Add implementation for resolve() missing from the HapiFhir library (#…

…984)

* Update HapiFhirImplementation.java

Testing different engine implementation to support resolve

* Create HapiFhirCustomEvaluationContext.java

adding dummy file

* Added resolveReference implementation

* Fixed tests

* Adding docs

* Added tests and method that goes through all fhir files in examples/test

* Fixed rules names

* Added integration tests

* Added comment

* Updated comment

* Create HapiFhirCustomEvaluationContextTest.groovy

* Update HapiFhirCustomEvaluationContext.java

Handle reference resolving if the input is provided but not a reference

* Moved method based on feedback

---------

Co-authored-by: Basilio Bogado <[email protected]>

etor/src/main/resources/rule_definitions.json

@@ -1,6 +1,6 @@
 {
   "rules": [ {
-      "name": "requiredReceiverId",
+      "name": "messageHasRequiredReceiverId",
       "description": "Message has required receiver id",
       "violationMessage": "Message doesn't have required receiver id",
       "conditions": [ ],
@@ -9,7 +9,7 @@
       ]
     },
     {
-      "name": "requiredReceiverId",
+      "name": "ORMHasRequiredCardNumber",
       "description": "ORM has required Card Number",
       "violationMessage": "ORM doesn't have required Card Number",
       "conditions": [

etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/ruleengine/RuleEngineIntegrationTest.groovy

@@ -14,12 +14,11 @@ import java.nio.file.Files
 import java.nio.file.Path
 
 class RuleEngineIntegrationTest extends Specification {
+    def testExampleFilesPath = "../examples/Test"
     def fhir = HapiFhirImplementation.getInstance()
     def engine = RuleEngine.getInstance()
     def mockLogger = Mock(Logger)
 
-    String fhirBody
-
     def setup() {
         TestApplicationContext.reset()
         TestApplicationContext.init()
@@ -33,15 +32,91 @@ class RuleEngineIntegrationTest extends Specification {
         TestApplicationContext.injectRegisteredImplementations()
     }
 
-    def "validation logs a warning when a validation fails"() {
+    def "validation logs a warning when at least one validation fails"() {
         given:
-        fhirBody = Files.readString(Path.of("../examples/Test/Orders/001_OML_O21_short.fhir"))
-        def bundle = fhir.parseResource(fhirBody, Bundle)
+        def bundle = new Bundle()
 
         when:
         engine.validate(new HapiFhirResource(bundle))
 
         then:
-        1 * mockLogger.logWarning(_ as String)
+        (1.._) * mockLogger.logWarning(_ as String)
+    }
+
+    def "validation doesn't break for any of the sample test messages"() {
+        given:
+        def exampleFhirResources = getExampleFhirResources("Orders")
+
+        when:
+        exampleFhirResources.each { resource ->
+            engine.validate(resource)
+        }
+
+        then:
+        noExceptionThrown()
+    }
+
+    def "validation rule with resolve() works as expected"() {
+        given:
+        def fhirResource = getExampleFhirResource("Orders/001_OML_O21_short.fhir")
+        def validation = "Bundle.entry.resource.ofType(MessageHeader).focus.resolve().category.exists()"
+        def rule = createValidationRule([], [validation])
+
+        when:
+        def applies = rule.isValid(fhirResource)
+
+        then:
+        applies
+    }
+
+    def "validation rules pass for test files"() {
+        given:
+        def fhirResource = getExampleFhirResource(testFile)
+        def rule = createValidationRule([], [validation])
+
+        expect:
+        rule.isValid(fhirResource)
+
+        where:
+        testFile | validation
+        "Orders/001_OML_O21_short.fhir"                                    | "Bundle.entry.resource.ofType(MessageHeader).focus.resolve().category.exists()"
+        "Orders/003_AL_ORM_O01_NBS_Fully_Populated_1_hl7_translation.fhir" | "Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().identifier.value.exists()"
+        // Once we fix the mapping for ORM from story #900 and update the FHIR files in /examples/Test/Orders, we can uncomment the below line
+        // "Orders/003_AL_ORM_O01_NBS_Fully_Populated_1_hl7_translation.fhir" | "Bundle.entry.resource.ofType(Observation).where(code.coding.code = '57723-9').value.coding.code.exists()"
+    }
+
+    def "validation rules fail for test files"() {
+        given:
+        def fhirResource = getExampleFhirResource(testFile)
+        def rule = createValidationRule([], [validation])
+
+        expect:
+        !rule.isValid(fhirResource)
+
+        where:
+        testFile | validation
+        "Orders/001_OML_O21_short.fhir" | "Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().identifier.value.exists()"
+        "Orders/001_OML_O21_short.fhir" | "Bundle.entry.resource.ofType(Observation).where(code.coding.code = '57723-9').value.coding.code.exists()"
+    }
+
+    Rule createValidationRule(List<String> ruleConditions, List<String> ruleValidations) {
+        return new ValidationRule(
+                name: "Rule name",
+                description: "Rule description",
+                violationMessage: "Rule warning message",
+                conditions: ruleConditions,
+                validations: ruleValidations,
+                )
+    }
+
+    List<HapiFhirResource> getExampleFhirResources(String messageType = "") {
+        return Files.walk(Path.of(testExampleFilesPath, messageType))
+                .filter { it.toString().endsWith(".fhir") }
+                .map { new HapiFhirResource(fhir.parseResource(Files.readString(it), Bundle))  }
+                .collect()
+    }
+
+    HapiFhirResource getExampleFhirResource(String relativeFilePath) {
+        return new HapiFhirResource(fhir.parseResource(Files.readString(Path.of(testExampleFilesPath, relativeFilePath)), Bundle))
     }
 }

shared/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiFhirCustomEvaluationContext.java

@@ -0,0 +1,30 @@
+package gov.hhs.cdc.trustedintermediary.external.hapi;
+
+import ca.uhn.fhir.fhirpath.IFhirPathEvaluationContext;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Reference;
+
+public class HapiFhirCustomEvaluationContext implements IFhirPathEvaluationContext {
+
+    /**
+     * When a FHIR path includes the "resolve()" method, this function is called to parse that into
+     * a Resource.
+     *
+     * @param theReference Id-based reference to the resource we're attempting to resolve.
+     * @param theContext Internally converted resource version of theReference.
+     * @return Reference resource if available, else null.
+     */
+    @Override
+    public IBase resolveReference(@Nonnull IIdType theReference, @Nullable IBase theContext) {
+        if (theContext != null) {
+            if (theContext.getClass() == Reference.class) {
+                return ((Reference) theContext).getResource();
+            }
+            return theContext;
+        }
+        return IFhirPathEvaluationContext.super.resolveReference(theReference, null);
+    }
+}

shared/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiFhirImplementation.java

@@ -13,14 +13,26 @@ public class HapiFhirImplementation implements HapiFhir {
 
     private static final HapiFhirImplementation INSTANCE = new HapiFhirImplementation();
     private static final FhirContext CONTEXT = FhirContext.forR4();
-    private static final IFhirPath PATH_ENGINE = CONTEXT.newFhirPath();
+
+    private static final IFhirPath PATH_ENGINE = createEngine();
 
     private HapiFhirImplementation() {}
 
     public static HapiFhirImplementation getInstance() {
         return INSTANCE;
     }
 
+    /**
+     * Creates FHIRPath engine with a custom evaluation context.
+     *
+     * @return Configured engine.
+     */
+    private static IFhirPath createEngine() {
+        var engine = CONTEXT.newFhirPath();
+        engine.setEvaluationContext(new HapiFhirCustomEvaluationContext());
+        return engine;
+    }
+
     @Override
     public <T extends IBaseResource> T parseResource(
             final String fhirResource, final Class<T> clazz) throws FhirParseException {

shared/src/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiFhirCustomEvaluationContextTest.groovy

@@ -0,0 +1,43 @@
+package gov.hhs.cdc.trustedintermediary.external.hapi
+
+import ca.uhn.fhir.model.primitive.IdDt
+import org.hl7.fhir.r4.model.Organization
+import org.hl7.fhir.r4.model.Reference
+import spock.lang.Specification
+
+class HapiFhirCustomEvaluationContextTest extends Specification {
+    def context = new HapiFhirCustomEvaluationContext()
+
+    def "resolveReference returns null if the context is NOT provided"() {
+        when:
+        def result = context.resolveReference(new IdDt(), null)
+
+        then:
+        result == null
+    }
+
+    def "resolveReference attempts to get a resource if the context is provided and is a reference"() {
+        given:
+        def refId = new IdDt()
+        def org = new Organization()
+        def theContext = new Reference(org)
+
+        when:
+        def result = context.resolveReference(refId, theContext)
+
+        then:
+        result == org
+    }
+
+    def "resolveReference returns the given context if it's NOT a reference"() {
+        given:
+        def refId = new IdDt()
+        def org = new Organization()
+
+        when:
+        def result = context.resolveReference(refId, org)
+
+        then:
+        result == org
+    }
+}

shared/src/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiFhirImplementationTest.groovy

@@ -75,26 +75,26 @@ class HapiFhirImplementationTest extends Specification {
         result == false
     }
 
-    def "evaluateCondition throws FhirPathExecutionException on empty string"() {
+    def "evaluateCondition throws Exception on empty string"() {
         given:
         def path = ""
 
         when:
         fhir.evaluateCondition(bundle as IBaseResource, path)
 
         then:
-        thrown(FhirPathExecutionException)
+        thrown(Exception)
     }
 
-    def "evaluateCondition throws FhirPathExecutionException on fake method"() {
+    def "evaluateCondition throws Exception on fake method"() {
         given:
         def path = "Bundle.entry[0].resource.BadMethod('blah')"
 
         when:
         fhir.evaluateCondition(bundle as IBaseResource, path)
 
         then:
-        thrown(FhirPathExecutionException)
+        thrown(Exception)
     }
 
     def "parseResource can convert a valid string to Bundle"() {