Flexporter - Update randomCode fn to take output type as an optional second param

src/main/java/App.java

@@ -220,6 +220,8 @@ public static void main(String[] args) throws Exception {
             if (flexporterMappingFile.exists()) {
               Mapping mapping = Mapping.parseMapping(flexporterMappingFile);
               exportOptions.addFlexporterMapping(mapping);
+              mapping.loadValueSets();
+
               // disable the graalVM warning when FlexporterJavascriptContext is instantiated
               System.getProperties().setProperty("polyglot.engine.WarnInterpreterOnly", "false");
             } else {

src/main/java/RunFlexporter.java

@@ -1,9 +1,6 @@
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
 
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
@@ -14,7 +11,6 @@
 import java.nio.file.StandardOpenOption;
 import java.util.ArrayDeque;
 import java.util.Arrays;
-import java.util.Map;
 import java.util.Queue;
 
 import org.apache.commons.io.FilenameUtils;
@@ -125,6 +121,7 @@ private static void convertFhir(File mappingFile, File igDirectory, File sourceF
       throws IOException {
 
     Mapping mapping = Mapping.parseMapping(mappingFile);
+    mapping.loadValueSets();
 
     if (igDirectory != null) {
       loadIG(igDirectory);

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

@@ -3385,7 +3385,7 @@ private static Type convertFhirDateTime(long datetime, boolean time) {
    * @param system The system identifier, such as a URI. Optional; may be null.
    * @return The converted CodeableConcept
    */
-  private static CodeableConcept mapCodeToCodeableConcept(Code from, String system) {
+  public static CodeableConcept mapCodeToCodeableConcept(Code from, String system) {
     CodeableConcept to = new CodeableConcept();
     system = system == null ? null : ExportHelper.getSystemURI(system);
     from.system = ExportHelper.getSystemURI(from.system);

src/main/java/org/mitre/synthea/export/flexporter/Actions.java

@@ -26,6 +26,7 @@
 import org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
+import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Meta;
@@ -822,7 +823,7 @@ private static Object getValue(Bundle bundle, String valueDef, Resource currentR
     } else if (flag.equals("getAttribute")) {
       return getAttribute(person, flagValues);
     } else if (flag.equals("randomCode")) {
-      return randomCode(flagValues[0]);
+      return randomCode(flagValues);
     }
 
     return null;
@@ -900,13 +901,22 @@ private static Base findValue(Bundle bundle, String... args) {
     return fieldValues.get(0);
   }
 
-  private static Map<String, String> randomCode(String valueSetUrl) {
+  private static Object randomCode(String... args) {
+    String valueSetUrl = args[0];
+    String outputType = (args.length > 1) ? args[1] : "Coding";
     Code code = RandomCodeGenerator.getCode(valueSetUrl,
         (int) (Math.random() * Integer.MAX_VALUE));
-    Map<String, String> codeAsMap = Map.of(
-         "system", code.system,
-         "code", code.code,
-         "display", code.display == null ? "" : code.display);
-    return codeAsMap;
+
+    if (outputType.equalsIgnoreCase("code")) {
+      return code.code;
+    } else if (outputType.equalsIgnoreCase("Coding")) {
+      return new Coding(code.system, code.code, code.display);
+    } else if (outputType.equalsIgnoreCase("CodeableConcept")) {
+      return FhirR4.mapCodeToCodeableConcept(code, null);
+    } else {
+      throw new IllegalArgumentException("Unexpected output type for randomCode: " + outputType
+          + ". Valid values are: code, Coding, CodeableConcept");
+    }
+
   }
 }

src/main/java/org/mitre/synthea/export/flexporter/Mapping.java

@@ -1,12 +1,17 @@
 package org.mitre.synthea.export.flexporter;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.InputStream;
 import java.util.List;
 import java.util.Map;
 
+import org.hl7.fhir.r4.model.ValueSet;
+import org.mitre.synthea.helpers.RandomCodeGenerator;
+import org.mitre.synthea.helpers.Utilities;
 import org.yaml.snakeyaml.Yaml;
 import org.yaml.snakeyaml.constructor.Constructor;
 
@@ -15,6 +20,7 @@ public class Mapping {
   public String applicability;
 
   public Map<String, Object> variables;
+  public List<Map<String, Object>> customValueSets;
 
