Fix merge conflict.

src/main/java/org/mitre/synthea/export/CSVExporter.java

@@ -297,7 +297,7 @@ private static List<String> propStringToList(String fileListString) {
    */
   private void writeCSVHeaders() throws IOException {
     patients.write("Id,BIRTHDATE,DEATHDATE,SSN,DRIVERS,PASSPORT,"
-        + "PREFIX,FIRST,LAST,SUFFIX,MAIDEN,MARITAL,RACE,ETHNICITY,GENDER,BIRTHPLACE,"
+        + "PREFIX,FIRST,MIDDLE,LAST,SUFFIX,MAIDEN,MARITAL,RACE,ETHNICITY,GENDER,BIRTHPLACE,"
         + "ADDRESS,CITY,STATE,COUNTY,FIPS,ZIP,LAT,LON,"
         + "HEALTHCARE_EXPENSES,HEALTHCARE_COVERAGE,INCOME");
     patients.write(NEWLINE);
@@ -625,6 +625,7 @@ private String patient(Person person, long time) throws IOException {
         Person.IDENTIFIER_PASSPORT,
         Person.NAME_PREFIX,
         Person.FIRST_NAME,
+        Person.MIDDLE_NAME,
         Person.LAST_NAME,
         Person.NAME_SUFFIX,
         Person.MAIDEN_NAME,
@@ -2021,4 +2022,4 @@ private OutputStreamWriter getWriter(Path outputDirectory, String filename, bool
     append = append && file.exists();
     return new OutputStreamWriter(new FileOutputStream(file, append), charset);
   }
-}
+}

src/main/java/org/mitre/synthea/export/ExportHelper.java

@@ -239,7 +239,7 @@ public static String getSystemURI(String system) {
   }
 
   /**
-   * Translate the the official FHIR system URI (e.g. http://snomed.info/sct)
+   * Translate the official FHIR system URI (e.g. http://snomed.info/sct)
    * into system name (e.g. SNOMED-CT).
    * @param uri http://snomed.info/sct, http://loinc.org, etc.
    * @return The internal short name used by Synthea, or "Unknown"

src/main/java/org/mitre/synthea/export/Exporter.java

@@ -1,6 +1,8 @@
 package org.mitre.synthea.export;
 
 import ca.uhn.fhir.parser.IParser;
+import com.google.common.base.Strings;
+
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
@@ -24,6 +26,8 @@
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
 
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.StringType;
 import org.mitre.synthea.engine.Generator;
 import org.mitre.synthea.export.flexporter.Actions;
 import org.mitre.synthea.export.flexporter.FhirPathUtils;
@@ -500,6 +504,34 @@ public static void runPostCompletionExports(Generator generator) {
    */
   public static void runPostCompletionExports(Generator generator, ExporterRuntimeOptions options) {
 
+    if (Config.getAsBoolean("exporter.fhir.bulk_data")) {
+      IParser parser = FhirR4.getContext().newJsonParser();
+      parser.setPrettyPrint(false);
+      Parameters parameters = new Parameters()
+              .addParameter("inputFormat","application/fhir+ndjson");
+      File outDirectory = getOutputFolder("fhir", null);
+
+      File[] files = outDirectory.listFiles(pathname -> pathname.getName().endsWith("ndjson"));
+
+      String configHostname = Config.get("exporter.fhir.bulk_data.parameter_hostname");
+      String hostname = Strings.isNullOrEmpty(configHostname)
+              ? "http://localhost:8080/" : configHostname;
+
+      for (File file : files) {
+        parameters.addParameter(
+                new Parameters.ParametersParameterComponent().setName("input")
+                        .addPart(new Parameters.ParametersParameterComponent()
+                                .setName("type")
+                                .setValue(new StringType(file.getName().split("\\.")[0])))
+                        .addPart(new Parameters.ParametersParameterComponent()
+                                .setName("url")
+                                .setValue(new StringType(hostname + file.getName()))));
+      }
+      overwriteFile(outDirectory.toPath().resolve("parameters.json"),
+          parser.encodeResourceToString(parameters));
+    }
+
+
     if (options.deferExports) {
       ExporterRuntimeOptions nonDeferredOptions = new ExporterRuntimeOptions(options);
       nonDeferredOptions.deferExports = false;

src/main/java/org/mitre/synthea/export/FhirR4.java

@@ -20,6 +20,7 @@
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.UUID;
 import java.util.stream.Collectors;
 
