Merge branch 'develop' into container-naming-fix

Author: stevenwinship

.github/workflows/deploy_beta_testing.yml

@@ -36,7 +36,7 @@ jobs:
         run: echo "war_file=$(ls *.war | head -1)">> $GITHUB_ENV
 
       - name: Upload war artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: built-app
           path: ./target/${{ env.war_file }}
@@ -50,7 +50,7 @@ jobs:
       - uses: actions/checkout@v5
 
       - name: Download war artifact
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v6
         with:
           name: built-app
           path: ./

.github/workflows/maven_unit_test.yml

@@ -62,7 +62,7 @@ jobs:
 
           # Upload the built war file. For download, it will be wrapped in a ZIP by GitHub.
           # See also https://github.com/actions/upload-artifact#zipped-artifact-downloads
-          - uses: actions/upload-artifact@v4
+          - uses: actions/upload-artifact@v5
             with:
                 name: dataverse-java${{ matrix.jdk }}.war
                 path: target/dataverse*.war
@@ -72,7 +72,7 @@ jobs:
           - run: |
                 tar -cvf java-builddir.tar target
                 tar -cvf java-m2-selection.tar ~/.m2/repository/io/gdcc/dataverse-*
-          - uses: actions/upload-artifact@v4
+          - uses: actions/upload-artifact@v5
             with:
                 name: java-artifacts
                 path: |
@@ -112,7 +112,7 @@ jobs:
                   cache: maven
 
             # Get the build output from the unit test job
-            - uses: actions/download-artifact@v5
+            - uses: actions/download-artifact@v6
               with:
                   name: java-artifacts
             - run: |
@@ -124,7 +124,7 @@ jobs:
 
             # Wrap up and send to coverage job
             - run: tar -cvf java-reportdir.tar target/site
-            - uses: actions/upload-artifact@v4
+            - uses: actions/upload-artifact@v5
               with:
                   name: java-reportdir
                   path: java-reportdir.tar
@@ -145,7 +145,7 @@ jobs:
                 cache: maven
 
           # Get the build output from the integration test job
-          - uses: actions/download-artifact@v5
+          - uses: actions/download-artifact@v6
             with:
                 name: java-reportdir
           - run: tar -xvf java-reportdir.tar

doc/release-notes/11771-update-dataset-license-api.md

@@ -0,0 +1,13 @@
+## New Endpoint: `/datasets/{id}/license`
+
+A new endpoint has been implemented to manage dataset licenses.
+
+### Functionality
+- Updates the license of a dataset by applying it to the draft version.
+- If no draft exists, a new one is automatically created.
+
+### Usage
+This endpoint supports two ways of defining a license:
+1. **Predefined License** – Provide the license name (e.g., `CC BY 4.0`).
+2. **Custom Terms of Use and Access** – Provide a JSON body with the `customTerms` object.
+    - All fields are optional **except** `termsOfUse`, which is required.

doc/release-notes/11865-suppress-host-dataverse-field.md

@@ -0,0 +1,3 @@
+### Suppression of the Host Dataverse field
+
+When creating a dataset, the _host dataverse_ field is not shown when the user can only add datasets to one collection.

doc/sphinx-guides/source/admin/integrations.rst

@@ -240,11 +240,6 @@ Discoverability
 
 A number of builtin features related to data discovery are listed under :doc:`discoverability` but you can further increase the discoverability of your data by setting up integrations.
 
-SHARE
-+++++
-
-`SHARE <http://www.share-research.org>`_ is building a free, open, data set about research and scholarly activities across their life cycle. It's possible to add a Dataverse installation as one of the `sources <https://share.osf.io/sources>`_ they include if you contact the SHARE team.
-
 Geodisy
 +++++++
 

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

@@ -4208,24 +4208,24 @@ Delete files from a dataset. This API call allows you to delete multiple files f
 
   curl -H "X-Dataverse-key:$API_TOKEN" -X PUT "$SERVER_URL/api/datasets/:persistentId/deleteFiles?persistentId=$PERSISTENT_IDENTIFIER" \
   -H "Content-Type: application/json" \
-  -d '{"fileIds": [1, 2, 3]}'
+  -d '[1, 2, 3]'
 
 The fully expanded example above (without environment variables) looks like this:
 
 .. code-block:: bash
 
   curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X PUT "https://demo.dataverse.org/api/datasets/:persistentId/deleteFiles?persistentId=doi:10.5072/FK2ABCDEF" \
   -H "Content-Type: application/json" \
-  -d '{"fileIds": [1, 2, 3]}'
+  -d '[1, 2, 3]'
 
-The ``fileIds`` in the JSON payload should be an array of file IDs that you want to delete from the dataset.
+The JSON payload should be an array of file IDs that you want to delete from the dataset.
 
