Merge branch 'master' into envelope-to-elem

BlueBrain · Jan 9, 2024 · 3ef239e · 3ef239e
2 parents 38a8220 + fe86350
commit 3ef239e
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Showing 59 changed files with 306 additions and 234 deletions.
diff --git a/.github/workflows/ci-delta-app.yml b/.github/workflows/ci-delta-app.yml
@@ -18,7 +18,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Checkout
         uses: actions/checkout@v4

diff --git a/.github/workflows/ci-delta-core.yml b/.github/workflows/ci-delta-core.yml
@@ -22,7 +22,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Checkout
         uses: actions/checkout@v4

diff --git a/.github/workflows/ci-delta-plugins.yml b/.github/workflows/ci-delta-plugins.yml
@@ -23,7 +23,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Checkout
         uses: actions/checkout@v4

diff --git a/.github/workflows/ci-delta-static-analysis.yml b/.github/workflows/ci-delta-static-analysis.yml
@@ -18,7 +18,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Checkout
         uses: actions/checkout@v4

diff --git a/.github/workflows/ci-docs-ext-links.yml b/.github/workflows/ci-docs-ext-links.yml
@@ -13,7 +13,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Checkout
         uses: actions/checkout@v4

diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml
@@ -17,7 +17,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Checkout
         uses: actions/checkout@v4

diff --git a/.github/workflows/ci-integration-tests.yml b/.github/workflows/ci-integration-tests.yml
@@ -19,7 +19,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Checkout
         uses: actions/checkout@v4

diff --git a/.github/workflows/ci-release-docker.yml b/.github/workflows/ci-release-docker.yml
@@ -19,7 +19,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Set up proxy for docker buildx
         run: |

diff --git a/.github/workflows/ci-release-sonatype.yml b/.github/workflows/ci-release-sonatype.yml
@@ -25,7 +25,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Publish To Sonatype
         run: sbt -Dsbt.color=always -Dsbt.supershell=false ci-release
diff --git a/.github/workflows/ci-snapshot.yml b/.github/workflows/ci-snapshot.yml
@@ -26,7 +26,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Set up proxy for docker buildx
         run: |

diff --git a/.github/workflows/ci-storage.yml b/.github/workflows/ci-storage.yml
@@ -18,7 +18,7 @@ jobs:
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           check-latest: true
       - name: Checkout
         uses: actions/checkout@v4

diff --git a/build.sbt b/build.sbt
@@ -40,22 +40,22 @@ val handleBarsVersion       = "4.3.1"
 val hikariVersion           = "5.1.0"
 val jenaVersion             = "4.2.0"
 val jsonldjavaVersion       = "0.13.6"
-val kamonVersion            = "2.6.6"
+val kamonVersion            = "2.7.0"
 val kanelaAgentVersion      = "1.0.18"
 val kindProjectorVersion    = "0.13.2"
 val log4catsVersion         = "2.6.0"
 val logbackVersion          = "1.4.14"
-val magnoliaVersion         = "1.1.6"
+val magnoliaVersion         = "1.1.8"
 val mockitoVersion          = "1.17.30"
 val munitVersion            = "1.0.0-M10"
 val munitCatsEffectVersion  = "2.0.0-M4"
-val nimbusJoseJwtVersion    = "9.37.1"
-val postgresJdbcVersion     = "42.7.0"
+val nimbusJoseJwtVersion    = "9.37.3"
+val postgresJdbcVersion     = "42.7.1"
 val pureconfigVersion       = "0.17.4"
 val scalaTestVersion        = "3.2.17"
 val scalaXmlVersion         = "2.2.0"
 val topBraidVersion         = "1.3.2" // 1.4.1 fails to validate some test schemas
-val testContainersVersion   = "1.19.1"
+val testContainersVersion   = "1.19.3"
 
 lazy val akkaActorTyped = "com.typesafe.akka" %% "akka-actor-typed" % akkaVersion
 
@@ -913,7 +913,7 @@ lazy val compilation = {
   Seq(
     scalaVersion                           := scalaCompilerVersion,
     scalacOptions                          ~= { options: Seq[String] => options.filterNot(Set("-Wself-implicit", "-Xlint:infer-any", "-Wnonunit-statement")) },
-    javaSpecificationVersion               := "17",
+    javaSpecificationVersion               := "21",
     javacOptions                          ++= Seq(
       "-source",
       javaSpecificationVersion.value,
@@ -977,7 +977,7 @@ lazy val servicePackaging = {
       else version.value
     },
     Docker / daemonUser   := "nexus",
-    dockerBaseImage       := "eclipse-temurin:17-jre",
+    dockerBaseImage       := "eclipse-temurin:21-jre",
     dockerBuildxPlatforms := Seq("linux/arm64/v8", "linux/amd64"),
     dockerExposedPorts    := Seq(8080),
     dockerUsername        := Some("bluebrain"),

diff --git a/...cala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphScopeInitialization.scala b/...cala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphScopeInitialization.scala
@@ -13,7 +13,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.organizations.model.Organization
 import ch.epfl.bluebrain.nexus.delta.sdk.projects.model.Project
 import ch.epfl.bluebrain.nexus.delta.sdk.{Defaults, ScopeInitialization}
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.Subject
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.{EntityType, Identity}
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{EntityType, Identity, IriFilter}
 
