Merge pull request #82 from srdc/handle-primitive-extensions

Handle primitive extensions and implement memberOf function

onfhir-path/src/main/scala/io/onfhir/path/FhirPathEnvironment.scala

@@ -1,7 +1,7 @@
 package io.onfhir.path
 
 import io.onfhir.api.service.{IFhirIdentityService, IFhirTerminologyService}
-import io.onfhir.api.validation.IReferenceResolver
+import io.onfhir.api.validation.{IFhirTerminologyValidator, IReferenceResolver}
 
 import scala.collection.mutable
 import scala.util.matching.Regex
@@ -23,6 +23,7 @@ case class FhirPathEnvironment(
                                 val functionLibraries:Map[String, IFhirPathFunctionLibraryFactory] = Map.empty,
                                 val terminologyService:Option[IFhirTerminologyService] = None,
                                 val identityService:Option[IFhirIdentityService] = None,
+                                val terminologyValidator: Option[IFhirTerminologyValidator] = None,
                                 val _index:Int = 0,
                                 val _total:Option[FhirPathResult] = None,
                                 val isContentFhir:Boolean = true

onfhir-path/src/main/scala/io/onfhir/path/FhirPathEvaluator.scala

@@ -6,7 +6,7 @@ import java.io.ByteArrayInputStream
 import java.nio.charset.StandardCharsets
 import java.time.{LocalTime, ZoneId}
 import java.time.temporal.Temporal
-import io.onfhir.api.validation.IReferenceResolver
+import io.onfhir.api.validation.{IFhirTerminologyValidator, IReferenceResolver}
 import io.onfhir.path.grammar.{FhirPathExprLexer, FhirPathExprParser}
 import org.antlr.v4.runtime.{CharStreams, CommonTokenStream}
 import org.json4s.JsonAST.{JArray, JBool, JValue}
@@ -25,6 +25,7 @@ case class FhirPathEvaluator (
                                functionLibraries:Map[String, IFhirPathFunctionLibraryFactory] = Map.empty,
                                terminologyService:Option[IFhirTerminologyService] = None,
                                identityService:Option[IFhirIdentityService] = None,
+                               terminologyValidator: Option[IFhirTerminologyValidator] = None,
                                isContentFhir:Boolean = true
                              ) {
   private val logger: Logger = LoggerFactory.getLogger(this.getClass)
@@ -103,7 +104,8 @@ case class FhirPathEvaluator (
         functionLibraries,
         terminologyService,
         identityService,
-        isContentFhir = isContentFhir
+        isContentFhir = isContentFhir,
+        terminologyValidator = terminologyValidator
       )
     val evaluator = new FhirPathExpressionEvaluator(environment, resource)
     evaluator.visit(expr)

onfhir-path/src/main/scala/io/onfhir/path/FhirPathExpressionEvaluator.scala

@@ -100,12 +100,28 @@ class FhirPathExpressionEvaluator(context:FhirPathEnvironment, current:Seq[FhirP
     *     */
   override def visitMemberInvocation(ctx: FhirPathExprParser.MemberInvocationContext):Seq[FhirPathResult] = {
     //Element path
-    val pathName = FhirPathLiteralEvaluator.parseIdentifier(ctx.identifier().getText) + targetType.getOrElse("") //if there is target type add it e.g. Observation.value as Quantity --> search for valueQuantity
+    var pathName = FhirPathLiteralEvaluator.parseIdentifier(ctx.identifier().getText) + targetType.getOrElse("") //if there is target type add it e.g. Observation.value as Quantity --> search for valueQuantity
 
     //Execute the path and return
     current
       .filter(_.isInstanceOf[FhirPathComplex]) //Only get the complex objects
       .flatMap(r => {
+        // Check if the current field is a complex type
+        val jsonValue = r.asInstanceOf[FhirPathComplex].json \ pathName
+        val isComplex: Boolean = jsonValue match {
+          case _: JObject => true         // Complex type
+          case _: JArray  => true         // Consider arrays as complex types
+          case _          => false        // Any primitive type (e.g., JString, JNumber, JBool)
+        }
+        if (!isComplex) {
+          // If the current field is not complex (i.e., it's a primitive type), check if the next token is an "extension"
+          if (isNextTokenExtension(ctx)) {
+            // If the next token is "extension", modify the path name to access the corresponding "_<field>" element
+            // This is necessary because FHIR stores extensions for primitive fields under a separate path prefixed with "_"
+            pathName = s"_$pathName"
+          }
+        }
+
         FhirPathValueTransformer.transform(r.asInstanceOf[FhirPathComplex].json \ pathName, context.isContentFhir) match { //Execute JSON path for each element
           //The field can be a multi valued so we should check if there is a field starting with the path
           case Nil if targetType.isEmpty && context.isContentFhir =>
@@ -503,4 +519,37 @@ class FhirPathExpressionEvaluator(context:FhirPathEnvironment, current:Seq[FhirP
     }
   }
 
