BlueBrain · shinyhappydan · Nov 9, 2023 · Nov 9, 2023 · Nov 9, 2023 · Nov 9, 2023
diff --git a/build.sbt b/build.sbt
@@ -47,8 +47,6 @@ val log4catsVersion         = "1.7.0"
 val logbackVersion          = "1.4.11"
 val magnoliaVersion         = "1.1.6"
 val mockitoVersion          = "1.17.27"
-val monixVersion            = "3.4.1"
-val monixBioVersion         = "1.2.0"
 val munitVersion            = "1.0.0-M10"
 val nimbusJoseJwtVersion    = "9.37"
 val postgresJdbcVersion     = "42.6.0"
@@ -113,7 +111,6 @@ lazy val log4cats           = "org.typelevel"                %% "log4cats-slf4j"
 lazy val logback            = "ch.qos.logback"                % "logback-classic"          % logbackVersion
 lazy val magnolia           = "com.softwaremill.magnolia1_2" %% "magnolia"                 % magnoliaVersion
 lazy val mockito            = "org.mockito"                  %% "mockito-scala"            % mockitoVersion
-lazy val monixBio           = "io.monix"                     %% "monix-bio"                % monixBioVersion
 lazy val munit              = "org.scalameta"                %% "munit"                    % munitVersion
 lazy val nimbusJoseJwt      = "com.nimbusds"                  % "nimbus-jose-jwt"          % nimbusJoseJwtVersion
 lazy val pureconfig         = "com.github.pureconfig"        %% "pureconfig"               % pureconfigVersion
@@ -212,7 +209,6 @@ lazy val kernel = project
       circeCore,
       circeParser,
       handleBars,
-      monixBio,
       nimbusJoseJwt,
       kamonCore,
       log4cats,
@@ -242,7 +238,6 @@ lazy val testkit = project
       ),
       catsRetry,
       doobiePostgres,
-      monixBio,
       munit,
       scalaTest,
       testContainers
@@ -267,7 +262,6 @@ lazy val sourcingPsql = project
       distageCore,
       fs2,
       fs2io,
-      monixBio,
       munit          % Test,
       catsEffectLaws % Test,
       logback        % Test
@@ -295,7 +289,6 @@ lazy val rdf = project
       jenaArq,
       jsonldjava,
       magnolia,
-      monixBio,
       topBraidShacl,
       akkaSlf4j   % Test,
       akkaTestKit % Test,
@@ -325,7 +318,6 @@ lazy val sdk = project
       circeGenericExtras,
       distageCore,
       fs2,
-      monixBio,
       akkaTestKitTyped % Test,
       akkaHttpTestKit  % Test,
       munit            % Test,
@@ -804,7 +796,6 @@ lazy val tests = project
       circeGenericExtras,
       fs2,
       logback,
-      monixBio,
       scalaLogging,
       akkaTestKit     % Test,
       akkaHttpTestKit % Test,

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/routes/OrganizationsRoutes.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/routes/OrganizationsRoutes.scala
@@ -5,15 +5,14 @@ import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.{Directive1, Route}
 import cats.effect.IO
 import cats.implicits._
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.RemoteContextResolution
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.encoder.JsonLdEncoder
 import ch.epfl.bluebrain.nexus.delta.rdf.utils.JsonKeyOrdering
 import ch.epfl.bluebrain.nexus.delta.routes.OrganizationsRoutes.OrganizationInput
 import ch.epfl.bluebrain.nexus.delta.sdk.OrganizationResource
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclCheck
-import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaDirectives._
 import ch.epfl.bluebrain.nexus.delta.sdk.circe.CirceUnmarshalling
+import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaDirectives._
 import ch.epfl.bluebrain.nexus.delta.sdk.directives.{AuthDirectives, DeltaSchemeDirectives}
 import ch.epfl.bluebrain.nexus.delta.sdk.identities.Identities
 import ch.epfl.bluebrain.nexus.delta.sdk.identities.model.Caller
@@ -71,7 +70,7 @@ final class OrganizationsRoutes(
           createdBy,
           updatedBy,
           label,
-          org => aclCheck.authorizeFor(org.label, orgs.read, allAcls).toUIO
+          org => aclCheck.authorizeFor(org.label, orgs.read, allAcls)
         )
       }
     }

