folder per provider

synthetichealth · Sep 8, 2023 · 2e5a557 · 2e5a557
1 parent 02955f2
commit 2e5a557
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Showing 3 changed files with 68 additions and 3 deletions.
diff --git a/src/main/java/org/mitre/synthea/export/Exporter.java b/src/main/java/org/mitre/synthea/export/Exporter.java
@@ -31,9 +31,11 @@
 import org.mitre.synthea.identity.Variant;
 import org.mitre.synthea.modules.DeathModule;
 import org.mitre.synthea.world.agents.Person;
+import org.mitre.synthea.world.agents.Provider;
 import org.mitre.synthea.world.concepts.Claim;
 import org.mitre.synthea.world.concepts.HealthRecord;
 import org.mitre.synthea.world.concepts.HealthRecord.Encounter;
+import org.mitre.synthea.world.concepts.HealthRecord.EncounterType;
 import org.mitre.synthea.world.concepts.HealthRecord.Observation;
 import org.mitre.synthea.world.concepts.HealthRecord.Report;
 
@@ -727,6 +729,15 @@ public static File getOutputFolder(String folderName, Person person) {
       folders.add(id.substring(0, 3));
     }
 
+    if (person != null && person.hasMultipleRecords
+        && Config.getAsBoolean("exporter.split_records.subfolders_by_provider")) {
+      // person.record has already been set to a single split record
+      Provider providerOrganization = person.record.provider;
+      // TODO: can this be null?
+      String providerId = providerOrganization.getResourceID();
+      folders.add(providerId);
+    }
+
     String baseDirectory = Config.get("exporter.baseDirectory");
 
     File f = Paths.get(baseDirectory, folders.toArray(new String[0])).toFile();

diff --git a/src/main/java/org/mitre/synthea/export/FhirR4.java b/src/main/java/org/mitre/synthea/export/FhirR4.java
@@ -2,7 +2,9 @@
 
 import ca.uhn.fhir.context.FhirContext;
 
+import com.google.common.collect.BiMap;
 import com.google.common.collect.HashBasedTable;
+import com.google.common.collect.HashBiMap;
 import com.google.common.collect.Table;
 import com.google.gson.Gson;
 import com.google.gson.JsonElement;
@@ -14,6 +16,7 @@
 import java.util.Calendar;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -127,7 +130,6 @@
 import org.hl7.fhir.r4.model.Type;
 import org.hl7.fhir.r4.model.codesystems.DoseRateType;
 
-import org.hl7.fhir.r4.model.codesystems.LocationPhysicalType;
 import org.hl7.fhir.utilities.xhtml.NodeType;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 
@@ -533,8 +535,8 @@ private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long
 
       Extension nationalityCodingExtension = new Extension("code");
       CodeableConcept nationalityCC = new CodeableConcept();
-      Coding nationalityCoding = new Coding();
-      nationalityCoding.setCode(nationality);
+      Coding nationalityCoding = nationalityToCoding(nationality);
+
       nationalityCC.addCoding(nationalityCoding);
       nationalityCodingExtension.setValue(nationalityCC);
       nationalityExtension.addExtension(nationalityCodingExtension);
@@ -720,6 +722,57 @@ private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long
     return newEntry(bundle, patientResource, (String) person.attributes.get(Person.ID));
   }
 
+  private static final BiMap<String, String> NATIONALITY_CODES = createNationalityCodeMap();
+
+  private static BiMap<String, String> createNationalityCodeMap() {
+    try {
+      String nationalityCodeData = Utilities.readResourceAndStripBOM("geography/nationalities.csv");
+      Iterator<LinkedHashMap<String,String>> lines =  SimpleCSV.parseLineByLine(nationalityCodeData);
+
+      BiMap<String, String> codeMap = HashBiMap.create();
+
+      while (lines.hasNext()) {
+        LinkedHashMap<String,String> line = lines.next();
+        codeMap.put(line.get("code").toUpperCase(), line.get("display").toLowerCase());
+      }
+      return codeMap;
+
+    } catch (Exception e) {
+      throw new ExceptionInInitializerError(e);
+    }
+  }
+
+  public static Coding nationalityToCoding(String nationality) {
+    Coding nationalityCoding = new Coding();
+    if (nationality == null) {
+      nationalityCoding.setCode("00");
+      nationalityCoding.setDisplay("Unknown");
+    } else if (nationality.length() == 2) {
+      // "B5", "E5", etc
+      nationalityCoding.setCode(nationality.toUpperCase());
+
+      String display = NATIONALITY_CODES.get(nationality.toUpperCase());
+      if (display != null) {
+        nationalityCoding.setDisplay(display);
+      }
+    } else {
+      // "English"
+      nationalityCoding.setDisplay(nationality);
+
+      String code = NATIONALITY_CODES.inverse().get(nationality);
+
+      if (code == null) {
+        code = NATIONALITY_CODES.inverse().get(nationality.toLowerCase());
+      }
+
+      if (code != null) {
+        nationalityCoding.setCode(code.toUpperCase());
+      }
+    }
+
+    return nationalityCoding;
+  }
+
   /**
    * Map the given Encounter into a FHIR Encounter resource, and add it to the given Bundle.
    *

diff --git a/src/main/resources/synthea.properties b/src/main/resources/synthea.properties
@@ -9,6 +9,7 @@ exporter.years_of_history = 10
 # split records allows patients to have one record per provider organization
 exporter.split_records = false
 exporter.split_records.duplicate_data = false
+exporter.split_records.subfolders_by_provider = true
 exporter.metadata.export = true
 exporter.ccda.export = false
 exporter.fhir.export = true