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Payara7.2026.6 Plus Multiple Library updates #12498

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f2ef1f9
library update config changes
qqmyers Jun 28, 2026
e8c1c4c
avoid line sep hardcoding
qqmyers Jun 30, 2026
e0040ab
payara update, jhove downgrade, DDI fix
qqmyers Jun 29, 2026
fcf6563
restore old jhove config
qqmyers Jun 29, 2026
3569d23
Merge remote-tracking branch 'IQSS/develop' into payara7.2026.6plus
qqmyers Jun 30, 2026
6f8eafd
payara version update in docs
qqmyers Jun 30, 2026
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6 changes: 3 additions & 3 deletions doc/sphinx-guides/source/installation/prerequisites.rst
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Expand Up @@ -44,7 +44,7 @@ On RHEL/derivative you can make Java 21 the default with the ``alternatives`` co
Payara
------

Payara 7.2026.2 is recommended. Newer versions might work fine. Regular updates are recommended.
Payara 7.2026.6 is recommended. Newer versions might work fine. Regular updates are recommended.

Installing Payara
=================
Expand All @@ -55,8 +55,8 @@ Installing Payara

- Download and install Payara (installed in ``/usr/local/payara7`` in the example commands below)::

# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/7.2026.2/payara-7.2026.2.zip
# unzip payara-7.2026.2.zip
# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/7.2026.6/payara-7.2026.6.zip
# unzip payara-7.2026.6.zip
# mv payara7 /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/
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13 changes: 7 additions & 6 deletions modules/dataverse-parent/pom.xml
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@@ -1,3 +1,4 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd;">
<modelVersion>4.0.0</modelVersion>
Expand Down Expand Up @@ -132,7 +133,7 @@

<properties>
<!-- This is a special Maven property name, do not change! -->
<revision>6.10.1</revision>
<revision>6.11</revision>

<target.java.version>21</target.java.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
Expand All @@ -149,12 +150,12 @@
<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>7.2026.2</payara.version>
<payara.version>7.2026.6</payara.version>
<postgresql.version>42.7.11</postgresql.version>
<solr.version>9.8.0</solr.version>
<solr.version>9.10.0</solr.version>
<postgresql.server.version>16</postgresql.server.version>
<aws.version>2.33.0</aws.version>
<google.library.version>26.30.0</google.library.version>
<aws.version>2.46.17</aws.version>
<google.library.version>26.69.0</google.library.version>

<!-- Basic libs, logging -->
<slf4j.version>1.7.35</slf4j.version>
Expand Down Expand Up @@ -418,7 +419,7 @@
<repository>
<id>unidata-all</id>
<name>Unidata All</name>
<url>https://artifacts.unidata.ucar.edu/repository/unidata-all/</url>
<url>https://artifacts.unidata.ucar.edu/repository/unidata-all</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
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29 changes: 16 additions & 13 deletions pom.xml
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Expand Up @@ -30,13 +30,13 @@
<!-- This will be switched within the container profile! -->
<packaging.type>war</packaging.type>

<reload4j.version>1.2.18.4</reload4j.version>
<flyway.version>10.19.0</flyway.version>
<reload4j.version>1.2.26</reload4j.version>
<flyway.version>12.9.0</flyway.version>
<auto-service.version>1.1.1</auto-service.version>
<jhove.version>1.20.1</jhove.version>
<poi.version>5.4.0</poi.version>
<tika.version>3.2.2</tika.version>
<netcdf.version>5.9.1</netcdf.version>
<poi.version>5.5.1</poi.version>
<tika.version>3.3.1</tika.version>
<netcdf.version>5.10.0</netcdf.version>

<openapi.infoTitle>Dataverse API</openapi.infoTitle>
<openapi.infoVersion>${project.version}</openapi.infoVersion>
Expand Down Expand Up @@ -108,7 +108,7 @@
<dependency>
<groupId>org.apache.james</groupId>
<artifactId>apache-mime4j-dom</artifactId>
<version>0.8.7</version>
<version>0.8.14</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
Expand Down Expand Up @@ -153,7 +153,7 @@
<dependency>
<groupId>org.apache.httpcomponents.client5</groupId>
<artifactId>httpclient5</artifactId>
<version>5.2.1</version>
<version>5.6.1</version>
</dependency>

<!-- BEGIN Data Deposit API v1 (SWORD v2) -->
Expand Down Expand Up @@ -215,7 +215,7 @@
<dependency>
<groupId>com.apicatalog</groupId>
<artifactId>titanium-json-ld</artifactId>
<version>1.4.0</version>
<version>1.7.0</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
Expand Down Expand Up @@ -404,7 +404,7 @@
<dependency>
<groupId>commons-validator</groupId>
<artifactId>commons-validator</artifactId>
<version>1.7</version>
<version>1.10.1</version>
</dependency>

