Add new non-macro-based update and set methods (#24)

* experiment

* sugar seems to work

* improvements

* bump bunch

* fix type ascencion in update method ; ignore test

* tidy naming

* we don't need macros for the extension/id methods now

* rm old primitive element macros

bench/src/test/scala/com/babylonhealth/lit/bench/RegressionBenchmark.scala

@@ -86,7 +86,7 @@ object RegressionBenchmarks6 extends RegressionBenchmark {
 object RegressionBenchmarks7 extends RegressionBenchmark {
   performance of "lit_resource" in {
     measure method "update" in {
-      using(singleTest) in (_ => sampleResource.updateType(_ => BUNDLE_TYPE.SEARCHSET))
+      using(singleTest) in (_ => sampleResource.update(_.`type`)(_ => BUNDLE_TYPE.SEARCHSET))
     }
   }
 

core/src/main/scala/com/babylonhealth/lit/core/CompanionFor.scala

@@ -10,8 +10,7 @@ import scala.util.{ Failure, Success, Try }
 import io.circe.{ Decoder, DecodingFailure, HCursor }
 import izumi.reflect.macrortti.LTag
 import org.slf4j.{ Logger, LoggerFactory }
-
-import com.babylonhealth.lit.core.model.{ Element, Resource, resourceTypeLookup, urlLookup }
+import com.babylonhealth.lit.core.model.{ Element, Extension, Resource, resourceTypeLookup, urlLookup }
 
 trait OptionSugar {
   implicit class RichT[T](val t: T) {
@@ -22,14 +21,44 @@ trait OptionSugar {
   }
 }
 
+case class ObjectAndCompanion[O <: FHIRObject: LTag: ClassTag, C <: CompanionFor[_]](o: O, c: C) {
+  def update[T](fieldSelection: C => FHIRComponentFieldMeta[T])(fn: T => T): O =
+    o.updateFromField[T, O](fieldSelection(c))(fn)
+  def set[T](fieldSelection: C => FHIRComponentFieldMeta[T])(value: T): O =
+    o.setFromField[T, O](fieldSelection(c))(value)
+  def updateIfExists[T](fieldSelection: C => FHIRComponentFieldMeta[Option[T]])(fn: T => T): O =
+    o.updateFromField[Option[T], O](fieldSelection(c))(_ map fn)
+  def updateAll[T](fieldSelection: C => FHIRComponentFieldMeta[LitSeq[T]])(fn: T => T): O =
+    o.updateFromField[LitSeq[T], O](fieldSelection(c))(_ map fn)
+  def updateExtensions(field: C => FHIRComponentFieldMeta[_])(update: LitSeq[Extension] => LitSeq[Extension]): O =
+    o.extensions.update(field(c))(update)
+  def updateIds(field: C => FHIRComponentFieldMeta[_])(update: Option[String] => Option[String]): O =
+    o.ids.update(field(c))(update)
+  def setExtensions(field: C => FHIRComponentFieldMeta[_])(extension: LitSeq[Extension]): O =
+    o.extensions.set(field(c))(extension)
+  def setIds(field: C => FHIRComponentFieldMeta[_])(id: Option[String]): O    = o.ids.set(field(c))(id)
+  def getExtensions(field: C => FHIRComponentFieldMeta[_]): LitSeq[Extension] = o.extensions.get(field(c))
+  def getIds(field: C => FHIRComponentFieldMeta[_]): Option[String]           = o.ids.get(field(c))
+}
+
 abstract class CompanionFor[-T <: FHIRObject: LTag](implicit val thisClassTag: ClassTag[T @uncheckedVariance])
     extends JsonDecoderHelpers
     with OptionSugar {
   type ResourceType >: T <: FHIRObject
+  type ParentType >: T <: FHIRObject
   private val log: Logger = LoggerFactory.getLogger(getClass)
   val thisName: String
   val profileUrl: Option[String] = None
 
