Merge 44d387b into 0b404c8

IQSS · Apr 15, 2024 · 98228c4 · 98228c4
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diff --git a/doc/sphinx-guides/source/admin/monitoring.rst b/doc/sphinx-guides/source/admin/monitoring.rst
@@ -154,7 +154,7 @@ Tips:
 MicroProfile Metrics endpoint
 -----------------------------
 
-Payara provides the metrics endpoint: <https://docs.payara.fish/community/docs/6.2023.9/Technical%20Documentation/MicroProfile/Metrics/Metrics%20Rest%20Endpoint.html>_
+Payara provides the metrics endpoint: <https://docs.payara.fish/community/docs/Technical%20Documentation/MicroProfile/Metrics/Metrics%20Rest%20Endpoint.html>_
 The metrics you can retrieve that way:
 - `index_permit_wait_time_seconds_mean` displays how long does it take to receive a permit to index a dataset.
 - `index_time_seconds` displays how long does it take to index a dataset.
diff --git a/doc/sphinx-guides/source/container/base-image.rst b/doc/sphinx-guides/source/container/base-image.rst
@@ -46,7 +46,7 @@ The base image provides:
 - CLI tools necessary to run Dataverse (i. e. ``curl`` or ``jq`` - see also :doc:`../installation/prerequisites` in Installation Guide)
 - Linux tools for analysis, monitoring and so on
 - `Jattach <https://github.com/apangin/jattach>`__ (attach to running JVM)
-- `wait-for <https://github.com/eficode/wait-for>`__ (tool to "wait for" a service to be available)
+- `wait4x <https://github.com/atkrad/wait4x>`__ (tool to "wait for" a service to be available)
 - `dumb-init <https://github.com/Yelp/dumb-init>`__ (see :ref:`below <base-entrypoint>` for details)
 
 This image is created as a "multi-arch image", see :ref:`below <base-multiarch>`.

diff --git a/doc/sphinx-guides/source/developers/classic-dev-env.rst b/doc/sphinx-guides/source/developers/classic-dev-env.rst
@@ -93,15 +93,15 @@ On Linux, install ``jq`` from your package manager or download a binary from htt
 Install Payara
 ~~~~~~~~~~~~~~
 
-Payara 6.2023.8 or higher is required.
+Payara 6.2024.4 or higher is required.
 
 To install Payara, run the following commands:
 
 ``cd /usr/local``
 
-``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip``
+``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2024.4/payara-6.2024.4.zip``
 
-``sudo unzip payara-6.2023.8.zip``
+``sudo unzip payara-6.2024.4.zip``
 
 ``sudo chown -R $USER /usr/local/payara6``
 

diff --git a/doc/sphinx-guides/source/installation/prerequisites.rst b/doc/sphinx-guides/source/installation/prerequisites.rst
@@ -44,7 +44,7 @@ On RHEL/derivative you can make Java 17 the default with the ``alternatives`` co
 Payara
 ------
 
-Payara 6.2023.8 is recommended. Newer versions might work fine. Regular updates are recommended.
+Payara 6.2024.4 is recommended. Newer versions might work fine. Regular updates are recommended.
 
 Installing Payara
 =================
@@ -55,8 +55,8 @@ Installing Payara
 
 - Download and install Payara (installed in ``/usr/local/payara6`` in the example commands below)::
 
-	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip
-	# unzip payara-6.2023.8.zip
+	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2024.4/payara-6.2024.4.zip
+	# unzip payara-6.2024.4.zip
 	# mv payara6 /usr/local
 
 If nexus.payara.fish is ever down for maintenance, Payara distributions are also available from https://repo1.maven.org/maven2/fish/payara/distributions/payara/

diff --git a/doc/sphinx-guides/source/qa/test-automation.md b/doc/sphinx-guides/source/qa/test-automation.md
@@ -52,7 +52,7 @@ Go to the end of the log and then scroll up, looking for the failure. A failed A
 
