Feat: add Reaktoro integration (#11)

* feat(all): integrate ReactionService & fix comments

* feat(tests): fix tests using service integration

* feat(reaktoro): add Reaktoro service & redo arch (separation of concerns)

* fix(preprocessor): fix  JSON decoding issue & improve services' pipelines

* feat(env): create .env example

* feat(reaktoro): integrate Reaktoro service & fix tests

* fix(docker): add repositories explicitly

* fix(reaktoro): include routes into the Main & fix tests

Dockerfile

@@ -20,7 +20,7 @@ RUN sbt update
 
 COPY src/ ./src/
 
-RUN sbt compile
+RUN sbt clean compile
 
 COPY . .
 

build.sbt

@@ -17,7 +17,7 @@ Test / scalaSource := baseDirectory.value / "src" / "test" / "scala"
 
 lazy val root = (project in file("."))
   .settings(
-    name := "chemist-flow",
+    name := ".",
     libraryDependencies ++= Seq(
       scalaLogging,
       scalaTest,
@@ -40,4 +40,13 @@ lazy val root = (project in file("."))
     )
   )
 
-resolvers += "Akka library repository".at("https://repo.akka.io/maven")
+scalacOptions ++= Seq(
+  "-Xmax-inlines", "64"
+)
+
+resolvers ++= Seq(
+  "Akka library repository" at "https://repo.akka.io/maven",
+  "Sonatype OSS Releases" at "https://oss.sonatype.org/content/repositories/releases/",
+  "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots/",
+  "Maven Central" at "https://repo1.maven.org/maven2/"
+)

examples/.env.example

@@ -0,0 +1,13 @@
+AKKA_LICENSE_KEY=...
+
+CHEMIST_FLOW_HOST=localhost
+CHEMIST_FLOW_PORT=8081
+
+POSTGRE_URL=jdbc:postgresql://localhost:5432/chemist_db
+POSTGRE_USER=chemist
+POSTGRE_PASSWORD=chemist_password
+POSTGRE_DRIVER=org.postgresql.Driver
+
+CHEMIST_PREPROCESSOR_BASE_URI=http://localhost:8080
+
+CHEMIST_ENGINE_BASE_URI=http://localhost:8082

project/plugins.sbt

@@ -1,4 +1,11 @@
 addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.0")
 addSbtPlugin("com.github.sbt" % "sbt-native-packager" % "1.10.4")
 addSbtPlugin("org.http4s" % "sbt-http4s-org" % "0.17.5")
-resolvers += "Scalafmt Releases" at "https://oss.sonatype.org/content/repositories/releases"
+
+resolvers ++= Seq(
+  "Scalafmt Releases" at "https://oss.sonatype.org/content/repositories/releases",
+  "Sonatype OSS Releases" at "https://oss.sonatype.org/content/repositories/releases",
+  "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots/",
+  "Maven Central" at "https://repo1.maven.org/maven2/",
+  "Akka repository" at "https://repo.akka.io/maven"
+)

src/main/scala/api/ServerBuilder.scala

@@ -1,12 +1,15 @@
 package api
 
 import cats.effect.{IO, Resource}
+
 import com.comcast.ip4s.{Host, Port}
+
 import org.http4s.server.Server
 import org.http4s.ember.server.EmberServerBuilder
+import org.http4s.HttpRoutes
 
 class ServerBuilder(
-  implicit endpoints: Endpoints
+  routes: HttpRoutes[IO]
 ) {
 
   def startServer(
@@ -17,7 +20,7 @@ class ServerBuilder(
       .default[IO]
       .withHost(host)
       .withPort(port)
-      .withHttpApp(ErrorHandler(endpoints.routes).orNotFound)
+      .withHttpApp(ErrorHandler(routes).orNotFound)
       .build
   }
 

