Merge pull request #1525 from synthetichealth/flexporter_updates_2024_10

Flexporter updates - October 2024

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

@@ -424,6 +424,12 @@ private static Map<String, Object> createFhirPathMapping(List<Map<String, Object
       String location = (String)field.get("location");
       Object valueDef = field.get("value");
       String transform = (String)field.get("transform");
+      String ifDef = (String)field.get("if");
+
+      if (ifDef != null && !FhirPathUtils.appliesToResource(sourceResource, ifDef)) {
+        // The "if" condition returned falsy, so don't evaluate this value/set this field
+        continue;
+      }
 
       if (valueDef == null) {
         // do nothing, leave it null
@@ -457,12 +463,15 @@ private static Map<String, Object> createFhirPathMapping(List<Map<String, Object
       } else if (valueDef instanceof Map<?,?>) {
         Map<String,Object> valueMap = (Map<String, Object>) valueDef;
 
-        populateFhirPathMapping(fhirPathMapping, location, valueMap);
+        populateFhirPathMapping(fhirPathMapping, location, valueMap, sourceBundle, sourceResource,
+            person, fjContext);
 
       } else if (valueDef instanceof List<?>) {
         List<Object> valueList = (List<Object>) valueDef;
 
-        populateFhirPathMapping(fhirPathMapping, location, valueList);
+        populateFhirPathMapping(fhirPathMapping, location, valueList, sourceBundle, sourceResource,
+            person, fjContext);
+
       } else {
         // unexpected type here - is it even possible to get anything else?
         String type = valueDef == null ? "null" : valueDef.getClass().toGenericString();
@@ -474,21 +483,32 @@ private static Map<String, Object> createFhirPathMapping(List<Map<String, Object
   }
 
   private static void populateFhirPathMapping(Map<String, Object> fhirPathMapping, String basePath,
-      Map<String, Object> valueMap) {
+      Map<String, Object> valueMap, Bundle sourceBundle, Resource sourceResource, Person person,
+      FlexporterJavascriptContext fjContext) {
     for (Map.Entry<String,Object> entry : valueMap.entrySet()) {
       String key = entry.getKey();
       Object value = entry.getValue();
 
       String path = basePath + "." + key;
 
       if (value instanceof String) {
+        String valueString = (String)value;
+
+        if (valueString.startsWith("$")) {
+          value = getValue(sourceBundle, valueString, sourceResource, person, fjContext);
+        }
+      }
+
+      if (value instanceof String || value instanceof Base) {
         fhirPathMapping.put(path, value);
       } else if (value instanceof Number) {
         fhirPathMapping.put(path, value.toString());
       } else if (value instanceof Map<?,?>) {
-        populateFhirPathMapping(fhirPathMapping, path, (Map<String, Object>) value);
+        populateFhirPathMapping(fhirPathMapping, path, (Map<String, Object>) value, sourceBundle,
+            sourceResource, person, fjContext);
       } else if (value instanceof List<?>) {
-        populateFhirPathMapping(fhirPathMapping, path, (List<Object>) value);
+        populateFhirPathMapping(fhirPathMapping, path, (List<Object>) value, sourceBundle,
+            sourceResource, person, fjContext);
       } else if (value != null) {
         System.err
             .println("Unexpected class found in populateFhirPathMapping[map]: " + value.getClass());
@@ -497,20 +517,23 @@ private static void populateFhirPathMapping(Map<String, Object> fhirPathMapping,
   }
 
   private static void populateFhirPathMapping(Map<String, Object> fhirPathMapping, String basePath,
-      List<Object> valueList) {
+      List<Object> valueList, Bundle sourceBundle, Resource sourceResource, Person person,
+      FlexporterJavascriptContext fjContext) {
     for (int i = 0; i < valueList.size(); i++) {
       Object value = valueList.get(i);
 
       String path = basePath + "[" + i + "]";
 
-      if (value instanceof String) {
+      if (value instanceof String || value instanceof Base) {
         fhirPathMapping.put(path, value);
       } else if (value instanceof Number) {
         fhirPathMapping.put(path, value.toString());
       } else if (value instanceof Map<?,?>) {
-        populateFhirPathMapping(fhirPathMapping, path, (Map<String, Object>) value);
+        populateFhirPathMapping(fhirPathMapping, path, (Map<String, Object>) value, sourceBundle,
+            sourceResource, person, fjContext);
       } else if (value instanceof List<?>) {
-        populateFhirPathMapping(fhirPathMapping, path, (List<Object>) value);
+        populateFhirPathMapping(fhirPathMapping, path, (List<Object>) value, sourceBundle,
+            sourceResource, person, fjContext);
       } else if (value != null) {
         System.err
             .println("Unexpected class found in populateFhirPathMapping[list]:" + value.getClass());
@@ -649,13 +672,9 @@ private static void dateFilter(Bundle bundle, String minDateStr, String maxDateS
    * Cascade (current), Delete reference field but leave object, Do nothing
    *
    * @param bundle FHIR Bundle to filter
-   * @param list List of resource types to delete, other types not listed will be kept
+   * @param list List of resource types or FHIRPath to delete, other types not listed will be kept
    */
   public static void deleteResources(Bundle bundle, List<String> list) {
-    // TODO: make this FHIRPath instead of just straight resource types
-
-    Set<String> resourceTypesToDelete = new HashSet<>(list);
-
     Set<String> deletedResourceIDs = new HashSet<>();
 
