BlueButton 2 RIF Exporter

.gitignore

@@ -16,6 +16,14 @@ bin/**
 # don't commit the autobuilt version file
 src/main/resources/version.txt
 
+# don't commit the code maps
+src/main/resources/export/condition_code_map.json
+src/main/resources/export/medication_code_map.json
+src/main/resources/export/drg_code_map.json
+src/main/resources/export/dme_code_map.json
+src/main/resources/export/hcpcs_code_map.json
+src/main/resources/export/betos_code_map.json
+
 # H2 database files
 **/*.mv.db
 **/*.trace.db
@@ -26,5 +34,5 @@ src/main/resources/version.txt
 .vscode/settings.json
 /build/
 
-src/main/resources/map.json
-
+# VS Code plugin files
+.history

build.gradle

@@ -25,6 +25,11 @@ repositories {
   }
 }
 
+// Uncomment to see deprecation warnings
+// tasks.withType(JavaCompile) {
+//   options.compilerArgs << "-Xlint:deprecation"
+// }
+
 checkstyle {
   toolVersion '8.4'
   //showViolations = true

config/checkstyle/checkstyle.xml

@@ -33,8 +33,10 @@
         <property name="eachLine" value="true"/>
     </module>
 
+    <module name="SuppressWarningsFilter" />
     <module name="TreeWalker">
         <module name="OuterTypeFilename"/>
+        <module name="SuppressWarningsHolder" />
         <module name="IllegalTokenText">
             <property name="tokens" value="STRING_LITERAL, CHAR_LITERAL"/>
             <property name="format" value="\\u00(09|0(a|A)|0(c|C)|0(d|D)|22|27|5(C|c))|\\(0(10|11|12|14|15|42|47)|134)"/>

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

@@ -631,6 +631,8 @@ public static class SetAttribute extends State {
     // For GMF 1.0 Support
     private Object value;
     private Code valueCode;
+    /** When the value of the attribute should be the value of another attribute. */
+    private String valueAttribute;
     private Range<Double> range;
     private String expression;
     private transient ThreadLocal<ExpressionProcessor> threadExpProcessor;
@@ -709,6 +711,11 @@ public boolean process(Person person, long time) {
         value = distribution.generate(person);
       } else if (valueCode != null) {
         value = valueCode;
+      } else if (valueAttribute != null) {
+        // the module is setting an attribute to be the value of an existing attribute
+        if (person.attributes.containsKey(valueAttribute)) {
+          value = person.attributes.get(valueAttribute);
+        }
       }
 
       if (value != null) {
@@ -845,8 +852,13 @@ public boolean process(Person person, long time) {
 
         if (reason != null) {
           if (person.attributes.containsKey(reason)) {
-            Entry condition = (Entry) person.attributes.get(reason);
-            encounter.reason = condition.codes.get(0);
+            Object value = person.attributes.get(reason);
+            if (value instanceof Entry) {
+              Entry condition = (Entry) person.attributes.get(reason);
+              encounter.reason = condition.codes.get(0);
+            } else if (value instanceof Code) {
+              encounter.reason = (Code) value;
+            }
           } else if (person.hadPriorState(reason)) {
             // loop through the present conditions, the condition "name" will match
             // the name of the ConditionOnset state (aka "reason")

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

@@ -175,10 +175,7 @@ private void loadLookupTable() {
       String fileName = Config.get("generate.lookup_tables") + lookupTableName;
       List<? extends Map<String, String>> lookupTable = null;
       try {
-        String csv = Utilities.readResource(fileName);
-        if (csv.startsWith("\uFEFF")) {
-          csv = csv.substring(1); // Removes BOM.
-        }
+        String csv = Utilities.readResourceAndStripBOM(fileName);
         lookupTable = SimpleCSV.parse(csv);
       } catch (IOException e) {
         e.printStackTrace();