src/main/scala/api/endpoints/flow/ReaktoroEndpoints.scala

@@ -0,0 +1,54 @@
+package api.endpoints.flow
+
+import cats.effect.IO
+
+import org.http4s.HttpRoutes
+import org.http4s.dsl.io._
+import org.http4s.server.Router
+import org.http4s.server.middleware.Logger
+import org.http4s.circe.CirceEntityEncoder.circeEntityEncoder
+import org.http4s.circe.CirceSensitiveDataEntityDecoder.circeEntityDecoder
+
+import io.circe.syntax._
+import io.circe.generic.auto.deriveEncoder
+
+import core.services.flow.ReaktoroService
+import core.domain.preprocessor.ReactionId
+import core.domain.flow.{DataBase, MoleculeAmountList}
+
+case class ComputePropsRequest(
+  reactionId: ReactionId,
+  database:   DataBase,
+  amounts:    MoleculeAmountList
+)
+
+object ComputePropsRequest {
+  import io.circe.{Decoder, Encoder}
+  import io.circe.generic.semiauto.{deriveDecoder, deriveEncoder}
+
+  implicit val decoder: Decoder[ComputePropsRequest] = deriveDecoder
+  implicit val encoder: Encoder[ComputePropsRequest] = deriveEncoder
+}
+
+class ReaktoroEndpoints(
+  reaktoroService: ReaktoroService[IO]
+) {
+
+  private val computeSystemPropsForReactionRoute: HttpRoutes[IO] = HttpRoutes.of[IO] {
+    case req @ POST -> Root / "system" / "properties" =>
+      req.as[ComputePropsRequest].flatMap {
+        case ComputePropsRequest(reactionId, database, amounts) =>
+          reaktoroService
+            .computeSystemPropsForReaction(reactionId, database, amounts)
+            .flatMap(result => Ok(result.asJson))
+            .handleErrorWith(ex => InternalServerError(("InternalError", ex.getMessage).asJson))
+      }
+  }
+
+  val routes: HttpRoutes[IO] = Logger.httpRoutes(logHeaders = true, logBody = true)(
+    Router(
+      "/api" -> computeSystemPropsForReactionRoute
+    )
+  )
+
+}

src/main/scala/api/endpoints/preprocessor/PreprocessorEndpoints.scala

@@ -0,0 +1,84 @@
+package api.endpoints.preprocessor
+
+import cats.effect.IO
+import cats.syntax.semigroupk.toSemigroupKOps
+
+import io.circe.syntax.EncoderOps
+
+import org.http4s.HttpRoutes
+import org.http4s.dsl.io._
+import org.http4s.server.Router
+import org.http4s.server.middleware.Logger
+import org.http4s.circe.CirceEntityEncoder.circeEntityEncoder
+import org.http4s.circe.CirceSensitiveDataEntityDecoder.circeEntityDecoder
+
+import core.services.preprocessor.{MechanismService, ReactionService}
+import core.domain.preprocessor.{MechanismDetails, Reaction, ReactionDetails}
+import core.errors.http.preprocessor.ReactionError
+
+class PreprocessorEndpoints(
+  reactionService:  ReactionService[IO],
+  mechanismService: MechanismService[IO]
+) {
+
+  private val getReactionRoute: HttpRoutes[IO] = HttpRoutes.of[IO] {
+    case GET -> Root / "reaction" / id =>
+      validateId(id) match {
+        case Some(validId) =>
+          reactionService.getReaction(validId).flatMap {
+            (reactionDetails: ReactionDetails) => Ok(reactionDetails.asJson)
+          }.handleErrorWith {
+            case _: ReactionError.NotFoundError => NotFound(("NotFound", s"Reaction with ID $validId not found"))
+            case ex                             => InternalServerError(("InternalError", ex.getMessage))
+          }
+        case None          => BadRequest(("BadRequest", "ID must be an integer"))
+      }
+  }
+
+  private val postReactionRoute: HttpRoutes[IO] = HttpRoutes.of[IO] {
+    case req @ POST -> Root / "reaction" =>
+      req.as[Reaction].flatMap { reaction =>
+        reactionService.createReaction(reaction).flatMap {
+          createdReaction => Created(createdReaction.asJson)
+        }.handleErrorWith {
+          case _: ReactionError.CreationError => BadRequest(("CreationError", "Failed to create reaction"))
+          case ex                             => InternalServerError(("InternalError", ex.getMessage))
+        }
+      }
+  }
+
+  private val deleteReactionRoute: HttpRoutes[IO] = HttpRoutes.of[IO] {
+    case DELETE -> Root / "reaction" / id =>
+      validateId(id) match {
+        case Some(validId) =>
+          reactionService.deleteReaction(validId).flatMap {
+            case Right(_)    => NoContent()
+            case Left(error) => BadRequest(("DeletionError", error.message))
+          }
+        case None          => BadRequest(("BadRequest", "ID must be an integer"))
+      }
+  }
+
+  private val getMechanismRoute: HttpRoutes[IO] = HttpRoutes.of[IO] {
+    case GET -> Root / "mechanism" / id =>
+      validateId(id) match {
+        case Some(validId) =>
+          mechanismService.getMechanism(validId).flatMap {
+            (mechanismDetails: MechanismDetails) => Ok(mechanismDetails.asJson)
+          }.handleErrorWith {
+            case _: ReactionError.NotFoundError => NotFound(("NotFound", s"Mechanism with ID $validId not found"))
+            case ex                             => InternalServerError(("InternalError", ex.getMessage))
+          }
+        case None          => BadRequest(("BadRequest", "ID must be an integer"))
+      }
+  }
+
+  private def validateId(id: String): Option[Int] = id.toIntOption
+
+  val routes: HttpRoutes[IO] = Logger.httpRoutes(logHeaders = false, logBody = true)(
+    Router(
+      "/api" -> (getReactionRoute <+> postReactionRoute <+> deleteReactionRoute <+> getMechanismRoute)
+    )
+  )
+
+}