Merge pull request IQSS#9764 from IQSS/8094-java-17

Upgrade to Java 17

.github/workflows/container_app_pr.yml

@@ -25,7 +25,7 @@ jobs:
                   ref: 'refs/pull/${{ github.event.client_payload.pull_request.number }}/merge'
             - uses: actions/setup-java@v3
               with:
-                  java-version: "11"
+                  java-version: "17"
                   distribution: 'adopt'
             - uses: actions/cache@v3
               with:

.github/workflows/container_app_push.yml

@@ -36,10 +36,10 @@ jobs:
             - name: Checkout repository
               uses: actions/checkout@v3
 
-            - name: Set up JDK 11
+            - name: Set up JDK
               uses: actions/setup-java@v3
               with:
-                  java-version: "11"
+                  java-version: "17"
                   distribution: temurin
                   cache: maven
 
@@ -109,7 +109,7 @@ jobs:
             - uses: actions/checkout@v3
             - uses: actions/setup-java@v3
               with:
-                  java-version: "11"
+                  java-version: "17"
                   distribution: temurin
 
             # Depending on context, we push to different targets. Login accordingly.

.github/workflows/container_base_push.yml

@@ -34,7 +34,7 @@ jobs:
             packages: read
         strategy:
             matrix:
-                jdk: [ '11' ]
+                jdk: [ '17' ]
         # Only run in upstream repo - avoid unnecessary runs in forks
         if: ${{ github.repository_owner == 'IQSS' }}
 

.github/workflows/deploy_beta_testing.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: actions/setup-java@v3
         with:
           distribution: 'zulu'
-          java-version: '11'
+          java-version: '17'
 
       - name: Enable API Session Auth feature flag
         working-directory: src/main/resources/META-INF

.github/workflows/maven_unit_test.yml

@@ -22,18 +22,9 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                jdk: [ '11' ]
+                jdk: [ '17' ]
                 experimental: [false]
                 status:  ["Stable"]
-                #
-                # JDK 17 builds disabled due to non-essential fails marking CI jobs as completely failed within
-                # Github Projects, PR lists etc. This was consensus on Slack #dv-tech. See issue #8094
-                # (This is a limitation of how Github is currently handling these things.)
-                #
-                #include:
-                #    - jdk: '17'
-                #      experimental: true
-                #      status: "Experimental"
         continue-on-error: ${{ matrix.experimental }}
         runs-on: ubuntu-latest
         steps:
@@ -68,6 +59,14 @@ jobs:
 
           # We don't want to cache the WAR file, so delete it
           - run: rm -rf ~/.m2/repository/edu/harvard/iq/dataverse
+
+          # 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@v3
+            with:
+                name: dataverse-java${{ matrix.jdk }}.war
+                path: target/dataverse*.war
+                retention-days: 7
     push-app-img:
         name: Publish App Image
         permissions:

.github/workflows/spi_release.yml

@@ -40,7 +40,7 @@ jobs:
             - uses: actions/checkout@v3
             - uses: actions/setup-java@v3
               with:
-                  java-version: '11'
+                  java-version: '17'
                   distribution: 'adopt'
                   server-id: ossrh
                   server-username: MAVEN_USERNAME
@@ -66,7 +66,7 @@ jobs:
             -   uses: actions/checkout@v3
             -   uses: actions/setup-java@v3
                 with:
-                    java-version: '11'
+                    java-version: '17'
                     distribution: 'adopt'
             -   uses: actions/cache@v2
                 with:
@@ -78,7 +78,7 @@ jobs:
             -   name: Set up Maven Central Repository
                 uses: actions/setup-java@v3
                 with:
-                    java-version: '11'
+                    java-version: '17'
                     distribution: 'adopt'
                     server-id: ossrh
                     server-username: MAVEN_USERNAME
@@ -91,4 +91,4 @@ jobs:
                 env:
                     MAVEN_USERNAME: ${{ secrets.DATAVERSEBOT_SONATYPE_USERNAME }}
                     MAVEN_PASSWORD: ${{ secrets.DATAVERSEBOT_SONATYPE_TOKEN }}
-                    MAVEN_GPG_PASSPHRASE: ${{ secrets.DATAVERSEBOT_GPG_PASSWORD }}
+                    MAVEN_GPG_PASSPHRASE: ${{ secrets.DATAVERSEBOT_GPG_PASSWORD }}

doc/release-notes/8094-java-17.md

@@ -0,0 +1 @@
+Java 17 or higher is now required.