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
@@ -6,14 +6,13 @@ import akka.http.scaladsl.server._
 import cats.data.OptionT
 import cats.effect.{ContextShift, IO}
 import cats.implicits._
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.RemoteContextResolution
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.encoder.JsonLdEncoder
 import ch.epfl.bluebrain.nexus.delta.rdf.utils.JsonKeyOrdering
 import ch.epfl.bluebrain.nexus.delta.sdk._
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclCheck
-import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaDirectives._
 import ch.epfl.bluebrain.nexus.delta.sdk.circe.CirceUnmarshalling
+import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaDirectives._
 import ch.epfl.bluebrain.nexus.delta.sdk.directives.{AuthDirectives, DeltaSchemeDirectives}
 import ch.epfl.bluebrain.nexus.delta.sdk.fusion.FusionConfig
 import ch.epfl.bluebrain.nexus.delta.sdk.identities.Identities
@@ -75,7 +74,7 @@ final class ProjectsRoutes(
           createdBy,
           updatedBy,
           label,
-          proj => aclCheck.authorizeFor(proj.ref, projectsPermissions.read, allAcls).toUIO
+          proj => aclCheck.authorizeFor(proj.ref, projectsPermissions.read, allAcls)
         )
       }
     }

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/routes/ResourcesRoutes.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/routes/ResourcesRoutes.scala
@@ -5,7 +5,6 @@ import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server._
 import cats.effect.IO
 import cats.syntax.all._
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.rdf.RdfError
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary.schemas
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.{ContextValue, RemoteContextResolution}
@@ -14,8 +13,8 @@ import ch.epfl.bluebrain.nexus.delta.rdf.utils.JsonKeyOrdering
 import ch.epfl.bluebrain.nexus.delta.routes.ResourcesRoutes.asSourceWithMetadata
 import ch.epfl.bluebrain.nexus.delta.sdk._
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclCheck
-import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaDirectives._
 import ch.epfl.bluebrain.nexus.delta.sdk.circe.CirceUnmarshalling
+import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaDirectives._
 import ch.epfl.bluebrain.nexus.delta.sdk.directives.{AuthDirectives, DeltaSchemeDirectives}
 import ch.epfl.bluebrain.nexus.delta.sdk.fusion.FusionConfig
 import ch.epfl.bluebrain.nexus.delta.sdk.identities.Identities
@@ -28,7 +27,6 @@ import ch.epfl.bluebrain.nexus.delta.sdk.resources.NexusSource.DecodingOption
 import ch.epfl.bluebrain.nexus.delta.sdk.resources.model.ResourceRejection.{InvalidJsonLdFormat, InvalidSchemaRejection, NoSchemaProvided, ResourceNotFound}
 import ch.epfl.bluebrain.nexus.delta.sdk.resources.model.{Resource, ResourceRejection}
 import ch.epfl.bluebrain.nexus.delta.sdk.resources.{NexusSource, Resources}
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.ProjectRef
 import io.circe.{Json, Printer}
 
 /**
@@ -68,9 +66,6 @@ final class ResourcesRoutes(
   implicit private def resourceFAJsonLdEncoder[A: JsonLdEncoder]: JsonLdEncoder[ResourceF[A]] =
     ResourceF.resourceFAJsonLdEncoder(ContextValue.empty)
 