 /**
   * The default creation of the default SparqlView as part of the project initialization.
@@ -38,8 +38,8 @@ class BlazegraphScopeInitialization(
   private def defaultValue: IndexingBlazegraphViewValue = IndexingBlazegraphViewValue(
     name = Some(defaults.name),
     description = Some(defaults.description),
-    resourceSchemas = Set.empty,
-    resourceTypes = Set.empty,
+    resourceSchemas = IriFilter.None,
+    resourceTypes = IriFilter.None,
     resourceTag = None,
     includeMetadata = true,
     includeDeprecated = true,

diff --git a/...rc/main/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/model/BlazegraphView.scala b/...rc/main/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/model/BlazegraphView.scala
@@ -13,7 +13,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.model.{BaseUri, IdSegmentRef, Tags}
 import ch.epfl.bluebrain.nexus.delta.sdk.permissions.model.Permission
 import ch.epfl.bluebrain.nexus.delta.sdk.syntax._
 import ch.epfl.bluebrain.nexus.delta.sdk.views.ViewRef
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.ProjectRef
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{IriFilter, ProjectRef}
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Tag.UserTag
 import io.circe.generic.extras.Configuration
 import io.circe.generic.extras.semiauto.deriveConfiguredEncoder
@@ -112,8 +112,8 @@ object BlazegraphView {
       description: Option[String],
       project: ProjectRef,
       uuid: UUID,
-      resourceSchemas: Set[Iri],
-      resourceTypes: Set[Iri],
+      resourceSchemas: IriFilter,
+      resourceTypes: IriFilter,
       resourceTag: Option[UserTag],
       includeMetadata: Boolean,
       includeDeprecated: Boolean,

diff --git a/...in/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/model/BlazegraphViewValue.scala b/...in/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/model/BlazegraphViewValue.scala
@@ -9,6 +9,7 @@ import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.decoder.{Configuration, JsonLdDe
 import ch.epfl.bluebrain.nexus.delta.sdk.permissions.model.Permission
 import ch.epfl.bluebrain.nexus.delta.sdk.views.ViewRef
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Tag.{Latest, UserTag}
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.IriFilter
 import ch.epfl.bluebrain.nexus.delta.sourcing.query.SelectFilter
 import ch.epfl.bluebrain.nexus.delta.sourcing.stream.PipeChain
 import io.circe.generic.extras.semiauto.deriveConfiguredEncoder
@@ -72,8 +73,8 @@ object BlazegraphViewValue {
   final case class IndexingBlazegraphViewValue(
       name: Option[String] = None,
       description: Option[String] = None,
-      resourceSchemas: Set[Iri] = Set.empty,
-      resourceTypes: Set[Iri] = Set.empty,
+      resourceSchemas: IriFilter = IriFilter.None,
+      resourceTypes: IriFilter = IriFilter.None,
       resourceTag: Option[UserTag] = None,
       includeMetadata: Boolean = false,
       includeDeprecated: Boolean = false,

diff --git a/.../ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphScopeInitializationSpec.scala b/.../ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphScopeInitializationSpec.scala
@@ -13,7 +13,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.projects.model.ApiMappings
 import ch.epfl.bluebrain.nexus.delta.sdk.resolvers.ResolverContextResolution
 import ch.epfl.bluebrain.nexus.delta.sdk.{ConfigFixtures, Defaults}
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.{Subject, User}
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.Label
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{IriFilter, Label}
 import ch.epfl.bluebrain.nexus.delta.sourcing.postgres.DoobieScalaTestFixture
 import ch.epfl.bluebrain.nexus.testkit.scalatest.ce.CatsEffectSpec
 
