Merge branch 'develop' into 11996-fix-settings

Author: landreev

doc/release-notes/11827-Payara-6.2025.10.md

@@ -0,0 +1,16 @@
+The recommended Payara version has been updated to Payara-6.2025.10
+
+Payara 6.2025.10 cannot be used with earlier versions of Dataverse, e.g. v6.8.
+
+Standard Payara upgrade instructions - as in the 6.7 release notes should be added, 
+but we should assure the instructions don't have you trying to run 6.8 with the latest Payara 
+and perhaps should explicitly note that you can't. 
+
+We should also change the 'standard' language related to Payara updates to include copying the
+*.p12 files from the distributed domain1/config directory into the Dataverse domain1/config directory,
+at least if/when they are different. Those files include base certs and over time using the old files
+can cause SSL errors. If the domain.xml file is old enough, it may also reference *.jks files instead
+of the *.p12 ones. That should also be fixed (domain.xml having those lines updated to reference *.p12 files).
+FWIW: I ran across this at TDL where a dev machine stopped being able to contact DataCite because the root
+cert used by DataCite today is not in the *.jks files that had been copied forward during Payara updates.)
+

doc/release-notes/11954-CVoC-for-textarea-inputs.md

@@ -0,0 +1,5 @@
+### External Vocabulary Mechanism enhancement
+
+- The external vocabulary mechanism (see https://github.com/gdcc/dataverse-external-vocab-support/) now supports 
+  assigning metadatablock dataset field types of fieldType textbox (multiline inputs) as managed fields. This new functionality is
+  being leveraged to support automated generation of citation text for Related Publications entries. (a url could be added once the work in the external vocabulary repo is done).

doc/release-notes/11987-storage-quotas-on-datasets.md

@@ -0,0 +1,4 @@
+It is now possible to define storage quotas on individual datasets. See the API guide for more information.
+The practical use case is for datasets in the top-level, root collection. This does not address the use case of a user creating multiple datasets. But there is an open dev. issue for adding per-user storage quotas as well.
+
+A convenience API `/api/datasets/{id}/uploadlimits` has been added to show the remaining storage and/or number of files quotas, if present.

doc/sphinx-guides/source/admin/dataverses-datasets.rst

@@ -271,6 +271,8 @@ The effective store can be seen using::
 
     curl http://$SERVER/api/datasets/$dataset-id/storageDriver
 
+The output of the API will include the id, label, type (for example, "file" or "s3") as well as the support for direct download and upload.
+
 To remove an assigned store, and allow the dataset to inherit the store from it's parent collection, use the following (only a superuser can do this) ::
 
     curl -H "X-Dataverse-key: $API_TOKEN" -X DELETE http://$SERVER/api/datasets/$dataset-id/storageDriver

doc/sphinx-guides/source/api/native-api.rst

@@ -1250,16 +1250,22 @@ Collection Storage Quotas
 
   curl -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/dataverses/$ID/storage/quota"
 
-Will output the storage quota allocated (in bytes), or a message indicating that the quota is not defined for the specific collection. The user identified by the API token must have the ``Manage`` permission on the collection. 
+Will output the storage quota allocated (in bytes), or a message indicating that the quota is not defined for the collection. If this is an unpublished collection, the user must have the ``ViewUnpublishedDataverse`` permission. 
+With an optional query parameter ``showInherited=true`` it will show the applicable quota potentially defined on the nearest parent when the collection does not have a quota configured directly.
 
+.. code-block:: 
+
+  curl -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/dataverses/$ID/storage/use"
+
+Will output the dynamically cached total storage size (in bytes) used by the collection. The user identified by the API token must have the ``Edit`` permission on the collection. 
 
 To set or change the storage allocation quota for a collection:
 
 .. code-block:: 
 
-  curl -X POST -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/dataverses/$ID/storage/quota/$SIZE_IN_BYTES"
+  curl -X PUT -H "X-Dataverse-key:$API_TOKEN" -d $SIZE_IN_BYTES "$SERVER_URL/api/dataverses/$ID/storage/quota"
 
-This is API is superuser-only.
+This API is superuser-only.
 
 
 To delete a storage quota configured for a collection:
@@ -1268,9 +1274,70 @@ To delete a storage quota configured for a collection:
 
   curl -X DELETE -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/dataverses/$ID/storage/quota"
 
