testing with primitives

synthetichealth · Mar 6, 2024 · 47fc1a9 · 47fc1a9
1 parent 32e75d9
commit 47fc1a9
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Showing 5 changed files with 66 additions and 15 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
@@ -10,9 +10,9 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -417,7 +417,8 @@ private static Map<String, Object> createFhirPathMapping(List<Map<String, Object
       Bundle sourceBundle, Resource sourceResource, Person person,
       FlexporterJavascriptContext fjContext) {
 
-    Map<String, Object> fhirPathMapping = new HashMap<>();
+    // linked hashmap to ensure lists are kept in order. could also use something like a treemap
+    Map<String, Object> fhirPathMapping = new LinkedHashMap<>();
 
     for (Map<String, Object> field : fields) {
       String location = (String)field.get("location");

diff --git a/src/main/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4.java b/src/main/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4.java
@@ -519,11 +519,9 @@ private void handleIndexFunctionNode(ExpressionNode fhirPath) {
 
         nextTier.nodes.add(containedNodes.get(index));
       }
-
-    } else if (nextTier.nodeDefinition instanceof RuntimePrimitiveDatatypeDefinition) {
-      // TODO: is this possible or necessary?
-      // review handlePrimitiveNode()
     }
+    // else if (nextTier.nodeDefinition instanceof RuntimePrimitiveDatatypeDefinition) {
+    // from testing this seems to not be necessary
 
     // push the created nextTier to the nodeStack
     this.nodeStack.push(nextTier);

diff --git a/src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java b/src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java
@@ -27,11 +27,13 @@
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
+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.DateTimeType;
 import org.hl7.fhir.r4.model.DateType;
 import org.hl7.fhir.r4.model.Encounter;
+import org.hl7.fhir.r4.model.Enumeration;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.Immunization;
@@ -40,6 +42,9 @@
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Period;
+import org.hl7.fhir.r4.model.PositiveIntType;
+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.Quantity;
 import org.hl7.fhir.r4.model.Resource;
@@ -352,6 +357,40 @@ void testSetValues_encounter_common(String actionName) {
     assertTrue(seen355);
   }
 
+  @Test
+  public void testSetValues_listOfPrimitives() {
+    Map<String, Object> action = getActionByName("testSetValues_listOfPrimitives");
+
+    PractitionerRole pr = new PractitionerRole();
+    Claim c = new Claim();
+    Bundle b = new Bundle();
+    b.addEntry().setResource(pr);
+    b.addEntry().setResource(c);
+
+    Actions.applyAction(b, action, null, null);
+
+    assertEquals(1, pr.getAvailableTime().size());
+
+    List<Enumeration<DaysOfWeek>> daysOfWeek = pr.getAvailableTimeFirstRep().getDaysOfWeek();
+    assertEquals(3, daysOfWeek.size());
+
+    assertEquals(DaysOfWeek.WED, daysOfWeek.get(0).getValue());
+    assertEquals(DaysOfWeek.THU, daysOfWeek.get(1).getValue());
+    assertEquals(DaysOfWeek.FRI, daysOfWeek.get(2).getValue());
+
+    assertEquals(1, c.getItem().size());
+    Claim.ItemComponent item = c.getItemFirstRep();
+
+    List<PositiveIntType> diagnosisSequence = item.getDiagnosisSequence();
+    assertEquals(6, diagnosisSequence.size());
+    assertEquals(1, diagnosisSequence.get(0).getValue().intValue());
+    assertEquals(1, diagnosisSequence.get(1).getValue().intValue());
+    assertEquals(2, diagnosisSequence.get(2).getValue().intValue());
+    assertEquals(3, diagnosisSequence.get(3).getValue().intValue());
+    assertEquals(5, diagnosisSequence.get(4).getValue().intValue());
+    assertEquals(8, diagnosisSequence.get(5).getValue().intValue());
+  }
+
   @Test
   public void testSetValues_deeplyNested() {
     Map<String, Object> action = getActionByName("testSetValues_deeplyNested");

diff --git a/src/test/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4Test.java b/src/test/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4Test.java
@@ -15,7 +15,6 @@
 import org.hl7.fhir.r4.model.HumanName.NameUse;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.StringType;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.mitre.synthea.export.FhirR4;
 
@@ -70,20 +69,13 @@ public void testArray1() {
     assertEquals("Bob", given.get(1).getValueAsString());
   }
 
-
-  @Ignore
   @Test
   public void testArray2() {
     Map<String, Object> fhirPathMapping = new HashMap<>();
 
     fhirPathMapping.put("Patient.name[0].given", "Billy");
     fhirPathMapping.put("Patient.name[1].given", "Bob");
 
-    // TODO: for some reason Patient.name.given[0] and given[1] work as expected (2 name strings in
-    // the 'given' array)
-    // but Patient.name[0].given and .name[1].given do not (same result, expected was 2 HumanName
-    // objects in the name array)
-
     Patient patient = createPatient(fhirPathMapping);
 
     List<HumanName> name = patient.getName();

diff --git a/src/test/resources/flexporter/test_mapping.yaml b/src/test/resources/flexporter/test_mapping.yaml
@@ -127,7 +127,28 @@ actions:
              - system: http://terminology.hl7.org/CodeSystem/service-type
                code: "355"
 
-
+
+ - name: testSetValues_listOfPrimitives
+   set_values:
+     - applicability: PractitionerRole
+       fields:
+         - location: PractitionerRole.availableTime.daysOfWeek
+           value:
+             - "wed"
+             - "thu"
+             - "fri"
+     - applicability: Claim
+       fields:
+         - location:  Claim.item.diagnosisSequence
+           value:
+             - 1
+             - 1
+             - 2
+             - 3
+             - 5
+             - 8
+
+
  - name: testSetValues_deeplyNested
    set_values:
      - applicability: Observation