Merge pull request #11128 from QualitativeDataRepository/IQSS/11126-Payara6.2024.12

Upgrade to Payara 6 2025.2

Author: ofahimIQSS

doc/release-notes/6.2025.2_update.md

@@ -0,0 +1,35 @@
+- Payara application server has been upgraded to version 6.2025.2. See #11126 and #11128.
+
+## Installation
+
+The following assumes the standard instructions to `export PAYARA=/usr/local/payara6`, undeploy v6.5, stop payara have been done already.
+
+### Upgrade to Payara 6.2025.2
+
+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/6.2025.2/Release%20Notes/Release%20Notes%206.2025.2.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 6.2025.2 (from https://www.payara.fish/downloads/payara-platform-community-edition/ or https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.2/payara-6.2025.2.zip), and unzip it in its place:
+
+```shell
+cd /usr/local
+unzip payara-6.2025.2.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 payara6.6.2024.6/glassfish/domains/domain1 payara6/glassfish/domains/
+```
+
+Deploy/install as normal
+

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 6.2025.2 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/6.2025.2/payara-6.2025.2.zip``
 
-``sudo unzip payara-6.2024.6.zip``
+``sudo unzip payara-6.2025.2.zip``
 
 ``sudo chown -R $USER /usr/local/payara6``
 

doc/sphinx-guides/source/developers/tips.rst

@@ -296,3 +296,14 @@ with the following code in ``SettingsWrapper.java``:
 A more serious example would be direct calls to PermissionServiceBean methods used in render logic expressions. This is something that has happened and caused some problems in real life. A simple permission service lookup (for example, whether a user is authorized to create a dataset in the current dataverse) can easily take 15 database queries. Repeated multiple times, this can quickly become a measurable delay in rendering the page. PermissionsWrapper must be used exclusively for any such lookups from JSF pages.
 
 See also :doc:`performance`.
+
+JSF1103 Errors
+~~~~~~~~~~~~~~
+
+Errors of the form ``JSF1103: The metadata facet must be a direct child of the view in viewId /dataverse.xhtml`` come from use of the f:metadata tag at the wrong depth in the .xhtml.
+
+Most/all known instances of the problem were corrected in https://github.com/IQSS/dataverse/pull/11128.
+
+Any page that used <ui:composition template="/dataverse_template.xhtml"> was including the f:metadata farther down in the tree rather than as a direct child of the view.
+As of Payara 6.2025.2, it is not clear that this error was resulting in changes to UI behavior, but the error messages were in the log.
+If you see these errors, this note and the examples in the PR will hopefully provide some insight as to how to fix them.

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 6.2025.2 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/6.2025.2/payara-6.2025.2.zip
+	# unzip payara-6.2025.2.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/6.2025.2/payara-6.2025.2.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>6.2025.2</payara.version>
         <postgresql.version>42.7.4</postgresql.version>
         <solr.version>9.8.0</solr.version>
         <aws.version>1.12.748</aws.version>

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

@@ -6235,7 +6235,7 @@ 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();
         }
@@ -6251,6 +6251,11 @@ 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}">