this.getGender());
+    attributes.put(Person.BIRTH_SEX, this.entity.getSexAtBirth());
+
+    // TODO
+//    attributes.put(Person.SOCIOECONOMIC_CATEGORY, ???)
+//    this.entity.getSocioeconomicLevel()
+
+    attributes.put(Person.RACE, this.entity.getSyntheaRace());
+    attributes.put(Person.ETHNICITY, this.entity.getSyntheaEthnicity());
+
     attributes.put(Person.STATE, this.state);
     attributes.put(Person.CITY, WordUtils.capitalizeFully(this.city));
     attributes.put(Person.ADDRESS, this.addressLines.stream()

diff --git a/src/main/java/org/mitre/synthea/world/agents/Person.java b/src/main/java/org/mitre/synthea/world/agents/Person.java
@@ -56,6 +56,8 @@ public class Person implements Serializable, RandomNumberGenerator, QuadTreeElem
   public static final String ETHNICITY = "ethnicity";
   public static final String FIRST_LANGUAGE = "first_language";
   public static final String GENDER = "gender";
+  public static final String BIRTH_SEX = "birth_sex";
+
   public static final String MULTIPLE_BIRTH_STATUS = "multiple_birth_status";
   public static final String TELECOM = "telecom";
   public static final String ID = "id";