Merge branch 'master' into resolver-priority

BlueBrain · Mar 28, 2024 · bd08d5f · bd08d5f
2 parents 2b0d888 + 6534494
commit bd08d5f
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Showing 26 changed files with 480 additions and 309 deletions.
diff --git a/.github/workflows/ci-delta-ship.yml b/.github/workflows/ci-delta-ship.yml
@@ -35,7 +35,6 @@ jobs:
       - name: Clean, build Delta & Storage images
         run: |
           sbt -Dsbt.color=always -Dsbt.supershell=false \
-            clean \
             app/Docker/publishLocal
       - name: Start services
         run: docker-compose -f tests/docker/docker-compose.yml up -d
@@ -46,4 +45,8 @@ jobs:
       - name: Unit tests
         run: |
           sbt -Dsbt.color=always -Dsbt.supershell=false \
-            ship-unit-tests
+            "ship/testOnly *Suite"
+      - name: Integration tests
+        run: |
+          sbt -Dsbt.color=always -Dsbt.supershell=false \
+            "ship/testOnly *Spec"
diff --git a/build.sbt b/build.sbt
@@ -27,16 +27,16 @@ val byteBuddyAgentVersion      = "1.10.17"
 val betterMonadicForVersion    = "0.3.1"
 val caffeineVersion            = "3.1.8"
 val catsEffectVersion          = "3.5.4"
-val catsRetryVersion           = "3.1.0"
+val catsRetryVersion           = "3.1.3"
 val catsVersion                = "2.10.0"
 val circeVersion               = "0.14.6"
 val circeOpticsVersion         = "0.15.0"
 val circeExtrasVersions        = "0.14.3"
 val classgraphVersion          = "4.8.168"
 val declineVersion             = "2.4.1"
-val distageVersion             = "1.2.6"
+val distageVersion             = "1.2.7"
 val doobieVersion              = "1.0.0-RC5"
-val fs2Version                 = "3.9.4"
+val fs2Version                 = "3.10.1"
 val googleAuthClientVersion    = "1.35.0"
 val handleBarsVersion          = "4.4.0"
 val hikariVersion              = "5.1.0"
@@ -52,7 +52,7 @@ val mockitoVersion             = "1.17.30"
 val munitVersion               = "1.0.0-M11"
 val munitCatsEffectVersion     = "2.0.0-M4"
 val nimbusJoseJwtVersion       = "9.37.3"
-val postgresJdbcVersion        = "42.7.2"
+val postgresJdbcVersion        = "42.7.3"
 val pureconfigVersion          = "0.17.6"
 val scalaTestVersion           = "3.2.18"
 val scalaXmlVersion            = "2.2.0"
@@ -729,16 +729,18 @@ lazy val delta = project
 lazy val ship = project
   .in(file("ship"))
   .settings(
-    name       := "nexus-ship",
-    moduleName := "nexus-ship"
+    name                     := "nexus-ship",
+    moduleName               := "nexus-ship",
+    Test / parallelExecution := false
   )
   .enablePlugins(UniversalPlugin, JavaAppPackaging, JavaAgent, DockerPlugin, BuildInfoPlugin)
   .settings(shared, compilation, servicePackaging, assertJavaVersion, kamonSettings, coverage, release)
   .dependsOn(
-    sdk                 % "compile->compile;test->test",
-    blazegraphPlugin    % "compile->compile",
-    elasticsearchPlugin % "compile->compile",
-    tests               % "test->compile;test->test"
+    sdk                  % "compile->compile;test->test",
+    blazegraphPlugin     % "compile->compile",
+    compositeViewsPlugin % "compile->compile",
+    elasticsearchPlugin  % "compile->compile",
+    tests                % "test->compile;test->test"
   )
   .settings(
     libraryDependencies ++= Seq(declineEffect),

