Update US Core v4 export and enforce physiology usage more consistently.

config/simulations/ecg.yml

@@ -37,7 +37,7 @@ charts:
       axisParamX: time
       axisLabelX: time (s)
       axisLabelY: Current (A)
-      lowerBoundY: -0.05
-      upperBoundY: 0.15
+      #lowerBoundY: -0.05
+      #upperBoundY: 0.15
       series:
         - param: zf

src/main/java/org/mitre/synthea/engine/Components.java

@@ -101,7 +101,7 @@ public static class SampledData implements Serializable {
     public Double lowerLimit; // Lower limit of detection
     public Double upperLimit; // Upper limit of detection
     public List<String> attributes; // Person attributes containing TimeSeriesData objects
-    public transient List<TimeSeriesData> series; // List of actual series data collections
+    public List<TimeSeriesData> series; // List of actual series data collections
 
     // Format for the output decimal numbers
     // See https://docs.oracle.com/javase/8/docs/api/java/text/DecimalFormat.html

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

@@ -1654,7 +1654,7 @@ private static BundleEntryComponent observation(RandomNumberGenerator rand,
       if (codeMappingUri != null) {
         meta.addProfile(codeMappingUri);
         if (!codeMappingUri.contains("/us/core/") && observation.category.equals("vital-signs")) {
-          meta.addProfile("http://hl7.org/fhir/StructureDefinition/vitalsigns");
+          meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs");
         }
       } else if (observation.report != null && observation.category.equals("laboratory")) {
         meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab");

src/main/java/org/mitre/synthea/helpers/TimeSeriesData.java

@@ -1,9 +1,10 @@
 package org.mitre.synthea.helpers;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
-public class TimeSeriesData {
+public class TimeSeriesData implements Serializable {
   /** Provides a collection of time series values as well as sampling metadata
    *  concerning those values.
    */

src/main/java/org/mitre/synthea/modules/LifecycleModule.java

@@ -849,7 +849,7 @@ private static double reverseCalculateCreatinine(Person person, double crcl, lon
       Config.getAsBoolean("lifecycle.death_by_natural_causes");
   protected static boolean ENABLE_DEATH_BY_LOSS_OF_CARE =
       Config.getAsBoolean("lifecycle.death_by_loss_of_care");
-  protected static boolean ENABLE_PHYSIOLOGY_GENERATORS =
+  public static boolean ENABLE_PHYSIOLOGY_GENERATORS =
       Config.getAsBoolean("physiology.generators.enabled", false);
 
   // Death From Natural Causes SNOMED Code

src/main/resources/us_core_mapping.csv

@@ -4,13 +4,12 @@ SYSTEM,CODE,URL
 "http://loinc.org","72166-2","http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus"
 "http://loinc.org","2708-6","http://hl7.org/fhir/us/core/StructureDefinition/us-core-pulse-oximetry"
 "http://loinc.org","59408-5","http://hl7.org/fhir/us/core/StructureDefinition/us-core-pulse-oximetry"
-"http://loinc.org","85353-1","http://hl7.org/fhir/StructureDefinition/vitalspanel"
-"http://loinc.org","9279-1","http://hl7.org/fhir/StructureDefinition/resprate"
-"http://loinc.org","8867-4","http://hl7.org/fhir/StructureDefinition/heartrate"
-"http://loinc.org","8310-5","http://hl7.org/fhir/StructureDefinition/bodytemp"
-"http://loinc.org","8331-1","http://hl7.org/fhir/StructureDefinition/bodytemp"
-"http://loinc.org","8302-2","http://hl7.org/fhir/StructureDefinition/bodyheight"
-"http://loinc.org","9843-4","http://hl7.org/fhir/StructureDefinition/headcircum"
-"http://loinc.org","29463-7","http://hl7.org/fhir/StructureDefinition/bodyweight"
-"http://loinc.org","39156-5","http://hl7.org/fhir/StructureDefinition/bmi"
-"http://loinc.org","85354-9","http://hl7.org/fhir/StructureDefinition/bp"
+"http://loinc.org","9279-1","http://hl7.org/fhir/us/core/StructureDefinition/us-core-respiratory-rate"
+"http://loinc.org","8867-4","http://hl7.org/fhir/us/core/StructureDefinition/us-core-heart-rate"
+"http://loinc.org","8310-5","http://hl7.org/fhir/us/core/StructureDefinition/us-core-body-temperature"
+"http://loinc.org","8302-2","http://hl7.org/fhir/us/core/StructureDefinition/us-core-body-height"
+"http://loinc.org","9843-4","http://hl7.org/fhir/us/core/StructureDefinition/us-core-head-circumference"
+"http://loinc.org","8289-1","http://hl7.org/fhir/us/core/StructureDefinition/head-occipital-frontal-circumference-percentile"
+"http://loinc.org","29463-7","http://hl7.org/fhir/us/core/StructureDefinition/us-core-body-weight"
+"http://loinc.org","39156-5","http://hl7.org/fhir/us/core/StructureDefinition/us-core-bmi"
+"http://loinc.org","85354-9","http://hl7.org/fhir/us/core/StructureDefinition/us-core-blood-pressure"

