chore: Jena & libs upgrade (#1079)

SwissDataScienceCenter · Aug 30, 2022 · 84633ee · 84633ee
1 parent ecb31c7
commit 84633ee
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Showing 24 changed files with 54 additions and 38 deletions.
diff --git a/acceptance-tests/project/build.properties b/acceptance-tests/project/build.properties
@@ -1 +1 @@
-sbt.version=1.7.0
+sbt.version=1.7.1
diff --git a/commit-event-service/Dockerfile b/commit-event-service/Dockerfile
@@ -10,7 +10,7 @@ COPY . .
 RUN export PATH="/usr/local/sbt/bin:$PATH" && \
     apk update && apk add --no-cache --virtual .build-dependencies bash wget tar git && \
     mkdir -p "/usr/local/sbt" && \
-    wget -qO  - "https://github.com/sbt/sbt/releases/download/v1.7.0/sbt-1.7.0.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
+    wget -qO  - "https://github.com/sbt/sbt/releases/download/v1.7.1/sbt-1.7.1.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
     sbt writeVersionToVersionSbt && \
     sbt writeVersionToVersionConf && \
     sbt "project commit-event-service" stage  && \

diff --git a/commit-event-service/build.sbt b/commit-event-service/build.sbt
@@ -18,4 +18,4 @@
 
 name := "commit-event-service"
 
-libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.2.11"
+libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.4.0"
diff --git a/...t-event-service/src/test/scala/io/renku/commiteventservice/events/EventEndpointSpec.scala b/...t-event-service/src/test/scala/io/renku/commiteventservice/events/EventEndpointSpec.scala
@@ -1,3 +1,21 @@
+/*
+ * Copyright 2022 Swiss Data Science Center (SDSC)
+ * A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+ * Eidgenössische Technische Hochschule Zürich (ETHZ).
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package io.renku.commiteventservice.events
 
 import cats.effect.IO

diff --git a/event-log/Dockerfile b/event-log/Dockerfile
@@ -10,7 +10,7 @@ COPY . .
 RUN export PATH="/usr/local/sbt/bin:$PATH" && \
     apk update && apk add --no-cache --virtual .build-dependencies bash wget tar git && \
     mkdir -p "/usr/local/sbt" && \
-    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.0/sbt-1.7.0.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
+    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.1/sbt-1.7.1.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
     sbt writeVersionToVersionSbt && \
     sbt writeVersionToVersionConf && \
     sbt "project event-log" stage && \

diff --git a/event-log/build.sbt b/event-log/build.sbt
@@ -20,4 +20,4 @@ name := "event-log"
 
 Test / fork := true
 
-libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.2.11"
+libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.4.0"
diff --git a/generators/build.sbt b/generators/build.sbt
@@ -19,8 +19,8 @@
 organization := "io.renku"
 name := "generators"
 
-libraryDependencies += "eu.timepit"     %% "refined"    % "0.9.29"
+libraryDependencies += "eu.timepit"     %% "refined"    % "0.10.1"
 libraryDependencies += "io.circe"       %% "circe-core" % "0.14.2"
 libraryDependencies += "io.renku"       %% "jsonld4s"   % "0.2.0"
 libraryDependencies += "org.typelevel"  %% "cats-core"  % "2.8.0"
-libraryDependencies += "org.scalacheck" %% "scalacheck" % "1.14.3" // version 1.15.1 is broken
+libraryDependencies += "org.scalacheck" %% "scalacheck" % "1.16.0"
diff --git a/graph-commons/build.sbt b/graph-commons/build.sbt
@@ -24,8 +24,8 @@ val pureConfigVersion = "0.17.1"
 libraryDependencies += "com.github.pureconfig" %% "pureconfig"      % pureConfigVersion
 libraryDependencies += "com.github.pureconfig" %% "pureconfig-cats" % pureConfigVersion
 
