ExposuresProvider · balhoff · Nov 15, 2022 · Nov 12, 2022
diff --git a/src/it/scala/org/renci/cam/it/ExampleQueriesEndpointTest.scala b/src/it/scala/org/renci/cam/it/ExampleQueriesEndpointTest.scala
@@ -75,13 +75,7 @@ object ExampleQueriesEndpointTest extends DefaultRunnableSpec {
               exampleJson <- ZIO.fromEither(io.circe.parser.parse(exampleText))
               example <- ZIO.fromEither(
                 {
-                  implicit val decoderIRI: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-                  implicit val keyDecoderIRI: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes)
-                  implicit val decoderBiolinkClass: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-                  implicit val decoderBiolinkPredicate: Decoder[BiolinkPredicate] =
-                    Implicits.biolinkPredicateDecoder(biolinkData.predicates)
-                  implicit lazy val decoderTRAPIAttribute: Decoder[TRAPIAttribute] = deriveDecoder[TRAPIAttribute]
-
+                  import biolinkData.implicits._
                   exampleJson.as[ExampleJsonFile]
                 }
               )
@@ -93,12 +87,7 @@ object ExampleQueriesEndpointTest extends DefaultRunnableSpec {
 
               // Prepare request for the CAM-KP-API endpoint.
               messageText = {
-                implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(biolinkData.prefixes)
-                implicit val iriKeyEncoder: KeyEncoder[IRI] = Implicits.iriKeyEncoder(biolinkData.prefixes)
-                implicit val biolinkClassEncoder: Encoder[BiolinkClass] = Implicits.biolinkClassEncoder
-                implicit val biolinkPredicateEncoder: Encoder[BiolinkPredicate] =
-                  Implicits.biolinkPredicateEncoder(biolinkData.prefixes)
-
+                import biolinkData.implicits._
                 TRAPIQuery(message = example.message, log_level = None).asJson.deepDropNullValues.noSpaces
               }
               // _ = println(s"messageText = ${messageText}")
@@ -115,13 +104,7 @@ object ExampleQueriesEndpointTest extends DefaultRunnableSpec {
               // Translate the response into a TRAPIResponse for testing.
               trapiResponse <- ZIO.fromEither(
                 {
-                  implicit val decoderIRI: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-                  implicit val keyDecoderIRI: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes)
-                  implicit val decoderBiolinkClass: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-                  implicit val decoderBiolinkPredicate: Decoder[BiolinkPredicate] =
-                    Implicits.biolinkPredicateDecoder(biolinkData.predicates)
-                  implicit lazy val decoderTRAPIAttribute: Decoder[TRAPIAttribute] = deriveDecoder[TRAPIAttribute]
-
+                  import biolinkData.implicits._
                   response.as[TRAPIResponse]
                 }
               )

diff --git a/src/it/scala/org/renci/cam/it/ImplicitsTest.scala b/src/it/scala/org/renci/cam/it/ImplicitsTest.scala
@@ -28,7 +28,7 @@ object ImplicitsTest extends DefaultRunnableSpec with LazyLogging {
       for {
         bl <- biolinkData
       } yield {
-        implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(bl.prefixes)
+        import bl.implicits._
         val json = iri.asJson.deepDropNullValues.noSpaces.replace("\"", "")
         assert(json)(equalTo("WB:WBGene00013878"))
       }
@@ -42,8 +42,7 @@ object ImplicitsTest extends DefaultRunnableSpec with LazyLogging {
       } yield {
         val dataAsList = """["biolink:participates_in","biolink:related_to"]"""
         val data = """"biolink:related_to""""
-        implicit val biolinkPredicateDecoder: Decoder[List[BiolinkPredicate]] =
-          Implicits.predicateOrPredicateListDecoder(biolinkData.predicates)
+        import biolinkData.implicits._
         val ret = decode[List[BiolinkPredicate]](data)
         val retWithListData = decode[List[BiolinkPredicate]](dataAsList)
         assert(ret.toOption.get)(contains(BiolinkPredicate("related_to"))) && assert(retWithListData.toOption.get)(