-This is API is superuser-only.
+This API is superuser-only.
+
+Storage Quotas on Individual Datasets
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: 
+
+  curl -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/datasets/$ID/storage/quota"
+
+Will output the storage quota allocated (in bytes), or a message indicating that the quota is not defined for this dataset. If this is an unpublished dataset, the user must have the ``ViewUnpublishedDataset`` permission.  
+With an optional query parameter ``showInherited=true`` it will show the applicable quota potentially defined on the nearest parent collection when the dataset does not have a quota configured directly.
+
+.. code-block:: 
+
+  curl -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/datasets/$ID/storage/use"
+
+Will output the dynamically cached total storage size (in bytes) used by the dataset. The user identified by the API token must have the ``Edit`` permission on the dataset.
+
+To set or change the storage allocation quota for a dataset:
+
+.. code-block:: 
+
+  curl -X PUT -H "X-Dataverse-key:$API_TOKEN" -d $SIZE_IN_BYTES "$SERVER_URL/api/datasets/$ID/storage/quota"
+
+This API is superuser-only.
+  
+
+To delete a storage quota configured for a dataset:
+
+.. code-block:: 
+
+  curl -X DELETE -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/datasets/$ID/storage/quota"
+
+This API is superuser-only.
+
+The following convenience API shows the dynamic values of the *remaining* storage size and/or file number quotas on the dataset, if present. For example:
+
+.. code-block::
+
+   curl  -H "X-Dataverse-key: $API_TOKEN" "http://localhost:8080/api/datasets/$dataset-id/uploadlimits" 
+   {
+     "status": "OK",
+     "data": {
+       "uploadLimits": {
+         "numberOfFilesRemaining": 20,
+         "storageQuotaRemaining": 1048576
+       }
+     } 
+   }
+
+Or, when neither limit is present: 
+
+.. code-block::
+
+   {
+     "status": "OK",
+     "data": {
+       "uploadLimits": {}
+     }
+   }
+
+This API requires the Edit permission on the dataset. 
 
-Use the ``/settings`` API to enable or disable the enforcement of storage quotas that are defined across the instance via the following setting. For example,
+Use the ``/settings`` API to enable or disable the enforcement of storage quotas that are defined across the instance via the following setting:
 
 .. code-block:: 
 

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 6.2025.3 or higher is required.
+Payara 6.2025.10 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/6.2025.3/payara-6.2025.3.zip``
+``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.10/payara-6.2025.10.zip``
 
-``sudo unzip payara-6.2025.3.zip``
+``sudo unzip payara-6.2025.10.zip``
 
 ``sudo chown -R $USER /usr/local/payara6``
 

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

@@ -10,27 +10,6 @@ Once you have finished securing and configuring your Dataverse installation, you
 .. contents:: |toctitle|
   :local:
 
-.. _comma-separated-config-values:
-
-Comma-separated configuration values
-------------------------------------
-
-Many configuration options (both MicroProfile/JVM settings and database settings) accept comma-separated lists. For all such settings, Dataverse applies consistent, lightweight parsing:
-
-- Whitespace immediately around commas is ignored (e.g., ``GET, POST`` is equivalent to ``GET,POST``).
-- Tokens are otherwise preserved exactly as typed. There is no quote parsing and no escape processing.
-- Embedded commas within a token are not supported.
-
-Examples include (but are not limited to):
-
-- :ref:`dataverse.cors.origin <dataverse.cors.origin>`
-- :ref:`dataverse.cors.methods <dataverse.cors.methods>`
-- :ref:`dataverse.cors.headers.allow <dataverse.cors.headers.allow>`
-- :ref:`dataverse.cors.headers.expose <dataverse.cors.headers.expose>`
-- :ref:`:UploadMethods`
-
-This behavior is implemented centrally and applies across all Dataverse settings that accept comma-separated values.
-
 .. _securing-your-installation:
 
 Securing Your Installation
@@ -2540,6 +2519,28 @@ Setting Up Integrations
 
 Before going live, you might want to consider setting up integrations to make it easier for your users to deposit or explore data. See the :doc:`/admin/integrations` section of the Admin Guide for details.
 
+.. _comma-separated-config-values:
+
+Comma-Separated Configuration Values
+------------------------------------
+
+Many configuration options (both MicroProfile/JVM settings and database settings) accept comma-separated lists. For all such settings, Dataverse applies consistent, lightweight parsing:
+
+- Whitespace immediately around commas is ignored (e.g., ``GET, POST`` is equivalent to ``GET,POST``).
+- Tokens are otherwise preserved exactly as typed. There is no quote parsing and no escape processing.
+- Embedded commas within a token are not supported.
+
+Examples include (but are not limited to):
+
+- :ref:`dataverse.cors.origin <dataverse.cors.origin>`
+- :ref:`dataverse.cors.methods <dataverse.cors.methods>`
+- :ref:`dataverse.cors.headers.allow <dataverse.cors.headers.allow>`
+- :ref:`dataverse.cors.headers.expose <dataverse.cors.headers.expose>`
+- :ref:`:UploadMethods`
+
+This behavior is implemented centrally and applies across all Dataverse settings that accept comma-separated values.
+
+
 .. _jvm-options:
 
 JVM Options

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 6.2025.3 is recommended. Newer versions might work fine. Regular updates are recommended.
+Payara 6.2025.10 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/6.2025.3/payara-6.2025.3.zip
-	# unzip payara-6.2025.3.zip
+	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.10/payara-6.2025.10.zip
+	# unzip payara-6.2025.10.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/6.2025.3/payara-6.2025.3.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/6.2025.10/payara-6.2025.10.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

@@ -149,7 +149,7 @@
         <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>6.2025.3</payara.version>
+        <payara.version>6.2025.10</payara.version>
         <postgresql.version>42.7.7</postgresql.version>
         <solr.version>9.8.0</solr.version>
         <postgresql.server.version>16</postgresql.server.version>