merge develop into master for 6.9 release

.github/actions/setup-maven/action.yml

@@ -23,7 +23,7 @@ runs:
         echo "JAVA_VERSION=$(grep '<target.java.version>' ${GITHUB_WORKSPACE}/modules/dataverse-parent/pom.xml | cut -f2 -d'>' | cut -f1 -d'<')" | tee -a ${GITHUB_ENV}
     - name: Set up JDK ${{ env.JAVA_VERSION }}
       id: setup-java
-      uses: actions/setup-java@v4
+      uses: actions/setup-java@v5
       with:
         java-version: ${{ env.JAVA_VERSION }}
         distribution: 'temurin'

.github/workflows/codeql.yml

@@ -71,7 +71,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
         build-mode: ${{ matrix.build-mode }}
@@ -99,6 +99,6 @@ jobs:
         exit 1
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4
       with:
         category: "/language:${{matrix.language}}"

.github/workflows/container_app_pr.yml

@@ -23,7 +23,7 @@ jobs:
             - uses: actions/checkout@v5
               with:
                   ref: 'refs/pull/${{ github.event.client_payload.pull_request.number }}/merge'
-            - uses: actions/setup-java@v4
+            - uses: actions/setup-java@v5
               with:
                   java-version: "17"
                   distribution: 'adopt'
@@ -86,7 +86,7 @@ jobs:
                       :ship: [See on GHCR](https://github.com/orgs/gdcc/packages/container). Use by referencing with full name as printed above, mind the registry name.
 
             # Leave a note when things have gone sideways
-            - uses: peter-evans/create-or-update-comment@v4
+            - uses: peter-evans/create-or-update-comment@v5
               if: ${{ failure() }}
               with:
                   issue-number: ${{ github.event.client_payload.pull_request.number }}

.github/workflows/container_maintenance.yml

@@ -218,7 +218,7 @@ jobs:
           cat "./modules/container-base/README.md"
       - name: Push description to DockerHub for base image
         if: ${{ ! inputs.dry_run && ! inputs.damp_run && toJSON(needs.base-image.outputs.rebuilt_images) != '[]' }}
-        uses: peter-evans/dockerhub-description@v4
+        uses: peter-evans/dockerhub-description@v5
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -243,7 +243,7 @@ jobs:
           cat "./src/main/docker/README.md"
       - name: Push description to DockerHub for application image
         if: ${{ ! inputs.dry_run && ! inputs.damp_run && toJSON(needs.application-image.outputs.rebuilt_images) != '[]' }}
-        uses: peter-evans/dockerhub-description@v4
+        uses: peter-evans/dockerhub-description@v5
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -268,7 +268,7 @@ jobs:
           cat "./modules/container-configbaker/README.md"
       - name: Push description to DockerHub for config baker image
         if: ${{ ! inputs.dry_run && ! inputs.damp_run && toJSON(needs.configbaker-image.outputs.rebuilt_images) != '[]' }}
-        uses: peter-evans/dockerhub-description@v4
+        uses: peter-evans/dockerhub-description@v5
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/deploy_beta_testing.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v5
 
-      - uses: actions/setup-java@v4
+      - uses: actions/setup-java@v5
         with:
           distribution: 'zulu'
           java-version: '17'
@@ -36,7 +36,7 @@ jobs:
         run: echo "war_file=$(ls *.war | head -1)">> $GITHUB_ENV
 
       - name: Upload war artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: built-app
           path: ./target/${{ env.war_file }}
@@ -50,7 +50,7 @@ jobs:
       - uses: actions/checkout@v5
 
       - name: Download war artifact
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v6
         with:
           name: built-app
           path: ./
@@ -69,7 +69,7 @@ jobs:
           overwrite: true
 
       - name: Execute payara war deployment remotely
-        uses: appleboy/[email protected].2
+        uses: appleboy/[email protected].3
         env:
           INPUT_WAR_FILE: ${{ env.war_file }}
         with:

.github/workflows/maven_cache_management.yml

@@ -36,7 +36,7 @@ jobs:
             - name: Determine Java version from Parent POM
               run: echo "JAVA_VERSION=$(grep '<target.java.version>' modules/dataverse-parent/pom.xml | cut -f2 -d'>' | cut -f1 -d'<')" >> ${GITHUB_ENV}
             - name: Set up JDK ${{ env.JAVA_VERSION }}
-              uses: actions/setup-java@v4
+              uses: actions/setup-java@v5
               with:
                   java-version: ${{ env.JAVA_VERSION }}
                   distribution: temurin

.github/workflows/maven_unit_test.yml

@@ -39,7 +39,7 @@ jobs:
           # Basic setup chores
           - uses: actions/checkout@v5
           - name: Set up JDK ${{ matrix.jdk }}
-            uses: actions/setup-java@v4
+            uses: actions/setup-java@v5
             with:
                 java-version: ${{ matrix.jdk }}
                 distribution: temurin
@@ -62,7 +62,7 @@ jobs:
 
           # Upload the built war file. For download, it will be wrapped in a ZIP by GitHub.
           # See also https://github.com/actions/upload-artifact#zipped-artifact-downloads
-          - uses: actions/upload-artifact@v4
+          - uses: actions/upload-artifact@v5
             with:
                 name: dataverse-java${{ matrix.jdk }}.war
                 path: target/dataverse*.war
@@ -72,7 +72,7 @@ jobs:
           - run: |
                 tar -cvf java-builddir.tar target
                 tar -cvf java-m2-selection.tar ~/.m2/repository/io/gdcc/dataverse-*
-          - uses: actions/upload-artifact@v4
+          - uses: actions/upload-artifact@v5
             with:
                 name: java-artifacts
                 path: |
@@ -105,14 +105,14 @@ jobs:
             # Basic setup chores
             - uses: actions/checkout@v5
             - name: Set up JDK ${{ matrix.jdk }}
-              uses: actions/setup-java@v4
+              uses: actions/setup-java@v5
               with:
                   java-version: ${{ matrix.jdk }}
                   distribution: temurin
                   cache: maven
 
             # Get the build output from the unit test job
-            - uses: actions/download-artifact@v5
+            - uses: actions/download-artifact@v6
               with:
                   name: java-artifacts
             - run: |
@@ -124,7 +124,7 @@ jobs:
 
             # Wrap up and send to coverage job
             - run: tar -cvf java-reportdir.tar target/site
-            - uses: actions/upload-artifact@v4
+            - uses: actions/upload-artifact@v5
               with:
                   name: java-reportdir
                   path: java-reportdir.tar
@@ -138,14 +138,14 @@ jobs:
             # TODO: As part of #10618 change to setup-maven custom action
             # Basic setup chores
           - uses: actions/checkout@v5
-          - uses: actions/setup-java@v4
+          - uses: actions/setup-java@v5
             with:
                 java-version: '17'
                 distribution: temurin
                 cache: maven
 
           # Get the build output from the integration test job
-          - uses: actions/download-artifact@v5
+          - uses: actions/download-artifact@v6
             with:
                 name: java-reportdir
           - run: tar -xvf java-reportdir.tar

.github/workflows/spi_release.yml

@@ -38,11 +38,11 @@ jobs:
         if: github.event_name == 'pull_request' && needs.check-secrets.outputs.available == 'true'
         steps:
             - uses: actions/checkout@v5
-            - uses: actions/setup-java@v4
+            - uses: actions/setup-java@v5
               with:
                   java-version: '17'
                   distribution: 'adopt'
-                  server-id: ossrh
+                  server-id: central
                   server-username: MAVEN_USERNAME
                   server-password: MAVEN_PASSWORD
             - uses: actions/cache@v4
@@ -64,7 +64,7 @@ jobs:
         if: github.event_name == 'push' && needs.check-secrets.outputs.available == 'true'
         steps:
             -   uses: actions/checkout@v5
-            -   uses: actions/setup-java@v4
+            -   uses: actions/setup-java@v5
                 with:
                     java-version: '17'
                     distribution: 'adopt'
@@ -76,11 +76,11 @@ jobs:
 
             # Running setup-java again overwrites the settings.xml - IT'S MANDATORY TO DO THIS SECOND SETUP!!!
             -   name: Set up Maven Central Repository
-                uses: actions/setup-java@v4
+                uses: actions/setup-java@v5
                 with:
                     java-version: '17'
                     distribution: 'adopt'
-                    server-id: ossrh
+                    server-id: central
                     server-username: MAVEN_USERNAME
                     server-password: MAVEN_PASSWORD
                     gpg-private-key: ${{ secrets.DATAVERSEBOT_GPG_KEY }}

conf/keycloak/builtin-users-spi/pom.xml

@@ -100,7 +100,7 @@
     </build>
 
     <properties>
-        <keycloak.version>26.3.2</keycloak.version>
+        <keycloak.version>26.3.4</keycloak.version>
         <java.version>17</java.version>
         <jakarta.persistence.version>3.2.0</jakarta.persistence.version>
         <mindrot.jbcrypt.version>0.4</mindrot.jbcrypt.version>

conf/mdc/counter_weekly.sh

@@ -0,0 +1,92 @@
+#!/bin/sh
+#counter_weekly.sh
+
+# This script iterates through all published Datasets in all Dataverses and calls the Make Data Count API to update their citations from DataCite
+# Note: Requires curl and jq for parsing JSON responses form curl
+
+# A recursive method to process each Dataverse
+processDV () {
+echo "Processing Dataverse ID#: $1"
+
+#Call the Dataverse API to get the contents of the Dataverse (without credentials, this will only list published datasets and dataverses
+DVCONTENTS=$(curl -s http://localhost:8080/api/dataverses/$1/contents)
+
+# Iterate over all datasets, pulling the value of their DOIs (as part of the persistentUrl) from the json returned
+for subds in $(echo "${DVCONTENTS}" | jq -r '.data[] | select(.type == "dataset") | .persistentUrl'); do
+
+#The authority/identifier are preceded by a protocol/host, i.e. https://doi.org/
+DOI=`expr "$subds" : '.*:\/\/\doi\.org\/\(.*\)'`
+
+# Call the Dataverse API for this dataset and capture both the response and HTTP status code
+HTTP_RESPONSE=$(curl -s -w "\n%{http_code}" -X POST "http://localhost:8080/api/admin/makeDataCount/:persistentId/updateCitationsForDataset?persistentId=doi:$DOI")
+
+# Extract the HTTP status code from the last line
+HTTP_STATUS=$(echo "$HTTP_RESPONSE" | tail -n1)
+# Extract the response body (everything except the last line)
+RESPONSE_BODY=$(echo "$HTTP_RESPONSE" | sed '$d')
+
+# Check the HTTP status code and report accordingly
+case $HTTP_STATUS in
+    200)
+        # Successfully queued
+        # Extract status from the nested data object
+        STATUS=$(echo "$RESPONSE_BODY" | jq -r '.data.status')
+
+        # Extract message from the nested data object
+        if echo "$RESPONSE_BODY" | jq -e '.data.message' > /dev/null 2>&1 && [ "$(echo "$RESPONSE_BODY" | jq -r '.data.message')" != "null" ]; then
+            MESSAGE=$(echo "$RESPONSE_BODY" | jq -r '.data.message')
+            echo "[SUCCESS] doi:$DOI - $STATUS: $MESSAGE"
+        else
+            # If message is missing or null, just show the status
+            echo "[SUCCESS] doi:$DOI - $STATUS: Citation update queued"
+        fi
+        ;;
+    400)
+        # Bad request
+        if echo "$RESPONSE_BODY" | jq -e '.message' > /dev/null 2>&1; then
+            ERROR=$(echo "$RESPONSE_BODY" | jq -r '.message')
+            echo "[ERROR 400] doi:$DOI - Bad request: $ERROR"
+        else
+            echo "[ERROR 400] doi:$DOI - Bad request"
+        fi
+        ;;
+    404)
+        # Not found
+        if echo "$RESPONSE_BODY" | jq -e '.message' > /dev/null 2>&1; then
+            ERROR=$(echo "$RESPONSE_BODY" | jq -r '.message')
+            echo "[ERROR 404] doi:$DOI - Not found: $ERROR"
+        else
+            echo "[ERROR 404] doi:$DOI - Not found"
+        fi
+        ;;
+    503)
+        # Service unavailable (queue full)
+        if echo "$RESPONSE_BODY" | jq -e '.message' > /dev/null 2>&1; then
+            ERROR=$(echo "$RESPONSE_BODY" | jq -r '.message')
+            echo "[ERROR 503] doi:$DOI - Service unavailable: $ERROR"
+        elif echo "$RESPONSE_BODY" | jq -e '.data.message' > /dev/null 2>&1; then
+            ERROR=$(echo "$RESPONSE_BODY" | jq -r '.data.message')
+            echo "[ERROR 503] doi:$DOI - Service unavailable: $ERROR"
+        else
+            echo "[ERROR 503] doi:$DOI - Service unavailable: Queue is full"
+        fi
+        ;;
+    *)
+        # Other error
+        echo "[ERROR $HTTP_STATUS] doi:$DOI - Unexpected error"
+        echo "Response: $RESPONSE_BODY"
+        ;;
+esac
+
+done
+
+# Now iterate over any child Dataverses and recursively process them
+for subdv in $(echo "${DVCONTENTS}" | jq -r '.data[] | select(.type == "dataverse") | .id'); do
+echo $subdv
+processDV $subdv
+done
+
+}
+
+# Call the function on the root dataverse to start processing 
+processDV 1