 You must have the appropriate permissions to delete files from the dataset.
 
 Upon success, the API will return a JSON response with a success message and the number of files deleted.
 
 The API call will report a 400 (BAD REQUEST) error if any of the files specified do not exist or are not in the latest version of the specified dataset.
-The ``fileIds`` in the JSON payload should be an array of file IDs that you want to delete from the dataset.
+The JSON payload should be an array of file IDs that you want to delete from the dataset.
 
 .. _api-dataset-role-assignment-history:
 
@@ -4357,6 +4357,53 @@ The CSV response for this call is the same as for the /api/datasets/{id}/assignm
 
 Note: This feature requires the "role-assignment-history" feature flag to be enabled (see :ref:`feature-flags`).
 
+Update Dataset License
+~~~~~~~~~~~~~~~~~~~~~~
+
+Updates the license of a dataset by applying it to the draft version, or by creating a draft if none exists.
+
+The JSON representation of a license can take two forms, depending on whether you want to specify a predefined license or define custom terms of use and access.
+
+To set a predefined license (e.g., CC BY 4.0), provide a JSON body with the license name:
+
+.. code-block:: json
+
+  {
+    "name": "CC BY 4.0"
+  }
+
+To define custom terms of use and access, provide a JSON body with the following properties. All fields within ``customTerms`` are optional, except for the ``termsOfUse`` field, which is required:
+
+.. code-block:: json
+
+  {
+    "customTerms": {
+        "termsOfUse": "Your terms of use",
+        "confidentialityDeclaration": "Your confidentiality declaration",
+        "specialPermissions": "Your special permissions",
+        "restrictions": "Your restrictions",
+        "citationRequirements": "Your citation requirements",
+        "depositorRequirements": "Your depositor requirements",
+        "conditions": "Your conditions",
+        "disclaimer": "Your disclaimer"
+    }
+  }
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export ID=3
+  export FILE_PATH=license.json
+
+  curl -H "X-Dataverse-key:$API_TOKEN" -X PUT "$SERVER_URL/api/datasets/$ID/license" -H "Content-type:application/json" --upload-file $FILE_PATH
+
+The fully expanded example above (without environment variables) looks like this:
+
+.. code-block:: bash
+
+  curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X PUT "https://demo.dataverse.org/api/datasets/3/license" -H "Content-type:application/json" --upload-file license.json
+
 Files
 -----
 

doc/sphinx-guides/source/container/dev-usage.rst

@@ -233,6 +233,13 @@ Hotswapping methods requires using JDWP (Debug Mode), but does not allow switchi
        **Requires IntelliJ Ultimate!**
        (Note that `free educational licenses <https://www.jetbrains.com/community/education/>`_ are available)
 
+       Go to settings, then plugins. Install "Payara Ultimate Tools". For more information:
+
+       - `plugin homepage <https://plugins.jetbrains.com/plugin/15114-payara-ultimate-tools>`_
+       - `docs <https://docs.payara.fish/community/docs/Technical%20Documentation/Ecosystem/IDE%20Integration/IntelliJ%20Plugin/Overview.html>`_
+       - `source <https://github.com/payara/ecosystem-intellij-plugin>`_
+       - `issues <https://github.com/payara/ecosystem-support>`_
+
        .. image:: img/intellij-payara-plugin-install.png
 
 #. Configure a connection to Payara:
@@ -284,6 +291,7 @@ Hotswapping methods requires using JDWP (Debug Mode), but does not allow switchi
 
         You might want to tweak the hot deploy behavior in the "Server" tab now.
         "Update action" can be found in the run window (see below).
+        By default it is "Hot Swap classes", which works fine, but as the screenshot shows you can also change it to "Redeploy".
         "Frame deactivation" means switching from IntelliJ window to something else, e.g. your browser.
         *Note: static resources like properties, XHTML etc will only update when redeploying!*
 
@@ -305,7 +313,11 @@ Hotswapping methods requires using JDWP (Debug Mode), but does not allow switchi
         See cheat sheet above for more options.
         Note that this command either assumes you built the :doc:`app-image` first or will download it from Docker Hub.
      .. group-tab:: IntelliJ
-        You can create a service configuration to automatically start services for you.
+        Note that you can skip this step if you're ok running the command under the "Maven" tab, which is this:
+
+        ``mvn -Pct docker:run -Dapp.skipDeploy``
+
+        In IntelliJ you can create a service configuration to automatically start services for you.
 