 ```
 TASK [dataverse : download payara zip] *****************************************
-fatal: [localhost]: FAILED! => {"changed": false, "dest": "/tmp/payara.zip", "elapsed": 10, "msg": "Request failed: <urlopen error timed out>", "url": "https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip"}
+fatal: [localhost]: FAILED! => {"changed": false, "dest": "/tmp/payara.zip", "elapsed": 10, "msg": "Request failed: <urlopen error timed out>", "url": "https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2024.4/payara-6.2024.4.zip"}
 ```
 
 In the example above, if Payara can't be downloaded, we're obviously going to have problems deploying Dataverse to it!

diff --git a/modules/container-base/src/main/docker/Dockerfile b/modules/container-base/src/main/docker/Dockerfile
@@ -69,6 +69,9 @@ ENV PATH="${PATH}:${PAYARA_DIR}/bin:${SCRIPT_DIR}" \
 ### PART 1: SYSTEM ###
 ARG UID=1000
 ARG GID=1000
+# Auto-populated by BuildKit / buildx
+#ARG TARGETARCH="amd64"
+ARG TARGETARCH
 USER root
 WORKDIR /
 SHELL ["/bin/bash", "-euo", "pipefail", "-c"]
@@ -90,10 +93,10 @@ RUN <<EOF
 
 EOF
 
-ARG JATTACH_VERSION="v2.1"
-ARG JATTACH_CHECKSUM="07885fdc782e02e7302c6d190f54c3930afa10a38140365adf54076ec1086a8e"
-ARG WAIT_FOR_VERSION="v2.2.3"
-ARG WAIT_FOR_CHECKSUM="70271181be69cd2c7265b2746f97fccfd7e8aa1059894138a775369c23589ff4"
+ARG JATTACH_VERSION="v2.2"
+ARG JATTACH_TGZ_CHECKSUM_AMD64="acd9e17f15749306be843df392063893e97bfecc5260eef73ee98f06e5cfe02f"
+ARG JATTACH_TGZ_CHECKSUM_ARM64="288ae5ed87ee7fe0e608c06db5a23a096a6217c9878ede53c4e33710bdcaab51"
+ARG WAIT4X_VERSION="v2.14.0"
 ARG PKGS="jq imagemagick curl unzip wget acl dirmngr gpg lsof procps netcat dumb-init"
 
 # Installing the packages in an extra container layer for better caching
@@ -103,15 +106,21 @@ RUN <<EOF
     apt-get install -qqy --no-install-recommends ${PKGS}
     rm -rf "/var/lib/apt/lists/*"
 
-    # Install jattach
-    curl -sSfL -o /usr/bin/jattach "https://github.com/apangin/jattach/releases/download/${JATTACH_VERSION}/jattach"
-    echo "${JATTACH_CHECKSUM} /usr/bin/jattach" | sha256sum -c -
-    chmod +x /usr/bin/jattach
-
-    # Install wait-for
-    curl -sSfL -o /usr/bin/wait-for "https://github.com/eficode/wait-for/releases/download/${WAIT_FOR_VERSION}/wait-for"
-    echo "${WAIT_FOR_CHECKSUM} /usr/bin/wait-for" | sha256sum -c -
-    chmod +x /usr/bin/wait-for
+    # Install jattach & wait4x
+    if [ "${TARGETARCH}" = "amd64" ]; then
+      curl -sSfL -o /usr/bin/jattach.tgz "https://github.com/jattach/jattach/releases/download/${JATTACH_VERSION}/jattach-linux-x64.tgz"
+      echo "${JATTACH_TGZ_CHECKSUM_AMD64} /usr/bin/jattach.tgz" | sha256sum -c -
+    elif [ "${TARGETARCH}" = "arm64" ]; then
+      curl -sSfL -o /usr/bin/jattach.tgz "https://github.com/jattach/jattach/releases/download/${JATTACH_VERSION}/jattach-linux-arm64.tgz"
+      echo "${JATTACH_TGZ_CHECKSUM_ARM64} /usr/bin/jattach.tgz" | sha256sum -c -
+    fi
+    tar -xzf /usr/bin/jattach.tgz -C /usr/bin && chmod +x /usr/bin/jattach
+
+    # Install wait4x
+    curl -sSfL -o /usr/bin/wait4x.tar.gz "https://github.com/atkrad/wait4x/releases/download/${WAIT4X_VERSION}/wait4x-linux-${TARGETARCH}.tar.gz"
+    curl -sSfL -o /tmp/w4x-checksum "https://github.com/atkrad/wait4x/releases/download/${WAIT4X_VERSION}/wait4x-linux-${TARGETARCH}.tar.gz.sha256sum"
+    echo "$(cat /tmp/w4x-checksum | cut -f1 -d" ") /usr/bin/wait4x.tar.gz" | sha256sum -c -
+    tar -xzf /usr/bin/wait4x.tar.gz -C /usr/bin && chmod +x /usr/bin/wait4x
 EOF
 
 ### PART 2: PAYARA ###
@@ -166,8 +175,6 @@ RUN <<EOF
     ${ASADMIN} create-jvm-options '-XX\:MetaspaceSize=${ENV=MEM_METASPACE_SIZE}'