+  final private[core] def leastParentWithField(
+      f: FHIRComponentFieldMeta[_],
+      chain: List[CompanionFor[_]] = Nil
+  ): CompanionFor[_ <: ResourceType] = {
+    if (fieldsMeta.contains(f)) this.asInstanceOf[CompanionFor[_ <: ResourceType]]
+    else if (parentType eq this)
+      throw new RuntimeException(s"Unable to find field matching $f in ${chain.map(_.thisName).mkString(" <: ")}")
+    else parentType.leastParentWithField(f, chain :+ this)
+  }
   //  private val m = runtimeMirror(getClass.getClassLoader)
   //  lazy val classConstructor: Constructor[_] =
   //    thisClassTag.runtimeClass.getDeclaredConstructor(fieldsMeta.map(f => m.runtimeClass(f.tt.tag.typeSymbol.asClass)): _*)
@@ -81,6 +110,8 @@ abstract class CompanionFor[-T <: FHIRObject: LTag](implicit val thisClassTag: C
 
   def fields(t: T): Seq[FHIRComponentField[_]]
 
+  val parentType: CompanionFor[ParentType]
+
   val baseType: CompanionFor[T]
 
   protected lazy val (refMetas, otherMetas) = fieldsMeta.partition(_.isRef) match {

core/src/main/scala/com/babylonhealth/lit/core/FHIRObject.scala

@@ -1,12 +1,12 @@
 package com.babylonhealth.lit.core
 
 import scala.collection.immutable.TreeMap
-import scala.reflect.ClassTag
+import scala.reflect.{ ClassTag, classTag }
 import scala.reflect.runtime.universe.{ RuntimeClass, typeOf }
 
 import cats.Monad
+import com.babylonhealth.lit.core
 import izumi.reflect.macrortti.LTag
-
 import com.babylonhealth.lit.core.TagSummoners.lTypeOf
 import com.babylonhealth.lit.core.model.{ Element, Extension, intSubSuffixes, stringSubSuffixes, typeSuffixMap }
 
@@ -34,6 +34,33 @@ abstract class FHIRObject(
   def updatePrimitiveAttributes(fn: FieldToElementLookup => FieldToElementLookup): this.type =
     withPrimitiveAttributes(fn(primitiveAttributes))
 
+  // This form is not typesafe (one can call it on any resource with any meta field), but it should either
+  // always or never throw on a given resourceType at a particular call-site.
+  // Prefer update/set/updateIfExists/updateAll from the implicitly-summoned `ObjectAndCompanion`
+  def updateFromField[T, UpType >: this.type <: FHIRObject: ClassTag: LTag](
+      field: FHIRComponentFieldMeta[T]
+  )(fn: T => T): UpType = {
+    val parent: CompanionFor[_ <: companion.ResourceType] = companion.leastParentWithField(field)
+    val currentValue = parent
+      .fieldsFromParent(this.asInstanceOf[parent.ResourceType])
+      .get // fieldsFromParent shouldn't be able to fail if upcasting...
+      .find(_.meta == field)
+      .get // leastParentWithField call should fail if this isn't found; this indicates an error in the value provided in `field` param
+      .value
+      .asInstanceOf[T]
+    val newVal = fn(currentValue)
+    withFieldUnsafe[T, companion.ResourceType](field.name, newVal)(
+      parent.thisClassTag.asInstanceOf[ClassTag[companion.ResourceType]],
+      parent.thisTypeTag.asInstanceOf[LTag[companion.ResourceType]]).asInstanceOf[UpType]
+  }
+  def setFromField[T, UpType >: this.type <: FHIRObject: ClassTag: LTag](
+      field: FHIRComponentFieldMeta[T]
+  )(newVal: T): UpType = {
+    val parent: CompanionFor[_ <: companion.ResourceType] = companion.leastParentWithField(field)
+    withFieldUnsafe[T, companion.ResourceType](field.name, newVal)(
+      parent.thisClassTag.asInstanceOf[ClassTag[companion.ResourceType]],
+      parent.thisTypeTag.asInstanceOf[LTag[companion.ResourceType]]).asInstanceOf[UpType]
+  }
   val extensions = new {
     def update(field: FHIRComponentFieldMeta[_])(
         update: LitSeq[Extension] => LitSeq[Extension]): FHIRObject.this.type = {
@@ -70,7 +97,7 @@ abstract class FHIRObject(
 
