diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index acf3b6452..3a878a6bf 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -16,10 +16,10 @@ jobs: steps: - uses: actions/checkout@v5 - - name: Set up JDK 11 + - name: Set up JDK 21 uses: actions/setup-java@v5 with: - java-version: '11' + java-version: '21' distribution: 'zulu' cache: maven diff --git a/Dockerfile b/Dockerfile index b921534cc..23da3f3b4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -32,7 +32,7 @@ # Install library dependencies before actually building source. # This caches libraries into an image layer that can be reused when only source code has changed. -FROM azul/zulu-openjdk-debian:11 as build_environment +FROM azul/zulu-openjdk-debian:21 as build_environment LABEL maintainer="Forrest Collman , Eric Trautman " RUN apt-get update && apt-get install -y maven @@ -85,7 +85,7 @@ RUN mkdir -p /root/render-lib && \ # Once web service application is built, set up jetty server and deploy application to it. # NOTE: jetty version should be kept in sync with values in render/render-ws/pom.xml and render/render-ws/src/main/scripts/install.sh -FROM jetty:10.0.13-jre11 as render-ws +FROM jetty:10.0.26-jre21 as render-ws # add packages not included in base image: # curl and coreutils are always needed for gnu readlink, tzdata is needed to set timezone diff --git a/docs/src/site/markdown/how-to/how-to-local-spark-intellij.md b/docs/src/site/markdown/how-to/how-to-local-spark-intellij.md index 1fb918a1c..3fd2594de 100644 --- a/docs/src/site/markdown/how-to/how-to-local-spark-intellij.md +++ b/docs/src/site/markdown/how-to/how-to-local-spark-intellij.md @@ -1,7 +1,7 @@ # How To: Run Spark Locally in IntelliJ It can be useful to run and test render spark clients within an IDE -[using a local master URL](https://spark.apache.org/docs/3.4.1/submitting-applications.html#master-urls). Unfortunately +[using a local master URL](https://spark.apache.org/docs/4.0.4/submitting-applications.html#master-urls). Unfortunately because we need to exclude spark libraries from the render-ws-spark-client fat jar, you'll need to add a few extra settings to your IntelliJ run configuration to get spark clients to run within the IDE. @@ -10,7 +10,7 @@ few extra settings to your IntelliJ run configuration to get spark clients to ru The hadoop client runtime library is required to run spark locally. If you don't already have it in a local directory, an easy way to install it is to: - Comment out the library's exclusion block in the -[render-ws-spark-client pom.xml](../../../../../render-ws-spark-client/pom.xml#L213-L216): +[render-ws-spark-client pom.xml](../../../../../render-ws-spark-client/pom.xml#L267-L270): ``` 2.1.3 - - 3.1.9 - - 2.14.3 + + 2.18.6 1.6.2 @@ -163,9 +164,9 @@ gpl_v2 Howard Hughes Medical Institute - - 11 - [11,] + + 21 + [21,] false @@ -179,7 +180,7 @@ maven-compiler-plugin - 11 + 21 diff --git a/render-app/pom.xml b/render-app/pom.xml index f1a5aca3b..52119274b 100644 --- a/render-app/pom.xml +++ b/render-app/pom.xml @@ -164,11 +164,11 @@ n5-hdf5 - + com.fasterxml.jackson.core jackson-databind - ${jackson-version} diff --git a/render-ws-java-client/pom.xml b/render-ws-java-client/pom.xml index 0599c6b3a..ce9ef8d82 100644 --- a/render-ws-java-client/pom.xml +++ b/render-ws-java-client/pom.xml @@ -230,11 +230,11 @@ ${n5-version} - + com.fasterxml.jackson.core jackson-databind - ${jackson-version} diff --git a/render-ws-spark-client/pom.xml b/render-ws-spark-client/pom.xml index fef7b6bf7..1d5945f74 100644 --- a/render-ws-spark-client/pom.xml +++ b/render-ws-spark-client/pom.xml @@ -183,38 +183,22 @@ org.janelia.saalfeldlab n5-spark - 3.7.3 + + 4.1.0 - + com.esotericsoftware kryo - - javax.validation - validation-api - - - - com.google.http-client - google-http-client-xml - - - - com.kjetland - mbknor-jackson-jsonschema_2.12 - - + com.fasterxml.jackson.core jackson-databind - ${jackson-version} @@ -222,7 +206,12 @@ org.apache.spark spark-core_2.13 - 3.4.1 + + 4.0.4 provided @@ -249,9 +238,9 @@ Comment out the hadoop-client-runtime exclusion below