         **IMPORTANT**: This requires installation of the `Docker plugin <https://plugins.jetbrains.com/plugin/7724-docker>`_.
 
@@ -362,7 +374,7 @@ Hotswapping methods requires using JDWP (Debug Mode), but does not allow switchi
 
         .. image:: img/intellij-payara-run-output.png
 
-        Manually hotswap classes in "Debug" mode via "Run" > "Debugging Actions" > "Reload Changed Classes".
+        Manually hotswap classes in "Debug" mode via "Run" > "Debugging Actions" > "Compile and Reload Modified Files".
 
         .. image:: img/intellij-payara-run-menu-reload.png
 

doc/sphinx-guides/source/developers/making-library-releases.rst

@@ -13,7 +13,9 @@ Note: See :doc:`making-releases` for Dataverse itself.
 We release Java libraries to Maven Central that are used by Dataverse (and perhaps `other <https://github.com/gdcc/xoai/issues/141>`_ `software <https://github.com/gdcc/xoai/issues/170>`_!):
 
 - https://central.sonatype.com/namespace/org.dataverse
+- https://central.sonatype.com/namespace/org.dataverse.test
 - https://central.sonatype.com/namespace/io.gdcc
+- https://central.sonatype.com/namespace/io.gdcc.export
 
 We release JavaScript/TypeScript libraries to npm:
 
@@ -109,60 +111,18 @@ Releasing a New Library to Maven Central
 At a high level:
 
 - Start with a snapshot release.
-- Use an existing pom.xml as a starting point.
-- Use existing GitHub Actions workflows as a starting point.
-- Create secrets in the new library's GitHub repo used by the workflow.
-- If you need an entire new namespace, look at previous issues such as https://issues.sonatype.org/browse/OSSRH-94575 and https://issues.sonatype.org/browse/OSSRH-94577
-
-Updating pom.xml for a Snapshot Release
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Before publishing a final version to Maven Central, you should publish a snapshot release or two. For each snapshot release you publish, the jar name will be unique each time (e.g. ``foobar-0.0.1-20240430.175110-3.jar``), so you can safely publish over and over with the same version number.
-
-We use the `Nexus Staging Maven Plugin <https://github.com/sonatype/nexus-maven-plugins/blob/main/staging/maven-plugin/README.md>`_ to push snapshot releases to https://s01.oss.sonatype.org/content/groups/staging/io/gdcc/ and https://s01.oss.sonatype.org/content/groups/staging/org/dataverse/
-
-Add the following to your pom.xml:
-
-.. code-block:: xml
+- Use an existing pom.xml as a starting point, such as from `Croissant <https://github.com/gdcc/exporter-croissant>`_, that inherits from the common Maven parent (https://github.com/gdcc/maven-parent). You can also play around with the "hello" project (https://github.com/gdcc/hello) and even make releases from it since it is designed to be a sandbox for publishing to Maven Central.
+- Use existing GitHub Actions workflows as a starting point, such as from `Croissant <https://github.com/gdcc/exporter-croissant>`_. As of this writing we have separate actions for ``maven-snapshot.yml`` and ``maven-release.yml``.
+- For repos under https://github.com/IQSS, create secrets in the new library's GitHub repo used by the workflow. This is necessary for the IQSS org because "organization secrets are not available for organizations on legacy per-repository billing plans." For repos under https://github.com/gdcc you can make use of shared secrets at the org level. These are the environment variables we use:
 
-    <version>0.0.1-SNAPSHOT</version>
+  - DATAVERSEBOT_GPG_KEY
 
-    <distributionManagement>
-        <snapshotRepository>
-            <id>ossrh</id>
-            <url>https://s01.oss.sonatype.org/content/repositories/snapshots</url>
-        </snapshotRepository>
-        <repository>
-            <id>ossrh</id>
-            <url>https://s01.oss.sonatype.org/service/local/staging/deploy/maven2/</url>
-        </repository>
-    </distributionManagement>
+  - DATAVERSEBOT_GPG_PASSWORD
 
