IQSS/11126 payara6.2025.1

doc/release-notes/6.2025.1_update.md

@@ -0,0 +1,206 @@
+- Payara application server has been upgraded to version 6.2025.1.
+
+## Installation
+
+The following assumes the standard instructions to undeploy v6.5, stop payara, `export PAYARA=/usr/local/payara6`, etc. have been done already.
+
+### Upgrade to Payara 6.2025.1
+
+Option 1: 
+
+The steps below reuse your existing domain directory with the new distribution. You may also want to review the Payara upgrade instructions as it could be helpful during any troubleshooting:
+[Payara Release Notes](https://docs.payara.fish/community/docs/6.2025.1/Release%20Notes/Release%20Notes%206.2025.1.html).
+We also recommend you ensure you followed all update instructions from the past releases regarding Payara.
+(The most recent Payara update was for [v6.3](https://github.com/IQSS/dataverse/releases/tag/v6.3).)
+
+Move the current Payara directory out of the way:
+
+```shell
+mv $PAYARA $PAYARA.6.2024.6
+```
+
+Download the new Payara version 6.2025.1 (from https://www.payara.fish/downloads/payara-platform-community-edition/), and unzip it in its place:
+
+```shell
+cd /usr/local
+unzip payara-6.2025.1.zip
+```
+
+Replace the brand new `payara/glassfish/domains/domain1` with your old, preserved domain1:
+
+```shell
+mv payara6/glassfish/domains/domain1 payara6/glassfish/domains/domain1_DIST
+mv payara6-2024.6/glassfish/domains/domain1 payara6/glassfish/domains/
+```
+
+Deploy/install as normal
+
+Option2 : Modify the default 6.2025.1 domain1 configuration for your Dataverse instance. (Removes obsolete options, gets updated certificate store, makes tracking your Dataverse-specific changes relative to the the Payara default easier.)
+
+1. Stop Payara 6, if running.
+
+    ``
+    sudo -u dataverse /usr/local/payara6/bin/asadmin stop-domain
+    ``
+1. Move your existing payara installation to a backup directory
+
+```shell
+mv $PAYARA $PAYARA.6.2024.6
+```
+
+1. Download Payara 6.2025.1 and unzip it
+
+```shell
+    cd /usr/local
+    curl -L -O https://nexus.payara.fish/repository/payara- community/fish/payara/distributions/payara/6.2025.1/payara-6.2025.1.zip
+    unzip payara-6.2025.1.zip
+```
+
+1. Change ownership of the unzipped Payara to your "service" user ("dataverse" by default)
+
+   `sudo chown -R dataverse /usr/local/payara6`
+
+1. Create a Dataverse-specific domain.xml file
+
+    i. Make a copy of the default domain.xml file (to be able to compare against later)
+
+   ``sudo -u dataverse cp /usr/local/payara6/glassfish/domains/domain1/config/domain.xml /usr/local/payara6/glassfish/domains/domain1/config/domain.xml.orig``
+
+    ii. Retrieve the domain.xml file for this version of Dataverse
+
+```shell
+    cd /usr/local/payara6/glassfish/domains/domain1/config
+    curl -L -O https://github.com/IQSS/dataverse/raw/refs/tags/v6.6/conf/payara/domain.xml
+``` 
+
+    iii. Copy Dataverse-related lines from your existing domain.xml to sections of the new domain.xml highlighted by `Dataverse-instance-specific` comments
+
+   `sudo egrep 'dataverse|doi|Xmx' /usr/local/$PAYARA.6.2024.6/glassfish/domains/domain1/config/domain.xml > lines.txt`
+
+   `sudo vi /usr/local/payara6/glassfish/domains/domain1/config/domain.xml`
+
+
+   The lines will appear in two sections, examples shown below (but your content will vary)
+
+
+   Section 1: system properties (under `<server name="server" config-ref="server-config">`
+
+
+   ```
+   <system-property name="dataverse.db.user" value="dvnuser"></system-property>
+
+   <system-property name="dataverse.db.host" value="localhost"></system-property>
+
+   <system-property name="dataverse.db.port" value="5432"></system-property>
+
+   <system-property name="dataverse.db.name" value="dvndb"></system-property>
+