diff --git a/src/it/scala/org/renci/cam/it/MetaKnowledgeGraphServiceTest.scala b/src/it/scala/org/renci/cam/it/MetaKnowledgeGraphServiceTest.scala
@@ -30,20 +30,7 @@ object MetaKnowledgeGraphServiceTest extends DefaultRunnableSpec with LazyLoggin
           .withHeaders(Accept(MediaType.application.json))
         response <- httpClient.expect[String](request)
       } yield {
-        implicit val iriKeyEncoder: KeyEncoder[BiolinkClass] = Implicits.biolinkClassKeyEncoder
-        implicit val iriKeyDecoder: KeyDecoder[BiolinkClass] = Implicits.biolinkClassKeyDecoder(biolinkData.classes)
-
-//        implicit val iriDecoder: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-//        implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(biolinkData.prefixes)
-
-//        logger.info("biolinkData.classes: {}", biolinkData.classes)
-        implicit val blClassDecoder: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-//        implicit val blClassEncoder: Encoder[BiolinkClass] = Implicits.biolinkClassEncoder
-
-//        logger.info("biolinkData.predicates: {}", biolinkData.predicates)
-        implicit val biolinkPredicateDecoder: Decoder[BiolinkPredicate] = Implicits.biolinkPredicateDecoder(biolinkData.predicates)
-//        implicit val biolinkPredicateEncoder: Encoder[BiolinkPredicate] = Implicits.biolinkPredicateEncoder(biolinkData.prefixes)
-
+        import biolinkData.implicits._
         val parsed = parser.parse(response).toOption.get
 //        logger.info("parsed: {}", parsed)
         val mkg = parsed.as[MetaKnowledgeGraph]

diff --git a/src/it/scala/org/renci/cam/it/ProdQueryServiceTest.scala b/src/it/scala/org/renci/cam/it/ProdQueryServiceTest.scala
@@ -29,10 +29,7 @@ object ProdQueryServiceTest extends DefaultRunnableSpec {
       httpClient <- HttpClient.client
       biolinkData <- Biolink.biolinkData
       encoded = {
-        implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(biolinkData.prefixes)
-        implicit val iriKeyEncoder: KeyEncoder[IRI] = Implicits.iriKeyEncoder(biolinkData.prefixes)
-        implicit val biolinkClassEncoder: Encoder[BiolinkClass] = Implicits.biolinkClassEncoder
-        implicit val biolinkPredicateEncoder: Encoder[BiolinkPredicate] = Implicits.biolinkPredicateEncoder(biolinkData.prefixes)
+        import biolinkData.implicits._
         trapiQuery.asJson.deepDropNullValues.noSpaces
       }
       _ = println("encoded: " + encoded)
@@ -57,10 +54,7 @@ object ProdQueryServiceTest extends DefaultRunnableSpec {
           .orElseFail(new Exception("failed to traverse down to context"))
 
       nodesMapResult = {
-        implicit val decoderIRI: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-        implicit val keyDecoderIRI: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes)
-        implicit val decoderTRAPINode: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-        implicit lazy val decoderTRAPIAttribute: Decoder[TRAPIAttribute] = deriveDecoder[TRAPIAttribute]
+        import biolinkData.implicits._
         knowledgeGraphNodesJson.as[Map[IRI, TRAPINode]]
       }
 
@@ -72,10 +66,7 @@ object ProdQueryServiceTest extends DefaultRunnableSpec {
           .orElseFail(new Exception("failed to traverse down to context"))
 
       edgesMapResult = {
-        implicit val decoderIRI: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-        implicit val keyDecoderIRI: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes)
-        implicit val decoderBiolinkClass: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-        implicit val decoderBiolinkPredicate: Decoder[BiolinkPredicate] = Implicits.biolinkPredicateDecoder(biolinkData.predicates)
+        import biolinkData.implicits._
         implicit lazy val decoderTRAPIAttribute: Decoder[TRAPIAttribute] = deriveDecoder[TRAPIAttribute]
         knowledgeGraphEdgesJson.as[Map[String, TRAPIEdge]]
       }

diff --git a/src/it/scala/org/renci/cam/it/QueryServiceTest.scala b/src/it/scala/org/renci/cam/it/QueryServiceTest.scala
@@ -27,10 +27,7 @@ object QueryServiceTest extends DefaultRunnableSpec {
       httpClient <- HttpClient.client
       biolinkData <- Biolink.biolinkData
       encoded = {
-        implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(biolinkData.prefixes)
-        implicit val iriKeyEncoder: KeyEncoder[IRI] = Implicits.iriKeyEncoder(biolinkData.prefixes)
-        implicit val biolinkClassEncoder: Encoder[BiolinkClass] = Implicits.biolinkClassEncoder
-        implicit val biolinkPredicateEncoder: Encoder[BiolinkPredicate] = Implicits.biolinkPredicateEncoder(biolinkData.prefixes)
+        import biolinkData.implicits._
         trapiQuery.asJson.deepDropNullValues.noSpaces
       }
       _ = println("encoded: " + encoded)

