Merge remote-tracking branch 'IQSS/develop' into IQSS/8053-fix_import

doc/release-notes/5.4-release-notes.md

@@ -274,6 +274,8 @@ Add the following JVM options to the `<config name="server-config"><java-config>
 
 `<jvm-options>[9|]--add-opens=java.logging/java.util.logging=ALL-UNNAMED</jvm-options>`  
 
+`<jvm-options>[1.8.0u251|]-Xbootclasspath/a:${com.sun.aas.installRoot}/lib/grizzly-npn-api.jar</jvm-options>`
+
 6\. Start Payara
 
 - `service payara start`

doc/release-notes/5.6-release-notes.md

@@ -50,6 +50,8 @@ Some changes in this release require an upgrade to Payara 5.2021.5 or higher. (S
 
 Instructions on how to update can be found in the [Payara documentation](https://docs.payara.fish/community/docs/5.2021.4/documentation/user-guides/upgrade-payara.html) We've included the necessary steps below, but we recommend that you review the Payara upgrade instructions as it could be helpful during any troubleshooting.
 
+Installations upgrading from a previous Payara version shouldn't encounter a logging configuration bug in Payara-5.2021.5, but if your server.log fills with repeated notes about logging configuration and WELD complaints about loading beans, see the paragraph on `logging.properties` in the [installation guide](https://guides.dataverse.org/en/5.6/installation/installation-main.html#running-the-dataverse-software-installer)
+
 ### Enhancement to DDI Metadata Exports
 
 To increase support for internationalization and to improve compliance with CESSDA requirements, DDI exports now have a holdings element with a URI attribute whose value is the URL form of the dataset PID.
@@ -106,15 +108,19 @@ In the following commands we assume that Payara 5 is installed in `/usr/local/pa
 
 5\. Replace the brand new payara/glassfish/domains/domain1 with your old, preserved `domain1`
 
-6\. Start Payara
+6\. In domain.xml, add/confirm the existence of the following JVM option to/in the `<config name="server-config"><java-config>` section:
+
+`<jvm-options>[1.8.0u251|]-Xbootclasspath/a:${com.sun.aas.installRoot}/lib/grizzly-npn-api.jar</jvm-options>`
+
+7\. Start Payara
 
 - `service payara start`
 
-7\. Deploy this version.
+8\. Deploy this version.
 
 - `$PAYARA/bin/asadmin deploy dataverse-5.6.war`
 
-8\. Restart payara
+9\. Restart payara
 
 - `service payara stop`
 - `service payara start`
@@ -125,6 +131,6 @@ In the following commands we assume that Payara 5 is installed in `/usr/local/pa
 
 Note that you can skip this step if your installation uses the default-style, randomly-generated six alphanumeric character-long identifiers for your datasets! This is the case with most Dataverse installations.
 
-The underlying database framework has been modified in this release, to make it easier for installations  to create custom procedures for generating identifier strings that suit their needs. Your current configuration will  be automatically updated by the database upgrade (Flyway) script incorporated in the release. No manual configuration changes should be necessary. However, after the upgrade, we recommend that you confirm that your installation can still create new datasets, and that they are still assigned sequential numeric identifiers. In the unlikely chance that this is no longer working, please re-create the stored procedure following the steps described in the documentation for the `:IdentifierGenerationStyle` setting in the *Configuration* section of the Installation Guide for this release (v5.6).
+The underlying database framework has been modified in this release, to make it easier for installations  to create custom procedures for generating identifier strings that suit their needs. Your current configuration will be automatically updated by the database upgrade (Flyway) script incorporated in the release. No manual configuration changes should be necessary. However, after the upgrade, we recommend that you confirm that your installation can still create new datasets, and that they are still assigned sequential numeric identifiers. In the unlikely chance that this is no longer working, please re-create the stored procedure following the steps described in the documentation for the `:IdentifierGenerationStyle` setting in the *Configuration* section of the Installation Guide for this release (v5.6).
 