   def fields: Seq[FHIRComponentField[_]] = companion.fields(this)
 
-  def companion: CompanionFor[this.type]
+  val companion: CompanionFor[this.type]
 
   def thisClassName: String // For HL7 classes, this should be the same as `thisTypeName`, but will differ for domain-specific subclasses
   def thisTypeName: String

core/src/main/scala/com/babylonhealth/lit/core/model/Address.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Address extends CompanionFor[Address] {
+  implicit def summonObjectAndCompanionAddress2002168585(o: Address): ObjectAndCompanion[Address, Address.type] =
+    ObjectAndCompanion(o, this)
   override type ResourceType = Address
+  override type ParentType   = Address
   override val baseType: CompanionFor[ResourceType] = Address
+  override val parentType: CompanionFor[ParentType] = Address
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Address")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/Age.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Age extends CompanionFor[Age] {
+  implicit def summonObjectAndCompanionAge_1092090844(o: Age): ObjectAndCompanion[Age, Age.type] =
+    ObjectAndCompanion(o, this)
   override type ResourceType = Age
+  override type ParentType   = Age
   override val baseType: CompanionFor[ResourceType] = Age
+  override val parentType: CompanionFor[ParentType] = Age
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Age")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/Annotation.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Annotation extends CompanionFor[Annotation] {
+  implicit def summonObjectAndCompanionAnnotation_1299111937(
+      o: Annotation): ObjectAndCompanion[Annotation, Annotation.type] = ObjectAndCompanion(o, this)
   override type ResourceType = Annotation
+  override type ParentType   = Annotation
   override val baseType: CompanionFor[ResourceType] = Annotation
+  override val parentType: CompanionFor[ParentType] = Annotation
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Annotation")
   type AuthorChoice = Choice[Union_1128709984]
   def apply(