@@ -69,8 +69,8 @@ class BlazegraphScopeInitializationSpec
       val resource = views.fetch(defaultViewId, project.ref).accepted
       resource.value match {
         case v: IndexingBlazegraphView  =>
-          v.resourceSchemas shouldBe empty
-          v.resourceTypes shouldBe empty
+          v.resourceSchemas shouldBe IriFilter.None
+          v.resourceTypes shouldBe IriFilter.None
           v.resourceTag shouldEqual None
           v.includeDeprecated shouldEqual true
           v.includeMetadata shouldEqual true

diff --git a/...t/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphViewDecodingSpec.scala b/...t/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphViewDecodingSpec.scala
@@ -13,7 +13,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.permissions.model.Permission
 import ch.epfl.bluebrain.nexus.delta.sdk.projects.model.{ApiMappings, ProjectContext}
 import ch.epfl.bluebrain.nexus.delta.sdk.views.ViewRef
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Tag.UserTag
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.{Label, ProjectRef}
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{IriFilter, Label, ProjectRef}
 import ch.epfl.bluebrain.nexus.testkit.scalatest.ce.CatsEffectSpec
 import io.circe.literal._
 
@@ -62,8 +62,8 @@ class BlazegraphViewDecodingSpec extends CatsEffectSpec with Fixtures {
         val expected    = IndexingBlazegraphViewValue(
           name = Some("viewName"),
           description = Some("viewDescription"),
-          resourceSchemas = Set(context.vocab / "Person"),
-          resourceTypes = Set(context.vocab / "Person"),
+          resourceSchemas = IriFilter.restrictedTo(context.vocab / "Person"),
+          resourceTypes = IriFilter.restrictedTo(context.vocab / "Person"),
           resourceTag = Some(UserTag.unsafe("release")),
           includeMetadata = false,
           includeDeprecated = false,

diff --git a/...src/test/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphViewsSpec.scala b/...src/test/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphViewsSpec.scala
@@ -19,7 +19,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.projects.model.ApiMappings
 import ch.epfl.bluebrain.nexus.delta.sdk.resolvers.ResolverContextResolution
 import ch.epfl.bluebrain.nexus.delta.sdk.views.ViewRef
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.{Authenticated, Group, User}
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.Label
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{IriFilter, Label}
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Tag.UserTag
 import ch.epfl.bluebrain.nexus.delta.sourcing.postgres.DoobieScalaTestFixture
 import ch.epfl.bluebrain.nexus.testkit.scalatest.ce.CatsEffectSpec
@@ -45,8 +45,8 @@ class BlazegraphViewsSpec extends CatsEffectSpec with DoobieScalaTestFixture wit
     val indexingValue  = IndexingBlazegraphViewValue(
       None,
       None,
-      Set.empty,
-      Set.empty,
+      IriFilter.None,
+      IriFilter.None,
       None,
       includeMetadata = false,
       includeDeprecated = false,

diff --git a/.../test/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphViewsStmSpec.scala b/.../test/scala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/BlazegraphViewsStmSpec.scala
@@ -17,7 +17,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.permissions.model.Permission
 import ch.epfl.bluebrain.nexus.delta.sdk.views.ViewRef
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.{Anonymous, Subject, User}
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Tag.UserTag
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.{Label, ProjectRef}
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{IriFilter, Label, ProjectRef}
 import ch.epfl.bluebrain.nexus.testkit.scalatest.ce.CatsEffectSpec
 import io.circe.Json
 
@@ -43,8 +43,8 @@ class BlazegraphViewsStmSpec extends CatsEffectSpec with Fixtures {
     val indexingValue            = IndexingBlazegraphViewValue(
       None,
       None,
-      Set.empty,
-      Set.empty,
+      IriFilter.None,
+      IriFilter.None,
       None,
       includeMetadata = false,
       includeDeprecated = false,

diff --git a/...cala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/indexing/IndexingViewDefSuite.scala b/...cala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/indexing/IndexingViewDefSuite.scala
@@ -14,7 +14,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.stream.GraphResourceStream
 import ch.epfl.bluebrain.nexus.delta.sdk.views.ViewRef
 import ch.epfl.bluebrain.nexus.delta.sourcing.config.BatchConfig
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.{Anonymous, Subject}
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.ProjectRef
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{IriFilter, ProjectRef}
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Tag.UserTag
 import ch.epfl.bluebrain.nexus.delta.sourcing.offset.Offset
 import ch.epfl.bluebrain.nexus.delta.sourcing.stream.ProjectionErr.CouldNotFindTypedPipeErr
@@ -49,10 +49,10 @@ class IndexingViewDefSuite extends NexusSuite {
 
   private val namespace = s"${prefix}_${uuid}_1"
 