diff --git a/src/it/scala/org/renci/cam/it/SerializationTest.scala b/src/it/scala/org/renci/cam/it/SerializationTest.scala
@@ -31,14 +31,7 @@ object SerializationTest extends DefaultRunnableSpec with LazyLogging {
       for {
         biolinkData <- Biolink.biolinkData
       } yield {
-
-        implicit val iriDecoder: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-        implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(biolinkData.prefixes)
-        implicit val biolinkClassEncoder: Encoder[BiolinkClass] = Implicits.biolinkClassEncoder
-        implicit val biolinkPredicateEncoder: Encoder[BiolinkPredicate] = Implicits.biolinkPredicateEncoder(biolinkData.prefixes)
-
-        implicit val iriKeyDecoder: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes)
-        implicit val iriKeyEncoder: KeyEncoder[IRI] = Implicits.iriKeyEncoder(biolinkData.prefixes)
+        import biolinkData.implicits._
 //        implicit val blClassKeyEncoder: KeyEncoder[BiolinkClass] = (blClass: BiolinkClass) => s"biolink:${blClass.shorthand}"
 //        implicit val blClassKeyDecoder: Decoder[TRAPIQueryNode] = new Decoder[TRAPIQueryNode] {
 //          final def apply(c: HCursor): Decoder.Result[TRAPIQueryNode] =

diff --git a/src/main/scala/org/renci/cam/Biolink.scala b/src/main/scala/org/renci/cam/Biolink.scala
@@ -7,7 +7,7 @@ import org.apache.commons.lang3.StringUtils
 import org.http4s.headers.Accept
 import org.http4s.implicits._
 import org.http4s.{MediaType, Method, Request}
-import org.renci.cam.domain.{BiolinkClass, BiolinkPredicate}
+import org.renci.cam.domain.{BiolinkClass, BiolinkPredicate, IRI}
 import zio._
 import zio.blocking.{effectBlockingIO, Blocking}
 import zio.interop.catz._
@@ -21,7 +21,22 @@ object Biolink extends LazyLogging {
   final case class BiolinkData(version: String,
                                prefixes: Map[String, String],
                                classes: List[BiolinkClass],
-                               predicates: List[BiolinkPredicate])
+                               predicates: List[BiolinkPredicate]) {
+
+    object implicits {
+      implicit val bcKeyDecoder: KeyDecoder[BiolinkClass] = Implicits.biolinkClassKeyDecoder(classes)
+      implicit val bcKeyEncoder: KeyEncoder[BiolinkClass] = Implicits.biolinkClassKeyEncoder
+      implicit val iriDecoder: Decoder[IRI] = Implicits.iriDecoder(prefixes)
+      implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(prefixes)
+      implicit val iriKeyDecoder: KeyDecoder[IRI] = Implicits.iriKeyDecoder(prefixes)
+      implicit val iriKeyEncoder: KeyEncoder[IRI] = Implicits.iriKeyEncoder(prefixes)
+      implicit val blClassDecoder: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(classes)
+      implicit val blClassEncoder: Encoder[BiolinkClass] = Implicits.biolinkClassEncoder
+      implicit val blPredicateDecoder: Decoder[BiolinkPredicate] = Implicits.biolinkPredicateDecoder(predicates)
+      implicit val blPredicateEncoder: Encoder[BiolinkPredicate] = Implicits.biolinkPredicateEncoder(prefixes)
+    }
+
+  }
 
   def makeUtilitiesLayer: ZLayer[Any, Throwable, Has[BiolinkData]] = getBiolinkData.toLayer
 

