Merge branch 'develop' into 11634-api-get-available-file-categories

Author: sekmiller

doc/release-notes/11534-link-permissions.md

@@ -0,0 +1 @@
+The [API for listing the collections a dataverse has been linked to](https://guides.dataverse.org/en/latest/admin/dataverses-datasets.html#list-dataverse-collection-links) (`api/dataverses/$dataverse-alias/links`) has been refactored to return a new Json format. This is a breaking API.

doc/release-notes/11633-list-dataverse-links-api-change.md

@@ -0,0 +1,11 @@
+## API Updates 
+
+### Support read/unread status for notifications
+
+The API for managing notifications has been extended. 
+
+- displayAsRead boolean added to "get all"
+- new GET unreadCount API endpoint
+- new PUT markAsRead API endpoint
+
+See also [the guides](https://dataverse-guide--11664.org.readthedocs.build/en/11664/api/native-api.html#notifications), #11650, and #11664.

doc/release-notes/11650-unread.md

@@ -118,7 +118,7 @@ Moves a dataset whose id is passed to a Dataverse collection whose alias is pass
 Link a Dataset
 ^^^^^^^^^^^^^^
 
-Creates a link between a dataset and a Dataverse collection (see the :ref:`dataset-linking` section of the User Guide for more information). Accessible to users with Link Dataset permission on the Dataverse collection. ::
+Creates a link between a dataset and a Dataverse collection (see the :ref:`dataset-linking` section of the User Guide for more information). ::
 
     curl -H "X-Dataverse-key: $API_TOKEN" -X PUT http://$SERVER/api/datasets/$linked-dataset-id/link/$linking-dataverse-alias
 
@@ -155,7 +155,7 @@ It returns a list in the following format (new format as of v6.4):
 Unlink a Dataset
 ^^^^^^^^^^^^^^^^
 
-Removes a link between a dataset and a Dataverse collection. Accessible to users with Link Dataset permission on the Dataverse collection. ::
+Removes a link between a dataset and a Dataverse collection. Accessible to users with Publish Dataset permissions. ::
 
     curl -H "X-Dataverse-key: $API_TOKEN" -X DELETE http://$SERVER/api/datasets/$linked-dataset-id/deleteLink/$linking-dataverse-alias
 

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

@@ -9,8 +9,10 @@ This API changelog is experimental and we would love feedback on its usefulness.
 
 v6.8
 ----
+
 - For POST /api/files/{id}/metadata passing an empty string ("description":"")  or array ("categories":[]) will no longer be ignored. Empty fields will now clear out the values in the file's metadata. To ignore the fields simply do not include them in the JSON string.
 - For PUT /api/datasets/{id}/editMetadata the query parameter "sourceInternalVersionNumber" has been removed and replaced with "sourceLastUpdateTime" to verify that the data being edited hasn't been modified and isn't stale.
+- For GET /api/dataverses/$dataverse-alias/links the Json response has changed breaking the backward compatibility of the API.
 
 v6.7
 ----

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

@@ -5947,6 +5947,8 @@ Notifications
 
 See :ref:`account-notifications` in the User Guide for an overview. For a list of all the notification types mentioned below (e.g. ASSIGNROLE), see :ref:`mute-notifications` in the Admin Guide.
 
+.. _get-all-notifications:
+
 Get All Notifications by User
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -5956,6 +5958,52 @@ Each user can get a dump of their notifications by passing in their API token:
 
   curl -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/notifications/all"
 