     ${ASADMIN} create-jvm-options '-XX\:MaxMetaspaceSize=${ENV=MEM_MAX_METASPACE_SIZE}'
     ${ASADMIN} create-jvm-options '-XX\:+IgnoreUnrecognizedVMOptions'
-    # Workaround for FISH-7722: Failed to deploy war with @Stateless https://github.com/payara/Payara/issues/6337
-    ${ASADMIN} create-jvm-options --add-opens=java.base/java.io=ALL-UNNAMED
     # Disable autodeploy and hot reload
     ${ASADMIN} set configs.config.server-config.admin-service.das-config.dynamic-reload-enabled="false"
     ${ASADMIN} set configs.config.server-config.admin-service.das-config.autodeploy-enabled="false"

diff --git a/modules/dataverse-parent/pom.xml b/modules/dataverse-parent/pom.xml
@@ -148,7 +148,7 @@
         <argLine>-Duser.timezone=${project.timezone} -Dfile.encoding=${project.build.sourceEncoding} -Duser.language=${project.language} -Duser.region=${project.region}</argLine>
 
         <!-- Major system components and dependencies -->
-        <payara.version>6.2023.8</payara.version>
+        <payara.version>6.2024.4</payara.version>
         <postgresql.version>42.7.2</postgresql.version>
         <solr.version>9.3.0</solr.version>
         <aws.version>1.12.290</aws.version>
@@ -386,18 +386,6 @@
                 <enabled>false</enabled>
             </snapshots>
         </repository>
-        <!-- This repository is about to being phased out. See https://github.com/payara/Payara_PatchedProjects/issues/366 -->
-        <repository>
-            <id>payara-patched-externals</id>
-            <name>Payara Patched Externals</name>
-            <url>https://raw.github.com/payara/Payara_PatchedProjects/master</url>
-            <releases>
-                <enabled>true</enabled>
-            </releases>
-            <snapshots>
-                <enabled>false</enabled>
-            </snapshots>
-        </repository>
         <repository>
             <id>central-repo</id>
             <name>Central Repository</name>

diff --git a/pom.xml b/pom.xml
@@ -213,9 +213,6 @@
             <groupId>fish.payara.api</groupId>
             <artifactId>payara-api</artifactId>
             <scope>provided</scope>
-            <!-- Note: The version was provided by Payara BOM till 6.2023.7, when they removed the Core BOM from it as
-                       meant for internal use only. Simply referencing the version property here solves the problem. -->
-            <version>${payara.version}</version>
         </dependency>
 
         <!-- JSON-P -->

diff --git a/scripts/installer/as-setup.sh b/scripts/installer/as-setup.sh
@@ -117,9 +117,6 @@ function preliminary_setup()
 
   ./asadmin $ASADMIN_OPTS create-jvm-options "-Ddataverse.timerServer=true"
 
-  # Workaround for FISH-7722: Failed to deploy war with @Stateless https://github.com/payara/Payara/issues/6337
-  ./asadmin $ASADMIN_OPTS create-jvm-options --add-opens=java.base/java.io=ALL-UNNAMED
-
   # enable comet support
   ./asadmin $ASADMIN_OPTS set server-config.network-config.protocols.protocol.http-listener-1.http.comet-support-enabled="true"
 

diff --git a/src/main/docker/scripts/init_3_wait_dataverse_db_host.sh b/src/main/docker/scripts/init_3_wait_dataverse_db_host.sh
@@ -1,4 +1,4 @@
 #It was reported on 9949 that on the first launch of the containers Dataverse would not be deployed on payara
 #this was caused by a race condition due postgress not being ready. A solion for docker compose was prepared
 #but didn't work due a compatibility issue on the Maven pluggin [https://github.com/fabric8io/docker-maven-plugin/issues/888]
-wait-for "${DATAVERSE_DB_HOST:-postgres}:${DATAVERSE_DB_PORT:-5432}" -t 120
+wait4x tcp "${DATAVERSE_DB_HOST:-postgres}:${DATAVERSE_DB_PORT:-5432}" -t 120s