+  /**
+   * Checks if the next member in the FHIRPath expression chain after the given context
+   * is the "extension" function.
+   *
+   * This function traverses up the parse tree to locate the parent context that contains
+   * the entire expression and checks if the token following the current context is ".extension".
+   *
+   * @param ctx The current `MemberInvocationContext` representing the current member.
+   * @return `true` if the next token in the chain is "extension", `false` otherwise.
+   */
+  private def isNextTokenExtension(ctx: FhirPathExprParser.MemberInvocationContext): Boolean = {
+    // Cache the current context's text to avoid duplicate calls
+    val currentText = ctx.getText
+    // Start with the parent context to traverse the tree
+    var parent = ctx.getParent
+    while (parent != null) {
+      val parentText = parent.getText
+      // Check if the current context's text differs from the parent's text
+      if (!parentText.contentEquals(currentText)) {
+        // Extract the substring after the current context in the parent's text
+        val nextToken = parentText.substring(parentText.indexOf(currentText) + currentText.length)
+        // Check if the next token starts with ".extension"
+        if (nextToken.startsWith(".extension")) {
+          return true
+        }
+        // Return false if the next token is not ".extension"
+        return false
+      }
+      // Move to the next parent in the parse tree
+      parent = parent.getParent
+    }
+    false
+  }
 }

onfhir-path/src/main/scala/io/onfhir/path/FhirPathFunctionEvaluator.scala

@@ -110,6 +110,43 @@ class FhirPathFunctionEvaluator(context: FhirPathEnvironment, current: Seq[FhirP
     result
   }
 
+  /**
+   * Validates if the current element belongs to a specified FHIR value set.
+   *
+   * This function checks whether the `code` from the current context is a member of
+   * the value set specified by the provided `urlExp`.
+   *
+   * @param urlExp The URL expression representing the FHIR value set to validate against.
+   * @return A sequence containing a single `FhirPathBoolean` result:
+   *         - `true` if the code is a member of the specified value set.
+   *         - `false` otherwise.
+   * @throws FhirPathException if `urlExp` does not return a valid URL.
+   */
+  @FhirPathFunction(
+    documentation = "\uD83D\uDCDC Returns whether the current element is a member of a specific value set.\n\n\uD83D\uDCDD <span style=\"color:#ff0000;\">_@param_</span> **`urlExp`**  \nThe URL of the FHIR value set to validate against.\n\n\uD83D\uDD19 <span style=\"color:#ff0000;\">_@return_</span>  \nA boolean indicating if the code is valid within the specified value set:\n```json\ntrue | false\n```\n\n\uD83D\uDCA1 **E.g.**  \n`code.memberOf(\"http://example.org/fhir/ValueSet/my-value-set\")`",
+    insertText = "memberOf(<urlExp>)", detail = "Validate if the current element belongs to a FHIR value set.", label = "memberOf", kind = "Method",  returnType = Seq("boolean"), inputType = Seq("string")
+  )
+  def memberOf(urlExp: ExpressionContext): Seq[FhirPathResult] = {
+    // Evaluate the URL expression and ensure it resolves to a single valid URL string
+    val url = new FhirPathExpressionEvaluator(context, current).visit(urlExp)
+    if (url.length != 1 || !url.head.isInstanceOf[FhirPathString]) {
+      throw new FhirPathException(
+        s"Invalid function call 'memberOf': expression ${urlExp.getText} does not return a valid URL!"
+      )
+    }
+
+    // Retrieve the terminology validator and validate the code against the specified value set
+    val isValid = context.terminologyValidator.get
+      .validateCodeAgainstValueSet(
+        vsUrl = url.head.asInstanceOf[FhirPathString].s,  // Value set URL
+        code = current.head.asInstanceOf[FhirPathString].s,  // Current code to validate
+        version = None,
+        codeSystem = None
+      )
+
+    // Return the validation result as a FhirPathBoolean
+    Seq(FhirPathBoolean(isValid))
+  }
 
   /**
    * Type functions, for these basic casting or type checking are done before calling the function on the left expression