core/src/main/scala/com/babylonhealth/lit/core/model/Attachment.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Attachment extends CompanionFor[Attachment] {
+  implicit def summonObjectAndCompanionAttachment1501498888(
+      o: Attachment): ObjectAndCompanion[Attachment, Attachment.type] = ObjectAndCompanion(o, this)
   override type ResourceType = Attachment
+  override type ParentType   = Attachment
   override val baseType: CompanionFor[ResourceType] = Attachment
+  override val parentType: CompanionFor[ParentType] = Attachment
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Attachment")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/BackboneElement.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object BackboneElement extends CompanionFor[BackboneElement] {
+  implicit def summonObjectAndCompanionBackboneElement_17315358(
+      o: BackboneElement): ObjectAndCompanion[BackboneElement, BackboneElement.type] = ObjectAndCompanion(o, this)
   override type ResourceType = BackboneElement
+  override type ParentType   = BackboneElement
   override val baseType: CompanionFor[ResourceType] = BackboneElement
+  override val parentType: CompanionFor[ParentType] = BackboneElement
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/BackboneElement")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/CodeableConcept.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object CodeableConcept extends CompanionFor[CodeableConcept] {
+  implicit def summonObjectAndCompanionCodeableConcept1231013185(
+      o: CodeableConcept): ObjectAndCompanion[CodeableConcept, CodeableConcept.type] = ObjectAndCompanion(o, this)
   override type ResourceType = CodeableConcept
+  override type ParentType   = CodeableConcept
   override val baseType: CompanionFor[ResourceType] = CodeableConcept
+  override val parentType: CompanionFor[ParentType] = CodeableConcept
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/CodeableConcept")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/Coding.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Coding extends CompanionFor[Coding] {
+  implicit def summonObjectAndCompanionCoding_462683970(o: Coding): ObjectAndCompanion[Coding, Coding.type] =
+    ObjectAndCompanion(o, this)
   override type ResourceType = Coding
+  override type ParentType   = Coding
   override val baseType: CompanionFor[ResourceType] = Coding
+  override val parentType: CompanionFor[ParentType] = Coding
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Coding")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/ContactDetail.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object ContactDetail extends CompanionFor[ContactDetail] {
+  implicit def summonObjectAndCompanionContactDetail_1828331805(
+      o: ContactDetail): ObjectAndCompanion[ContactDetail, ContactDetail.type] = ObjectAndCompanion(o, this)
   override type ResourceType = ContactDetail
+  override type ParentType   = ContactDetail
   override val baseType: CompanionFor[ResourceType] = ContactDetail
+  override val parentType: CompanionFor[ParentType] = ContactDetail
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/ContactDetail")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/ContactPoint.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object ContactPoint extends CompanionFor[ContactPoint] {
+  implicit def summonObjectAndCompanionContactPoint_1318533811(
+      o: ContactPoint): ObjectAndCompanion[ContactPoint, ContactPoint.type] = ObjectAndCompanion(o, this)
   override type ResourceType = ContactPoint
+  override type ParentType   = ContactPoint
   override val baseType: CompanionFor[ResourceType] = ContactPoint
+  override val parentType: CompanionFor[ParentType] = ContactPoint
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/ContactPoint")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/Contributor.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Contributor extends CompanionFor[Contributor] {
+  implicit def summonObjectAndCompanionContributor_1606151921(
+      o: Contributor): ObjectAndCompanion[Contributor, Contributor.type] = ObjectAndCompanion(o, this)
   override type ResourceType = Contributor
+  override type ParentType   = Contributor
   override val baseType: CompanionFor[ResourceType] = Contributor
+  override val parentType: CompanionFor[ParentType] = Contributor
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Contributor")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/Count.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Count extends CompanionFor[Count] {
+  implicit def summonObjectAndCompanionCount195454229(o: Count): ObjectAndCompanion[Count, Count.type] =
+    ObjectAndCompanion(o, this)
   override type ResourceType = Count
+  override type ParentType   = Count
   override val baseType: CompanionFor[ResourceType] = Count
+  override val parentType: CompanionFor[ParentType] = Count
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Count")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/DataRequirement.scala

@@ -21,12 +21,20 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object DataRequirement extends CompanionFor[DataRequirement] {
+  implicit def summonObjectAndCompanionDataRequirement1813028335(
+      o: DataRequirement): ObjectAndCompanion[DataRequirement, DataRequirement.type] = ObjectAndCompanion(o, this)
   override type ResourceType = DataRequirement
+  override type ParentType   = DataRequirement
   override val baseType: CompanionFor[ResourceType] = DataRequirement
+  override val parentType: CompanionFor[ParentType] = DataRequirement
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/DataRequirement")
   object DateFilter extends CompanionFor[DateFilter] {
+    implicit def summonObjectAndCompanionDateFilter167096238(
+        o: DateFilter): ObjectAndCompanion[DateFilter, DateFilter.type] = ObjectAndCompanion(o, this)
     override type ResourceType = DateFilter
-    type ValueChoice           = Choice[Union_1947777294]
+    override type ParentType   = DateFilter
+    override val parentType: CompanionFor[ResourceType] = DateFilter
+    type ValueChoice = Choice[Union_1947777294]
     def apply(
         id: Option[String] = None,
         path: Option[String] = None,
@@ -89,7 +97,11 @@ object DataRequirement extends CompanionFor[DataRequirement] {
       override val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo] = FHIRObject.emptyAtts)
       extends Element(id = id, extension = extension)
   object CodeFilter extends CompanionFor[CodeFilter] {
+    implicit def summonObjectAndCompanionCodeFilter540025153(
+        o: CodeFilter): ObjectAndCompanion[CodeFilter, CodeFilter.type] = ObjectAndCompanion(o, this)
     override type ResourceType = CodeFilter
+    override type ParentType   = CodeFilter
+    override val parentType: CompanionFor[ResourceType] = CodeFilter
     def apply(
         id: Option[String] = None,
         path: Option[String] = None,
@@ -159,7 +171,11 @@ object DataRequirement extends CompanionFor[DataRequirement] {
       override val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo] = FHIRObject.emptyAtts)
       extends Element(id = id, extension = extension)
   object Sort extends CompanionFor[Sort] {
+    implicit def summonObjectAndCompanionSort725645701(o: Sort): ObjectAndCompanion[Sort, Sort.type] =
+      ObjectAndCompanion(o, this)
     override type ResourceType = Sort
+    override type ParentType   = Sort
+    override val parentType: CompanionFor[ResourceType] = Sort
     def apply(
         id: Option[String] = None,
         path: String,