@@ -188,18 +189,28 @@ public class FhirR4 {
   protected static boolean TRANSACTION_BUNDLE =
       Config.getAsBoolean("exporter.fhir.transaction_bundle");
 
-  /* For the most part the US Core changes from v4 -> v5 are backwards compatible,
-   * so for those cases just check USE_US_CORE_IG.
-   * If there are version differences then use USE_US_CORE_(#) to separate them out.
-   */
   protected static boolean USE_US_CORE_IG =
       Config.getAsBoolean("exporter.fhir.use_us_core_ig");
   protected static String US_CORE_VERSION =
-      Config.get("exporter.fhir.us_core_version", "5.0.1");
+      Config.get("exporter.fhir.us_core_version", "6.1.0");
 
   private static Table<String, String, String> US_CORE_MAPPING;
+  private static final Table<String, String, String> US_CORE_3_MAPPING;
   private static final Table<String, String, String> US_CORE_4_MAPPING;
   private static final Table<String, String, String> US_CORE_5_MAPPING;
+  private static final Table<String, String, String> US_CORE_6_MAPPING;
+
+  public static enum USCoreVersion {
+    v311, v400, v501, v610
+  }
+
+  protected static boolean useUSCore3() {
+    boolean useUSCore3 = USE_US_CORE_IG && US_CORE_VERSION.startsWith("3");
+    if (useUSCore3) {
+      US_CORE_MAPPING = US_CORE_3_MAPPING;
+    }
+    return useUSCore3;
+  }
 
   protected static boolean useUSCore4() {
     boolean useUSCore4 = USE_US_CORE_IG && US_CORE_VERSION.startsWith("4");
@@ -217,6 +228,14 @@ protected static boolean useUSCore5() {
     return useUSCore5;
   }
 
+  protected static boolean useUSCore6() {
+    boolean useUSCore6 = USE_US_CORE_IG && US_CORE_VERSION.startsWith("6");
+    if (useUSCore6) {
+      US_CORE_MAPPING = US_CORE_6_MAPPING;
+    }
+    return useUSCore6;
+  }
+
   private static final String COUNTRY_CODE = Config.get("generate.geography.country_code");
 
   private static final Table<String, String, String> SHR_MAPPING =
@@ -229,15 +248,21 @@ protected static boolean useUSCore5() {
     reloadIncludeExclude();
 
     Map<String, Table<String, String, String>> usCoreMappings =
-        loadMappingWithVersions("us_core_mapping.csv", "4", "5");
+        loadMappingWithVersions("us_core_mapping.csv", "3", "4", "5", "6");
 
+    US_CORE_3_MAPPING = usCoreMappings.get("3");
     US_CORE_4_MAPPING = usCoreMappings.get("4");
     US_CORE_5_MAPPING = usCoreMappings.get("5");
+    US_CORE_6_MAPPING = usCoreMappings.get("6");
 
-    if (US_CORE_VERSION.startsWith("4")) {
+    if (US_CORE_VERSION.startsWith("3")) {
+      US_CORE_MAPPING = US_CORE_3_MAPPING;
+    } else if (US_CORE_VERSION.startsWith("4")) {
       US_CORE_MAPPING = US_CORE_4_MAPPING;
     } else if (US_CORE_VERSION.startsWith("5")) {
       US_CORE_MAPPING = US_CORE_5_MAPPING;
+    } else if (US_CORE_VERSION.startsWith("6")) {
+      US_CORE_MAPPING = US_CORE_6_MAPPING;
     }
   }
 
@@ -364,17 +389,15 @@ private static Table<String, String, String> loadMapping(String filename) {
       String url = line.get("URL");
       String version = line.get("VERSION");
 
