add custom ValueSets to flexporter mapping file

Author: dehall

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/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/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

@@ -85,6 +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
@@ -825,21 +826,6 @@ public void testRandomCode() {
     Bundle b = new Bundle();
     b.setType(BundleType.COLLECTION);
 
-    ValueSet statusVs = constructValueSet(
-        "http://hl7.org/fhir/encounter-status",
-        "planned", "finished", "cancelled");
-    RandomCodeGenerator.loadValueSet("http://example.org/encounterStatus", statusVs);
-
-    ValueSet classVs = constructValueSet(
-        "http://terminology.hl7.org/CodeSystem/v3-ActCode",
-        "AMB", "EMER", "ACUTE");
-    RandomCodeGenerator.loadValueSet("http://example.org/encounterClass", classVs);
-
-    ValueSet typeVs = constructValueSet(
-        "http://terminology.hl7.org/CodeSystem/encounter-type",
-        "ADMS", "OKI");
-    RandomCodeGenerator.loadValueSet("http://example.org/encounterType", typeVs);
-
     Map<String, Object> action = getActionByName("testRandomCode");
     Actions.applyAction(b, action, null, null);
 
@@ -865,20 +851,4 @@ public void testRandomCode() {
     code = typeCoding.getCode();
     assertTrue(code.equals("ADMS") || code.equals("OKI"));
   }
-
-  private ValueSet constructValueSet(String system, String... codes) {
-    ValueSet vs = new ValueSet();
-
-    // populates the codes so that they can be read in RandomCodeGenerator.loadValueSet
-    ConceptSetComponent csc = new ConceptSetComponent();
-    csc.setSystem(system);
-    for (String code : codes) {
-      csc.addConcept().setCode(code).setDisplay(code);
-    }
-
-    vs.getCompose().getInclude().add(csc);
-
-    return vs;
-  }
-
 }

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