core/src/main/scala/com/babylonhealth/lit/core/model/Distance.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Distance extends CompanionFor[Distance] {
+  implicit def summonObjectAndCompanionDistance952422758(o: Distance): ObjectAndCompanion[Distance, Distance.type] =
+    ObjectAndCompanion(o, this)
   override type ResourceType = Distance
+  override type ParentType   = Distance
   override val baseType: CompanionFor[ResourceType] = Distance
+  override val parentType: CompanionFor[ParentType] = Distance
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Distance")
   def apply(
       id: Option[String] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/Dosage.scala

@@ -21,13 +21,21 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Dosage extends CompanionFor[Dosage] {
+  implicit def summonObjectAndCompanionDosage_588073389(o: Dosage): ObjectAndCompanion[Dosage, Dosage.type] =
+    ObjectAndCompanion(o, this)
   override type ResourceType = Dosage
+  override type ParentType   = Dosage
   override val baseType: CompanionFor[ResourceType] = Dosage
+  override val parentType: CompanionFor[ParentType] = Dosage
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Dosage")
   object DoseAndRate extends CompanionFor[DoseAndRate] {
+    implicit def summonObjectAndCompanionDoseAndRate_228242847(
+        o: DoseAndRate): ObjectAndCompanion[DoseAndRate, DoseAndRate.type] = ObjectAndCompanion(o, this)
     override type ResourceType = DoseAndRate
-    type DoseChoice            = Choice[Union01639511888]
-    type RateChoice            = Choice[Union_0575082635]
+    override type ParentType   = DoseAndRate
+    override val parentType: CompanionFor[ResourceType] = DoseAndRate
+    type DoseChoice = Choice[Union01639511888]
+    type RateChoice = Choice[Union_0575082635]
     def apply(
         id: Option[String] = None,
         `type`: Option[CodeableConcept] = None,

core/src/main/scala/com/babylonhealth/lit/core/model/Duration.scala

@@ -21,8 +21,12 @@ import com.babylonhealth.lit.{ core }
 import com.babylonhealth.lit.macros.POJOBoilerplate
 
 object Duration extends CompanionFor[Duration] {
+  implicit def summonObjectAndCompanionDuration1993583550(o: Duration): ObjectAndCompanion[Duration, Duration.type] =
+    ObjectAndCompanion(o, this)
   override type ResourceType = Duration
+  override type ParentType   = Duration
   override val baseType: CompanionFor[ResourceType] = Duration
+  override val parentType: CompanionFor[ParentType] = Duration
   override val profileUrl: Option[String]           = Some("http://hl7.org/fhir/StructureDefinition/Duration")
   def apply(
       id: Option[String] = None,