-      if (StringUtils.isBlank(version)) {
-        // blank means applies to ALL versions
-        versions.values().forEach(table -> table.put(system, code, url));
-      } else {
-        Table<String, String, String> mappingTable = versions.get(version);
-        if (mappingTable == null) {
-          throw new IllegalArgumentException("Error in loading mapping from file " + filename
-              + ". File contains row with version '" + version
-              + "' but supported version numbers are: " + String.join(",", supportedVersions));
+      for (Entry<String, Table<String, String, String>> e : versions.entrySet()) {
+        String versionKey = e.getKey();
+        Table<String, String, String> mappingTable = e.getValue();
+
+        if (StringUtils.isBlank(version) || version.contains(versionKey)) {
+          // blank means applies to ALL versions
+          // version.contains allows for things like "4,5,6"
+          mappingTable.put(system, code, url);
         }
-        mappingTable.put(system, code, url);
       }
     }
 
@@ -1649,7 +1672,7 @@ private static BundleEntryComponent condition(
 
     if (USE_US_CORE_IG) {
       Meta meta = new Meta();
-      if (useUSCore5()) {
+      if (useUSCore5() || useUSCore6()) {
         meta.addProfile(
             "http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis");
       } else {
@@ -1880,29 +1903,51 @@ private static BundleEntryComponent observation(
         meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab");
       }
 
-      if (useUSCore5() && observation.category != null) {
-        switch (observation.category) {
-          case "imaging":
-            meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging");
-            break;
-          case "social-history":
-            meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-social-history");
-            break;
-          case "survey":
-            meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey");
-            // note that the -sdoh-assessment profile is a subset of -survey,
-            // those are handled by code in US_CORE_MAPPING above
-            break;
-          case "exam":
-            // this one is a little nebulous -- are all exams also clinical tests?
-            meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test");
-
-            observationResource.addCategory().addCoding().setCode("clinical-test")
-                .setSystem("http://hl7.org/fhir/us/core/CodeSystem/us-core-observation-category")
-                .setDisplay("Clinical Test");
-            break;
-          default:
-            // do nothing
+      if (observation.category != null) {
+        if (useUSCore6()) {
+          switch (observation.category) {
+            case "imaging":
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-result");
+              break;
+            case "social-history":
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-simple-observation");
+              break;
+            case "survey":
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-screening-assessment");
+              break;
+            case "exam":
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-result");
+              break;
+            case "laboratory":
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab");
+              break;
+            default:
+              // do nothing
+          }
+        } else if (useUSCore5()) {
+          switch (observation.category) {
+            case "imaging":
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging");
+              break;
+            case "social-history":
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-social-history");
+              break;
+            case "survey":
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey");
+              // note that the -sdoh-assessment profile is a subset of -survey,
+              // those are handled by code in US_CORE_MAPPING above
+              break;
+            case "exam":
+              // this one is a little nebulous -- are all exams also clinical tests?
+              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test");
+
+              observationResource.addCategory().addCoding().setCode("clinical-test")
+                  .setSystem("http://hl7.org/fhir/us/core/CodeSystem/us-core-observation-category")
+                  .setDisplay("Clinical Test");
+              break;
+            default:
+              // do nothing
+          }
         }
       }
 

src/main/java/org/mitre/synthea/export/rif/BeneficiaryExporter.java

@@ -511,7 +511,7 @@ String getDualEligibilityCode(Person person, boolean medicareAge,
   }
 
   /**
-   * The the current beneficiary ID code (CRNT_BIC).
+   * The current beneficiary ID code (CRNT_BIC).
    * @param person The person.
    * @param ageThisYear The person's current age (at the end of the year).
    * @param disabled If the person is disabled according to SSD.