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
@@ -3,7 +3,6 @@ package ch.epfl.bluebrain.nexus.delta.routes
 import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.server.{Directive1, Route}
 import cats.effect.IO
-import cats.effect.unsafe.implicits._
 import cats.implicits._
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.RemoteContextResolution
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.encoder.JsonLdEncoder
@@ -12,8 +11,8 @@ import ch.epfl.bluebrain.nexus.delta.routes.OrganizationsRoutes.OrganizationInpu
 import ch.epfl.bluebrain.nexus.delta.sdk.OrganizationResource
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclCheck
 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
+import ch.epfl.bluebrain.nexus.delta.sdk.directives.DeltaDirectives._
 import ch.epfl.bluebrain.nexus.delta.sdk.identities.Identities
 import ch.epfl.bluebrain.nexus.delta.sdk.identities.model.Caller
 import ch.epfl.bluebrain.nexus.delta.sdk.implicits._
@@ -59,17 +58,15 @@ final class OrganizationsRoutes(
   import baseUri.prefixSegment
 
   private def orgsSearchParams(implicit caller: Caller): Directive1[OrganizationSearchParams] =
-    onSuccess(aclCheck.fetchAll.unsafeToFuture()).flatMap { allAcls =>
-      (searchParams & parameter("label".?)).tmap { case (deprecated, rev, createdBy, updatedBy, label) =>
-        OrganizationSearchParams(
-          deprecated,
-          rev,
-          createdBy,
-          updatedBy,
-          label,
-          org => aclCheck.authorizeFor(org.label, orgs.read, allAcls)
-        )
-      }
+    (searchParams & parameter("label".?)).tmap { case (deprecated, rev, createdBy, updatedBy, label) =>
+      OrganizationSearchParams(
+        deprecated,
+        rev,
+        createdBy,
+        updatedBy,
+        label,
+        org => aclCheck.authorizeFor(org.label, orgs.read)
+      )
     }
 
   private def emitMetadata(value: IO[OrganizationResource]) = {

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
@@ -60,18 +60,16 @@ final class ProjectsRoutes(
   implicit val paginationConfig: PaginationConfig = config.pagination
 
   private def projectsSearchParams(implicit caller: Caller): Directive1[ProjectSearchParams] = {
-    onSuccess(aclCheck.fetchAll.unsafeToFuture()).flatMap { allAcls =>
-      (searchParams & parameter("label".?)).tmap { case (deprecated, rev, createdBy, updatedBy, label) =>
-        ProjectSearchParams(
-          None,
-          deprecated,
-          rev,
-          createdBy,
-          updatedBy,
-          label,
-          proj => aclCheck.authorizeFor(proj.ref, ReadProjects, allAcls)
-        )
-      }
+    (searchParams & parameter("label".?)).tmap { case (deprecated, rev, createdBy, updatedBy, label) =>
+      ProjectSearchParams(
+        None,
+        deprecated,
+        rev,
+        createdBy,
+        updatedBy,
+        label,
+        proj => aclCheck.authorizeFor(proj.ref, ReadProjects)
+      )
     }
   }
 

diff --git a/.../src/main/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeViews.scala b/.../src/main/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeViews.scala
@@ -5,7 +5,6 @@ import ch.epfl.bluebrain.nexus.delta.kernel.kamon.KamonMetricComponent
 import ch.epfl.bluebrain.nexus.delta.kernel.search.Pagination.FromPagination
 import ch.epfl.bluebrain.nexus.delta.kernel.utils.UUIDF
 import ch.epfl.bluebrain.nexus.delta.plugins.compositeviews.CompositeViews._
-import ch.epfl.bluebrain.nexus.delta.plugins.compositeviews.config.CompositeViewsConfig
 import ch.epfl.bluebrain.nexus.delta.plugins.compositeviews.indexing.CompositeViewDef
 import ch.epfl.bluebrain.nexus.delta.plugins.compositeviews.indexing.CompositeViewDef.{ActiveViewDef, DeprecatedViewDef}
 import ch.epfl.bluebrain.nexus.delta.plugins.compositeviews.model.CompositeViewCommand._
@@ -27,13 +26,16 @@ import ch.epfl.bluebrain.nexus.delta.sdk.projects.{FetchContext, Projects}
 import ch.epfl.bluebrain.nexus.delta.sdk.resolvers.ResolverContextResolution
 import ch.epfl.bluebrain.nexus.delta.sdk.views.IndexingRev
 import ch.epfl.bluebrain.nexus.delta.sourcing._
+import ch.epfl.bluebrain.nexus.delta.sourcing.config.EventLogConfig
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.EntityDependency.DependsOn
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.Subject
 import ch.epfl.bluebrain.nexus.delta.sourcing.model._
 import ch.epfl.bluebrain.nexus.delta.sourcing.offset.Offset
 import ch.epfl.bluebrain.nexus.delta.sourcing.stream.Elem
 import io.circe.Json
 