-  private def indexUIO(project: ProjectRef, resource: ResourceF[Resource], mode: IndexingMode) =
-    index(project, resource, mode).toUIO
-
   def routes: Route =
     baseUriPrefix(baseUri.prefix) {
       pathPrefix("resources") {
@@ -85,7 +80,7 @@ final class ResourcesRoutes(
                       Created,
                       resources
                         .create(project, resourceSchema, source.value, tag)
-                        .flatTap(indexUIO(project, _, mode))
+                        .flatTap(index(project, _, mode))
                         .map(_.void)
                         .attemptNarrow[ResourceRejection]
                     )
@@ -102,7 +97,7 @@ final class ResourcesRoutes(
                           Created,
                           resources
                             .create(project, schema, source.value, tag)
-                            .flatTap(indexUIO(project, _, mode))
+                            .flatTap(index(project, _, mode))
                             .map(_.void)
                             .attemptNarrow[ResourceRejection]
                             .rejectWhen(wrongJsonOrNotFound)
@@ -124,7 +119,7 @@ final class ResourcesRoutes(
                                     Created,
                                     resources
                                       .create(resource, project, schema, source.value, tag)
-                                      .flatTap(indexUIO(project, _, mode))
+                                      .flatTap(index(project, _, mode))
                                       .map(_.void)
                                       .attemptNarrow[ResourceRejection]
                                       .rejectWhen(wrongJsonOrNotFound)
@@ -134,7 +129,7 @@ final class ResourcesRoutes(
                                   emit(
                                     resources
                                       .update(resource, project, schemaOpt, rev, source.value, tag)
-                                      .flatTap(indexUIO(project, _, mode))
+                                      .flatTap(index(project, _, mode))
                                       .map(_.void)
                                       .attemptNarrow[ResourceRejection]
                                       .rejectWhen(wrongJsonOrNotFound)
@@ -148,7 +143,7 @@ final class ResourcesRoutes(
                               emit(
                                 resources
                                   .deprecate(resource, project, schemaOpt, rev)
-                                  .flatTap(indexUIO(project, _, mode))
+                                  .flatTap(index(project, _, mode))
                                   .map(_.void)
                                   .attemptNarrow[ResourceRejection]
                                   .rejectWhen(wrongJsonOrNotFound)
@@ -178,7 +173,7 @@ final class ResourcesRoutes(
                           emit(
                             resources
                               .undeprecate(resource, project, schemaOpt, rev)
-                              .flatTap(indexUIO(project, _, mode))
+                              .flatTap(index(project, _, mode))
                               .map(_.void)
                               .attemptNarrow[ResourceRejection]
                               .rejectWhen(wrongJsonOrNotFound)
@@ -193,7 +188,7 @@ final class ResourcesRoutes(
                               .flatMap { schema =>
                                 resources
                                   .updateAttachedSchema(resource, project, schema)
-                                  .flatTap(indexUIO(project, _, mode))
+                                  .flatTap(index(project, _, mode))
                               }
                               .attemptNarrow[ResourceRejection]
                               .rejectWhen(wrongJsonOrNotFound)
@@ -207,7 +202,7 @@ final class ResourcesRoutes(
                             OK,
                             resources
                               .refresh(resource, project, schemaOpt)
-                              .flatTap(indexUIO(project, _, mode))
+                              .flatTap(index(project, _, mode))
                               .map(_.void)
                               .attemptNarrow[ResourceRejection]
                               .rejectWhen(wrongJsonOrNotFound)
@@ -273,7 +268,7 @@ final class ResourcesRoutes(
                                   Created,
                                   resources
                                     .tag(resource, project, schemaOpt, tag, tagRev, rev)
-                                    .flatTap(indexUIO(project, _, mode))
+                                    .flatTap(index(project, _, mode))
                                     .map(_.void)
                                     .attemptNarrow[ResourceRejection]
                                     .rejectWhen(wrongJsonOrNotFound)
@@ -289,7 +284,7 @@ final class ResourcesRoutes(
                             emit(
                               resources
                                 .deleteTag(resource, project, schemaOpt, tag, rev)
-                                .flatTap(indexUIO(project, _, mode))
+                                .flatTap(index(project, _, mode))
                                 .map(_.void)
                                 .attemptNarrow[ResourceRejection]
                                 .rejectOn[ResourceNotFound]

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/routes/UserPermissionsRoutes.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/routes/UserPermissionsRoutes.scala
@@ -3,7 +3,6 @@ package ch.epfl.bluebrain.nexus.delta.routes
 import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.Route
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration.MigrateEffectSyntax
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclCheck
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.model.AclAddress
 import ch.epfl.bluebrain.nexus.delta.sdk.circe.CirceUnmarshalling
@@ -26,8 +25,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.permissions.model.Permission
 final class UserPermissionsRoutes(identities: Identities, aclCheck: AclCheck, storages: StoragePermissionProvider)(
     implicit baseUri: BaseUri
 ) extends AuthDirectives(identities, aclCheck)
-    with CirceUnmarshalling
-    with MigrateEffectSyntax {
+    with CirceUnmarshalling {
 
   def routes: Route =
     baseUriPrefix(baseUri.prefix) {

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/AclsModule.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/AclsModule.scala
@@ -18,7 +18,6 @@ import ch.epfl.bluebrain.nexus.delta.sdk.permissions.{Permissions, StoragePermis
 import ch.epfl.bluebrain.nexus.delta.sdk.sse.SseEncoder
 import ch.epfl.bluebrain.nexus.delta.sourcing.Transactors
 import izumi.distage.model.definition.{Id, ModuleDef}
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 
 /**
   * Acls module wiring config.
@@ -37,7 +36,7 @@ object AclsModule extends ModuleDef {
         timer: Timer[IO]
     ) =>
       acls.AclsImpl(
-        permissions.fetchPermissionSet.toUIO,
+        permissions.fetchPermissionSet,
         AclsImpl.findUnknownRealms(xas),
         permissions.minimum,
         config.acls,