src/main/java/org/mitre/synthea/modules/covid/C19Vaccine.java

@@ -40,16 +40,15 @@ public enum EUASet {
    */
   public static void initialize() {
     EUAs.put(EUASet.PFIZER,
-        new C19Vaccine("SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, "
-            + "preservative free, 30 mcg/0.3mL dose", "208", true, 0.531,
+        new C19Vaccine("COVID-19, mRNA, LNP-S, PF, 30 mcg/0.3 mL dose",
+            "208", true, 0.531,
             Utilities.convertTime("days", 21)));
     EUAs.put(EUASet.MODERNA,
-        new C19Vaccine("SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, "
-            + "preservative free, 100 mcg/0.5mL dose", "207", true, 0.398,
+        new C19Vaccine("COVID-19, mRNA, LNP-S, PF, 100 mcg/0.5mL dose or 50 mcg/0.25mL dose",
+            "207", true, 0.398,
             Utilities.convertTime("days", 28)));
     EUAs.put(EUASet.JANSSEN,
-        new C19Vaccine("SARS-COV-2 (COVID-19) vaccine, vector non-replicating, "
-            + "recombinant spike protein-Ad26, preservative free, 0.5 mL",
+        new C19Vaccine("COVID-19 vaccine, vector-nr, rS-Ad26, PF, 0.5 mL",
             "212", false, 0.071, 0));
 
     List<Pair<EUASet, Double>> pmf = EUAs.entrySet().stream()

src/main/resources/costs/procedures.csv

@@ -36,7 +36,7 @@ CODE,MIN,MODE,MAX,COMMENTS
 167995008,3048.51,6097.0171,12194.03,Sputum microscopy (procedure)
 91602002,7753.63,15507.25552,31014.51,Thoracentesis (procedure)
 432231006,7753.63,15507.25552,31014.51,Fine needle aspiration biopsy of lung (procedure)
-173160006,4245.28,8490.5551,16981.11,Diagnostic fiberoptic bronchoscopy (procedure)
+85765000,4245.28,8490.5551,16981.11,Fiberoptic bronchoscopy (procedure)
 698354004,5103.68,10207.35977,20414.72,Magnetic resonance imaging for measurement of brain volume (procedure)
 430193006,250.00,500,1000.00,Medication Reconciliation (procedure)
 180030006,10671.22,21342.44596,42684.89,Amputation of right foot

src/main/resources/modules/lung_cancer.json

@@ -409,8 +409,8 @@
       "codes": [
         {
           "system": "SNOMED-CT",
-          "code": "173160006",
-          "display": "Diagnostic fiberoptic bronchoscopy (procedure)"
+          "code": "85765000",
+          "display": "Fiberoptic bronchoscopy (procedure)"
         }
       ],
       "direct_transition": "End_Diagnosis_Encounter_III"

src/main/resources/modules/sepsis.json

@@ -291,8 +291,13 @@
       "codes": [
         {
           "system": "LOINC",
-          "code": "2713-6",
-          "display": "Oxygen saturation Calculated from oxygen partial pressure in Blood"
+          "code": "2708-6",
+          "display": "Oxygen saturation in Arterial blood"
+        },
+        {
+          "system": "LOINC",
+          "code": "59408-5",
+          "display": "Oxygen saturation in Arterial blood by Pulse oximetry"
         }
       ],
       "direct_transition": "Lactate_Level1",

src/main/resources/modules/veteran_lung_cancer.json

@@ -309,8 +309,8 @@
       "codes": [
         {
           "system": "SNOMED-CT",
-          "code": "173160006",
-          "display": "Diagnostic fiberoptic bronchoscopy (procedure)"
+          "code": "85765000",
+          "display": "Fiberoptic bronchoscopy (procedure)"
         }
       ],
       "direct_transition": "End_Diagnosis_Encounter_III"

src/main/resources/synthea.properties

@@ -22,6 +22,8 @@ exporter.fhir.us_core_version = 5.0.1
 exporter.fhir.transaction_bundle = true
 # using bulk_data=true will ignore exporter.pretty_print
 exporter.fhir.bulk_data = false
+# hostname embedded into the generated parameters file. Defaults to http://localhost:8000/
+#exporter.fhir.bulk_data.parameter_hostname = http://example.org/
 # included_ and excluded_resources list out the resource types to include/exclude in the csv exporters.
 # only one of these may be set at a time, if both are set then both will be ignored.
 # if neither is set, then all resource types will be included.