+   <system-property name="dataverse.db.password" value="dvnsecret"></system-property>
+
+   ```
+
+
+   Note: if you used the Dataverse installer, you won't have a `dataverse.db.password` property. See "Create password aliases" below
+
+
+   Section 2: JVM options (under `<java-config classpath-suffix="" debug-options="-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=9009" system-classpath="">`, the one under `<config name="server-config">`, not under `<config name="default-config">`
+
+
+   Add the remaining lines (starting with `<jvm-options>` )from lines.txt created above, e.g.
+
+
+   ```
+
+   <jvm-options>-Ddataverse.files.directory=/usr/local/dvn/data</jvm-options
+
+   <jvm-options>-Ddataverse.files.file.type=file</jvm-options
+
+   <jvm-options>-Ddataverse.files.file.label=file</jvm-options
+
+   <jvm-options>-Ddataverse.files.file.directory=/usr/local/dvn/data</jvm-options
+
+   <jvm-options>-Ddataverse.rserve.host=localhost</jvm-options
+
+   <jvm-options>-Ddataverse.rserve.port=6311</jvm-options
+
+   <jvm-options>-Ddataverse.rserve.user=rserve</jvm-options
+
+   <jvm-options>-Ddataverse.rserve.password=rserve</jvm-options
+
+   <jvm-options>-Ddataverse.auth.password-reset-timeout-in-minutes=60</jvm-options
+
+   <jvm-options>-Ddataverse.timerServer=true</jvm-options
+
+   <jvm-options>-Ddataverse.fqdn=dev1.dataverse.org</jvm-options
+
+   <jvm-options>-Ddataverse.siteUrl=https://dev1.dataverse.org</jvm-options
+
+   <jvm-options>-Ddataverse.files.storage-driver-id=file</jvm-options
+
+   <jvm-options>-Ddoi.username=testaccount</jvm-options
+
+   <jvm-options>-Ddoi.password=notmypassword</jvm-options
+
+   <jvm-options>-Ddoi.baseurlstring=https://mds.test.datacite.org/</jvm-options
+
+   <jvm-options>-Ddoi.dataciterestapiurlstring=https://api.test.datacite.org</jvm-options
+
+   ```
+
+   - If you've enabled access logging or any other site-specific configuration, be sure to preserve them. For instance, the default domain.xml include
+
+
+   ```
+
+        <http-service
+
+        <access-log></access-log
+
+   ```
+
+
+   but you may wish to include
+
+
+   ```
+
+        <http-service access-logging-enabled="true"
+
+        <access-log format="%client.name% %datetime% %request% %status% %response.length% %header.user-agent% %header.referer% %cookie.JSESSIONID% %header.x-forwarded-for%"></access-log
+
+   ```
+
+
+   Be sure to keep a previous copy of your domain.xml for reference
+
+
+1. Update additional files from your existing Payara configuration
+
+    i. Copy jhove files
+
+    `jhove.conf` and `jhoveConfig.xsd`
+
+
+   `sudo cp /usr/local/$PAYARA.6.2024.6/glassfish/domains/domain1/config/jhove* /usr/local/payara6/glassfish/domains/domain1/config/`
+
+    ii. Replace the default `domain-passwords` files with yours
+
+
+   `sudo cp /usr/local/$PAYARA.6.2024.6/glassfish/domains/domain1/config/domain-passwords /usr/local/payara6/glassfish/domains/domain1/config/`
+
+    iii. Optional: add any dataverse specific lines in your existing logging.properties file to the default one
+
+   `sudo vi /usr/local/payara6/glassfish/domains/domain1/config/logging.properties`
+
+    iv. Assure all config files are owned by the dataverse user
+
+   `sudo chown dataverse /usr/local/payara6/glassfish/domains/domain1/config/*`
+
+1. Copy/move logos and other files from  from your old domain to the new one, e.g.
+
+
+   `sudo -u dataverse mv -r /usr/local/$PAYARA.6.2024.6/glassfish/domains/domain1/docroot /usr/local/payara6/glassfish/domains/domain1`
+
+   `sudo -u dataverse mv -r /usr/local/$PAYARA.6.2024.6/glassfish/domains/domain1/files /usr/local/payara6/glassfish/domains/domain1`
+
+   `sudo -u dataverse mv -r /usr/local/$PAYARA.6.2024.6/glassfish/domains/domain1/logs /usr/local/payara6/glassfish/domains/logs`

