feat: Added GeneAlterationReference to allow modelling which gene is …

…the relevant one in the referenced variant object; fix: Corrected linter errors in Tests

build.sbt

@@ -45,6 +45,7 @@ lazy val compilerOptions = Seq(
   "-language:experimental.macros",
   "-language:higherKinds",
   "-language:implicitConversions",
+  "-language:postfixOps",
   "-Ymacro-annotations",
 
   // Warnings as errors!
@@ -75,11 +76,11 @@ lazy val compilerOptions = Seq(
   "-Wunused:locals",
   "-Wunused:patvars",
   "-Wunused:privates",
-  "-Wunused:implicits",
   "-Wvalue-discard",
 
   // Deactivated to avoid many false positives from 'evidence' parameters in context bounds
 //  "-Wunused:params",
+//  "-Wunused:implicits",
 )
 
 

src/main/scala/de/dnpm/dip/coding/Coding.scala

@@ -453,4 +453,10 @@ object Coding
         coding => css.values.contains(coding.system)
       )
 
+
+  implicit def codingToCoproductCoding[S, C <: Coproduct](coding: Coding[S])(
+    implicit sel: shapeless.ops.coproduct.Selector[C,S]
+  ): Coding[C] =
+    coding.asInstanceOf[Coding[C]]
+
 }

src/main/scala/de/dnpm/dip/model/BaseCompleters.scala

@@ -20,6 +20,8 @@ import de.dnpm.dip.coding.{
   UnregisteredMedication
 }
 import de.dnpm.dip.coding.hgvs.HGVS
+import de.dnpm.dip.coding.hgnc.HGNC
+
 
 
 trait BaseCompleters
@@ -159,4 +161,15 @@ trait BaseCompleters
           )                              // if not all CodeSystemProviders are in scope, so csps is sure to contain all systems
     )
 
+
+  implicit def geneAlterationReferenceCompleter[T](
+    implicit hgnc: CodeSystemProvider[HGNC,Id,Applicative[Id]]
+  ): Completer[GeneAlterationReference[T]] =
+    Completer.of(
+      ref => ref.copy(
+        gene = ref.gene.complete
+      )
+    )
+
+
 }

src/main/scala/de/dnpm/dip/model/GeneAlterationReference.scala

@@ -0,0 +1,54 @@
+package de.dnpm.dip.model
+
+
+import de.dnpm.dip.coding.Coding
+import de.dnpm.dip.coding.hgnc.HGNC
+import play.api.libs.json.{
+  Json,
+  Reads,
+  OWrites
+}
+
+/*
+ * Conceptually equivalent to FHIR "CodeableReference", to specify the
+ * (clinically) relevant gene in a variant supporting a recommendation
+ *
+ * Gene is kept optional because in SNVs it is already implicitly defined,
+ * and thus needn't be specified again, but for CNVs or Fusions, which can
+ * affect multiple or 2 genes, respectively,
+ * it should be specified to remove ambiguity
+ *
+ */
+
+final case class GeneAlterationReference[+Variant]
+(
+  gene: Option[Coding[HGNC]],
+  variant: Reference[Variant],
+  display: Option[String]
+)
+
+object GeneAlterationReference
+{
+
+  def apply[T <: { def id: Id[T] }](
+    gene: Option[Coding[HGNC]],
+    variant: T
+  ): GeneAlterationReference[T] =
+    GeneAlterationReference(
+      gene,
+      Reference.to(variant),
+      None
+    )
+
+
+  implicit def reads[T]: Reads[GeneAlterationReference[T]] =
+    Json.reads[GeneAlterationReference[T]]
+      // For (temporary) backward compatibility, fall back to parsing as a normal reference
+      .orElse(
+        Reads.of[Reference[T]].map(GeneAlterationReference(None,_,None))
+      )
+
+  implicit def writes[T: Reference.TypeName]: OWrites[GeneAlterationReference[T]] =
+    Json.writes[GeneAlterationReference[T]]
+
+}

src/main/scala/de/dnpm/dip/model/Recommendation.scala

@@ -17,8 +17,8 @@ trait Recommendation
   val id: Id[Recommendation]
   val patient: Reference[Patient]
   val issuedOn: LocalDate
-  val supportingVariants: Option[List[Reference[_]]]
-//  val supportingAlterations: Option[List[GeneAlterationReference[_]]]
+//  val supportingVariants: Option[List[Reference[_]]]
+  val supportingVariants: Option[List[GeneAlterationReference[_]]]
 }
 
 

src/main/scala/de/dnpm/dip/model/json/BaseSchemas.scala

@@ -18,6 +18,7 @@ import de.dnpm.dip.coding.{
   Code,
   Coding,
 }
+import de.dnpm.dip.coding.hgnc.HGNC
 import de.dnpm.dip.model.{
   Age,
   ExternalId,
@@ -27,6 +28,7 @@ import de.dnpm.dip.model.{
   PubMed,
   OpenEndPeriod,
   Reference,
+  GeneAlterationReference,
   UnitOfTime
 }
 import shapeless.{
@@ -86,6 +88,14 @@ trait BaseSchemas
     .toDefinition("Reference")
 
 
+  implicit def geneAlterationReferenceSchema[T]: Schema[GeneAlterationReference[T]] =
+    Schema.`object`[GeneAlterationReference[T]](
+      Field("gene",Json.schema[Coding[HGNC]],false),
+      Field("variant",Json.schema[Reference[T]],true)
+    )
+    .toDefinition("GeneAlterationReference")
+
+
   implicit val publicationReferenceSchema: Schema[Reference[Publication]] =
     Schema.`object`[Reference[Publication]](
       Field(

src/test/scala/de/dnpm/dip/coding/CodeTests.scala

@@ -3,8 +3,6 @@ package de.dnpm.dip.coding
 
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.must.Matchers._
-import org.scalatest.Inspectors._
-import de.dnpm.dip.coding.icd.ICD10GM
 
 
 sealed trait Dummy

src/test/scala/de/dnpm/dip/model/CompleterTests.scala

@@ -6,8 +6,6 @@ import org.scalatest.matchers.must.Matchers._
 import de.dnpm.dip.util.Completer
 import de.dnpm.dip.coding.Coding
 import java.time.LocalDate
-import java.util.UUID.randomUUID
-
 
 
 class CompleterTests extends AnyFlatSpec

src/test/scala/de/dnpm/dip/model/JsonSerializationTests.scala

@@ -4,11 +4,7 @@ package de.dnpm.dip.model
 import scala.util.chaining._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.must.Matchers._
-import play.api.libs.json.{
-  Json,
-  JsError,
-  JsSuccess
-}
+import play.api.libs.json.Json
 import de.dnpm.dip.coding.Coding
 
 

src/test/scala/de/dnpm/dip/model/ValueSetTests.scala

@@ -5,8 +5,6 @@ import java.net.URI
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.must.Matchers._
 import de.dnpm.dip.coding.{
-  Coding,
-  CodeSystem,
   CodeSystems,
   ValueSet
 }
@@ -39,14 +37,6 @@ class ValueSetTests extends AnyFlatSpec
       CodeSystems[Systems].values.values.flatMap(_.concepts).size
     )
 
-/*
-    val valueSet =
-      composer.expand[(VitalStatus.Value,Gender.Value)]
-      
-    valueSet.codings.size must equal (
-      CodeSystems[(VitalStatus.Value,Gender.Value)].values.flatMap(_.concepts).size
-    )
-*/
   }