-   <plugin>
-       <groupId>org.sonatype.plugins</groupId>
-       <artifactId>nexus-staging-maven-plugin</artifactId>
-       <version>${nexus-staging.version}</version>
-       <extensions>true</extensions>
-       <configuration>
-           <serverId>ossrh</serverId>
-           <nexusUrl>https://s01.oss.sonatype.org</nexusUrl>
-           <autoReleaseAfterClose>true</autoReleaseAfterClose>
-       </configuration>
-   </plugin>
+  - DATAVERSEBOT_SONATYPE_TOKEN
 
-Configuring Secrets
-~~~~~~~~~~~~~~~~~~~
-
-In GitHub, you will likely need to configure the following secrets:
-
-- DATAVERSEBOT_GPG_KEY
-- DATAVERSEBOT_GPG_PASSWORD
-- DATAVERSEBOT_SONATYPE_TOKEN
-- DATAVERSEBOT_SONATYPE_USERNAME
-
-Note that some of these secrets might be configured at the org level (e.g. gdcc or IQSS).
-
-Many of the automated tasks are performed by the dataversebot account on GitHub: https://github.com/dataversebot
+  - DATAVERSEBOT_SONATYPE_USERNAME
+- If you need an entire new namespace, look at previous issues such as https://issues.sonatype.org/browse/OSSRH-94575 and https://issues.sonatype.org/browse/OSSRH-94577
 
 npm (JavaScript/TypeScript)
 ---------------------------

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

@@ -115,6 +115,23 @@ See the :ref:`payara` section of :doc:`prerequisites` for details and init scrip
 
 Related to this is that you should remove ``/root/.payara/pass`` to ensure that Payara isn't ever accidentally started as root. Without the password, Payara won't be able to start as root, which is a good thing.
 
+.. _payara-ports-localhost-only:
+
+Restricting Payara's Ports to localhost
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In the recommended setup of Dataverse, you do not expose Payara's ports directly to the Internet. Rather, you front Payara with a proxy such as Apache.
+
+If you are running Payara and your proxy on the same server, we recommend having Payara listen only to localhost, which is how your proxy talks to it, with the following command:
+
+``./asadmin set server-config.network-config.network-listeners.network-listener.http-listener-1.address=127.0.0.1``
+
+(You should **NOT** use the configuration option above if you are running in a load-balanced environment, or otherwise have your proxy on a different host than Payara.)
+
+To test that Payara is now only listening on localhost, try hitting port 8080 from the Internet. Payara should not respond.
+
+See also :ref:`network-ports`.
+
 .. _secure-password-storage:
 
 Secure Password Storage
@@ -246,6 +263,8 @@ If you are running an installation with Apache and Payara on the same server, an
 
 You should **NOT** use the configuration option above if you are running in a load-balanced environment, or otherwise have the web server on a different host than the application server.
 
+This security tip is also mentioned at :ref:`payara-ports-localhost-only`.
+
 .. _root-collection-permissions:
 
 Root Dataverse Collection Permissions

doc/sphinx-guides/source/user/dataset-management.rst

@@ -704,7 +704,7 @@ If you have a Contributor role (can edit metadata, upload files, and edit files,
 Preview URL to Review Unpublished Dataset
 =========================================
 
-Creating a Preview URL for a draft version of your dataset allows you to share your dataset (for viewing and downloading of files) before it is published to a wide group of individuals who may not have a user account on the Dataverse installation. Anyone you send the Preview URL to will not have to log into the Dataverse installation to view the unpublished dataset. Once a dataset has been published you may create new General Preview URLs for subsequent draft versions, but the Anonymous Preview URL will no longer be available.
+Creating a Preview URL for a draft version of your dataset allows you to share your dataset (for viewing and downloading files, including :ref:`restricted <restricted-files>` and :ref:`embargoed <embargoes>` files) before it is published to a wide group of people who might not have a user account on the Dataverse installation. Anyone you send the Preview URL to will not have to log in to the Dataverse installation to view the unpublished dataset. Once a dataset has been published, you may create new General Preview URLs for subsequent draft versions, but the Anonymous Preview URL will no longer be available.
 
 **Note:** To create a Preview URL, you must have the *ManageDatasetPermissions* permission for your draft dataset, usually given by the :ref:`roles <permissions>` *Curator* or *Administrator*.
 
@@ -726,6 +726,8 @@ To disable a Preview URL and to revoke access, follow the same steps as above un
 
 Note that only one Preview URL (normal or with anonymized access) can be configured per dataset at a time. 
 
+.. _embargoes:
+
 Embargoes
 =========