-libraryDependencies += "eu.timepit"   %% "refined-pureconfig" % "0.9.29"
-libraryDependencies += "io.sentry"     % "sentry-logback"     % "6.1.2"
+libraryDependencies += "eu.timepit"   %% "refined-pureconfig" % "0.10.1"
+libraryDependencies += "io.sentry"     % "sentry-logback"     % "6.4.0"
 libraryDependencies += "org.tpolecat" %% "skunk-core"         % "0.3.1"
 
 val http4sVersion = "0.23.12"
@@ -36,11 +36,11 @@ libraryDependencies += "org.http4s" %% "http4s-dsl"                % http4sVersi
 libraryDependencies += "org.http4s" %% "http4s-prometheus-metrics" % http4sVersion
 libraryDependencies += "org.http4s" %% "http4s-server"             % http4sVersion
 
-libraryDependencies += "org.typelevel" %% "cats-effect"   % "3.3.5"
-libraryDependencies += "org.typelevel" %% "log4cats-core" % "2.3.2"
+libraryDependencies += "org.typelevel" %% "cats-effect"   % "3.3.14"
+libraryDependencies += "org.typelevel" %% "log4cats-core" % "2.4.0"
 
 // Test dependencies
-val testContainersScalaVersion = "0.40.8"
+val testContainersScalaVersion = "0.40.10"
 libraryDependencies += "com.dimafeng"          %% "testcontainers-scala-scalatest"  % testContainersScalaVersion % Test
 libraryDependencies += "com.dimafeng"          %% "testcontainers-scala-postgresql" % testContainersScalaVersion % Test
 libraryDependencies += "com.github.tomakehurst" % "wiremock-jre8"                   % "2.33.2"                   % Test

diff --git a/graph-commons/src/test/scala/io/renku/triplesstore/InMemoryJena.scala b/graph-commons/src/test/scala/io/renku/triplesstore/InMemoryJena.scala
@@ -45,13 +45,13 @@ trait InMemoryJena {
   lazy val container: SingleContainer[_] = maybeJenaFixedPort match {
     case None =>
       GenericContainer(
-        dockerImage = "renku/renku-jena:0.0.16",
+        dockerImage = "renku/renku-jena:0.0.17",
         exposedPorts = Seq(3030),
         waitStrategy = Wait forHttp "/$/ping"
       )
     case Some(fixedPort) =>
       FixedHostPortGenericContainer(
-        imageName = "renku/renku-jena:0.0.16",
+        imageName = "renku/renku-jena:0.0.17",
         exposedPorts = Seq(3030),
         exposedHostPort = fixedPort.value,
         exposedContainerPort = fixedPort.value,

diff --git a/helm-chart/renku-graph/requirements.yaml b/helm-chart/renku-graph/requirements.yaml
@@ -3,6 +3,6 @@ dependencies:
   version: "0.0.3"
   repository: "https://swissdatasciencecenter.github.io/helm-charts/"
 - name: renku-jena
-  version: "0.0.16"
+  version: "0.0.17"
   repository: "https://swissdatasciencecenter.github.io/helm-charts/"
   alias: jena
diff --git a/helm-chart/renku-graph/values.yaml b/helm-chart/renku-graph/values.yaml
@@ -30,7 +30,7 @@ jena:
   image:
     repository: renku/renku-jena
     pullPolicy: IfNotPresent
-    tag: '0.0.16'
+    tag: '0.0.17'
   users:
     admin:
       ## Admin user password

diff --git a/knowledge-graph/Dockerfile b/knowledge-graph/Dockerfile
@@ -10,7 +10,7 @@ COPY . .
 RUN export PATH="/usr/local/sbt/bin:$PATH" && \
     apk update && apk add --no-cache --virtual .build-dependencies bash wget tar git && \
     mkdir -p "/usr/local/sbt" && \
-    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.0/sbt-1.7.0.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
+    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.1/sbt-1.7.1.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
     sbt writeVersionToVersionSbt && \
     sbt writeVersionToVersionConf && \
     sbt "project knowledge-graph" stage && \

diff --git a/knowledge-graph/build.sbt b/knowledge-graph/build.sbt
@@ -22,13 +22,13 @@ Test / fork := true
 
 // log4j-core is needed only by widoco
 libraryDependencies += "org.apache.logging.log4j" % "log4j-core"      % "2.18.0"
-libraryDependencies += "ch.qos.logback"           % "logback-classic" % "1.2.11"
+libraryDependencies += "ch.qos.logback"           % "logback-classic" % "1.4.0"
 
 libraryDependencies += "com.github.dgarijo" % "widoco" % "1.4.17"
 