onfhir-path/src/test/resources/patient2.json

@@ -0,0 +1,105 @@
+{
+  "_gender": {
+    "extension": [
+      {
+        "url": "http://fhir.de/StructureDefinition/gender-amtlich-de",
+        "valueCoding": {
+          "code": "D",
+          "display": "divers",
+          "system": "http://fhir.de/CodeSystem/gender-amtlich-de"
+        }
+      }
+    ]
+  },
+  "address": [
+    {
+      "city": "Köln",
+      "country": "DE",
+      "line": [
+        "Teststraße 2"
+      ],
+      "postalCode": "50823",
+      "type": "both",
+      "extension": [
+        {
+          "url": "http://example.org/fhir/StructureDefinition/address-description",
+          "valueString": "This is the primary residence address."
+        },
+        {
+          "url": "http://example.org/fhir/StructureDefinition/address-verified",
+          "valueBoolean": true
+        }
+      ]
+    }
+  ],
+  "birthDate": "1998-09-19",
+  "gender": "other",
+  "id": "ExamplePatientPatientMinimal",
+  "identifier": [
+    {
+      "assigner": {
+        "display": "Charité – Universitätsmedizin Berlin",
+        "identifier": {
+          "system": "http://fhir.de/NamingSystem/arge-ik/iknr",
+          "value": "261101015",
+          "extension": [
+            {
+              "url": "http://example.org/fhir/StructureDefinition/identifier-verified",
+              "valueBoolean": true
+            }
+          ]
+        }
+      },
+      "system": "https://www.example.org/fhir/sid/patienten",
+      "type": {
+        "coding": [
+          {
+            "code": "MR",
+            "system": "http://terminology.hl7.org/CodeSystem/v2-0203"
+          }
+        ]
+      },
+      "use": "usual",
+      "value": "42285243"
+    },
+    {
+      "assigner": {
+        "identifier": {
+          "system": "http://fhir.de/sid/arge-ik/iknr",
+          "use": "official",
+          "value": "260326822"
+        }
+      },
+      "system": "http://fhir.de/sid/gkv/kvid-10",
+      "type": {
+        "coding": [
+          {
+            "code": "KVZ10",
+            "system": "http://fhir.de/CodeSystem/identifier-type-de-basis"
+          }
+        ]
+      },
+      "use": "official",
+      "value": "A999999999"
+    }
+  ],
+  "managingOrganization": {
+    "reference": "Organization/Charite-Universitaetsmedizin-Berlin"
+  },
+  "meta": {
+    "profile": [
+      "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient"
+    ]
+  },
+  "name": [
+    {
+      "family": "Van-der-Dussen",
+      "given": [
+        "Julia",
+        "Maja"
+      ],
+      "use": "official"
+    }
+  ],
+  "resourceType": "Patient"
+}

onfhir-path/src/test/scala/io/onfhir/path/FhirPathEvaluatorTest.scala

@@ -33,6 +33,8 @@ class FhirPathEvaluatorTest extends Specification {
 
   val encounter = Source.fromInputStream(getClass.getResourceAsStream("/encounter.json")).mkString.parseJson
 
+  val patient = Source.fromInputStream(getClass.getResourceAsStream("/patient2.json")).mkString.parseJson
+
   val emptyBundle = Source.fromInputStream(getClass.getResourceAsStream("/emptybundle.json")).mkString.parseJson
 
   val medicationAdministration = Source.fromInputStream(getClass.getResourceAsStream("/med-adm.json")).mkString.parseJson
@@ -661,6 +663,19 @@ class FhirPathEvaluatorTest extends Specification {
       results2 mustEqual Seq(10)
     }
 
+    "evaluate primitive extensions" in {
+      val evaluator = FhirPathEvaluator().withDefaultFunctionLibraries()
+
+      val result = evaluator.evaluateBoolean("gender.extension('http://fhir.de/StructureDefinition/gender-amtlich-de').exists()", patient).head
+      result mustEqual true
+      val result2 = evaluator.evaluateBoolean("birthDate.extension('http://fhir.de/StructureDefinition/birthdate').exists()", patient).head
+      result2 mustEqual false
+      val result3 = evaluator.evaluateBoolean("address[0].extension('http://example.org/fhir/StructureDefinition/address-verified').exists()", patient).head
+      result3 mustEqual true
+      val result4 = evaluator.evaluateBoolean("identifier[0].assigner.identifier.extension('http://example.org/fhir/StructureDefinition/identifier-verified').exists()", patient).head
+      result4 mustEqual true
+    }
+
     "evaluate new constraints in FHIR 4.0.1" in {
       var result = FhirPathEvaluator().satisfies("empty() or ($this = '*') or (toInteger() >= 0)", JString("*"))
       result mustEqual true

onfhir-validation/src/main/scala/io/onfhir/validation/ConstraintsRestriction.scala

@@ -13,7 +13,7 @@ import org.json4s.JsonAST.JValue
  */
 case class ConstraintsRestriction(fhirConstraints: Seq[FhirConstraint]) extends FhirRestriction {
   override def evaluate(value: JValue, fhirContentValidator: AbstractFhirContentValidator): Seq[ConstraintFailure] = {
-    val fhirPathEvaluator = FhirPathEvaluator.apply(fhirContentValidator.referenceResolver)
+    val fhirPathEvaluator = FhirPathEvaluator.apply(referenceResolver = fhirContentValidator.referenceResolver, terminologyValidator = Some(fhirContentValidator.terminologyValidator))
     fhirConstraints.flatMap(_.evaluate(value, fhirPathEvaluator))
   }
 }