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 6.2024.6 or higher is required.
+Payara 6.2025.1 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/6.2024.6/payara-6.2024.6.zip``
+``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.1/payara-6.2025.1.zip``
 
-``sudo unzip payara-6.2024.6.zip``
+``sudo unzip payara-6.2025.1.zip``
 
 ``sudo chown -R $USER /usr/local/payara6``
 

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 6.2024.6 is recommended. Newer versions might work fine. Regular updates are recommended.
+Payara 6.2025.1 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/6.2024.6/payara-6.2024.6.zip
-	# unzip payara-6.2024.6.zip
+	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.1/payara-6.2025.1.zip
+	# unzip payara-6.2025.1.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/

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/6.2024.6/payara-6.2024.6.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/6.2025.1/payara-6.2025.1.zip"}
 ```
 
 In the example above, if Payara can't be downloaded, we're obviously going to have problems deploying Dataverse to it!

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>6.2024.6</payara.version>
+        <payara.version>6.2025.1</payara.version>
         <postgresql.version>42.7.4</postgresql.version>
         <solr.version>9.4.1</solr.version>
         <aws.version>1.12.748</aws.version>

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

@@ -6214,7 +6214,7 @@ public String getEffectiveMetadataLanguage(boolean ofParent) {
 
     public String getLocaleDisplayName(String code) {
         String displayName = settingsWrapper.getBaseMetadataLanguageMap(false).get(code);
-        if(displayName==null && !code.equals(DvObjectContainer.UNDEFINED_CODE)) {
+        if(displayName==null && code!=null && !code.equals(DvObjectContainer.UNDEFINED_CODE)) {
             //Default (for cases such as :when a Dataset has a metadatalanguage code but :MetadataLanguages is no longer defined).
             displayName = new Locale(code).getDisplayName();
         }
@@ -6230,6 +6230,11 @@ public List<String> getVocabScripts() {
     }
 
     public String getFieldLanguage(String languages) {
+        //Prevent NPE in Payara 6-2024-12 with CVoc
+        logger.info("Languages: " + languages);
+        if(languages==null) {
+            languages="";
+        }
         return fieldService.getFieldLanguage(languages,session.getLocaleCode());
     }
 

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

@@ -209,19 +209,17 @@ public String getLocaleTitle() {
 
     public void initLocale() {
 
-        if(FacesContext.getCurrentInstance() == null) {
-            localeCode = "en";
-        }
-        else if (FacesContext.getCurrentInstance().getViewRoot() == null ) {
-            localeCode = FacesContext.getCurrentInstance().getExternalContext().getRequestLocale().getLanguage();
-        }
-        else if (FacesContext.getCurrentInstance().getViewRoot().getLocale().getLanguage().equals("en_US")) {
-            localeCode = "en";
-        }
-        else {
-            localeCode = FacesContext.getCurrentInstance().getViewRoot().getLocale().getLanguage();
+
+        localeCode = "en";
+        if (FacesContext.getCurrentInstance() != null) {
+            if (FacesContext.getCurrentInstance().getViewRoot() == null) {
+                localeCode = FacesContext.getCurrentInstance().getExternalContext().getRequestLocale().getLanguage();
+            } else if (FacesContext.getCurrentInstance().getViewRoot().getLocale().getLanguage().equals("en_US")) {
+                localeCode = "en";
+            } else {
+                localeCode = FacesContext.getCurrentInstance().getViewRoot().getLocale().getLanguage();
+            }
         }
-
         logger.fine("init: locale set to "+localeCode);
     }
 

src/main/webapp/ThemeAndWidgets.xhtml

@@ -15,12 +15,14 @@
             <ui:param name="dataverse" value="#{themeWidgetFragment.editDv}"/>  
 