src/test/java/org/mitre/synthea/TestHelper.java

@@ -18,6 +18,7 @@
 
 import org.mitre.synthea.engine.Generator;
 import org.mitre.synthea.engine.Module;
+import org.mitre.synthea.engine.State;
 import org.mitre.synthea.helpers.Config;
 import org.mitre.synthea.helpers.Utilities;
 import org.mitre.synthea.world.agents.Person;
@@ -149,6 +150,10 @@ public static long years(long numYears) {
   public static synchronized Person[] getGeneratedPeople() throws IOException,
       ClassNotFoundException {
     if (serializedPatients == null) {
+      // Ensure Physiology state is enabled
+      boolean physStateEnabled = State.ENABLE_PHYSIOLOGY_STATE;
+      State.ENABLE_PHYSIOLOGY_STATE = true;
+
       int numberOfPeople = 10;
       Generator generator = new Generator(numberOfPeople);
       generator.options.overflow = false;
@@ -162,12 +167,14 @@ public static synchronized Person[] getGeneratedPeople() throws IOException,
       oos.writeObject(people);
       oos.close();
       serializedPatients = baos.toByteArray();
+
+      // Reset state after exporter test.
+      State.ENABLE_PHYSIOLOGY_STATE = physStateEnabled;
     }
     ByteArrayInputStream bais = new ByteArrayInputStream(serializedPatients);
     ObjectInputStream ois = new ObjectInputStream(bais);
     Person[] rehydrated = (Person[]) ois.readObject();
     ois.close();
     return rehydrated;
   }
-
 }

src/test/java/org/mitre/synthea/export/FHIRDSTU2ExporterTest.java

@@ -23,8 +23,8 @@
 
 import org.apache.commons.codec.binary.Base64;
 import org.hl7.fhir.dstu3.model.DiagnosticReport;
-import org.junit.After;
-import org.junit.Before;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
@@ -46,7 +46,7 @@
  * Uses HAPI FHIR project to validate FHIR export. http://hapifhir.io/doc_validation.html
  */
 public class FHIRDSTU2ExporterTest {
-  private boolean physStateEnabled;
+  private static boolean physStateEnabled;
 
   /**
    * Temporary folder for any exported files, guaranteed to be deleted at the end of the test.
@@ -57,8 +57,8 @@ public class FHIRDSTU2ExporterTest {
   /**
    * Setup state for exporter test.
    */
-  @Before
-  public void setup() {
+  @BeforeClass
+  public static void setup() {
     // Ensure Physiology state is enabled
     physStateEnabled = State.ENABLE_PHYSIOLOGY_STATE;
     State.ENABLE_PHYSIOLOGY_STATE = true;
@@ -67,8 +67,8 @@ public void setup() {
   /**
    * Reset state after exporter test.
    */
-  @After
-  public void tearDown() {
+  @AfterClass
+  public static void tearDown() {
     State.ENABLE_PHYSIOLOGY_STATE = physStateEnabled;
   }
 

src/test/java/org/mitre/synthea/export/FHIRR4ExporterTest.java

@@ -18,13 +18,12 @@
 import org.apache.commons.codec.binary.Base64;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Media;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.SampledData;
-import org.junit.After;
-import org.junit.Before;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
@@ -47,7 +46,7 @@
  * Uses HAPI FHIR project to validate FHIR export. http://hapifhir.io/doc_validation.html
  */
 public class FHIRR4ExporterTest {
-  private boolean physStateEnabled;
+  private static boolean physStateEnabled;
 
   /**
    * Temporary folder for any exported files, guaranteed to be deleted at the end of the test.
@@ -58,8 +57,8 @@ public class FHIRR4ExporterTest {
   /**
    * Setup state for exporter test.
    */
-  @Before
-  public void setup() {
+  @BeforeClass
+  public static void setup() {
     // Ensure Physiology state is enabled
     physStateEnabled = State.ENABLE_PHYSIOLOGY_STATE;
     State.ENABLE_PHYSIOLOGY_STATE = true;
@@ -68,8 +67,8 @@ public void setup() {
   /**
    * Reset state after exporter test.
    */
-  @After
-  public void tearDown() {
+  @AfterClass
+  public static void tearDown() {
     State.ENABLE_PHYSIOLOGY_STATE = physStateEnabled;
   }
 

src/test/java/org/mitre/synthea/export/FHIRSTU3ExporterTest.java

@@ -23,9 +23,9 @@
 import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Quantity;
 import org.hl7.fhir.dstu3.model.SampledData;
-import org.junit.After;
+import org.junit.AfterClass;
 import org.junit.Assert;
-import org.junit.Before;
+import org.junit.BeforeClass;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
@@ -48,7 +48,7 @@
  * Uses HAPI FHIR project to validate FHIR export. http://hapifhir.io/doc_validation.html
  */
 public class FHIRSTU3ExporterTest {
-  private boolean physStateEnabled;
+  private static boolean physStateEnabled;
 
   /**
    * Temporary folder for any exported files, guaranteed to be deleted at the end of the test.
@@ -59,8 +59,8 @@ public class FHIRSTU3ExporterTest {
   /**
    * Setup state for exporter test.
    */
-  @Before
-  public void setup() {
+  @BeforeClass
+  public static void setup() {
     // Ensure Physiology state is enabled
     physStateEnabled = State.ENABLE_PHYSIOLOGY_STATE;
     State.ENABLE_PHYSIOLOGY_STATE = true;
@@ -69,8 +69,8 @@ public void setup() {
   /**
    * Reset state after exporter test.
    */
-  @After
-  public void tearDown() {
+  @AfterClass
+  public static void tearDown() {
     State.ENABLE_PHYSIOLOGY_STATE = physStateEnabled;
   }