-  private val filterByTypeConfig = FilterByTypeConfig(Set(nxv + "PullRequest"))
+  private val filterByTypeConfig = FilterByTypeConfig(IriFilter.restrictedTo(nxv + "PullRequest"))
   private val indexing           = IndexingBlazegraphViewValue(
     resourceTag = Some(UserTag.unsafe("some.tag")),
-    resourceTypes = Set(nxv + "PullRequest")
+    resourceTypes = IriFilter.restrictedTo(nxv + "PullRequest")
   )
 
   private val aggregate =

diff --git a/...ala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/model/BlazegraphViewValueSuite.scala b/...ala/ch/epfl/bluebrain/nexus/delta/plugins/blazegraph/model/BlazegraphViewValueSuite.scala
@@ -2,6 +2,7 @@ package ch.epfl.bluebrain.nexus.delta.plugins.blazegraph.model
 
 import ch.epfl.bluebrain.nexus.delta.plugins.blazegraph.model.BlazegraphViewValue.{nextIndexingRev, IndexingBlazegraphViewValue}
 import ch.epfl.bluebrain.nexus.delta.rdf.IriOrBNode.Iri
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.IriFilter
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Tag.UserTag
 import munit.FunSuite
 
@@ -21,8 +22,8 @@ class BlazegraphViewValueSuite extends FunSuite {
 
   test("Views with different reindexing fields") {
     val viewValues = List(
-      viewValue.copy(resourceSchemas = Set(Iri.unsafe("http://localhost/schema"))),
-      viewValue.copy(resourceTypes = Set(Iri.unsafe("https://localhost/type"))),
+      viewValue.copy(resourceSchemas = IriFilter.restrictedTo(Iri.unsafe("http://localhost/schema"))),
+      viewValue.copy(resourceTypes = IriFilter.restrictedTo(Iri.unsafe("https://localhost/type"))),
       viewValue.copy(resourceTag = Some(UserTag.unsafe("tag"))),
       viewValue.copy(includeMetadata = true),
       viewValue.copy(includeDeprecated = true)

diff --git a/...fl/bluebrain/nexus/delta/plugins/blazegraph/model/BlazegraphViewsSerializationSuite.scala b/...fl/bluebrain/nexus/delta/plugins/blazegraph/model/BlazegraphViewsSerializationSuite.scala
@@ -14,7 +14,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.sse.SseEncoder.SseData
 import ch.epfl.bluebrain.nexus.delta.sdk.views.ViewRef
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.{Subject, User}
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Tag.UserTag
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.{Label, ProjectRef}
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{IriFilter, Label, ProjectRef}
 import io.circe.{Json, JsonObject}
 
 import java.time.Instant
@@ -32,8 +32,8 @@ class BlazegraphViewsSerializationSuite extends SerializationSuite {
   private val indexingValue    = IndexingBlazegraphViewValue(
     Some("viewName"),
     Some("viewDescription"),
-    Set(nxv + "some-schema"),
-    Set(nxv + "SomeType"),
+    IriFilter.restrictedTo(nxv + "some-schema"),
+    IriFilter.restrictedTo(nxv + "SomeType"),
     Some(UserTag.unsafe("some.tag")),
     includeMetadata = false,
     includeDeprecated = false,

diff --git a/.../main/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/client/DeltaClient.scala b/.../main/scala/ch/epfl/bluebrain/nexus/delta/plugins/compositeviews/client/DeltaClient.scala
@@ -21,7 +21,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.http.HttpClientError.HttpClientStatusEr
 import ch.epfl.bluebrain.nexus.delta.sdk.projects.model.ProjectStatistics
 import ch.epfl.bluebrain.nexus.delta.sdk.stream.StreamConverter
 import ch.epfl.bluebrain.nexus.delta.sdk.syntax._
-import ch.epfl.bluebrain.nexus.delta.sourcing.model.ElemStream
+import ch.epfl.bluebrain.nexus.delta.sourcing.model.{ElemStream, IriFilter}
 import ch.epfl.bluebrain.nexus.delta.sourcing.offset.Offset
 import ch.epfl.bluebrain.nexus.delta.sourcing.offset.Offset.Start
 import ch.epfl.bluebrain.nexus.delta.sourcing.stream.{Elem, RemainingElems}
@@ -149,9 +149,10 @@ object DeltaClient {
         }
     }
 
-    private def typeQuery(types: Set[Iri])               =
-      if (types.isEmpty) Query.Empty
-      else Query(types.map(t => "type" -> t.toString).toList: _*)
+    private def typeQuery(restriction: IriFilter) = restriction match {
+      case IriFilter.None           => Query.Empty
+      case IriFilter.Include(types) => Query(types.map(t => "type" -> t.toString).toList: _*)
+    }
 
     private def elemAddress(source: RemoteProjectSource) =
       (source.endpoint / "elems" / source.project.organization.value / source.project.project.value)