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
@@ -33,7 +33,6 @@ import ch.epfl.bluebrain.nexus.delta.sourcing.config.{DatabaseConfig, Projection
 import ch.megard.akka.http.cors.scaladsl.settings.CorsSettings
 import com.typesafe.config.Config
 import izumi.distage.model.definition.{Id, ModuleDef}
-import monix.bio.UIO
 import org.slf4j.{Logger, LoggerFactory}
 
 import scala.concurrent.duration.DurationInt
@@ -106,7 +105,6 @@ class DeltaModule(appCfg: AppConfig, config: Config)(implicit classLoader: Class
     new JsonLdJavaApi(appCfg.jsonLdApi)(contextShift)
   }
 
-  make[Clock[UIO]].from(Clock[UIO])
   make[Clock[IO]].from(Clock.create[IO])
   make[UUIDF].from(UUIDF.random)
   make[JsonKeyOrdering].from(

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/EventsModule.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/EventsModule.scala
@@ -3,7 +3,6 @@ package ch.epfl.bluebrain.nexus.delta.wiring
 import cats.effect.{ContextShift, IO, 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.rdf.jsonld.context.RemoteContextResolution
 import ch.epfl.bluebrain.nexus.delta.rdf.utils.JsonKeyOrdering
 import ch.epfl.bluebrain.nexus.delta.routes.{ElemRoutes, EventsRoutes}
@@ -13,7 +12,6 @@ import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaSchemeDirectives
 import ch.epfl.bluebrain.nexus.delta.sdk.identities.Identities
 import ch.epfl.bluebrain.nexus.delta.sdk.model.BaseUri
 import ch.epfl.bluebrain.nexus.delta.sdk.organizations.Organizations
-import ch.epfl.bluebrain.nexus.delta.sdk.organizations.model.OrganizationRejection
 import ch.epfl.bluebrain.nexus.delta.sdk.projects.Projects
 import ch.epfl.bluebrain.nexus.delta.sdk.sse.{SseElemStream, SseEncoder, SseEventLog}
 import ch.epfl.bluebrain.nexus.delta.sourcing.Transactors
@@ -37,7 +35,7 @@ object EventsModule extends ModuleDef {
     ) =>
       SseEventLog(
         sseEncoders,
-        organizations.fetch(_).void.toBIO[OrganizationRejection],
+        organizations.fetch(_).void,
         projects.fetch(_).map { p => (p.value.organizationUuid, p.value.uuid) },
         config.sse,
         xas

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/MultiFetchModule.scala b/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/MultiFetchModule.scala
@@ -1,7 +1,6 @@
 package ch.epfl.bluebrain.nexus.delta.wiring
 
 import ch.epfl.bluebrain.nexus.delta.Main.pluginsMaxPriority
-import ch.epfl.bluebrain.nexus.delta.kernel.effect.migration._
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.RemoteContextResolution
 import ch.epfl.bluebrain.nexus.delta.rdf.utils.JsonKeyOrdering
 import ch.epfl.bluebrain.nexus.delta.routes.MultiFetchRoutes
@@ -23,7 +22,7 @@ object MultiFetchModule extends ModuleDef {
     ) =>
       MultiFetch(
         aclCheck,
-        (input: MultiFetchRequest.Input) => shifts.fetch(input.id, input.project).toUIO
+        (input: MultiFetchRequest.Input) => shifts.fetch(input.id, input.project)
       )
   }
 

diff --git a/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/config/AppConfigSpec.scala b/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/config/AppConfigSpec.scala
@@ -1,6 +1,6 @@
 package ch.epfl.bluebrain.nexus.delta.config
 
-import ch.epfl.bluebrain.nexus.delta.kernel.utils.CatsEffectsClasspathResourceUtils
+import ch.epfl.bluebrain.nexus.delta.kernel.utils.ClasspathResourceUtils
 import ch.epfl.bluebrain.nexus.testkit.scalatest.ce.CatsEffectSpec
 import com.typesafe.config.impl.ConfigImpl
 import org.scalatest.BeforeAndAfterAll
@@ -26,7 +26,7 @@ class AppConfigSpec extends CatsEffectSpec with BeforeAndAfterAll {
 
   "AppConfig" should {
 
-    val externalConfigPath = CatsEffectsClasspathResourceUtils.absolutePath("/config/external.conf").accepted
+    val externalConfigPath = ClasspathResourceUtils.absolutePath("/config/external.conf").accepted
 
     "load conf" in {
       val (conf, _) = AppConfig.load().accepted