+import scala.concurrent.duration.FiniteDuration
+
 /**
   * Composite views resource lifecycle operations.
   */
@@ -467,7 +469,8 @@ object CompositeViews {
       fetchContext: FetchContext,
       contextResolution: ResolverContextResolution,
       validate: ValidateCompositeView,
-      config: CompositeViewsConfig,
+      minIntervalRebuild: FiniteDuration,
+      eventLogConfig: EventLogConfig,
       xas: Transactors,
       clock: Clock[IO]
   )(implicit
@@ -476,13 +479,13 @@ object CompositeViews {
   ): IO[CompositeViews] =
     IO
       .delay(
-        CompositeViewFieldsJsonLdSourceDecoder(uuidF, contextResolution, config.minIntervalRebuild)
+        CompositeViewFieldsJsonLdSourceDecoder(uuidF, contextResolution, minIntervalRebuild)
       )
       .map { sourceDecoder =>
         new CompositeViews(
           ScopedEventLog(
             definition(validate, clock),
-            config.eventLog,
+            eventLogConfig,
             xas
           ),
           fetchContext,

diff --git a/...ala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeViewsPluginModule.scala b/...ala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeViewsPluginModule.scala
@@ -129,7 +129,8 @@ class CompositeViewsPluginModule(priority: Int) extends ModuleDef {
         fetchContext,
         contextResolution,
         validate,
-        config,
+        config.minIntervalRebuild,
+        config.eventLog,
         xas,
         clock
       )(

diff --git a/...cala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/model/CompositeViewFields.scala b/...cala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/model/CompositeViewFields.scala
@@ -4,9 +4,11 @@ import cats.data.NonEmptyList
 import ch.epfl.bluebrain.nexus.delta.plugins.compositeviews.model.CompositeView.RebuildStrategy
 import ch.epfl.bluebrain.nexus.delta.rdf.IriOrBNode.Iri
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.JsonLdContext.keywords
-import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.decoder.JsonLdDecoder
+import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.decoder.{Configuration, JsonLdDecoder}
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.decoder.JsonLdDecoderError.ParsingFailure
+import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.decoder.configuration.semiauto.deriveConfigJsonLdDecoder
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.decoder.semiauto.deriveDefaultJsonLdDecoder
+import ch.epfl.bluebrain.nexus.delta.rdf.syntax.iriStringContextSyntax
 import ch.epfl.bluebrain.nexus.delta.sdk.model.BaseUri
 import io.circe.syntax.EncoderOps
 import io.circe.{Encoder, Json}
@@ -73,6 +75,12 @@ object CompositeViewFields {
         }
       deriveDefaultJsonLdDecoder[RebuildStrategy]
     }
-    deriveDefaultJsonLdDecoder[CompositeViewFields]
+
+    val ctx             = Configuration.default.context
+      .addAliasIdType("description", iri"http://schema.org/description")
+      .addAliasIdType("name", iri"http://schema.org/name")
+    implicit val config = Configuration.default.copy(context = ctx)
+
+    deriveConfigJsonLdDecoder[CompositeViewFields]
   }
 }
diff --git a/.../test/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeViewsSpec.scala b/.../test/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/CompositeViewsSpec.scala
@@ -52,7 +52,8 @@ class CompositeViewsSpec
       fetchContext,
       ResolverContextResolution(rcr),
       alwaysValidate,
-      config,
+      config.minIntervalRebuild,
+      config.eventLog,
       xas,
       clock
     ).accepted