doc/sphinx-guides/source/container/base-image.rst

@@ -41,7 +41,7 @@ Image Contents
 
 The base image provides:
 
-- `Eclipse Temurin JRE using Java 11 <https://adoptium.net/temurin/releases?version=11>`_
+- `Eclipse Temurin JRE using Java 17 <https://adoptium.net/temurin/releases?version=17>`_
 - `Payara Community Application Server <https://docs.payara.fish/community>`_
 - 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

doc/sphinx-guides/source/developers/dev-environment.rst

@@ -12,7 +12,7 @@ These instructions are oriented around Docker but the "classic" instructions we
 Quickstart
 ----------
 
-First, install Java 11, Maven, and Docker.
+First, install Java 17, Maven, and Docker.
 
 After cloning the `dataverse repo <https://github.com/IQSS/dataverse>`_, run this:
 
@@ -30,7 +30,7 @@ Detailed Steps
 Install Java
 ~~~~~~~~~~~~
 
-The Dataverse Software requires Java 11.
+The Dataverse Software requires Java 17.
 
 On Mac and Windows, we suggest downloading OpenJDK from https://adoptium.net (formerly `AdoptOpenJDK <https://adoptopenjdk.net>`_) or `SDKMAN <https://sdkman.io>`_.
 

doc/sphinx-guides/source/installation/prerequisites.rst

@@ -19,7 +19,7 @@ We assume you plan to run your Dataverse installation on Linux and we recommend
 Java
 ----
 
-The Dataverse Software requires Java SE 11 (or higher).
+The Dataverse Software requires Java SE 17 (or higher).
 
 Installing Java
 ===============
@@ -30,11 +30,11 @@ The Oracle JDK can be downloaded from http://www.oracle.com/technetwork/java/jav
 
 On a RHEL/derivative, install OpenJDK (devel version) using yum::
 
-	# sudo yum install java-11-openjdk
+	# sudo yum install java-17-openjdk
 
-If you have multiple versions of Java installed, Java 11 should be the default when ``java`` is invoked from the command line. You can test this by running ``java -version``.
+If you have multiple versions of Java installed, Java 17 should be the default when ``java`` is invoked from the command line. You can test this by running ``java -version``.
 
-On RHEL/derivative you can make Java 11 the default with the ``alternatives`` command, having it prompt you to select the version of Java from a list::
+On RHEL/derivative you can make Java 17 the default with the ``alternatives`` command, having it prompt you to select the version of Java from a list::
 
         # alternatives --config java
 

modules/container-base/src/main/docker/Dockerfile

@@ -164,6 +164,8 @@ 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"

modules/dataverse-parent/pom.xml

@@ -133,7 +133,7 @@
         <!-- This is a special Maven property name, do not change! -->
         <revision>5.14</revision>
 
-        <target.java.version>11</target.java.version>
+        <target.java.version>17</target.java.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <additionalparam>-Xdoclint:none</additionalparam>
         <!-- Needed to avoid IDEA IDE compilation failures. See commits in GH #5059 -->

pom.xml

@@ -573,9 +573,9 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.jayway.restassured</groupId>
+            <groupId>io.rest-assured</groupId>
             <artifactId>rest-assured</artifactId>
-            <version>2.4.0</version>
+            <version>5.3.1</version>
             <scope>test</scope>
         </dependency>
         <dependency>

scripts/installer/as-setup.sh

@@ -116,6 +116,9 @@ 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"
 

scripts/installer/install.py

@@ -252,8 +252,8 @@
    # 1d. check java version
    java_version = subprocess.check_output(["java", "-version"], stderr=subprocess.STDOUT).decode()
    print("Found java version "+java_version)
-   if not re.search('(1.8|11)', java_version):
-      sys.exit("Dataverse requires OpenJDK 1.8 or 11. Please make sure it's in your PATH, and try again.")
+   if not re.search('(17)', java_version):
+      sys.exit("Dataverse requires OpenJDK 17. Please make sure it's in your PATH, and try again.")
 
    # 1e. check if the setup scripts - setup-all.sh, are available as well, maybe?
    # @todo (?)

src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java

@@ -1814,7 +1814,7 @@ public String getPublicationDateAsString() {
     // So something will need to be modified to accommodate this. -- L.A.  
     /**
      * We call the export format "Schema.org JSON-LD" and extensive Javadoc can
-     * be found in {@link SchemaDotOrgExporter}.
+     * be found in {@link edu.harvard.iq.dataverse.export.SchemaDotOrgExporter}.
      */
     public String getJsonLd() {
         // We show published datasets only for "datePublished" field below.

src/main/java/edu/harvard/iq/dataverse/dataaccess/FileAccessIO.java

@@ -565,21 +565,26 @@ private String getDatasetDirectory() throws IOException {
         if (isDirectAccess()) {
             throw new IOException("No DvObject defined in the Data Access Object");
         }
-
-        Path datasetDirectoryPath=null;
 
+        String authorityForFS = null;
+        String identifierForFS = null;
         if (dvObject instanceof Dataset) {
-            datasetDirectoryPath = Paths.get(this.getDataset().getAuthorityForFileStorage(), this.getDataset().getIdentifierForFileStorage());
+            authorityForFS = this.getDataset().getAuthorityForFileStorage();
+            identifierForFS = this.getDataset().getIdentifierForFileStorage();
         } else if (dvObject instanceof DataFile) {
-            datasetDirectoryPath = Paths.get(this.getDataFile().getOwner().getAuthorityForFileStorage(), this.getDataFile().getOwner().getIdentifierForFileStorage());
+            authorityForFS = this.getDataFile().getOwner().getAuthorityForFileStorage();
+            identifierForFS = this.getDataFile().getOwner().getIdentifierForFileStorage();
         } else if (dvObject instanceof Dataverse) {
             throw new IOException("FileAccessIO: Dataverses are not a supported dvObject");
         }
-            
-        if (datasetDirectoryPath == null) {
+
+        if (authorityForFS == null || identifierForFS == null) {
             throw new IOException("Could not determine the filesystem directory of the parent dataset.");
         }
-        String datasetDirectory = Paths.get(getFilesRootDirectory(), datasetDirectoryPath.toString()).toString();
+
+        // Determine the final directory tree. As of JDK 16, the first component of the path MUST be non-null
+        // (we check for that via the setting), but also the others make no sense if they are null.
+        String datasetDirectory = Paths.get(getFilesRootDirectory(), authorityForFS, identifierForFS).toString();
 
         if (dvObject.getStorageIdentifier() == null || dvObject.getStorageIdentifier().isEmpty()) {
             throw new IOException("Data Access: No local storage identifier defined for this datafile.");

src/test/java/edu/harvard/iq/dataverse/api/AccessIT.java

@@ -5,10 +5,10 @@
  */
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.RestAssured;
-import static com.jayway.restassured.RestAssured.given;
-import com.jayway.restassured.path.json.JsonPath;
-import com.jayway.restassured.response.Response;
+import io.restassured.RestAssured;
+import static io.restassured.RestAssured.given;
+import io.restassured.path.json.JsonPath;
+import io.restassured.response.Response;
 import edu.harvard.iq.dataverse.DataFile;
 import edu.harvard.iq.dataverse.util.FileUtil;
 import java.io.IOException;

src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java

@@ -1,8 +1,8 @@
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.RestAssured;
-import com.jayway.restassured.path.json.JsonPath;
-import com.jayway.restassured.response.Response;
+import io.restassured.RestAssured;
+import io.restassured.path.json.JsonPath;
+import io.restassured.response.Response;
 import edu.harvard.iq.dataverse.DataFile;
 import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinAuthenticationProvider;
 import edu.harvard.iq.dataverse.authorization.providers.oauth2.impl.GitHubOAuth2AP;

src/test/java/edu/harvard/iq/dataverse/api/AuxiliaryFilesIT.java

@@ -1,8 +1,8 @@
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.RestAssured;
-import com.jayway.restassured.path.json.JsonPath;
-import com.jayway.restassured.response.Response;
+import io.restassured.RestAssured;
+import io.restassured.path.json.JsonPath;
+import io.restassured.response.Response;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;

src/test/java/edu/harvard/iq/dataverse/api/BagIT.java

@@ -1,7 +1,7 @@
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.RestAssured;
-import com.jayway.restassured.response.Response;
+import io.restassured.RestAssured;
+import io.restassured.response.Response;
 import edu.harvard.iq.dataverse.engine.command.impl.LocalSubmitToArchiveCommand;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import static jakarta.ws.rs.core.Response.Status.CREATED;

src/test/java/edu/harvard/iq/dataverse/api/BatchImportIT.java

@@ -1,9 +1,9 @@
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.RestAssured;
-import com.jayway.restassured.path.json.JsonPath;
+import io.restassured.RestAssured;
+import io.restassured.path.json.JsonPath;
 import java.io.File;
-import com.jayway.restassured.response.Response;
+import io.restassured.response.Response;
 import java.util.logging.Logger;
 import org.junit.BeforeClass;
 import org.junit.Test;

src/test/java/edu/harvard/iq/dataverse/api/BuiltinUsersIT.java

@@ -1,10 +1,10 @@
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.RestAssured;
-import static com.jayway.restassured.RestAssured.given;
-import com.jayway.restassured.http.ContentType;
-import com.jayway.restassured.path.json.JsonPath;
-import com.jayway.restassured.response.Response;
+import io.restassured.RestAssured;
+import static io.restassured.RestAssured.given;
+import io.restassured.http.ContentType;
+import io.restassured.path.json.JsonPath;
+import io.restassured.response.Response;
 import edu.harvard.iq.dataverse.api.auth.ApiKeyAuthMechanism;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import java.util.AbstractMap;

src/test/java/edu/harvard/iq/dataverse/api/ConfirmEmailIT.java

@@ -1,9 +1,9 @@
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.RestAssured;
-import static com.jayway.restassured.RestAssured.given;
-import com.jayway.restassured.path.json.JsonPath;
-import com.jayway.restassured.response.Response;
+import io.restassured.RestAssured;
+import static io.restassured.RestAssured.given;
+import io.restassured.path.json.JsonPath;
+import io.restassured.response.Response;
 import java.util.logging.Logger;
 import static junit.framework.Assert.assertEquals;
 import org.junit.BeforeClass;

src/test/java/edu/harvard/iq/dataverse/api/DataCiteIT.java

@@ -1,7 +1,7 @@
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.path.json.JsonPath;
-import com.jayway.restassured.response.Response;
+import io.restassured.path.json.JsonPath;
+import io.restassured.response.Response;
 import static junit.framework.Assert.assertEquals;
 import static org.hamcrest.CoreMatchers.equalTo;
 import org.junit.Test;

src/test/java/edu/harvard/iq/dataverse/api/DataRetrieverApiIT.java

@@ -1,7 +1,7 @@
 package edu.harvard.iq.dataverse.api;
 
-import com.jayway.restassured.RestAssured;
-import com.jayway.restassured.response.Response;
+import io.restassured.RestAssured;
+import io.restassured.response.Response;
 import edu.harvard.iq.dataverse.api.auth.ApiKeyAuthMechanism;
 import org.junit.BeforeClass;
 import org.junit.Test;