and run mvn compile to pull it into your local .m2/repository. The compile will fail because of the enforcer no-duplicate-classes rule but the jar will get pulled. - Once $HOME/.m2/repository/org/apache/hadoop/hadoop-client-runtime/3.3.4/hadoop-client-runtime-3.3.4.jar exists, + Once $HOME/.m2/repository/org/apache/hadoop/hadoop-client-runtime/3.4.1/hadoop-client-runtime-3.4.1.jar exists, uncomment the exclusion and run mvn clean package. - Finally, add the hadoop-client-runtime-3.3.4.jar to IntelliJ run configurations to run local Spark jobs from IDE. + Finally, add the hadoop-client-runtime-3.4.1.jar to IntelliJ run configurations to run local Spark jobs from IDE. Note that the hadoop version will change with Spark version changes. Hopefully, whoever updates Spark will also update this comment with the new corresponding hadoop version and .m2 path. diff --git a/render-ws/pom.xml b/render-ws/pom.xml index 6785ea5db..fbb5ceafe 100644 --- a/render-ws/pom.xml +++ b/render-ws/pom.xml @@ -102,11 +102,11 @@ ${n5-version} - + com.fasterxml.jackson.core jackson-databind - ${jackson-version} @@ -161,16 +161,23 @@ resteasy-servlet-initializer + com.fasterxml.jackson.jaxrs jackson-jaxrs-json-provider - ${jackson-version} + ${jackson.version} jakarta.activation jakarta.activation-api + + + javax.xml.bind + jaxb-api + @@ -247,7 +254,7 @@ 4.7.9.Final - 10.0.13 + 10.0.26 4.4.1 gpl_v2 Howard Hughes Medical Institute diff --git a/render-ws/src/main/scripts/install.sh b/render-ws/src/main/scripts/install.sh index fb25d24b4..653d3fa03 100755 --- a/render-ws/src/main/scripts/install.sh +++ b/render-ws/src/main/scripts/install.sh @@ -1,6 +1,6 @@ #!/bin/bash -JETTY_VERSION="10.0.13" # NOTE: jetty version should be kept in sync with values in render/render-ws/pom.xml and render/Dockerfile +JETTY_VERSION="10.0.26" # NOTE: jetty version should be kept in sync with values in render/render-ws/pom.xml and render/Dockerfile JETTY_DIST="jetty-home-${JETTY_VERSION}" # URLs for Jetty 10, SLF4J 1.7, Logback 1.1, and Swagger 2.1 MAVEN_CENTRAL_URL="https://repo1.maven.org" @@ -91,7 +91,7 @@ JETTY_WRAPPER_SCRIPT="${JETTY_BASE}/jetty_wrapper.sh" sed " s~/opt/local/jetty_home~${JETTY_HOME}~ s~/opt/local/jetty_base~${JETTY_BASE}~ - s~/misc/sc/jdks/zulu11~${JAVA_HOME}~ + s~/misc/sc/jdks/zulu21~${JAVA_HOME}~ " "${SCRIPTS_DIR}"/jetty/jetty_wrapper.sh > "${JETTY_WRAPPER_SCRIPT}" chmod 755 "${JETTY_WRAPPER_SCRIPT}" diff --git a/render-ws/src/main/scripts/jdk-vars.sh b/render-ws/src/main/scripts/jdk-vars.sh index ca88833a7..68f4c3fa7 100755 --- a/render-ws/src/main/scripts/jdk-vars.sh +++ b/render-ws/src/main/scripts/jdk-vars.sh @@ -1,8 +1,8 @@ #!/bin/bash -export JDK_VERSION="zulu11.78.15-ca-jdk11.0.26-linux_x64" +export JDK_VERSION="zulu21.52.15-ca-jdk21.0.12-linux_x64" # URL for JDK # You can find latest Linux x64 download links at: -# https://www.azul.com/downloads/?version=java-11-lts&os=linux&architecture=x86-64-bit&package=jdk&show-old-builds=true#zulu +# https://www.azul.com/downloads/?version=java-21-lts&os=linux&architecture=x86-64-bit&package=jdk&show-old-builds=true#zulu export JDK_URL="https://cdn.azul.com/zulu/bin/${JDK_VERSION}.tar.gz" \ No newline at end of file diff --git a/render-ws/src/main/scripts/jetty/jetty_wrapper.sh b/render-ws/src/main/scripts/jetty/jetty_wrapper.sh index 81a1b0d07..1a42783be 100755 --- a/render-ws/src/main/scripts/jetty/jetty_wrapper.sh +++ b/render-ws/src/main/scripts/jetty/jetty_wrapper.sh @@ -21,7 +21,7 @@ export JETTY_STATE="${JETTY_RUN}/jetty.state" # JETTY_USER # JETTY_SHELL -export JAVA_HOME="/misc/sc/jdks/zulu11" +export JAVA_HOME="/misc/sc/jdks/zulu21" export PATH="${JAVA_HOME}/bin:${PATH}" export JAVA="${JAVA_HOME}/bin/java" export JAVA_OPTIONS="-Xms${JETTY_MIN_AND_MAX_MEMORY} -Xmx${JETTY_MIN_AND_MAX_MEMORY} -server -Djava.awt.headless=true" diff --git a/trakem2-scripts/pom.xml b/trakem2-scripts/pom.xml index 1f171b9f3..c15e4809d 100644 --- a/trakem2-scripts/pom.xml +++ b/trakem2-scripts/pom.xml @@ -238,11 +238,11 @@ ${n5-version} - + com.fasterxml.jackson.core jackson-databind - ${jackson-version}