diff --git a/...h/epfl/bluebrain/nexus/delta/plugins/compositeviews/routes/CompositeViewsRoutesSpec.scala b/...h/epfl/bluebrain/nexus/delta/plugins/compositeviews/routes/CompositeViewsRoutesSpec.scala
@@ -50,7 +50,8 @@ class CompositeViewsRoutesSpec extends CompositeViewsRoutesFixtures {
     fetchContext,
     ResolverContextResolution(rcr),
     alwaysValidate,
-    config,
+    config.minIntervalRebuild,
+    config.eventLog,
     xas,
     clock
   ).accepted

diff --git a/.../ch/epfl/bluebrain/nexus/delta/plugins/elasticsearch/client/ElasticSearchClientSpec.scala b/.../ch/epfl/bluebrain/nexus/delta/plugins/elasticsearch/client/ElasticSearchClientSpec.scala
@@ -4,6 +4,7 @@ import akka.actor.ActorSystem
 import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.model.Uri.Query
 import akka.testkit.TestKit
+import cats.effect.IO
 import cats.implicits._
 import ch.epfl.bluebrain.nexus.delta.kernel.search.Pagination.FromPagination
 import ch.epfl.bluebrain.nexus.delta.plugins.elasticsearch.ScalaTestElasticSearchClientSetup
@@ -23,7 +24,7 @@ import ch.epfl.bluebrain.nexus.testkit.CirceLiteral
 import ch.epfl.bluebrain.nexus.testkit.elasticsearch.ElasticSearchDocker
 import ch.epfl.bluebrain.nexus.testkit.scalatest.ce.CatsEffectSpec
 import io.circe.{Json, JsonObject}
-import org.scalatest.DoNotDiscover
+import org.scalatest.{Assertion, DoNotDiscover}
 import org.scalatest.concurrent.Eventually
 
 import scala.concurrent.duration._
@@ -260,23 +261,25 @@ class ElasticSearchClientSpec(override val docker: ElasticSearchDocker)
         ElasticSearchAction.Update(index, "1", json"""{ "doc" : {"field2" : "value2"} }""")
       )
 
+      def theCountShouldBe(count: Long): IO[Assertion] =
+        esClient.count(index.value).map(_ shouldEqual count)
+
       {
         for {
           // Indexing and checking count
-          _        <- esClient.bulk(operations)
-          _        <- esClient.refresh(index)
-          original <- esClient.count(index.value)
-          _         = original shouldEqual 2L
+          _    <- esClient.bulk(operations)
+          _    <- esClient.refresh(index)
+          _    <- eventually { theCountShouldBe(2L) }
           // Deleting document matching the given query
-          query     = jobj"""{"query": {"bool": {"must": {"term": {"field1": 3} } } } }"""
-          _        <- esClient.deleteByQuery(query, index)
+          query = jobj"""{"query": {"bool": {"must": {"term": {"field1": 3} } } } }"""
+          _    <- esClient.deleteByQuery(query, index)
           // Checking docs again
-          newCount <- esClient.count(index.value)
-          _         = newCount shouldEqual 1L
-          doc1     <- esClient.getSource[Json](index, "1").attemptNarrow[HttpClientError]
-          _         = doc1.rightValue
-          doc2     <- esClient.getSource[Json](index, "2").attemptNarrow[HttpClientError]
-          _         = doc2.leftValue.errorCode.value shouldEqual StatusCodes.NotFound
+          _    <- esClient.refresh(index)
+          _    <- eventually { theCountShouldBe(1L) }
+          doc1 <- esClient.getSource[Json](index, "1").attemptNarrow[HttpClientError]
+          _     = doc1.rightValue
+          doc2 <- esClient.getSource[Json](index, "2").attemptNarrow[HttpClientError]
+          _     = doc2.leftValue.errorCode.value shouldEqual StatusCodes.NotFound
         } yield ()
       }.accepted
     }

diff --git a/...st/scala/ch/epfl/bluebrain/nexus/delta/plugins/search/SearchScopeInitializationSpec.scala b/...st/scala/ch/epfl/bluebrain/nexus/delta/plugins/search/SearchScopeInitializationSpec.scala
@@ -35,7 +35,8 @@ class SearchScopeInitializationSpec
     fetchContext,
     ResolverContextResolution(rcr),
     alwaysValidate,
-    config,
+    config.minIntervalRebuild,
+    config.eventLog,
     xas,
     clock
   ).accepted