16052: enable FHIR transforms to change bundle with custom FHIR funct…

…ions (#16053)

* 16052: enable FHIR transforms to change bundle with custom FHIR functions

* 16052: enable FHIR transforms to change bundle with custom FHIR functions

* fixup! Merge branch 'platform/kalish/16052-custom-fhir-function-for-transforms' of github.com:CDCgov/prime-reportstream into platform/kalish/16052-custom-fhir-function-for-transforms

* Fix Version generation and killFunc in build.gradle

* fixup! 16052: enable FHIR transforms to change bundle with custom FHIR functions

* fixup! 16052: enable FHIR transforms to change bundle with custom FHIR functions

* fixup! Fix Version generation and killFunc in build.gradle

prime-router/build.gradle.kts

@@ -271,16 +271,17 @@ sourceSets.create("testIntegration") {
     runtimeClasspath += sourceSets["main"].output
 }
 
-// Add generated version object
-sourceSets["main"].java.srcDir("$buildDir/generated-src/version")
-
 val compileTestIntegrationKotlin: KotlinCompile by tasks
 compileTestIntegrationKotlin.kotlinOptions.jvmTarget = appJvmTarget
 
 val testIntegrationImplementation: Configuration by configurations.getting {
     extendsFrom(configurations["testImplementation"])
 }
 
+tasks.withType<KotlinCompile> {
+    mustRunAfter("generateVersionObject")
+}
+
 configurations["testIntegrationRuntimeOnly"].extendsFrom(configurations["runtimeOnly"])
 
 tasks.register<Test>("testIntegration") {
@@ -353,7 +354,7 @@ tasks.withType<Test>().configureEach {
 }
 
 tasks.processResources {
-    dependsOn("generateVersionObject")
+    mustRunAfter("generateVersionObject")
     // Set the proper build values in the build.properties file
     filesMatching("build.properties") {
         val dateFormatter = DateTimeFormatter.ofPattern("yyyyMMdd")
@@ -427,7 +428,7 @@ tasks.register<JavaExec>("primeCLI") {
     // Use arguments passed by another task in the project.extra["cliArgs"] property.
     doFirst {
         if (project.extra.has("cliArgs") && project.extra["cliArgs"] is List<*>) {
-            args = (project.extra["cliArgs"] as List<*>).filterIsInstance(String::class.java)
+            args = (project.extra["cliArgs"] as List<*>).filterIsInstance<String>()
         } else if (args.isNullOrEmpty()) {
             args = listOf("-h")
             println("primeCLI Gradle task usage: gradle primeCLI --args='<args>'")
@@ -521,12 +522,13 @@ tasks.register("generateVersionFile") {
     }
 }
 
-tasks.register("generateVersionObject") {
-    val sourceDir = file("$buildDir/generated-src/version")
-    val sourceFile = file("$sourceDir/Version.kt")
-    sourceDir.mkdirs()
-    sourceFile.writeText(
-        """
+val generateVersionObject = tasks.register("generateVersionObject") {
+    doLast {
+        val sourceDir = file("$buildDir/generated-src/version/src/main/kotlin/gov/cdc/prime/router")
+        val sourceFile = file("$sourceDir/Version.kt")
+        sourceDir.mkdirs()
+        sourceFile.writeText(
+            """
         package gov.cdc.prime.router.version
         
         /**
@@ -537,7 +539,12 @@ tasks.register("generateVersionObject") {
           const val commitId = "$commitId"
         }
     """.trimIndent()
-    )
+        )
+    }
+}
+sourceSets.getByName("main").kotlin.srcDir("$buildDir/generated-src/version/src/main/kotlin")
+tasks.named("compileKotlin").configure {
+    dependsOn(generateVersionObject)
 }
 
 val azureResourcesTmpDir = File(buildDir, "$azureFunctionsDir-resources/$azureAppName")
@@ -645,7 +652,6 @@ task<Exec>("uploadSwaggerUI") {
 }
 
 tasks.register("killFunc") {
-    doLast {
         val processName = "func"
         if (org.gradle.internal.os.OperatingSystem.current().isWindows) {
             exec {
@@ -658,7 +664,6 @@ tasks.register("killFunc") {
                 commandLine = listOf("sh", "-c", "pkill -9 $processName || true")
             }
         }
-    }
 }
 
 tasks.register("run") {
@@ -772,6 +777,7 @@ tasks.named<nu.studer.gradle.jooq.JooqGenerate>("generateJooq") {
 tasks.register("compile") {
     group = rootProject.description ?: ""
     description = "Compile the code"
+    dependsOn("generateVersionObject")
     dependsOn("compileKotlin")
 }
 

prime-router/docs/universal-pipeline/translate.md

@@ -38,7 +38,8 @@ The two kinds of transforms work the same at a high level. The schema enumerates
 