+The expected OK (200) response looks something like this:
+
+.. code-block:: text
+
+  {
+      "status": "OK",
+      "data": {
+          "notifications": [
+              {
+                  "id": 38,
+                  "type": "CREATEACC",
+                  "displayAsRead": true,
+                  "subjectText": "Root: Your account has been created",
+                  "messageText": "Hello, \nWelcome to...",
+                  "sentTimestamp": "2025-07-21T19:15:37Z"
+              }
+  ...
+
+Get Unread Count
+~~~~~~~~~~~~~~~~
+
+You can get a count of your unread notifications as shown below.
+
+.. code-block:: bash
+
+  curl -H "X-Dataverse-key:$API_TOKEN" -X GET "$SERVER_URL/api/notifications/unreadCount"
+
+Mark Notification As Read
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+After finding the ID of a notification using :ref:`get-all-notifications`, you can pass it to the "markAsRead" API endpoint as shown below. Note that this endpoint is idempotent; you can mark an already-read notification as read over and over.
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export NOTIFICATION_ID=555
+
+  curl -H "X-Dataverse-key:$API_TOKEN" -X PUT "$SERVER_URL/api/notifications/$NOTIFICATION_ID/markAsRead"
+
+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/notifications/555/markAsRead"
+
 Delete Notification by User
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

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

@@ -215,7 +215,7 @@ Dataset linking allows a Dataverse collection owner to "link" their Dataverse co
 
 For example, researchers working on a collaborative study across institutions can each link their own individual institutional Dataverse collections to the one collaborative dataset, making it easier for interested parties from each institution to find the study.
 
-In order to link a dataset, you will need your account to have the "Link Dataset" permission on the Dataverse collection that is doing the linking. If you created the Dataverse collection then you should have this permission already, but if not then you will need to ask the admin of that Dataverse collection to assign that permission to your account. You do not need any special permissions on the dataset being linked.
+In order to link a dataset, you will need your account to have the "Publish Dataset" permission on the Dataverse collection that is doing the linking. If you created the Dataverse collection then you should have this permission already, but if not then you will need to ask the admin of that Dataverse collection to assign that permission to your account. You do not need any special permissions on the dataset being linked.
 
 To link a dataset to your Dataverse collection, you must navigate to that dataset and click the white "Link" button in the upper-right corner of the dataset page. This will open up a window where you can type in the name of the Dataverse collection that you would like to link the dataset to. Select your Dataverse collection and click the save button. This will establish the link, and the dataset will now appear under your Dataverse collection.
 

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

@@ -1,14 +1,13 @@
 {
     "alias":"curator",
     "name":"Curator",
-    "description":"For datasets, a person who can edit License + Terms, edit Permissions, and publish and link datasets.",
+    "description":"For datasets, a person who can edit License + Terms, edit Permissions, and publish datasets.",
     "permissions":[
         "ViewUnpublishedDataset",
         "EditDataset",
         "DownloadFile",
         "DeleteDatasetDraft",
         "PublishDataset",
-        "LinkDataset",
         "ManageDatasetPermissions",
         "ManageFilePermissions",
         "AddDataverse",

scripts/api/data/role-curator.json

@@ -512,7 +512,7 @@ public List<Dataverse> filterDataversesForLinking(String query, DataverseRequest
 
         for (Dataverse res : results) {
             if (!remove.contains(res)) {
-                if (this.permissionService.requestOn(req, res).has(Permission.LinkDataset)) {
+                if (this.permissionService.requestOn(req, res).has(Permission.PublishDataset)) {
                     dataverseList.add(res);
                 }
             }
@@ -525,7 +525,7 @@ public List<Dataverse> filterDataversesForUnLinking(String query, DataverseReque
         List<Dataverse> dataverseList = new ArrayList<>();
         if (alreadyLinkeddv_ids != null && !alreadyLinkeddv_ids.isEmpty()) {
             alreadyLinkeddv_ids.stream().map((testDVId) -> this.find(testDVId)).forEachOrdered((dataverse) -> {
-                if (this.permissionService.requestOn(req, dataverse).has(Permission.LinkDataset)) {
+                if (this.permissionService.requestOn(req, dataverse).has(Permission.PublishDataset)) {
                     dataverseList.add(dataverse);
                 }
             });

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

@@ -87,7 +87,12 @@ public UserNotification find(Object pk) {
     public UserNotification save(UserNotification userNotification) {
         return em.merge(userNotification);
     }
-    
+
+    public UserNotification markAsRead(UserNotification userNotification) {
+        userNotification.setReadNotification(true);
+        return em.merge(userNotification);
+    }
+
     public void delete(UserNotification userNotification) {
         em.remove(em.merge(userNotification));
     }