 (Running the script supplied there will NOT overwrite the position on the sequence you are currently using!)

doc/sphinx-guides/source/_static/installation/files/usr/local/payara5/glassfish/domains/domain1/config/logging.properties

@@ -0,0 +1,166 @@
+#
+# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+#
+# Copyright (c) 2013 Oracle and/or its affiliates. All rights reserved.
+#
+# The contents of this file are subject to the terms of either the GNU
+# General Public License Version 2 only ("GPL") or the Common Development
+# and Distribution License("CDDL") (collectively, the "License").  You
+# may not use this file except in compliance with the License.  You can
+# obtain a copy of the License at
+# https://glassfish.dev.java.net/public/CDDL+GPL_1_1.html
+# or packager/legal/LICENSE.txt.  See the License for the specific
+# language governing permissions and limitations under the License.
+#
+# When distributing the software, include this License Header Notice in each
+# file and include the License file at packager/legal/LICENSE.txt.
+#
+# GPL Classpath Exception:
+# Oracle designates this particular file as subject to the "Classpath"
+# exception as provided by Oracle in the GPL Version 2 section of the License
+# file that accompanied this code.
+#
+# Modifications:
+# If applicable, add the following below the License Header, with the fields
+# enclosed by brackets [] replaced by your own identifying information:
+# "Portions Copyright [year] [name of copyright owner]"
+#
+# Contributor(s):
+# If you wish your version of this file to be governed by only the CDDL or
+# only the GPL Version 2, indicate your decision by adding "[Contributor]
+# elects to include this software in this distribution under the [CDDL or GPL
+# Version 2] license."  If you don't indicate a single choice of license, a
+# recipient has the option to distribute your version of this file under
+# either the CDDL, the GPL Version 2 or to extend the choice of license to
+# its licensees as provided above.  However, if you add GPL Version 2 code
+# and therefore, elected the GPL Version 2 license, then the option applies
+# only if the new code is made subject to such option by the copyright
+# holder.
+#
+# Portions Copyright [2016-2021] [Payara Foundation and/or its affiliates]
+
+#GlassFish logging.properties list
+#Update June 13 2012
+
+#All attributes details
+handlers=java.util.logging.ConsoleHandler
+handlerServices=com.sun.enterprise.server.logging.GFFileHandler,com.sun.enterprise.server.logging.SyslogHandler
+java.util.logging.ConsoleHandler.formatter=com.sun.enterprise.server.logging.UniformLogFormatter
+java.util.logging.FileHandler.count=1
+java.util.logging.FileHandler.formatter=java.util.logging.XMLFormatter
+java.util.logging.FileHandler.limit=50000
+java.util.logging.FileHandler.pattern=%h/java%u.log
+com.sun.enterprise.server.logging.GFFileHandler.compressOnRotation=false
+com.sun.enterprise.server.logging.GFFileHandler.excludeFields=
+com.sun.enterprise.server.logging.GFFileHandler.file=${com.sun.aas.instanceRoot}/logs/server.log
+com.sun.enterprise.server.logging.GFFileHandler.flushFrequency=1
+com.sun.enterprise.server.logging.GFFileHandler.formatter=com.sun.enterprise.server.logging.ODLLogFormatter
+com.sun.enterprise.server.logging.GFFileHandler.level=ALL
+com.sun.enterprise.server.logging.GFFileHandler.logStandardStreams=true
+com.sun.enterprise.server.logging.GFFileHandler.logtoConsole=false
+com.sun.enterprise.server.logging.GFFileHandler.logtoFile=true
+com.sun.enterprise.server.logging.GFFileHandler.maxHistoryFiles=0
+com.sun.enterprise.server.logging.GFFileHandler.multiLineMode=true
+com.sun.enterprise.server.logging.GFFileHandler.retainErrorsStasticsForHours=0
+com.sun.enterprise.server.logging.GFFileHandler.rotationLimitInBytes=2000000
+com.sun.enterprise.server.logging.GFFileHandler.rotationOnDateChange=false
+com.sun.enterprise.server.logging.GFFileHandler.rotationTimelimitInMinutes=0
+com.sun.enterprise.server.logging.SyslogHandler.level=ALL
+com.sun.enterprise.server.logging.SyslogHandler.useSystemLogging=false
+log4j.logger.org.hibernate.validator.util.Version=warn
+com.sun.enterprise.server.logging.UniformLogFormatter.ansiColor=true
+
+#Payara Notification logging properties
+fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.compressOnRotation=false
+fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.file=${com.sun.aas.instanceRoot}/logs/notification.log
+fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.formatter=com.sun.enterprise.server.logging.ODLLogFormatter
+fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.logtoFile=true
+fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.maxHistoryFiles=0
+fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.rotationLimitInBytes=2000000
+fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.rotationOnDateChange=false
+fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.rotationTimelimitInMinutes=0
+fish.payara.deprecated.jsonlogformatter.underscoreprefix=false
+
+#All log level details
+
+.level=INFO
+ShoalLogger.level=CONFIG
+com.hazelcast.level=WARNING
+java.util.logging.ConsoleHandler.level=FINEST
+javax.enterprise.resource.corba.level=INFO
+javax.enterprise.resource.javamail.level=INFO
+javax.enterprise.resource.jdo.level=INFO
+javax.enterprise.resource.jms.level=INFO
+javax.enterprise.resource.jta.level=INFO
+javax.enterprise.resource.resourceadapter.level=INFO
+javax.enterprise.resource.sqltrace.level=FINE
+javax.enterprise.resource.webcontainer.jsf.application.level=INFO
+javax.enterprise.resource.webcontainer.jsf.config.level=INFO
+javax.enterprise.resource.webcontainer.jsf.context.level=INFO
+javax.enterprise.resource.webcontainer.jsf.facelets.level=INFO
+javax.enterprise.resource.webcontainer.jsf.lifecycle.level=INFO
+javax.enterprise.resource.webcontainer.jsf.managedbean.level=INFO
+javax.enterprise.resource.webcontainer.jsf.renderkit.level=INFO
+javax.enterprise.resource.webcontainer.jsf.resource.level=INFO
+javax.enterprise.resource.webcontainer.jsf.taglib.level=INFO
+javax.enterprise.resource.webcontainer.jsf.timing.level=INFO
+javax.enterprise.system.container.cmp.level=INFO
+javax.enterprise.system.container.ejb.level=INFO
+javax.enterprise.system.container.ejb.mdb.level=INFO
+javax.enterprise.system.container.web.level=INFO
+javax.enterprise.system.core.classloading.level=INFO
+javax.enterprise.system.core.config.level=INFO
+javax.enterprise.system.core.level=INFO
+javax.enterprise.system.core.security.level=INFO
+javax.enterprise.system.core.selfmanagement.level=INFO
+javax.enterprise.system.core.transaction.level=INFO
+javax.enterprise.system.level=INFO
+javax.enterprise.system.ssl.security.level=INFO
+javax.enterprise.system.tools.admin.level=INFO
+javax.enterprise.system.tools.backup.level=INFO
+javax.enterprise.system.tools.deployment.common.level=WARNING
+javax.enterprise.system.tools.deployment.dol.level=WARNING
+javax.enterprise.system.tools.deployment.level=INFO
+javax.enterprise.system.util.level=INFO
+javax.enterprise.system.webservices.registry.level=INFO
+javax.enterprise.system.webservices.rpc.level=INFO
+javax.enterprise.system.webservices.saaj.level=INFO
+javax.level=INFO
+javax.mail.level=INFO
+javax.org.glassfish.persistence.level=INFO
+org.apache.catalina.level=INFO
+org.apache.coyote.level=INFO
+org.apache.jasper.level=INFO
+org.eclipse.persistence.session.level=INFO
+org.glassfish.admingui.level=INFO
+org.glassfish.naming.level=INFO
+org.jvnet.hk2.osgiadapter.level=INFO
+
+javax.enterprise.resource.corba.level=INFO
+javax.enterprise.resource.jta.level=INFO
+javax.enterprise.system.webservices.saaj.level=INFO
+javax.enterprise.system.container.ejb.level=INFO
+javax.enterprise.system.container.ejb.mdb.level=INFO
+javax.enterprise.resource.javamail.level=INFO
+javax.enterprise.system.webservices.rpc.level=INFO
+javax.enterprise.system.container.web.level=INFO
+javax.enterprise.resource.jms.level=INFO
+javax.enterprise.system.webservices.registry.level=INFO
+javax.enterprise.resource.webcontainer.jsf.application.level=INFO
+javax.enterprise.resource.webcontainer.jsf.resource.level=INFO
+javax.enterprise.resource.webcontainer.jsf.config.level=INFO
+javax.enterprise.resource.webcontainer.jsf.context.level=INFO
+javax.enterprise.resource.webcontainer.jsf.facelets.level=INFO
+javax.enterprise.resource.webcontainer.jsf.lifecycle.level=INFO
+javax.enterprise.resource.webcontainer.jsf.managedbean.level=INFO
+javax.enterprise.resource.webcontainer.jsf.renderkit.level=INFO
+javax.enterprise.resource.webcontainer.jsf.taglib.level=INFO
+javax.enterprise.resource.webcontainer.jsf.timing.level=INFO
+javax.org.glassfish.persistence.level=INFO
+javax.enterprise.system.tools.backup.level=INFO
+javax.mail.level=INFO
+org.glassfish.admingui.level=INFO
+org.glassfish.naming.level=INFO
+org.eclipse.persistence.session.level=INFO
+javax.enterprise.system.tools.deployment.dol.level=WARNING
+javax.enterprise.system.tools.deployment.common.level=WARNING