 - contains a FHIR path to the resource that needs to be transformed
 - a condition specifying whether the resource should be transformed
-- how the resource should get transformed
+- how the resource should get transformed; a resource can be transformed either by setting it to a value or applying a 
+FHIR function
 
 The primary difference between the FHIR and HL7 schemas is that the HL7 converter has special handling for converting
 a FHIR resource into an HL7 segment or component.

prime-router/metadata/json_schema/fhir/fhir-to-fhir-transform.json

@@ -67,6 +67,9 @@
               "type": "string"
             }
           },
+          "function": {
+            "type": "string"
+          },
           "valueSet": {
             "anyOf": [
               {

prime-router/src/main/kotlin/config/validation/Validations.kt

@@ -113,6 +113,9 @@ object FhirToFhirTransformValidation : KonformValidation<FhirTransformSchema>()
                     addConstraint("Invalid FHIR path: {value}", test = ::validFhirPath)
                 }
             }
+            addConstraint("Value and function cannot both be set") { element ->
+                !(element.value != null && element.function != null)
+            }
         }
     }
 }

prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirTransformer.kt

@@ -114,19 +114,32 @@ class FhirTransformer(
                 eligibleFocusResources.forEach { singleFocusResource ->
                     elementContext.focusResource = singleFocusResource
                     val value = getValue(element, bundle, singleFocusResource, elementContext)
+                    val function = element.function
+                    if (value != null && function != null) {
+                        throw SchemaException("Element can only set function or value")
+                    }
+                    val bundleProperty = element.bundleProperty
+                        ?: throw SchemaException("bundleProperty must be set for element ${element.name}")
                     if (value != null) {
-                        val bundleProperty = element.bundleProperty
-                            ?: throw SchemaException("bundleProperty must be set for element ${element.name}")
                         updateBundle(
                             bundleProperty,
                             value,
                             elementContext,
                             bundle,
                             singleFocusResource
                         )
+                    } else if (function != null) {
+                        updateBundle(
+                            bundleProperty,
+                            function,
+                            elementContext,
+                            bundle,
+                            singleFocusResource
+                        )
                     } else {
                         logger.warn(
-                            "Element ${element.name} is updating a bundle property, but did not specify a value"
+                            "Element ${element.name} is updating a bundle property," +
+                                " but did not specify a value or function"
                         )
                     }
                     debugMsg += "condition: true, resourceType: ${singleFocusResource.fhirType()}, " +
@@ -298,7 +311,32 @@ class FhirTransformer(
             focusResource,
             null
         )
-        setBundleProperty(penultimateElements, lastElement, value)
+        setBundleProperty(penultimateElements, lastElement, value, context)
+    }
+
+    /**
+     * Updates a bundle by setting a value at a specified spot
+     *
+     * @param bundleProperty the property to update
+     * @param function the function to apply to the bundle property
+     * @param context the context to evaluate the bundle under
+     * @param focusResource the focus resource for any FHIR path evaluations
+     */
+    internal fun updateBundle(
+        bundleProperty: String,
+        function: String,
+        context: CustomContext,
+        bundle: Bundle,
+        focusResource: Base,
+    ) {
+        val (lastElement, penultimateElements) = createMissingElementsInBundleProperty(
+            bundleProperty,
+            context,
+            bundle,
+            focusResource,
+            null
+        )
+        applyFunction(penultimateElements, lastElement, function, context, bundle)
     }
 
     /**
@@ -350,7 +388,29 @@ class FhirTransformer(
             focusResource,
             appendToElements
         )
-        setBundleProperty(bundlePenultimateElements, lastBundlePropertyElement, value)
+        setBundleProperty(bundlePenultimateElements, lastBundlePropertyElement, value, context)
+    }
+
+    /**
+     * Updates a list of [Base] by applying the passed FHIR [function]
+     *
+     * @param elementsToUpdate the list of [Base] to update
+     * @param propertyName the property to set on each element
+     * @param function the function to apply
+     */
+    private fun applyFunction(
+        elementsToUpdate: List<Base>,
+        propertyName: String,
+        function: String,
+        context: CustomContext,
+        bundle: Bundle,
+    ) {
+        elementsToUpdate.forEach { penultimateElement ->
+            val propertyInfo = extractChildProperty(propertyName, context, penultimateElement)
+            FhirPathUtils.evaluate(
+                context, penultimateElement, bundle, "%resource.${propertyInfo.propertyString}.$function"
+            )
+        }
     }
 
