fix: Replace HashMap with ordered collections to fix indeterministic PersonTest

- Use LinkedHashSet in ClinicalNoteExporter for deterministic clinical note ordering
- Use ConcurrentSkipListMap for Person.chronicMedications
- Use LinkedHashMap in HealthRecord and Demographics

Author: zyu49

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

@@ -6,6 +6,7 @@
 
 import java.io.StringWriter;
 import java.util.HashSet;
+import java.util.LinkedHashSet;
 import java.util.Set;
 
 import org.mitre.synthea.modules.LifecycleModule;
@@ -67,10 +68,10 @@ public static String export(Person person) {
   public static String export(Person person, Encounter encounter) {
     // The export templates fill in the record by accessing the attributes
     // of the Person, so we add a few attributes just for the purposes of export.
-    Set<String> activeAllergies = new HashSet<String>();
-    Set<String> activeConditions = new HashSet<String>();
-    Set<String> activeMedications = new HashSet<String>();
-    Set<String> activeProcedures = new HashSet<String>();
+    Set<String> activeAllergies = new LinkedHashSet<String>();
+    Set<String> activeConditions = new LinkedHashSet<String>();
+    Set<String> activeMedications = new LinkedHashSet<String>();
+    Set<String> activeProcedures = new LinkedHashSet<String>();
 
     // need to loop through record until THIS encounter
     // to get previous data, since "present" is what is present

src/main/java/org/mitre/synthea/world/agents/Person.java

@@ -17,6 +17,7 @@
 import java.util.Set;
 import java.util.UUID;
 import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentSkipListMap;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.tuple.Pair;
@@ -254,10 +255,10 @@ public Person(long seed) {
     /* initialized the onsetConditions field */
     onsetConditionRecord = new ExpressedConditionRecord(this);
     /* Chronic Medications which will be renewed at each Wellness Encounter */
-    chronicMedications = new ConcurrentHashMap<String, HealthRecord.Medication>();
+    chronicMedications = new ConcurrentSkipListMap<String, HealthRecord.Medication>();
     hasMultipleRecords = Config.getAsBoolean("exporter.split_records", false);
     if (hasMultipleRecords) {
-      records = new ConcurrentHashMap<String, HealthRecord>();
+      records = new ConcurrentSkipListMap<String, HealthRecord>();
     }
     this.initializeDefaultHealthRecords();
     coverage = new CoverageRecord(this);

src/main/java/org/mitre/synthea/world/concepts/HealthRecord.java

@@ -15,6 +15,7 @@
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.LinkedHashSet;
@@ -1054,7 +1055,7 @@ public Allergy(long start, String type) {
   public HealthRecord(Person person) {
     this.person = person;
     encounters = new ArrayList<Encounter>();
-    present = new HashMap<String, Entry>();
+    present = new LinkedHashMap<String, Entry>();
     if (person.attributes.get(Person.HOUSEHOLD) != null) {
       this.demographicsAtRecordCreation = new HashMap<String,Object>(person.attributes);
     }

src/main/java/org/mitre/synthea/world/geography/Demographics.java

@@ -7,6 +7,7 @@
 import java.io.Serializable;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -266,7 +267,7 @@ public String languageFromRaceAndEthnicity(String race, String ethnicity,
   public int pickIncome(RandomNumberGenerator random) {
     // lazy-load in case this randomcollection isn't necessary
     if (incomeDistribution == null) {
-      Map<String, Double> tempIncome = new HashMap<>(income);
+      Map<String, Double> tempIncome = new LinkedHashMap<>(income);
       tempIncome.remove("mean");
       tempIncome.remove("median");
       incomeDistribution = buildRandomCollectionFromMap(tempIncome);
@@ -486,7 +487,7 @@ private static Demographics csvLineToDemographics(Map<String,String> line) {
     d.state = line.get("STNAME");
     d.county = line.get("CTYNAME");
 
-    d.ages = new HashMap<String, Double>();
+    d.ages = new LinkedHashMap<String, Double>();
 
     int i = 1;
     for (String ageGroup : CSV_AGE_GROUPS) {
@@ -497,13 +498,13 @@ private static Demographics csvLineToDemographics(Map<String,String> line) {
     }
     nonZeroDefaults(d.ages);
 
-    d.gender = new HashMap<String, Double>();
+    d.gender = new LinkedHashMap<String, Double>();
     d.gender.put("male", Double.parseDouble(line.get("TOT_MALE")));
     d.gender.put("female", Double.parseDouble(line.get("TOT_FEMALE")));
     nonZeroDefaults(d.gender);
 
     double percentageTotal = 0;
-    d.race = new HashMap<String, Double>();
+    d.race = new LinkedHashMap<String, Double>();
     for (String race : CSV_RACES) {
       double percentage = Double.parseDouble(line.get(race));
       d.race.put(race.toLowerCase(), percentage);
@@ -524,7 +525,7 @@ private static Demographics csvLineToDemographics(Map<String,String> line) {
     }
     nonZeroDefaults(d.race);
 
-    d.income = new HashMap<String, Double>();
+    d.income = new LinkedHashMap<String, Double>();
     for (String income : CSV_INCOMES) {
       String incomeString = line.get(income);
       if (incomeString.isEmpty()) {
@@ -536,7 +537,7 @@ private static Demographics csvLineToDemographics(Map<String,String> line) {
     }
     nonZeroDefaults(d.income);
 
-    d.education = new HashMap<String, Double>();
+    d.education = new LinkedHashMap<String, Double>();
     for (String education : CSV_EDUCATIONS) {
       String educationString = line.get(education);
       if (educationString.isEmpty()) {