-libraryDependencies += "io.swagger.parser.v3" % "swagger-parser" % "2.0.33"
+libraryDependencies += "io.swagger.parser.v3" % "swagger-parser" % "2.1.2"
 
-libraryDependencies += "org.sangria-graphql" %% "sangria"       % "3.0.1"
+libraryDependencies += "org.sangria-graphql" %% "sangria"       % "3.2.0"
 libraryDependencies += "org.sangria-graphql" %% "sangria-circe" % "1.3.2"
 
 resolvers += "jitpack" at "https://jitpack.io"
diff --git a/project/build.properties b/project/build.properties
@@ -1 +1 @@
-sbt.version=1.7.0
+sbt.version=1.7.1
diff --git a/project/plugins.sbt b/project/plugins.sbt
@@ -18,8 +18,8 @@
 
 addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.4.6")
 
-addSbtPlugin("com.github.sbt" % "sbt-native-packager" % "1.9.9")
+addSbtPlugin("com.github.sbt" % "sbt-native-packager" % "1.9.11")
 
-addSbtPlugin("de.heikoseeberger" % "sbt-header" % "5.6.0")
+addSbtPlugin("de.heikoseeberger" % "sbt-header" % "5.7.0")
 
 addSbtPlugin("com.github.sbt" % "sbt-release" % "1.1.0")
diff --git a/tiny-types/build.sbt b/tiny-types/build.sbt
@@ -19,7 +19,7 @@
 organization := "io.renku"
 name := "tiny-types"
 
-libraryDependencies += "eu.timepit" %% "refined" % "0.9.29"
+libraryDependencies += "eu.timepit" %% "refined" % "0.10.1"
 
 val circeVersion = "0.14.1"
 libraryDependencies += "io.circe" %% "circe-core"    % circeVersion
@@ -34,6 +34,6 @@ val catsVersion = "2.8.0"
 libraryDependencies += "org.typelevel" %% "cats-core" % catsVersion
 libraryDependencies += "org.typelevel" %% "cats-free" % catsVersion
 
-libraryDependencies += "org.scalacheck"    %% "scalacheck"      % "1.14.3"  % Test // version 1.15.1 is broken
-libraryDependencies += "org.scalatest"     %% "scalatest"       % "3.2.12"  % Test
+libraryDependencies += "org.scalacheck"    %% "scalacheck"      % "1.16.0"  % Test
+libraryDependencies += "org.scalatest"     %% "scalatest"       % "3.2.13"  % Test
 libraryDependencies += "org.scalatestplus" %% "scalacheck-1-14" % "3.2.2.0" % Test
diff --git a/token-repository/Dockerfile b/token-repository/Dockerfile
@@ -10,7 +10,7 @@ COPY . .
 RUN export PATH="/usr/local/sbt/bin:$PATH" && \
     apk update && apk add --no-cache --virtual .build-dependencies bash wget tar git && \
     mkdir -p "/usr/local/sbt" && \
-    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.0/sbt-1.7.0.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
+    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.1/sbt-1.7.1.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
     sbt writeVersionToVersionSbt && \
     sbt writeVersionToVersionConf && \
     sbt "project token-repository" stage && \

diff --git a/token-repository/build.sbt b/token-repository/build.sbt
@@ -20,4 +20,4 @@ name := "token-repository"
 
 Test / fork := true
 
-libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.2.11"
+libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.4.0"
diff --git a/triples-generator/Dockerfile b/triples-generator/Dockerfile
@@ -10,7 +10,7 @@ COPY . .
 RUN export PATH="/usr/local/sbt/bin:$PATH" && \
     apk update && apk add --no-cache --virtual .build-dependencies bash wget tar git && \
     mkdir -p "/usr/local/sbt" && \
-    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.0/sbt-1.7.0.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
+    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.1/sbt-1.7.1.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
     sbt writeVersionToVersionSbt && \
     sbt writeVersionToVersionConf && \
     sbt "project triples-generator" stage && \

diff --git a/triples-generator/build.sbt b/triples-generator/build.sbt
@@ -20,5 +20,5 @@ name := "triples-generator"
 