     /**
@@ -364,8 +424,13 @@ class FhirTransformer(
         elementsToUpdate: List<Base>,
         propertyName: String,
         value: Base,
+        context: CustomContext,
     ) {
         elementsToUpdate.forEach { penultimateElement ->
+            val propertyInfo = extractChildProperty(propertyName, context, penultimateElement)
+            if (propertyInfo.index != null) {
+                throw SchemaException("Schema is attempting to set a value for a particular index which is not allowed")
+            }
             val property = penultimateElement.getNamedProperty(propertyName)
             val newValue = FhirBundleUtils.convertFhirType(value, value.fhirType(), property.typeCode, logger)
                 penultimateElement.setProperty(propertyName, newValue.copy())

prime-router/src/main/kotlin/fhirengine/translation/hl7/schema/fhirTransform/FhirTransformSchema.kt

@@ -74,6 +74,7 @@ class FhirTransformSchemaElement(
     debug: Boolean = false,
     var bundleProperty: String? = null,
     val appendToProperty: String? = null,
+    var function: String? = null,
 
     ) : ConfigSchemaElement<Bundle, Bundle, FhirTransformSchemaElement, FhirTransformSchema>(
     name = name,
@@ -105,6 +106,7 @@ class FhirTransformSchemaElement(
         bundleProperty: String? = null,
         action: FhirTransformSchemaElementAction,
         appendToProperty: String? = null,
+        function: String? = null,
     ) : this(
         name,
         condition,
@@ -118,7 +120,8 @@ class FhirTransformSchemaElement(
         valueSet,
         debug,
         bundleProperty,
-        appendToProperty
+        appendToProperty,
+        function
     ) {
       this.action = action
     }

prime-router/src/main/kotlin/fhirengine/translation/hl7/utils/CustomFHIRFunctions.kt

@@ -9,6 +9,7 @@ import org.hl7.fhir.r4.model.Base
 import org.hl7.fhir.r4.model.BaseDateTimeType
 import org.hl7.fhir.r4.model.BooleanType
 import org.hl7.fhir.r4.model.DateTimeType
+import org.hl7.fhir.r4.model.HumanName
 import org.hl7.fhir.r4.model.IntegerType
 import org.hl7.fhir.r4.model.StringType
 import java.time.DateTimeException
@@ -37,6 +38,7 @@ object CustomFHIRFunctions : FhirPathFunctions {
         HasPhoneNumberExtension,
         ChangeTimezone,
         ConvertDateToAge,
+        DeidentifyHumanName,
         ;
 
         companion object {
@@ -122,6 +124,14 @@ object CustomFHIRFunctions : FhirPathFunctions {
                 )
             }
 
+            CustomFHIRFunctionNames.DeidentifyHumanName -> {
+                FunctionDetails(
+                    "removes PII from a name",
+                    0,
+                    1
+                )
+            }
+
             else -> additionalFunctions?.resolveFunction(functionName)
         }
     }
@@ -185,6 +195,10 @@ object CustomFHIRFunctions : FhirPathFunctions {
                     convertDateToAge(focus, parameters)
                 }
 
+                CustomFHIRFunctionNames.DeidentifyHumanName -> {
+                    deidentifyHumanName(focus, parameters)
+                }
+
                 else -> additionalFunctions?.executeFunction(focus, functionName, parameters)
                     ?: throw IllegalStateException("Tried to execute invalid FHIR Path function $functionName")
             }
@@ -353,6 +367,22 @@ object CustomFHIRFunctions : FhirPathFunctions {
         return if (type != null) mutableListOf(StringType(type)) else mutableListOf()
     }
 
+    fun deidentifyHumanName(focus: MutableList<Base>, parameters: MutableList<MutableList<Base>>?): MutableList<Base> {
+        val deidentifiedValue = parameters?.firstOrNull()?.filterIsInstance<StringType>()?.firstOrNull()?.value ?: ""
+        focus.filterIsInstance<HumanName>().forEach { name ->
+            if (deidentifiedValue.isNotEmpty()) {
+                val updatedGiven = name.given.map { StringType(deidentifiedValue) }
+                name.setGiven(updatedGiven.toMutableList())
+            } else {
+                name.setGiven(emptyList())
+            }
+
+            name.setFamily(deidentifiedValue)
+        }
+
+        return focus
+    }
+
     /**
      * Get the ID type for the value in [focus].
      * @return a list with one value denoting the ID type, or an empty list