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

@@ -675,6 +675,21 @@ The presence of the :ref:`:Languages` database setting adds a dropdown in the he
 
 ``curl http://localhost:8080/api/admin/settings/:Languages -X PUT -d '[{"locale":"en","title":"English"},{"locale":"fr","title":"Français"}]'``
 
+When a user selects one of the available choices, the Dataverse user interfaces will be translated into that language (assuming you also configure the "lang" directory and populate it with translations as described below).
+
+Allowing the Language Used for Dataset Metadata to be Specified
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+Since dataset metadata can only be entered in one language, and administrators may wish to limit which languages metadata can be entered in, Dataverse also offers a separate setting defining allowed metadata languages. 
+The presence of the :ref:`:MetadataLanguages` database setting identifies the available options (which can be different from those in the :Languages setting above, with fewer or more options). 
+Dataverse collection admins can select from these options to indicate which language should be used for new Datasets created with that specific collection.
+
+When creating or editing a dataset, users will be asked to enter the metadata in that language. The metadata language selected will also be shown when dataset metadata is viewed and will be included in metadata exports (as appropriate for each format) for published datasets:
+
+``curl http://localhost:8080/api/admin/settings/:MetadataLanguages -X PUT -d '[{"locale":"en","title":"English"},{"locale":"fr","title":"Français"}]'``
+
+Note that metadata selected from Controlled Vocabularies will also display in the metadata language of the dataset, but only if translations have been configured, i.e. you configure the "lang" directory and populate it with translations as described below).
+
 Configuring the "lang" Directory
 ++++++++++++++++++++++++++++++++
 
@@ -1595,7 +1610,7 @@ By default this setting is absent and the Dataverse Software assumes it to be fa
 .. _:HandleAuthHandle:
 
 :HandleAuthHandle
-+++++++++++++++++++++++++
++++++++++++++++++
 
 Specific for Handle PIDs. Set this setting to <prefix>/<suffix> to be used on a global handle service when the public key is NOT stored in the default handle.
 By default this setting is absent and the Dataverse Software assumes it to be not set. If the public key for instance is stored in handle: 21.T12996/USER01.
@@ -2209,6 +2224,16 @@ in the header.
 
 See :ref:`i18n` for a curl example and related settings.
 
+.. _:MetadataLanguages:
+
+:MetadataLanguages
+++++++++++++++++++
+
+Sets which languages can be used when entering dataset metadata. 
+
+See :ref:`i18n` for further discussion, a curl example, and related settings.
+
+
 :InheritParentRoleAssignments
 +++++++++++++++++++++++++++++
 

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

@@ -100,6 +100,10 @@ The Dataverse Software uses JHOVE_ to help identify the file format (CSV, PNG, e
 
 .. _JHOVE: http://jhove.openpreservation.org
 
+**A note about Payara-5.2021.5:** as of this writing there exists a logging configuration bug in Payara-5.2021.5. Any change to the logging configuration results in the contents of ``/usr/local/payara/glassfish/domains/domain1/config/logging.properties`` getting clobbered. In the absence of a proper logging configuration, Payara logs a number of WELD INFO entries on Payara launch, then proceeds to attempt to update its logging configuration approximately twice a second. This will result in unnecessarily junked-up system logs.
+
+This bug appears to be triggered in new Payara installations during the Dataverse installation routine. As the ``default-logging.properties`` file doesn't match the ``logging.proprties`` file distributed with Payara, we are offering :download:`a copy of it here<../_static/installation/files/usr/local/payara5/glassfish/domains/domain1/config/logging.properties>`. Simply stopping Payara, replacing the file, and starting Payara should correct the issue.
+
 Logging In
 ----------