 Test / fork := true
 
-libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.2.11"
+libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.4.0"
 libraryDependencies += "com.lihaoyi"   %% "ammonite-ops"    % "2.4.1"
diff --git a/...iplesgenerator/events/consumers/tsmigrationrequest/migrations/MultipleDSDateCreated.scala b/...iplesgenerator/events/consumers/tsmigrationrequest/migrations/MultipleDSDateCreated.scala
@@ -22,11 +22,10 @@ package migrations
 import cats.effect.Async
 import cats.syntax.all._
 import eu.timepit.refined.auto._
-import io.renku.graph.model.Schemas.schema
+import io.renku.graph.model.Schemas.{schema, xsd}
 import io.renku.metrics.MetricsRegistry
 import io.renku.triplesstore.SparqlQuery.Prefixes
 import io.renku.triplesstore.{SparqlQuery, SparqlQueryTimeRecorder}
-import io.renku.triplesgenerator.events.consumers.tsmigrationrequest.Migration
 import org.typelevel.log4cats.Logger
 import tooling.UpdateQueryMigration
 
@@ -38,20 +37,19 @@ private object MultipleDSDateCreated {
   private lazy val name = Migration.Name("Multiple DateCreated on DS")
   private[migrations] lazy val query = SparqlQuery.of(
     name.asRefined,
-    Prefixes of schema -> "schema",
+    Prefixes of (schema -> "schema", xsd -> "xsd"),
     s"""|DELETE { ?dsId schema:dateCreated ?date }
         |WHERE {
         |  SELECT ?dsId ?date
         |  WHERE {
         |    {
-        |      SELECT ?dsId (MIN(?date) as ?minDate)
+        |      SELECT ?dsId (MIN(xsd:dateTime(?date)) as ?minDate)
         |      WHERE {
         |        ?dsId a schema:Dataset;
         |              schema:dateCreated ?date.
         |      }
         |      GROUP BY ?dsId
         |      HAVING (COUNT(?date) > 1)
-        |      ORDER BY ?dsId
         |    }
         |    ?dsId schema:dateCreated ?date.
         |    FILTER ( ?date != ?minDate )

diff --git a/...sgenerator/events/consumers/tsmigrationrequest/migrations/MultipleDSDateCreatedSpec.scala b/...sgenerator/events/consumers/tsmigrationrequest/migrations/MultipleDSDateCreatedSpec.scala
@@ -29,9 +29,9 @@ import io.renku.graph.model.testentities._
 import io.renku.interpreters.TestLogger
 import io.renku.logging.TestSparqlQueryTimeRecorder
 import io.renku.metrics.MetricsRegistry
+import io.renku.testtools.IOSpec
 import io.renku.triplesstore.SparqlQuery.Prefixes
 import io.renku.triplesstore._
-import io.renku.testtools.IOSpec
 import org.scalamock.scalatest.MockFactory
 import org.scalatest.matchers.should
 import org.scalatest.wordspec.AnyWordSpec

diff --git a/webhook-service/Dockerfile b/webhook-service/Dockerfile
@@ -10,7 +10,7 @@ COPY . .
 RUN export PATH="/usr/local/sbt/bin:$PATH" && \
     apk update && apk add --no-cache --virtual .build-dependencies bash wget tar git && \
     mkdir -p "/usr/local/sbt" && \
-    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.0/sbt-1.7.0.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
+    wget -qO - "https://github.com/sbt/sbt/releases/download/v1.7.1/sbt-1.7.1.tgz" | tar xz -C /usr/local/sbt --strip-components=1 && \
     sbt writeVersionToVersionSbt && \
     sbt writeVersionToVersionConf && \
     sbt "project webhook-service" stage  && \

diff --git a/webhook-service/build.sbt b/webhook-service/build.sbt
@@ -18,4 +18,4 @@
 
 name := "webhook-service"
 
-libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.2.11"
+libraryDependencies += "ch.qos.logback" % "logback-classic" % "1.4.0"