cleanup

synthetichealth · Jun 22, 2023 · d637bec · d637bec
1 parent 1fd3c6c
commit d637bec
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Showing 4 changed files with 28 additions and 8 deletions.
diff --git a/src/main/java/org/mitre/synthea/export/flexporter/Actions.java b/src/main/java/org/mitre/synthea/export/flexporter/Actions.java
@@ -217,6 +217,7 @@ public static void createResource(Bundle bundle, List<Map<String, Object>> resou
       }
 
       List<String> profiles = (List<String>) newResourceDef.get("profiles");
+      List<Map<String, Object>> fields = (List<Map<String, Object>>) newResourceDef.get("fields");
 
       List<Base> basedOnResources;
       List<Map<String, Object>> writeback;
@@ -269,13 +270,32 @@ public static void createResource(Bundle bundle, List<Map<String, Object>> resou
           basedOnResources.add(dummyEncounter);
         }
 
+        if (!basedOnResources.isEmpty()) {
+          // rewrite "State.entered" to "Encounter.period.start", etc
+          // so that the end user doesn't have to know we used an Encounter
+
+          for (Map<String, Object> field : fields) {
+            Object valueDef = field.get("value");
+            if (valueDef instanceof String && ((String) valueDef).startsWith("$")) {
+              String value = (String) valueDef;
+              if (value.contains("State.")) {
+                value = value
+                    .replace("State.entered", "Encounter.period.start")
+                    .replace("State.exited", "Encounter.period.end");
+
+                field.put("value", value);
+              }
+            }
+          }
+
+        }
+
         writeback = null;
       } else {
         basedOnResources = Collections.singletonList(null);
         writeback = null;
       }
 
-      List<Map<String, Object>> fields = (List<Map<String, Object>>) newResourceDef.get("fields");
 
       for (Base basedOnItem : basedOnResources) {
         // IMPORTANT: basedOnItem may be null
@@ -373,7 +393,8 @@ private static Map<String, Object> createFhirPathMapping(List<Map<String, Object
 
       } else {
         // unexpected type here - is it even possible to get anything else?
-        System.err.println("Unhandled type in createFhirPathMapping: " + valueDef.getClass());
+        String type = valueDef == null ? "null" : valueDef.getClass().toGenericString();
+        System.err.println("Unhandled type in createFhirPathMapping: " + type);
       }
     }
 
@@ -405,7 +426,7 @@ private static void populateFhirPathMapping(Map<String, Object> fhirPathMapping,
    * @param bundle FHIR Bundle to filter
    * @param list List of resource types to retain, all other types not listed will be removed
    */
-  public static void keepResources(Bundle bundle, List<String> list) {
+  private static void keepResources(Bundle bundle, List<String> list) {
     // TODO: make this FHIRPath instead of just straight resource types
 
     Set<String> resourceTypesToKeep = new HashSet<>(list);
@@ -430,7 +451,7 @@ public static void keepResources(Bundle bundle, List<String> list) {
     }
   }
 
-  public static void shiftDates(Bundle bundle, String amountString) {
+  private static void shiftDates(Bundle bundle, String amountString) {
     if (amountString == null) {
       return;
     }
@@ -463,7 +484,7 @@ public static void shiftDates(Bundle bundle, String amountString) {
     }
   }
 
-  public static void dateFilter(Bundle bundle, String minDateStr, String maxDateStr) {
+  private static void dateFilter(Bundle bundle, String minDateStr, String maxDateStr) {
     if (minDateStr == null && maxDateStr == null) {
       return;
     }

diff --git a/src/main/java/org/mitre/synthea/export/flexporter/FieldWrapper.java b/src/main/java/org/mitre/synthea/export/flexporter/FieldWrapper.java
@@ -87,7 +87,6 @@ public void set(Resource resource, IBase value) {
 
 
   public static class DateFieldWrapper extends FieldWrapper {
-
     public DateFieldWrapper(String fieldPath) {
       super(fieldPath);
     }

diff --git a/src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java b/src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java
@@ -563,7 +563,7 @@ public void testCreateResources_createBasedOnState() throws Exception {
          # - location: MedicationRequest.medicationCodeableConcept
          #   value: $getField([Procedure.code])
          - location: MedicationRequest.authoredOn
-           value: $getField([Encounter.period.start])
+           value: $getField([State.entered])
      */
 
     Resource newResource = entries.get(1).getResource();

diff --git a/src/test/resources/flexporter/test_mapping.yaml b/src/test/resources/flexporter/test_mapping.yaml
@@ -151,7 +151,7 @@ actions:
          # - location: MedicationRequest.medicationCodeableConcept
          #   value: $getField([Procedure.code])
          - location: MedicationRequest.authoredOn
-           value: $getField([Encounter.period.start])
+           value: $getField([State.entered])
 
  - name: testCreateResources_getAttribute
    create_resource: