Merge pull request #931 from synthetichealth/c19-updates

COVID-19 Related Updates

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

@@ -42,6 +42,7 @@
 import org.mitre.synthea.modules.LifecycleModule;
 import org.mitre.synthea.modules.QualityOfLifeModule;
 import org.mitre.synthea.modules.WeightLossModule;
+import org.mitre.synthea.modules.covid.C19ImmunizationModule;
 import org.mitre.synthea.world.agents.Person;
 
 /**
@@ -72,6 +73,7 @@ private static Map<String, ModuleSupplier> loadModules() {
     retVal.put("Cardiovascular Disease", new ModuleSupplier(new CardiovascularDiseaseModule()));
     retVal.put("Quality Of Life", new ModuleSupplier(new QualityOfLifeModule()));
     retVal.put("Weight Loss", new ModuleSupplier(new WeightLossModule()));
+    retVal.put("COVID-19 Immunization Module", new ModuleSupplier(new C19ImmunizationModule()));
 
     Properties moduleOverrides = getModuleOverrides();
 

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

@@ -40,6 +40,7 @@
 import org.mitre.synthea.modules.Immunizations;
 import org.mitre.synthea.modules.LifecycleModule;
 import org.mitre.synthea.modules.QualityOfLifeModule;
+import org.mitre.synthea.modules.covid.C19ImmunizationModule;
 import org.mitre.synthea.world.agents.Person;
 
 /**
@@ -149,6 +150,7 @@ public static Map<String,Inventory> getAttributeInventory() throws Exception {
     Immunizations.inventoryAttributes(attributes);
     LifecycleModule.inventoryAttributes(attributes);
     QualityOfLifeModule.inventoryAttributes(attributes);
+    C19ImmunizationModule.inventoryAttributes(attributes);
 
     return attributes;
   }

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

@@ -0,0 +1,45 @@
+package org.mitre.synthea.helpers;
+
+import java.util.List;
+
+import org.apache.commons.math3.distribution.EnumeratedDistribution;
+import org.apache.commons.math3.exception.MathArithmeticException;
+import org.apache.commons.math3.exception.NotANumberException;
+import org.apache.commons.math3.exception.NotFiniteNumberException;
+import org.apache.commons.math3.exception.NotPositiveException;
+import org.apache.commons.math3.util.Pair;
+import org.mitre.synthea.world.agents.Person;
+
+/**
+ * Class that wraps EnumeratedDistribution for thread safe use in Synthea. In several places in
+ * Synthea, EnumeratedDistributions are used following a
+ * <a href="https://en.wikipedia.org/wiki/Singleton_pattern">singleton pattern</a>. One distribution
+ * is used in a particular aspect of simulation. To support reproducibility of simulations, its
+ * source of randomness is reseeded for each individual. Since multiple threads may be accessing
+ * the distribution at the same time, it would be possible to reseed the distribution in one thread
+ * but sample on that seed in another thread. This class offers a synchronized method to prevent
+ * that with the handy side benefit that it takes the well-known and loved Synthea Person as a
+ * source of randomness.
+ * @param <T> The type to be returned when sampling from the distribiution.
+ */
+public class SyncedEnumeratedDistro<T> extends EnumeratedDistribution {
+  /**
+   * Just calls super. Look at the docs for EnumeratedDistributed for more details.
+   * @param pmf List of pairs of values and their weight in the distribution.
+   */
+  public SyncedEnumeratedDistro(List<Pair<T, Double>> pmf) throws NotPositiveException,
+      MathArithmeticException, NotFiniteNumberException, NotANumberException {
+    super(pmf);
+  }
+
+  /**
+   * Sample from the distribution after it has been reseeded using the Person provided as a source
+   * of randomness.
+   * @param person Where the randomness comes from
+   * @return a value from the distribution based on a weighted, random selection
+   */
+  public synchronized T syncedReseededSample(Person person) {
+    reseedRandomGenerator(person.randLong());
+    return (T) sample();
+  }
+}