Merge remote-tracking branch 'upstream/master' into 4469-migrate-json…

…ld-serialization
BlueBrain · Nov 9, 2023 · bb09923 · bb09923
2 parents 6c4ec0c + 4a8dd54
commit bb09923
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Showing 112 changed files with 568 additions and 997 deletions.
diff --git a/...p/src/main/scala/ch/epfl/bluebrain/nexus/delta/dependency/PostgresServiceDependency.scala b/...p/src/main/scala/ch/epfl/bluebrain/nexus/delta/dependency/PostgresServiceDependency.scala
@@ -20,7 +20,7 @@ class PostgresServiceDependency(xas: Transactors) extends ServiceDependency {
     sql"select version()"
       .query[String]
       .to[List]
-      .transact(xas.readCE)
+      .transact(xas.read)
       .map {
         case versionString :: _ =>
           versionString match {

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/routes/ProjectsRoutes.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/routes/ProjectsRoutes.scala
@@ -161,7 +161,7 @@ final class ProjectsRoutes(
                   // Project statistics
                   (pathPrefix("statistics") & get & pathEndOrSingleSlash) {
                     authorizeFor(ref, resources.read).apply {
-                      val stats = projectsStatistics.get(ref).toCatsIO
+                      val stats = projectsStatistics.get(ref)
                       emit(
                         OptionT(stats).toRight[ProjectRejection](ProjectNotFound(ref)).value
                       )

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/DeltaModule.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/DeltaModule.scala
@@ -11,7 +11,6 @@ import cats.data.NonEmptyList
 import cats.effect.{Clock, ContextShift, IO, Resource, Sync, Timer}
 import ch.epfl.bluebrain.nexus.delta.Main.pluginsMaxPriority
 import ch.epfl.bluebrain.nexus.delta.config.AppConfig
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.kernel.utils.UUIDF
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary.contexts
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.{JsonLdApi, JsonLdJavaApi}
@@ -65,8 +64,8 @@ class DeltaModule(appCfg: AppConfig, config: Config)(implicit classLoader: Class
 
   implicit val scheduler: Scheduler = Scheduler.global
 
-  make[Transactors].fromResource {
-    Transactors.init(appCfg.database).mapK(taskToIoK)
+  make[Transactors].fromResource { (cs: ContextShift[IO]) =>
+    Transactors.init(appCfg.database)(classLoader, cs)
   }
 
   make[List[PluginDescription]].from { (pluginsDef: List[PluginDef]) => pluginsDef.map(_.info) }

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/ProjectsModule.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/ProjectsModule.scala
@@ -4,7 +4,6 @@ import cats.effect.{Clock, ContextShift, IO, Timer}
 import cats.implicits._
 import ch.epfl.bluebrain.nexus.delta.Main.pluginsMaxPriority
 import ch.epfl.bluebrain.nexus.delta.config.AppConfig
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.kernel.utils.UUIDF
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary.contexts
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.{ContextValue, RemoteContextResolution}
@@ -77,7 +76,7 @@ object ProjectsModule extends ModuleDef {
   }
 
   make[ProjectsStatistics].fromEffect { (xas: Transactors) =>
-    toCatsIO(ProjectsStatistics(xas))
+    ProjectsStatistics(xas)
   }
 
   make[ProjectProvisioning].from {

diff --git a/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/MainSuite.scala b/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/MainSuite.scala
@@ -7,14 +7,14 @@ import ch.epfl.bluebrain.nexus.delta.sdk.plugin.PluginDef
 import ch.epfl.bluebrain.nexus.delta.sourcing.postgres.Doobie._
 import ch.epfl.bluebrain.nexus.delta.wiring.DeltaModule
 import ch.epfl.bluebrain.nexus.testkit.elasticsearch.ElasticSearchContainer
-import ch.epfl.bluebrain.nexus.testkit.mu.bio.ResourceFixture
+import ch.epfl.bluebrain.nexus.testkit.mu.ce.ResourceFixture
 import ch.epfl.bluebrain.nexus.testkit.mu.ce.CatsEffectSuite
+import ch.epfl.bluebrain.nexus.testkit.mu.ce.ResourceFixture.IOFixture
 import ch.epfl.bluebrain.nexus.testkit.postgres.PostgresContainer
 import com.typesafe.config.impl.ConfigImpl
 import izumi.distage.model.definition.{Module, ModuleDef}
 import izumi.distage.model.plan.Roots
 import izumi.distage.planning.solver.PlanVerifier
-import monix.bio.Task
 import munit.AnyFixture
 
 import java.nio.file.{Files, Paths}
@@ -73,7 +73,7 @@ object MainSuite {
   trait Fixture { self: CatsEffectSuite =>
 