     Iterator<BundleEntryComponent> itr = bundle.getEntry().iterator();
@@ -665,9 +684,14 @@ public static void deleteResources(Bundle bundle, List<String> list) {
 
       Resource resource = entry.getResource();
       String resourceType = resource.getResourceType().toString();
-      if (resourceTypesToDelete.contains(resourceType)) {
-        deletedResourceIDs.add(resource.getId());
-        itr.remove();
+
+      for (String applicability : list) {
+        if (applicability.equals(resourceType)
+            || FhirPathUtils.appliesToResource(resource, applicability)) {
+          deletedResourceIDs.add(resource.getId());
+          itr.remove();
+          break;
+        }
       }
     }
 

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

@@ -30,6 +30,7 @@
 import org.hl7.fhir.r4.model.Claim;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Condition;
 import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.DateType;
 import org.hl7.fhir.r4.model.Encounter;
@@ -46,6 +47,7 @@
 import org.hl7.fhir.r4.model.PractitionerRole;
 import org.hl7.fhir.r4.model.PractitionerRole.DaysOfWeek;
 import org.hl7.fhir.r4.model.Procedure;
+import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ResourceType;
@@ -486,21 +488,34 @@ public void testKeepResources() throws Exception {
 
   @Test
   public void testDeleteResources() throws Exception {
-    Bundle b = loadFixtureBundle("sample_complete_patient.json");
+    Bundle b = new Bundle();
+    b.addEntry().setResource(new Provenance());
+
+    Condition c1 = new Condition();
+    c1.setCode(new CodeableConcept(new Coding("http://snomed.info/sct", "15777000", "Prediabetes")));
+    b.addEntry().setResource(c1);
 
-    long countProvenance = b.getEntry().stream()
-        .filter(bec -> bec.getResource().getResourceType() == ResourceType.Provenance).count();
+    Condition c2 = new Condition();
+    c2.setCode(new CodeableConcept(new Coding("http://snomed.info/sct", "444814009", "Viral sinusitis")));
+    b.addEntry().setResource(c2);
+
+    Condition c3 = new Condition();
+    c3.setCode(new CodeableConcept(new Coding("http://snomed.info/sct", "49727002", "Cough (finding)")));
+    b.addEntry().setResource(c3);
 
-    // this is just making sure the fixture actually contains the thing we want to delete
-    assertEquals(1, countProvenance);
     Map<String, Object> action = getActionByName("testDeleteResources");
 
     Actions.applyAction(b, action, null, null);
 
-    countProvenance = b.getEntry().stream()
-        .filter(bec -> bec.getResource().getResourceType() == ResourceType.Provenance).count();
+    // provenance, c1, and c2 should be deleted by the rule. c3 should stay
+    assertEquals(1, b.getEntry().size());
 
-    assertEquals(0, countProvenance);
+    Resource r = b.getEntryFirstRep().getResource();
+    // this would work as of today but not guaranteed
+    // assertTrue(r == c3);
+    assertTrue(r instanceof Condition);
+    Condition conditionOut = (Condition)r;
+    assertEquals("49727002", conditionOut.getCode().getCodingFirstRep().getCode());
   }
 
   @Test
@@ -752,6 +767,32 @@ public void testCreateResources_createBasedOnState() throws Exception {
     assertEquals(120_000L, mr.getAuthoredOn().toInstant().toEpochMilli());
   }
 
+  @Test
+  public void testCreateResources_if() throws Exception {
+    Bundle b = new Bundle();
+    b.setType(BundleType.COLLECTION);
+
+    Procedure p1 = new Procedure();
+    p1.setPerformed(new Period().setStart(new Date(0)));
+    b.addEntry().setResource(p1);
+
+    Procedure p2 = new Procedure();
+    p2.setPerformed(new DateTimeType("2024-10-01T12:34:56"));
+    b.addEntry().setResource(p2);
+
+    Map<String, Object> action = getActionByName("testCreateResources_if");
+
+    Actions.applyAction(b, action, null, null);
+
+    assertEquals(4, b.getEntry().size());
+
+    ServiceRequest sr1 = (ServiceRequest)b.getEntry().get(2).getResource();
+    assertTrue(sr1.getAuthoredOn().getTime() == 0);
+
+    ServiceRequest sr2 = (ServiceRequest)b.getEntry().get(3).getResource();
+    DateTimeType sr2AuthoredOn = sr2.getAuthoredOnElement();
+    assertEquals("2024-10-01T12:34:56", sr2AuthoredOn.getValueAsString());
+  }
 
   @Test
   public void testGetAttribute() throws Exception {

src/test/resources/flexporter/test_mapping.yaml

@@ -267,6 +267,20 @@ actions:
          - location: Patient.name.family
            value: $getAttribute([last_name])
 
+ - name: testCreateResources_if
+   create_resource:
+     - resourceType: ServiceRequest
+       based_on:
+         resource: Procedure
+       fields:
+         - if: Procedure.performed.ofType(Period)
+           location: ServiceRequest.authoredOn
+           value: $getField([Procedure.performed.start]) # period choice type
+         - if: Procedure.performed.ofType(dateTime)
+           location: ServiceRequest.authoredOn
+           value: $getField([Procedure.performed]) # datetime choice type
+
+
  - name: testExecuteScript
    execute_script:
      - apply_to: bundle
@@ -300,6 +314,7 @@ actions:
  - name: testDeleteResources
    delete_resources:
      - Provenance
+     - Condition.code.coding.where($this.code in ('15777000' | '444814009'))
 
  - name: testDeleteResourcesCascade
    delete_resources: