flexporter enhancements

src/main/java/App.java

@@ -208,6 +208,8 @@ public static void main(String[] args) throws Exception {
             if (flexporterMappingFile.exists()) {
               Mapping mapping = Mapping.parseMapping(flexporterMappingFile);
               exportOptions.addFlexporterMapping(mapping);
+              // disable the graalVM warning when FlexporterJavascriptContext is instantiated
+              System.getProperties().setProperty("polyglot.engine.WarnInterpreterOnly", "false");
             } else {
               throw new FileNotFoundException(String.format(
                   "Specified flexporter mapping file (%s) does not exist", value));

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

@@ -3,7 +3,9 @@
 import ca.uhn.fhir.parser.IParser;
 
 import java.time.Duration;
+import java.time.Instant;
 import java.time.LocalDateTime;
+import java.time.ZoneOffset;
 import java.time.temporal.TemporalAmount;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -28,6 +30,7 @@
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Meta;
 import org.hl7.fhir.r4.model.Period;
+import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Resource;
 import org.mitre.synthea.engine.State;
 import org.mitre.synthea.export.FhirR4;
@@ -269,9 +272,13 @@ public static void createResource(Bundle bundle, List<Map<String, Object>> resou
             period.setEndElement(new DateTimeType(new Date(exited)));
           }
           dummyEncounter.setPeriod(period);
-          // TODO: figure out what encounter, if any, was active at this time
-          // and set the dummy.partOf as a reference to it
-          // dummyEncounter.setPartOf(new Reference("urn:uuid:" + enc.uuid.toString()));
+
+          Encounter encounterAtThatState = findEncounterAtState(instance, bundle);
+          if (encounterAtThatState != null) {
+            dummyEncounter.setPartOf(new Reference("urn:uuid:" + encounterAtThatState.getId()));
+            dummyEncounter.setParticipant(encounterAtThatState.getParticipant());
+            // TODO: copy any other fields over?
+          }
 
           basedOnResources.add(dummyEncounter);
         }
@@ -328,6 +335,7 @@ public static void createResource(Bundle bundle, List<Map<String, Object>> resou
         BundleEntryComponent newEntry = bundle.addEntry();
 
         newEntry.setResource(createdResource);
+        newEntry.setFullUrl("urn:uuid:" + createdResource.getId());
 
         if (bundle.getType().equals(BundleType.TRANSACTION)) {
           BundleEntryRequestComponent request = newEntry.getRequest();
@@ -351,6 +359,59 @@ public static void createResource(Bundle bundle, List<Map<String, Object>> resou
     }
   }
 
+  /**
+   * Helper method to find the Encounter that was active as of the given State.
+   * If the state type is Encounter, returns the Encounter it started.
+   * May return null if there was no Encounter active when the state was hit,
+   * or may return surprising results if the encounter was active in a different module.
+   */
+  private static Encounter findEncounterAtState(State state, Bundle bundle) {
+    Encounter encounterAtThatState = null;
+
+    if (state instanceof State.Encounter) {
+      String uuid = state.entry.uuid.toString();
+      for (BundleEntryComponent entry : bundle.getEntry())  {
+        Resource r = entry.getResource();
+        if (r instanceof Encounter && r.getId().equals(uuid)) {
+          encounterAtThatState = (Encounter) r;
+          break;
+        }
+      }
+
+    } else if (state.entered != null) {
+      LocalDateTime stateEntered =
+          Instant.ofEpochMilli(state.entered).atOffset(ZoneOffset.UTC).toLocalDateTime();
+
+      for (BundleEntryComponent entry : bundle.getEntry())  {
+        Resource r = entry.getResource();
+        if (r instanceof Encounter) {
+          Encounter currEnc = (Encounter)r;
+          Period period = currEnc.getPeriod();
+          Date startDt = period.getStart();
+          LocalDateTime encStart = startDt.toInstant().atOffset(ZoneOffset.UTC).toLocalDateTime();
+
+          Date endDt = period.getEnd();
+
+          if (endDt == null) {
+            // the Encounter is still open
+            if (stateEntered.isAfter(encStart) || stateEntered.isEqual(encStart)) {
+              encounterAtThatState = (Encounter) r;
+              break;
+            }
+          } else {
+            LocalDateTime encEnd = endDt.toInstant().atOffset(ZoneOffset.UTC).toLocalDateTime();
+            if ((stateEntered.isAfter(encStart) || stateEntered.isEqual(encStart))
+                && (stateEntered.isBefore(encEnd) || stateEntered.isEqual(encEnd))) {
+              encounterAtThatState = (Encounter) r;
+              break;
+            }
+          }
+        }
+      }
+    }
+    return encounterAtThatState;
+  }
+
 
   private static Map<String, Object> createFhirPathMapping(List<Map<String, Object>> fields,
       Bundle sourceBundle, Resource sourceResource, Person person,

src/main/resources/modules/heart/acs_discharge_meds.json

@@ -11,14 +11,13 @@
     },
     "Aspirin Check": {
       "type": "Simple",
-      "remarks": ["TODO: fix to Active Allergy after merging"],
       "complex_transition": [
         {
           "condition": {
             "condition_type": "Or",
             "conditions": [
               {
-                "condition_type": "Active Condition",
+                "condition_type": "Active Allergy",
                 "codes": [
                   {
                     "system": "RxNorm",
@@ -41,7 +40,7 @@
           },
           "distributions": [
             {
-              "transition": "BB Check",
+              "transition": "No_Aspirin",
               "distribution": 1
             }
           ]
@@ -53,7 +52,7 @@
               "distribution": 0.98
             },
             {
-              "transition": "BB Check",
+              "transition": "No_Aspirin",
               "distribution": 0.02
             }
           ]
@@ -315,6 +314,10 @@
     },
     "Terminal": {
       "type": "Terminal"
+    },
+    "No_Aspirin": {
+      "type": "Simple",
+      "direct_transition": "BB Check"
     }
   },
   "gmf_version": 2

src/test/resources/flexporter/qicore_minimal.yaml

@@ -44,7 +44,6 @@ actions:
      applicability: Claim
 
 
-
  - name: Set Missing Values
    set_values:
      - applicability: Immunization
@@ -64,6 +63,3 @@ actions:
        fields:
          - location: Procedure.extension.where(url='http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded').valueDateTime
            value: $getField([Procedure.performed])
-
-
-

src/test/resources/flexporter/qicore_withnotdone.yaml

@@ -0,0 +1,105 @@
+---
+# name is just a friendly name for this mapping
+name: QI Core With "Not Done" Instances
+
+# applicability determines whether this mapping applies to a given file.
+# for now the assumption is 1 file = 1 synthea patient bundle.
+applicability: true
+
+actions:
+ - name: Apply Profiles
+   # v1: define specific profiles and an applicability statement on when to apply them
+   # v1.1: allow specifying a field from the profile to key off of (ex. mCode TNMPrimaryTumorCategory.code)
+   # maybe v2 will automatically infer?
+   # some of the challenges to keep in mind:
+   #  - what if the resource doesn't conform to the profile yet? 
+   #    we should make sure we can take other actions before applying profiles, 
+   #    or manually specify where to apply profiles so that we can apply other fixes based on profile later.
+   profiles:
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-patient
+     applicability: Patient
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-encounter
+     applicability: Encounter
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-condition-encounter-diagnosis
+     applicability: Condition
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-observation
+     applicability: Observation
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-procedure
+     applicability: Procedure
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationrequest
+     applicability: MedicationRequest
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-immunization
+     applicability: Immunization
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-careplan
+     applicability: CarePlan
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-imagingstudy
+     applicability: ImagingStudy
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-device
+     applicability: Device
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-practitioner
+     applicability: Practitioner
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-allergyintolerance
+     applicability: AllergyIntolerance
+   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-claim
+     applicability: Claim
+
+
+ - name: Set Missing Values
+   set_values:
+     - applicability: Immunization
+       fields:
+         - location: Immunization.recorded
+           value: $getField([Immunization.occurrence])
+           # TODO: occurrence is a choice type,
+           # it would be nice to put "occurrenceDateTime" here
+           # since that's what's actually in the JSON
+           # but that doesn't seem to work with HAPI's FhirPath
+
+     - applicability: Procedure.performed.ofType(Period)
+       fields:
+         - location: Procedure.extension.where(url='http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded').valueDateTime
+           value: $getField([Procedure.performed.start])
+     - applicability: Procedure.performed.ofType(dateTime)
+       fields:
+         - location: Procedure.extension.where(url='http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded').valueDateTime
+           value: $getField([Procedure.performed])
+
+ - name: QICore NotDone Instances
+   create_resource:
+     - resourceType: MedicationRequest
+       based_on: 
+         module: Myocardial Infarction
+         # note the module has to be a top-level module,
+         # but the state can be a state name from a submodule
+         state: No_Aspirin
+       fields:
+         - location: MedicationRequest.meta.profile
+           value: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationnotrequested
+         - location: MedicationRequest.doNotPerform
+           value: "true"
+         - location: MedicationRequest.status
+           value: completed
+         - location: MedicationRequest.intent
+           value: order
+         - location: MedicationRequest.subject.reference
+           value: $findRef([Patient])
+         - location: MedicationRequest.authoredOn
+           value: $getField([State.entered]) 
+           # State.entered refers to the start of the based_on state
+         - location: MedicationRequest.requester.reference
+           value: $getField([Encounter.participant.individual.reference])
+         - location: MedicationRequest.reasonCode.coding
+           value:
+               system: http://snomedct.io
+               code: "183966005"
+               display: "Drug treatment not indicated (situation)"
+         - location: MedicationRequest.medicationCodeableConcept.extension
+           value:
+               url: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-notDoneValueSet
+               valueCanonical: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.196.11.1211
+               # VS is "Aspirin and Other Antiplatelets"
+
+
+
+
+