     // Overload config via system properties
-    private def acquire(postgres: PostgresContainer, elastic: ElasticSearchContainer) = Task.delay {
+    private def acquire(postgres: PostgresContainer, elastic: ElasticSearchContainer): IO[Unit] = IO.delay {
       val resourceTypesFile = Files.createTempFile("resource-types", ".json")
       Files.writeString(resourceTypesFile, """["https://neuroshapes.org/Entity"]""")
       val mappingFile       = Files.createTempFile("mapping", ".json")
@@ -105,7 +105,7 @@ object MainSuite {
     }
 
     // Resetting system properties
-    private def release = Task.delay {
+    private def release = IO.delay {
       System.clearProperty("app.defaults.database.access.host")
       System.clearProperty("app.defaults.database.access.port")
       System.clearProperty("app.defaults.database.access.username")
@@ -131,7 +131,7 @@ object MainSuite {
         _        <- Resource.make(acquire(postgres, elastic))(_ => release)
       } yield ()
 
-    val main: ResourceFixture.TaskFixture[Unit] = ResourceFixture.suiteLocal("main", resource())
+    val main: IOFixture[Unit] = ResourceFixture.suiteLocal("main", resource())
 
   }
 

diff --git a/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/routes/ProjectsRoutesSpec.scala b/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/routes/ProjectsRoutesSpec.scala
@@ -7,7 +7,7 @@ import akka.http.scaladsl.server.Route
 import cats.effect.IO
 import ch.epfl.bluebrain.nexus.delta.kernel.utils.{UUIDF, UrlUtils}
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclSimpleCheck
-import ch.epfl.bluebrain.nexus.delta.sdk.acls.model.{AclAddress, AclRejection}
+import ch.epfl.bluebrain.nexus.delta.sdk.acls.model.AclAddress
 import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaSchemeDirectives
 import ch.epfl.bluebrain.nexus.delta.sdk.generators.ProjectGen.defaultApiMappings
 import ch.epfl.bluebrain.nexus.delta.sdk.identities.IdentitiesDummy
@@ -26,8 +26,6 @@ import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.{Anonymous, Authent
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.{Label, ProjectRef}
 import ch.epfl.bluebrain.nexus.testkit.ce.IOFromMap
 import io.circe.Json
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
-import monix.bio.UIO
 
 import java.time.Instant
 import java.util.UUID
@@ -93,13 +91,13 @@ class ProjectsRoutesSpec extends BaseRouteSpec with IOFromMap {
   private val projectStats = ProjectStatistics(10, 10, Instant.EPOCH)
 
   private val projectsStatistics: ProjectsStatistics = {
-    case `ref` => UIO.some(projectStats)
-    case _     => UIO.none
+    case `ref` => IO.pure(Some(projectStats))
+    case _     => IO.none
   }
 
-  private lazy val projects     = ProjectsImpl(fetchOrg, _ => UIO.unit, Set.empty, defaultApiMappings, projectsConfig, xas)
+  private lazy val projects     = ProjectsImpl(fetchOrg, _ => IO.unit, Set.empty, defaultApiMappings, projectsConfig, xas)
   private lazy val provisioning =
-    ProjectProvisioning(aclCheck.append(_).toBIO[AclRejection], projects, provisioningConfig)
+    ProjectProvisioning(aclCheck.append, projects, provisioningConfig)
   private lazy val routes       = Route.seal(
     ProjectsRoutes(
       identities,

diff --git a/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/routes/QuotasRoutesSpec.scala b/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/routes/QuotasRoutesSpec.scala
@@ -3,6 +3,7 @@ package ch.epfl.bluebrain.nexus.delta.routes
 import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.model.headers.OAuth2BearerToken
 import akka.http.scaladsl.server.Route
+import cats.effect.IO
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary.contexts
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclSimpleCheck
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.model.AclAddress
@@ -15,7 +16,6 @@ import ch.epfl.bluebrain.nexus.delta.sdk.quotas.{QuotasConfig, QuotasImpl}
 import ch.epfl.bluebrain.nexus.delta.sdk.utils.BaseRouteSpec
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.{Anonymous, Authenticated, Group, User}
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.{Label, ProjectRef}
-import monix.bio.UIO
 
 class QuotasRoutesSpec extends BaseRouteSpec {
 
@@ -35,7 +35,7 @@ class QuotasRoutesSpec extends BaseRouteSpec {
     ServiceAccount(User("internal", Label.unsafe("sa")))
   )
 
-  private val projectsStatistics: ProjectsStatistics = (_ => UIO.none)
+  private val projectsStatistics: ProjectsStatistics = (_ => IO.none)
 
   private val quotas = new QuotasImpl(projectsStatistics)