<dependency>
Expand Down Expand Up @@ -463,6 +463,9 @@
<version>${poi.version}</version>
</dependency>
<dependency>
<!-- jhove 1.34 currently includes an old version of apache commons-compress
if we update, the commons-compress dependency below needs to go above this
(or an exclude is needed) -->
<groupId>org.openpreservation.jhove</groupId>
<artifactId>jhove-core</artifactId>
<version>${jhove.version}</version>
Expand Down Expand Up @@ -496,7 +499,7 @@
<dependency>
<groupId>edu.ucsb.nceas</groupId>
<artifactId>ezid</artifactId>
<version>1.0.0</version>
<version>1.0.3</version>
<type>jar</type>
<exclusions>
<exclusion>
Expand Down Expand Up @@ -524,7 +527,7 @@
<dependency>
<groupId>org.javaswift</groupId>
<artifactId>joss</artifactId>
<version>0.10.0</version>
<version>0.10.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
Expand All @@ -541,7 +544,7 @@
<dependency>
<groupId>com.nimbusds</groupId>
<artifactId>oauth2-oidc-sdk</artifactId>
<version>11.22.1</version>
<version>11.30.1</version>
</dependency>
<!-- Caching library, current main use case is for OIDC authentication -->
<dependency>
Expand Down Expand Up @@ -1104,7 +1107,7 @@
<artifactId>maven-checkstyle-plugin</artifactId>
<configuration>
<configLocation>checkstyle.xml</configLocation>
<encoding>UTF-8</encoding>
<inputEncoding>UTF-8</inputEncoding>
<consoleOutput>true</consoleOutput>
</configuration>
</plugin>
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2 changes: 1 addition & 1 deletion src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtil.java
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Expand Up @@ -2021,7 +2021,7 @@ public static void datasetHtmlDDI(InputStream datafile, OutputStream outputStrea
Document document = builder.parse(datafile);

// Use a Transformer for output
TransformerFactory tFactory = TransformerFactory.newInstance();
TransformerFactory tFactory = TransformerFactory.newDefaultInstance();
// Set secure processing feature
tFactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
tFactory.setAttribute(XMLConstants.ACCESS_EXTERNAL_STYLESHEET, "");
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/edu/harvard/iq/dataverse/util/xml/XmlPrinter.java
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Expand Up @@ -18,7 +18,7 @@ public class XmlPrinter {

static public String prettyPrintXml(String xml) {
try {
TransformerFactory tf = TransformerFactory.newInstance();
TransformerFactory tf = TransformerFactory.newDefaultInstance();
// Set secure processing feature
tf.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);

Expand Down
2 changes: 1 addition & 1 deletion src/test/java/edu/harvard/iq/dataverse/sitemap/SiteMapUtilTest.java
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Expand Up @@ -173,7 +173,7 @@ void testHugeSiteMap() throws IOException, ParseException, SAXException {
String sitemapString = XmlPrinter.prettyPrintXml(new String(Files.readAllBytes(Paths.get(sitemapFile.getAbsolutePath())), StandardCharsets.UTF_8));
// System.out.println("sitemap: " + sitemapString);

String[] lines = sitemapString.split("\n");
String[] lines = sitemapString.split("\r?\n");
for (int i = 0; i < lines.length; i++) {
String line = lines[i].strip();
if (StringUtils.isNotBlank(line)) {
Expand Down
27 changes: 15 additions & 12 deletions src/test/java/edu/harvard/iq/dataverse/util/JhoveFileTypeTest.java
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Expand Up @@ -2,6 +2,8 @@

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.commons.io.FileUtils;
Expand All @@ -13,7 +15,7 @@
public class JhoveFileTypeTest {

static JhoveFileType jhoveFileType;
static String baseDirForConfigFiles = "/tmp";
static Path baseDirForConfigFiles;
static File png;
static File gif;
static File jpg;
Expand All @@ -25,11 +27,18 @@ public class JhoveFileTypeTest {
static File ipynb;

@BeforeAll
public static void setUpClass() {
System.setProperty("com.sun.aas.instanceRoot", baseDirForConfigFiles);
jhoveFileType = new JhoveFileType();
copyConfigIntoPlace();
public static void setUpClass() throws IOException {
baseDirForConfigFiles = Files.createTempDirectory("dataverse-test-");
System.setProperty("com.sun.aas.instanceRoot", baseDirForConfigFiles.toString());

Path configDir = baseDirForConfigFiles.resolve("config");
Files.createDirectories(configDir);

Files.copy(
Path.of("conf", "jhove", "jhove.conf"),
configDir.resolve("jhove.conf")
);
jhoveFileType = new JhoveFileType();
png = new File("src/test/resources/images/coffeeshop.png");
gif = new File("src/main/webapp/resources/images/ajax-loading.gif");
jpg = new File("src/main/webapp/resources/images/dataverseproject_logo.jpg");
Expand Down Expand Up @@ -78,13 +87,7 @@ public void testGetJhoveConfigFile() {
}

private static void copyConfigIntoPlace() {
String testFile1Src = "conf/jhove/jhove.conf";
String testFile1Tmp = baseDirForConfigFiles + "/config/jhove.conf";
try {
FileUtils.copyFile(new File(testFile1Src), new File(testFile1Tmp));
} catch (IOException ex) {
Logger.getLogger(JhoveFileTypeTest.class.getName()).log(Level.SEVERE, null, ex);
}
// Not needed anymore due to new setup
}

}
9 changes: 5 additions & 4 deletions src/test/java/edu/harvard/iq/dataverse/util/xml/XmlPrinterTest.java
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Expand Up @@ -7,11 +7,12 @@ public class XmlPrinterTest {

@Test
public void testPrettyPrintXmlShort() {
String lineSep = System.lineSeparator();
String xml = "<foo><bar>baz</bar></foo>";
String expResult = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ "<foo>\n"
+ " <bar>baz</bar>\n"
+ "</foo>\n";
String expResult = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" + lineSep
+ "<foo>" + lineSep
+ " <bar>baz</bar>" + lineSep
+ "</foo>" + lineSep;
String result = XmlPrinter.prettyPrintXml(xml);
assertEquals(expResult, result);
}
Expand Down
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