   /**
    * Each action is a {@code Map>String,?>}. Nested fields within the YAML become ArrayLists and
@@ -34,4 +40,20 @@ public static Mapping parseMapping(File mappingFile) throws FileNotFoundExceptio
 
     return yaml.loadAs(selectorInputSteam, Mapping.class);
   }
+
+  /**
+   * Load the custom ValueSets that this mapping defines, so that the codes can be selected
+   * in RandomCodeGenerator.
+   */
+  public void loadValueSets() {
+    try {
+      if (this.customValueSets != null) {
+        List<ValueSet> valueSets =
+            Utilities.parseYamlToResources(this.customValueSets, ValueSet.class);
+        valueSets.forEach(vs -> RandomCodeGenerator.loadValueSet(null, vs));
+      }
+    } catch (JsonProcessingException e) {
+      throw new RuntimeException(e);
+    }
+  }
 }

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

@@ -18,6 +18,8 @@
 import okhttp3.ResponseBody;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.validator.routines.UrlValidator;
+import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent;
 import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
@@ -117,8 +119,25 @@ private static synchronized void expandValueSet(String valueSetUri) {
         ResponseBody body = response.body();
         if (body != null) {
           IParser parser = FhirR4.getContext().newJsonParser();
-          ValueSet valueSet = (ValueSet) parser.parseResource(body.charStream());
-          loadValueSet(valueSetUri, valueSet);
+          Resource resource = (Resource) parser.parseResource(body.charStream());
+          if (resource instanceof ValueSet) {
+            loadValueSet(valueSetUri, (ValueSet)resource);
+          } else if (resource instanceof OperationOutcome) {
+            OperationOutcome oo = (OperationOutcome)resource;
+            parser.setPrettyPrint(true);
+            System.err.println(parser.encodeResourceToString(oo));
+            String details = oo.getIssueFirstRep().getDetails().getText();
+
+            throw new RuntimeException(
+                "Received OperationOutcome in ValueSet expand response. Detail: "
+                + details + ". See log for full resource");
+          } else {
+            parser.setPrettyPrint(true);
+            System.err.println(parser.encodeResourceToString(resource));
+            throw new RuntimeException(
+                "Unexpected resourceType received in expand ValueSet response: "
+                + resource.getResourceType() + ". See log for full resource");
+          }
         } else {
           throw new RuntimeException("Value Set Expansion contained no body");
         }

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

@@ -1,5 +1,9 @@
 package org.mitre.synthea.helpers;
 
+import ca.uhn.fhir.parser.IParser;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.base.Charsets;
 import com.google.common.io.Resources;
 import com.google.gson.FieldNamingPolicy;
@@ -36,9 +40,11 @@
 import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.Range;
+import org.hl7.fhir.r4.model.Resource;
 import org.mitre.synthea.engine.Logic;
 import org.mitre.synthea.engine.Module;
 import org.mitre.synthea.engine.State;
+import org.mitre.synthea.export.FhirR4;
 import org.mitre.synthea.world.concepts.HealthRecord.Code;
 
 public class Utilities {
@@ -669,4 +675,36 @@ public static void enableReadingURIFromJar(URI uri) throws IOException {
       }
     }
   }
+
+  /**
+   * Helper method to parse FHIR resources from YAML.
+   * This is a workaround since the FHIR model classes don't work with our YAML parser.
+   *
+   * @param <T> Resource type contained in the YAML
+   * @param yaml List of pre-parsed YAML as Map&lt;String, Object&gt;
+   * @param resourceClass Specific resource class, must not be Resource
+   * @return List of parsed resources
+   * @throws JsonProcessingException (should never happen)
+   */
+  public static <T extends Resource> List<T> parseYamlToResources(
+      List<Map<String, Object>> yaml, Class<T> resourceClass)
+          throws JsonProcessingException {
+    if (yaml.isEmpty()) {
+      return Collections.emptyList();
+    }
+    ObjectMapper jsonMapper = new ObjectMapper();
+    IParser jsonParser = FhirR4.getContext().newJsonParser();
+    List<T> results = new ArrayList<>();
+    for (Map<String, Object> singleYaml : yaml) {
+      if (!singleYaml.containsKey("resourceType")) {
+        // allows the YAML to be cleaner by letting the resourceType be implied
+        singleYaml.put("resourceType", resourceClass.getSimpleName());
+      }
+      String resourceJson = jsonMapper.writeValueAsString(singleYaml);
+      @SuppressWarnings("unchecked")
+      T resource = (T) jsonParser.parseResource(resourceJson);
+      results.add(resource);
+    }
+    return results;
+  }
 }