diff --git a/src/main/scala/org/renci/cam/Server.scala b/src/main/scala/org/renci/cam/Server.scala
@@ -4,6 +4,7 @@ import cats.implicits._
 import com.typesafe.scalalogging.LazyLogging
 import io.circe._
 import io.circe.generic.auto._
+import io.circe.generic.semiauto.{deriveDecoder, deriveEncoder}
 import io.circe.yaml.syntax._
 import org.http4s._
 import org.http4s.blaze.server.BlazeServerBuilder
@@ -53,19 +54,7 @@ object Server extends App with LazyLogging {
       .errorOut(stringBody)
       .out(
         {
-
-          implicit val bcKeyDecoder: KeyDecoder[BiolinkClass] = Implicits.biolinkClassKeyDecoder(biolinkData.classes)
-          implicit val bcKeyEncoder: KeyEncoder[BiolinkClass] = Implicits.biolinkClassKeyEncoder
-
-          implicit val iriDecoder: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-          implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(biolinkData.prefixes)
-
-          implicit val blClassDecoder: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-          implicit val blClassEncoder: Encoder[BiolinkClass] = Implicits.biolinkClassEncoder
-
-          implicit val blPredicateDecoder: Decoder[BiolinkPredicate] = Implicits.biolinkPredicateDecoder(biolinkData.predicates)
-          implicit val blPredicateEncoder: Encoder[BiolinkPredicate] = Implicits.biolinkPredicateEncoder(biolinkData.prefixes)
-
+          import biolinkData.implicits._
           jsonBody[MetaKnowledgeGraph]
         }
       )
@@ -86,19 +75,7 @@ object Server extends App with LazyLogging {
     for {
       biolinkData <- biolinkData
     } yield {
-      implicit val iriDecoder: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-      implicit val iriEncoder: Encoder[IRI] = Implicits.iriEncoder(biolinkData.prefixes)
-
-      implicit val iriKeyEncoder: KeyEncoder[IRI] = Implicits.iriKeyEncoder(biolinkData.prefixes)
-      implicit val iriKeyDecoder: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes)
-
-      implicit val biolinkClassEncoder: Encoder[BiolinkClass] = Implicits.biolinkClassEncoder
-      implicit val biolinkClassDecoder: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-
-      implicit val biolinkPredicateEncoder: Encoder[BiolinkPredicate] = Implicits.biolinkPredicateEncoder(biolinkData.prefixes)
-      implicit val biolinkPredicateDecoder: Decoder[List[BiolinkPredicate]] =
-        Implicits.predicateOrPredicateListDecoder(biolinkData.predicates)
-
+      import biolinkData.implicits._
       val example = {
         // This example asks what biological process or activities positively regulate GO:0004707
         // (MAP kinase activity, see http://purl.obolibrary.org/obo/GO_0004707)

diff --git a/src/test/scala/org/renci/cam/test/TRAPITest.scala b/src/test/scala/org/renci/cam/test/TRAPITest.scala
@@ -72,11 +72,7 @@ object TRAPITest extends DefaultRunnableSpec with LazyLogging {
 
           trapiResponse <- ZIO.fromEither(
             {
-              implicit val decoderIRI: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-              implicit val keyDecoderIRI: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes)
-              implicit val decoderBiolinkClass: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-              implicit val decoderBiolinkPredicate: Decoder[BiolinkPredicate] =
-                Implicits.biolinkPredicateDecoder(biolinkData.predicates)
+              import biolinkData.implicits._
               implicit lazy val decoderTRAPIAttribute: Decoder[TRAPIAttribute] = deriveDecoder[TRAPIAttribute]
 
               trapiResponseJson.as[TRAPIResponse]
@@ -152,13 +148,8 @@ object TRAPITest extends DefaultRunnableSpec with LazyLogging {
 
         trapiResponse <- ZIO.fromEither(
           {
-            implicit val decoderIRI: Decoder[IRI] = Implicits.iriDecoder(biolinkData.prefixes)
-            implicit val keyDecoderIRI: KeyDecoder[IRI] = Implicits.iriKeyDecoder(biolinkData.prefixes)
-            implicit val decoderBiolinkClass: Decoder[BiolinkClass] = Implicits.biolinkClassDecoder(biolinkData.classes)
-            implicit val decoderBiolinkPredicate: Decoder[BiolinkPredicate] =
-              Implicits.biolinkPredicateDecoder(biolinkData.predicates)
+            import biolinkData.implicits._
             implicit lazy val decoderTRAPIAttribute: Decoder[TRAPIAttribute] = deriveDecoder[TRAPIAttribute]
-
             trapiResponseJson.as[TRAPIResponse]
           }
         )