             <ui:param name="showMessagePanel" value="#{true}"/>
-            <ui:define name="body">
+            <ui:define name="metadata">
                 <f:metadata>
                     <f:viewParam name="id" value="#{themeWidgetFragment.editDv.id}"/>
                     <f:viewAction action="#{themeWidgetFragment.initEditDv}"/>
                     <f:viewAction action="#{dataverseHeaderFragment.initBreadcrumbs(themeWidgetFragment.editDv, bundle['dataverse.option.themeAndWidgets'])}"/>
                 </f:metadata>
+            </ui:define>
+            <ui:define name="body">
                 <h:form id="themeWidgetsForm">
                     <ui:include src="themeAndWidgetsFragment.xhtml"/>
                 </h:form>

src/main/webapp/confirmemail.xhtml

@@ -14,12 +14,14 @@
             <ui:param name="dataverse" value="#{dataverseServiceBean.findRootDataverse()}"/>
             <ui:param name="showDataverseHeader" value="false"/>
             <ui:param name="loginRedirectPage" value="dataverse.xhtml"/>
-            <ui:define name="body">
+            <ui:define name="metadata">
                 <f:metadata>
                     <f:viewParam name="token" value="#{ConfirmEmailPage.token}"/>
                     <f:viewAction action="#{dataverseSession.updateLocaleInViewRoot}"/>
                     <f:viewAction action="#{ConfirmEmailPage.init}" />
                 </f:metadata>
+            </ui:define>
+            <ui:define name="body">
 
                 <!--This is just the button. The error message is added via addErrorMessage in the backing bean.-->
                 <h:form styleClass="form-horizontal" rendered="#{ConfirmEmailPage.invalidToken}">

src/main/webapp/dashboard.xhtml

@@ -12,13 +12,15 @@
         <ui:composition template="/dataverse_template.xhtml">
             <ui:param name="pageTitle" value="#{bundle['dashboard.title']} - #{dataverseServiceBean.findRootDataverse().name}"/>
             <ui:param name="showDataverseHeader" value="false"/>
-            <ui:define name="body">
+            <ui:define name="metadata">
                 <f:metadata>
                     <f:viewParam name="dataverseId" value="#{dashboardPage.dataverseId}"/>
                     <f:viewAction action="#{dataverseSession.updateLocaleInViewRoot}"/>
                     <f:viewAction action="#{dashboardPage.init}"/>
                     <f:viewAction action="#{dataverseHeaderFragment.initBreadcrumbs(dataverseServiceBean.findRootDataverse(), bundle['dashboard.title'])}"/>
                 </f:metadata>
+            </ui:define>
+            <ui:define name="body">
 
                 <div id="dashboard-block" class="content">
                     <div class="container">

src/main/webapp/dataset-widgets.xhtml

@@ -15,13 +15,15 @@
             <ui:param name="dataverse" value="#{DatasetWidgetsPage.dataset.owner}"/>
             <ui:param name="dataset" value="#{DatasetWidgetsPage.dataset}"/>
             <ui:param name="showMessagePanel" value="#{true}"/>
-            <ui:define name="body">
+            <ui:define name="metadata">
                 <f:metadata>
                     <f:viewParam name="datasetId" value="#{DatasetWidgetsPage.datasetId}"/>
                     <f:viewAction action="#{dataverseSession.updateLocaleInViewRoot}"/>
                     <f:viewAction action="#{DatasetWidgetsPage.init}" />
                     <f:viewAction action="#{dataverseHeaderFragment.initBreadcrumbs(DatasetWidgetsPage.dataset, bundle['dataset.thumbnailsAndWidget.breadcrumbs.title'])}"/>
                 </f:metadata>
+            </ui:define>
+            <ui:define name="body">
                 <h:form id="themeWidgetsForm" styleClass="row form-horizontal">
                 <p:tabView rendered="#{themeWidgetFragment.editDv!=null}" id="themeWidgetsTabView" widgetVar="content">
                     <p:tab id="thumbnailsTab" title="#{bundle['dataset.thumbnailsAndWidget.thumbnails.title']}">