src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java

@@ -54,12 +54,15 @@
 import org.hl7.fhir.r4.model.ServiceRequest;
 import org.hl7.fhir.r4.model.TimeType;
 import org.hl7.fhir.r4.model.Type;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.mitre.synthea.engine.Module;
 import org.mitre.synthea.engine.State;
 import org.mitre.synthea.export.FhirR4;
+import org.mitre.synthea.helpers.RandomCodeGenerator;
 import org.mitre.synthea.world.agents.Person;
 
 public class ActionsTest {
@@ -82,6 +85,7 @@ public static void setupClass() throws FileNotFoundException {
     File file = new File(classLoader.getResource("flexporter/test_mapping.yaml").getFile());
 
     testMapping = Mapping.parseMapping(file);
+    testMapping.loadValueSets();
   }
 
   @AfterClass
@@ -817,4 +821,34 @@ public void testGetAttribute() throws Exception {
     assertEquals("Robert Rainbow", name.getText());
   }
 
+  @Test
+  public void testRandomCode() {
+    Bundle b = new Bundle();
+    b.setType(BundleType.COLLECTION);
+
+    Map<String, Object> action = getActionByName("testRandomCode");
+    Actions.applyAction(b, action, null, null);
+
+    Encounter e = (Encounter) b.getEntryFirstRep().getResource();
+
+    Encounter.EncounterStatus status = e.getStatus();
+    assertNotNull(status);
+    assertTrue(status == Encounter.EncounterStatus.PLANNED
+        || status == Encounter.EncounterStatus.FINISHED
+        || status == Encounter.EncounterStatus.CANCELLED);
+
+    Coding encClass = e.getClass_();
+    assertNotNull(encClass);
+    assertEquals("http://terminology.hl7.org/CodeSystem/v3-ActCode", encClass.getSystem());
+    String code = encClass.getCode();
+    assertTrue(code.equals("AMB") || code.equals("EMER") || code.equals("ACUTE"));
+
+    CodeableConcept type = e.getTypeFirstRep();
+    assertNotNull(type);
+    Coding typeCoding = type.getCodingFirstRep();
+    assertNotNull(typeCoding);
+    assertEquals("http://terminology.hl7.org/CodeSystem/encounter-type", typeCoding.getSystem());
+    code = typeCoding.getCode();
+    assertTrue(code.equals("ADMS") || code.equals("OKI"));
+  }
 }

src/test/resources/flexporter/test_mapping.yaml

@@ -6,6 +6,49 @@ name: Random Testing
 # for now the assumption is 1 file = 1 synthea patient bundle.
 applicability: true
 
+# Not a huge fan of this format, but it's better than defining yet another custom syntax
+customValueSets:
+ - url: whats-for-dinner
+   compose:
+     include:
+       - system: http://snomed.info/sct
+         concept:
+           - code: 227360002
+             display: Pinto beans (substance)
+           - code: 227319009
+             display: Baked beans canned in tomato sauce with burgers (substance) 
+ - url: http://example.org/encounterStatus
+   compose:
+     include:
+       - system: http://hl7.org/fhir/encounter-status
+         concept:
+           - code: planned
+             display: Planned
+           - code: finished
+             display: Finished
+           - code: cancelled
+             display: Cancelled
+ - url: http://example.org/encounterClass
+   compose:
+     include:
+       - system: http://terminology.hl7.org/CodeSystem/v3-ActCode
+         concept:
+           - code: AMB
+             display: ambulatory
+           - code: EMER
+             display: emergency
+           - code: ACUTE
+             display: inpatient acute
+ - url: http://example.org/encounterType
+   compose:
+     include:
+       - system: http://terminology.hl7.org/CodeSystem/encounter-type
+         concept:
+           - code: ADMS
+             display: Annual diabetes mellitus screening
+           - code: OKI
+             display: Outpatient Kenacort injection
+
 actions:
  - name: Apply Profiles
    # v1: define specific profiles and an applicability statement on when to apply them
@@ -280,6 +323,17 @@ actions:
            location: ServiceRequest.authoredOn
            value: $getField([Procedure.performed]) # datetime choice type
 
+ - name: testRandomCode
+   create_resource: 
+     - resourceType: Encounter
+       fields:
+         - location: Encounter.status
+           value: $randomCode([http://example.org/encounterStatus,code])
+         - location: Encounter.class
+           value: $randomCode([http://example.org/encounterClass])
+         - location: Encounter.type
+           value: $randomCode([http://example.org/encounterType,CodeableConcept])
+
 
  - name: testExecuteScript
    execute_script: