Merge remote-tracking branch 'origin/main' into issue-9317

atmire · May 24, 2024 · e6c24ae · e6c24ae
2 parents c0b18cd + 4802307
commit e6c24ae
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -49,7 +49,7 @@ jobs:
 
       # https://github.com/actions/setup-java
       - name: Install JDK ${{ matrix.java }}
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{ matrix.java }}
           distribution: 'temurin'
@@ -65,14 +65,14 @@ jobs:
       # (This artifact is downloadable at the bottom of any job's summary page)
       - name: Upload Results of ${{ matrix.type }} to Artifact
         if: ${{ failure() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.type }} results
           path: ${{ matrix.resultsdir }}
 
       # Upload code coverage report to artifact, so that it can be shared with the 'codecov' job (see below)
       - name: Upload code coverage report to Artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.type }} coverage report
           path: 'dspace/target/site/jacoco-aggregate/jacoco.xml'
@@ -91,7 +91,7 @@ jobs:
 
       # Download artifacts from previous 'tests' job
       - name: Download coverage artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
 
       # Now attempt upload to Codecov using its action.
       # NOTE: We use a retry action to retry the Codecov upload if it fails the first time.
@@ -101,10 +101,11 @@ jobs:
       - name: Upload coverage to Codecov.io
         uses: Wandalen/[email protected]
         with:
-          action: codecov/codecov-action@v3
+          action: codecov/codecov-action@v4
           # Ensure codecov-action throws an error when it fails to upload
           with: |
             fail_ci_if_error: true
+            token: ${{ secrets.CODECOV_TOKEN }}
           # Try re-running action 5 times max
           attempt_limit: 5
           # Run again in 30 seconds

diff --git a/.github/workflows/codescan.yml b/.github/workflows/codescan.yml
@@ -39,7 +39,7 @@ jobs:
 
       # https://github.com/actions/setup-java
       - name: Install JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'temurin'

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -43,7 +43,7 @@ jobs:
     needs: dspace-dependencies
     uses: ./.github/workflows/reusable-docker-build.yml
     with:
-      build_id: dspace
+      build_id: dspace-prod
       image_name: dspace/dspace
       dockerfile_path: ./Dockerfile
     secrets:
@@ -120,7 +120,7 @@ jobs:
     if: github.repository == 'dspace/dspace'
     uses: ./.github/workflows/reusable-docker-build.yml
     with:
-      build_id: dspace-postgres-pgcrypto
+      build_id: dspace-postgres-pgcrypto-prod
       image_name: dspace/dspace-postgres-pgcrypto
       # Must build out of subdirectory to have access to install script for pgcrypto.
       # NOTE: this context will build the image based on the Dockerfile in the specified directory

diff --git a/.github/workflows/issue_opened.yml b/.github/workflows/issue_opened.yml
@@ -16,7 +16,7 @@ jobs:
       # Only add to project board if issue is flagged as "needs triage" or has no labels
       # NOTE: By default we flag new issues as "needs triage" in our issue template
       if: (contains(github.event.issue.labels.*.name, 'needs triage') || join(github.event.issue.labels.*.name) == '')
-      uses: actions/add-to-project@v0.5.0
+      uses: actions/add-to-project@v1.0.0
       # Note, the authentication token below is an ORG level Secret. 
       # It must be created/recreated manually via a personal access token with admin:org, project, public_repo permissions
       # See: https://docs.github.com/en/actions/configuring-and-managing-workflows/authenticating-with-the-github_token#permissions-for-the-github_token

diff --git a/.github/workflows/pull_request_opened.yml b/.github/workflows/pull_request_opened.yml
@@ -21,4 +21,4 @@ jobs:
     # Assign the PR to whomever created it. This is useful for visualizing assignments on project boards
     # See https://github.com/toshimaru/auto-author-assign
     - name: Assign PR to creator
-      uses: toshimaru/auto-author-assign@v2.0.1
+      uses: toshimaru/auto-author-assign@v2.1.0
diff --git a/.github/workflows/reusable-docker-build.yml b/.github/workflows/reusable-docker-build.yml
@@ -68,9 +68,9 @@ env:
   # See "Redeploy" steps below for more details.
   REDEPLOY_SANDBOX_URL: ${{ secrets.REDEPLOY_SANDBOX_URL }}
   REDEPLOY_DEMO_URL: ${{ secrets.REDEPLOY_DEMO_URL }}
-  # Current DSpace maintenance branch (and architecture) which is deployed to demo.dspace.org / sandbox.dspace.org
-  # (NOTE: No deployment branch specified for sandbox.dspace.org as it uses the default_branch)
+  # Current DSpace branches (and architecture) which are deployed to demo.dspace.org & sandbox.dspace.org respectively
   DEPLOY_DEMO_BRANCH: 'dspace-7_x'
+  DEPLOY_SANDBOX_BRANCH: 'main'
   DEPLOY_ARCH: 'linux/amd64'
 
 jobs:
@@ -93,6 +93,14 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
+      # This step converts the slashes in the "arch" matrix values above into dashes & saves to env.ARCH_NAME
+      # E.g. "linux/amd64" becomes "linux-amd64"
+      # This is necessary because all upload artifacts CANNOT have special chars (like slashes)
+      - name: Prepare
+        run: |
+          platform=${{ matrix.arch }}
+          echo "ARCH_NAME=${platform//\//-}" >> $GITHUB_ENV
+
       # https://github.com/actions/checkout
       - name: Checkout codebase
         uses: actions/checkout@v4
@@ -152,9 +160,9 @@ jobs:
       # Upload digest to an artifact, so that it can be used in manifest below
       - name: Upload Docker build digest to artifact
         if: ${{ ! matrix.isPr }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: digests-${{ inputs.build_id }}
+          name: digests-${{ inputs.build_id }}-${{ env.ARCH_NAME }}
           path: /tmp/digests/*
           if-no-files-found: error
           retention-days: 1
@@ -166,13 +174,13 @@ jobs:
           !matrix.isPR &&
           env.REDEPLOY_SANDBOX_URL != '' &&
           matrix.arch == env.DEPLOY_ARCH &&
-          github.ref_name == github.event.repository.default_branch
+          github.ref_name == env.DEPLOY_SANDBOX_BRANCH
         run: |
           curl -X POST $REDEPLOY_SANDBOX_URL
 
       # If this build is NOT a PR and passed in a REDEPLOY_DEMO_URL secret,
       # Then redeploy https://demo.dspace.org if this build is for our deployment architecture and demo branch.
-      - name: Redeploy demo.dspace.org (based on maintenace branch)
+      - name: Redeploy demo.dspace.org (based on maintenance branch)
         if: |
           !matrix.isPR &&
           env.REDEPLOY_DEMO_URL != '' &&
@@ -192,10 +200,12 @@ jobs:
       - docker-build
     steps:
       - name: Download Docker build digests
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: digests-${{ inputs.build_id }}
           path: /tmp/digests
+          # Download digests for both AMD64 and ARM64 into same directory
+          pattern: digests-${{ inputs.build_id }}-*
+          merge-multiple: true
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3

diff --git a/Dockerfile b/Dockerfile
@@ -27,9 +27,11 @@ ENV MAVEN_FLAGS="-P-test-environment -Denforcer.skip=true -Dcheckstyle.skip=true
 RUN mvn --no-transfer-progress package ${MAVEN_FLAGS} && \
   mv /app/dspace/target/${TARGET_DIR}/* /install && \
   mvn clean
+# Remove the server webapp to keep image small.
+RUN rm -rf /install/webapps/server/
 
 # Step 2 - Run Ant Deploy
-FROM openjdk:${JDK_VERSION}-slim as ant_build
+FROM eclipse-temurin:${JDK_VERSION} as ant_build
 ARG TARGET_DIR=dspace-installer
 # COPY the /install directory from 'build' container to /dspace-src in this container
 COPY --from=build /install /dspace-src
@@ -49,23 +51,16 @@ RUN mkdir $ANT_HOME && \
 # Run necessary 'ant' deploy scripts
 RUN ant init_installation update_configs update_code update_webapps
 
-# Step 3 - Run tomcat
-# Create a new tomcat image that does not retain the the build directory contents
-FROM tomcat:10-jdk${JDK_VERSION}
+# Step 3 - Start up DSpace via Runnable JAR
+FROM eclipse-temurin:${JDK_VERSION}
 # NOTE: DSPACE_INSTALL must align with the "dspace.dir" default configuration.
 ENV DSPACE_INSTALL=/dspace
 # Copy the /dspace directory from 'ant_build' container to /dspace in this container
 COPY --from=ant_build /dspace $DSPACE_INSTALL
-# Expose Tomcat port and AJP port
-EXPOSE 8080 8009
+WORKDIR $DSPACE_INSTALL
+# Expose Tomcat port
+EXPOSE 8080
 # Give java extra memory (2GB)
 ENV JAVA_OPTS=-Xmx2000m
-
-# Link the DSpace 'server' webapp into Tomcat's webapps directory.
-# This ensures that when we start Tomcat, it runs from /server path (e.g. http://localhost:8080/server/)
-RUN ln -s $DSPACE_INSTALL/webapps/server   /usr/local/tomcat/webapps/server
-# If you wish to run "server" webapp off the ROOT path, then comment out the above RUN, and uncomment the below RUN.
-# You also MUST update the 'dspace.server.url' configuration to match.
-# Please note that server webapp should only run on one path at a time.
-#RUN mv /usr/local/tomcat/webapps/ROOT /usr/local/tomcat/webapps/ROOT.bk && \
-#    ln -s $DSPACE_INSTALL/webapps/server   /usr/local/tomcat/webapps/ROOT
+# On startup, run DSpace Runnable JAR
+ENTRYPOINT ["java", "-jar", "webapps/server-boot.jar", "--dspace.dir=$DSPACE_INSTALL"]
diff --git a/Dockerfile.cli b/Dockerfile.cli
@@ -25,7 +25,7 @@ RUN mvn --no-transfer-progress package && \
   mvn clean
 
 # Step 2 - Run Ant Deploy
-FROM openjdk:${JDK_VERSION}-slim as ant_build
+FROM eclipse-temurin:${JDK_VERSION} as ant_build
 ARG TARGET_DIR=dspace-installer
 # COPY the /install directory from 'build' container to /dspace-src in this container
 COPY --from=build /install /dspace-src
@@ -34,9 +34,9 @@ WORKDIR /dspace-src
 ENV ANT_VERSION 1.10.13
 ENV ANT_HOME /tmp/ant-$ANT_VERSION
 ENV PATH $ANT_HOME/bin:$PATH
-# Need wget to install ant, and unzip for managing AIPs
+# Need wget to install ant
 RUN apt-get update \
-    && apt-get install -y --no-install-recommends wget unzip \
+    && apt-get install -y --no-install-recommends wget \
     && apt-get purge -y --auto-remove \
     && rm -rf /var/lib/apt/lists/*
 # Download and install 'ant'
@@ -46,10 +46,15 @@ RUN mkdir $ANT_HOME && \
 RUN ant init_installation update_configs update_code
 
 # Step 3 - Run jdk
-FROM openjdk:${JDK_VERSION}
+FROM eclipse-temurin:${JDK_VERSION}
 # NOTE: DSPACE_INSTALL must align with the "dspace.dir" default configuration.
 ENV DSPACE_INSTALL=/dspace
 # Copy the /dspace directory from 'ant_build' container to /dspace in this container
 COPY --from=ant_build /dspace $DSPACE_INSTALL
 # Give java extra memory (1GB)
 ENV JAVA_OPTS=-Xmx1000m
+# Install unzip for AIPs
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends unzip \
+    && apt-get purge -y --auto-remove \
+    && rm -rf /var/lib/apt/lists/*
diff --git a/Dockerfile.dependencies b/Dockerfile.dependencies
@@ -7,7 +7,7 @@
 ARG JDK_VERSION=17
 
 # Step 1 - Run Maven Build
-FROM maven:3-openjdk-${JDK_VERSION}-slim as build
+FROM maven:3-eclipse-temurin-${JDK_VERSION} as build
 ARG TARGET_DIR=dspace-installer
 WORKDIR /app
 # Create the 'dspace' user account & home directory

diff --git a/Dockerfile.test b/Dockerfile.test
@@ -26,9 +26,11 @@ ADD --chown=dspace . /app/
 RUN mvn --no-transfer-progress package && \
   mv /app/dspace/target/${TARGET_DIR}/* /install && \
   mvn clean
+# Remove the server webapp to keep image small. Rename runnable JAR to server-boot.jar.
+RUN rm -rf /install/webapps/server/
 
 # Step 2 - Run Ant Deploy
-FROM openjdk:${JDK_VERSION}-slim as ant_build
+FROM eclipse-temurin:${JDK_VERSION} as ant_build
 ARG TARGET_DIR=dspace-installer
 # COPY the /install directory from 'build' container to /dspace-src in this container
 COPY --from=build /install /dspace-src
@@ -48,29 +50,18 @@ RUN mkdir $ANT_HOME && \
 # Run necessary 'ant' deploy scripts
 RUN ant init_installation update_configs update_code update_webapps
 
-# Step 3 - Run tomcat
-# Create a new tomcat image that does not retain the the build directory contents
-FROM tomcat:10-jdk${JDK_VERSION}
+# Step 3 - Start up DSpace via Runnable JAR
+FROM eclipse-temurin:${JDK_VERSION}
+# NOTE: DSPACE_INSTALL must align with the "dspace.dir" default configuration.
 ENV DSPACE_INSTALL=/dspace
-ENV TOMCAT_INSTALL=/usr/local/tomcat
-# Copy the /dspace directory from 'ant_build' containger to /dspace in this container
+# Copy the /dspace directory from 'ant_build' container to /dspace in this container
 COPY --from=ant_build /dspace $DSPACE_INSTALL
-# Enable the AJP connector in Tomcat's server.xml
-# NOTE: secretRequired="false" should only be used when AJP is NOT accessible from an external network. But, secretRequired="true" isn't supported by mod_proxy_ajp until Apache 2.5
-RUN sed -i '/Service name="Catalina".*/a \\n    <Connector protocol="AJP/1.3" port="8009" address="0.0.0.0" redirectPort="8443" URIEncoding="UTF-8" secretRequired="false" />' $TOMCAT_INSTALL/conf/server.xml
-# Expose Tomcat port and AJP port
-EXPOSE 8080 8009 8000
+WORKDIR $DSPACE_INSTALL
+# Expose Tomcat port and debugging port
+EXPOSE 8080 8000
 # Give java extra memory (2GB)
 ENV JAVA_OPTS=-Xmx2000m
 # Set up debugging
 ENV CATALINA_OPTS=-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=*:8000
-
-# Link the DSpace 'server' webapp into Tomcat's webapps directory.
-# This ensures that when we start Tomcat, it runs from /server path (e.g. http://localhost:8080/server/)
-RUN ln -s $DSPACE_INSTALL/webapps/server   /usr/local/tomcat/webapps/server
-# If you wish to run "server" webapp off the ROOT path, then comment out the above RUN, and uncomment the below RUN.
-# You also MUST update the 'dspace.server.url' configuration to match.
-# Please note that server webapp should only run on one path at a time.
-#RUN mv /usr/local/tomcat/webapps/ROOT /usr/local/tomcat/webapps/ROOT.bk && \
-#    ln -s $DSPACE_INSTALL/webapps/server   /usr/local/tomcat/webapps/ROOT
-
+# On startup, run DSpace Runnable JAR
+ENTRYPOINT ["java", "-jar", "webapps/server-boot.jar", "--dspace.dir=$DSPACE_INSTALL"]
diff --git a/docker-compose-cli.yml b/docker-compose-cli.yml
@@ -1,4 +1,3 @@
-version: "3.7"
 networks:
   # Default to using network named 'dspacenet' from docker-compose.yml.
   # Its full name will be prepended with the project name (e.g. "-p d7" means it will be named "d7_dspacenet")

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,4 +1,3 @@
-version: '3.7'
 networks:
   dspacenet:
     ipam:
@@ -40,8 +39,6 @@ services:
     ports:
     - published: 8080
       target: 8080
-    - published: 8009
-      target: 8009
     - published: 8000
       target: 8000
     stdin_open: true
@@ -55,14 +52,14 @@ services:
     # Ensure that the database is ready BEFORE starting tomcat
     # 1. While a TCP connection to dspacedb port 5432 is not available, continue to sleep
     # 2. Then, run database migration to init database tables
-    # 3. Finally, start Tomcat
+    # 3. Finally, start DSpace
     entrypoint:
     - /bin/bash
     - '-c'
     - |
       while (!</dev/tcp/dspacedb/5432) > /dev/null 2>&1; do sleep 1; done;
       /dspace/bin/dspace database migrate
-      catalina.sh run
+      java -jar /dspace/webapps/server-boot.jar --dspace.dir=/dspace
   # DSpace PostgreSQL database container
   dspacedb:
     container_name: dspacedb

diff --git a/dspace-api/pom.xml b/dspace-api/pom.xml
@@ -458,7 +458,12 @@
             <artifactId>commons-validator</artifactId>
         </dependency>
         <dependency>
-            <groupId>com.sun.mail</groupId>
+            <groupId>jakarta.mail</groupId>
+            <artifactId>jakarta.mail-api</artifactId>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.angus</groupId>
             <artifactId>jakarta.mail</artifactId>
         </dependency>
         <dependency>
@@ -733,27 +738,16 @@
 
         <!-- TODO: This may need to be replaced with the "orcid-model" artifact once this ticket is resolved:
              https://github.com/ORCID/orcid-model/issues/50 -->
+        <!-- Maintained at https://github.com/DSpace/orcid-model -->
         <dependency>
-            <groupId>org.orcid</groupId>
+            <groupId>org.dspace</groupId>
             <artifactId>orcid-model-jakarta</artifactId>
             <version>3.3.0</version>
             <exclusions>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.jarkarta.rs</groupId>
-                    <artifactId>jackson-jakarta-rs-json-provider</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.yaml</groupId>
-                    <artifactId>snakeyaml</artifactId>
-                </exclusion>
                 <exclusion>
                     <groupId>org.javassist</groupId>
                     <artifactId>javassist</artifactId>
                 </exclusion>
-                <exclusion>
-                    <groupId>io.swagger.core.v3</groupId>
-                    <artifactId>swagger-jaxrs2-jakarta</artifactId>
-                </exclusion>
             </exclusions>
         </dependency>
 
@@ -906,7 +900,7 @@
           <dependency>
               <groupId>org.xmlunit</groupId>
               <artifactId>xmlunit-core</artifactId>
-              <version>2.9.1</version>
+              <version>2.10.0</version>
               <scope>test</scope>
           </dependency>
           <dependency>