Merge branch 'develop' into 12258-publish-submit-contains-files

Author: stevenwinship

doc/release-notes/12014-croissant-1.1.md

@@ -0,0 +1,25 @@
+### Croissant 1.1 (Summary Statistics)
+
+The Croissant metadata export format has been updated from version 1.0 to 1.1.
+
+Summary statistics (mean, min, max, etc.) are now included for tabular files that were successfully ingested.
+
+You can download an example Croissant file from the [Supported Metadata Export Formats](https://dataverse-guide--12214.org.readthedocs.build/en/12214/user/dataset-management.html#supported-metadata-export-formats) section of the guides.
+
+Minor backward-incompatible changes were made, which are noted below.
+
+See #12014 and #12214
+
+## Backward Incompatible Changes
+
+Generally speaking, see the [API Changelog](https://guides.dataverse.org/en/latest/api/changelog.html) for a list of backward-incompatible API changes.
+
+Minor changes in the `croissant` format are noted in the [API changelog](https://dataverse-guide--12214.org.readthedocs.build/en/12214/api/changelog.html).
+
+## Upgrade Instructions
+
+1. Re-export metadata export formats
+
+   We re-export because the Croissant format was updated.
+
+   `curl http://localhost:8080/api/admin/metadata/reExportAll`

doc/release-notes/12070-datacite-getmetadata.md

@@ -0,0 +1,11 @@
+Incremental improvements have been made to the process of registering dataset metadata with DataCite. If your instance is using DataCite, please make sure you have a valid DataCite REST API url configured, since it is now required.
+
+The JVM option(s) in question are `dataverse.pid.*.datacite.rest-api-url` if the recommended, new-style pid configuration is used, or `doi.dataciterestapiurlstring` if the legacy settings are in place. In the latter case however, this may be a good occasion to switch to the new configuration setup.
+
+For instances using registered DataCite authorities in production the url should be:
+
+```<jvm-options>-Ddataverse.pid.<providername>.datacite.rest-api-url=https://api.datacite.org</jvm-options>```
+
+Or, for test and development instances:
+
+```<jvm-options>-Ddataverse.pid.<providername>.datacite.rest-api-url=https://api.test.datacite.org</jvm-options>```

doc/release-notes/12112-get-default-contributor-role.md

@@ -0,0 +1 @@
+A new API endpoint for getting the default contributor role of a collection (`GET /api/dataverses/$ID/defaultContributorRole`) was added.

doc/release-notes/12268-direct-upload-support-legacy-lowercase-dois.md

@@ -0,0 +1 @@
+Fixed a problem with S3 direct upload to datasets which using lower- or mixed-case PID authority/identifier in the database and to datasets using an alternative identifier for file storage.

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

@@ -14,6 +14,8 @@ v6.11
 
   - **/api/datasets/{Id}/submitForReview**
 
+- The Croissant :ref:`metadata export format <metadata-export-formats>` has been updated from version 1.0 to 1.1, which is reflected in the ``conformsTo`` property. ``@vocab`` and ``sc`` properties now use "http" as `recommended <https://github.com/mlcommons/croissant/pull/929#pullrequestreview-3079137662>`_. The unused ``wd`` property has been dropped.
+
 v6.10
 -----
 - The following GET APIs will now return ``400`` if a required Guestbook Response is not supplied. A Guestbook Response can be passed to these APIs in the JSON body using a POST call. See the notes under :ref:`basic-file-access` and :ref:`download-by-dataset-by-version` for details.

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

@@ -525,7 +525,7 @@ The fully expanded example above (without environment variables) looks like this
 Assign Default Role to User Creating a Dataset in a Dataverse Collection
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Assign a default role to a user creating a dataset in a Dataverse collection ``id`` where ``roleAlias`` is the database alias of the role to be assigned:
+Assign a default role to a user creating a dataset in a Dataverse collection ``id`` where ``roleAlias`` is the database alias of the role to be assigned (requires ``ManageDataversePermissions``):
 
 .. code-block:: bash
 
@@ -544,6 +544,27 @@ The fully expanded example above (without environment variables) looks like this
 
 Note: You may use "none" as the ``ROLE_ALIAS``. This will prevent a user who creates a dataset from having any role on that dataset. It is not recommended for Dataverse collections with human contributors.
 
+.. _get-default-contributor-role-on-a-dataverse-api:
+
+Get Default Role Assigned to User Creating a Dataset in a Dataverse Collection
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Get the default role that is assigned to a user creating a dataset in a Dataverse collection ``id`` (requires ``ManageDataversePermissions``):
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export ID=root
+
+  curl -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/dataverses/$ID/defaultContributorRole"
+
+The fully expanded example above (without environment variables) looks like this:
+
+.. code-block:: bash
+
+  curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" "https://demo.dataverse.org/api/dataverses/root/defaultContributorRole"
+
 .. _assign-role-on-a-dataverse-api:
 
 Assign a New Role on a Dataverse Collection

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

@@ -28,7 +28,7 @@ Supported Metadata Export Formats
 
 Once a dataset has been published, its metadata can be exported in a variety of other metadata standards and formats, which help make datasets more :doc:`discoverable </admin/discoverability>` and usable in other systems, such as other data repositories. On each dataset page's metadata tab, the following exports are available:
 
-- Croissant
+- Croissant (example: :download:`max-croissant.json <../../../../src/test/resources/croissant/max/expected/max-croissant.json>`)
 - Dublin Core
 - DDI (Data Documentation Initiative Codebook 2.5)
 - DDI HTML Codebook (A more human-readable, HTML version of the DDI Codebook 2.5 metadata export)

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

@@ -662,6 +662,10 @@ public String getIdentifierForFileStorage(){
         return retVal;         
     }
 
+    public String getGlobalIdForFileStorageAsString() {
+        return getProtocolForFileStorage() + ":" + getAuthorityForFileStorage() + "/" + getIdentifierForFileStorage();
+    }
+
     public String getNextMajorVersionString() {
         // Never need to get the next major version for harvested studies.
         if (isHarvested()) {

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

@@ -1706,7 +1706,7 @@ public void requestDirectUploadUrls() {
         String storageIdentifier = null;
         try {
             storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation());
-            urls = s3io.generateTemporaryS3UploadUrls(dataset.getGlobalId().asString(), storageIdentifier, fileSize);
+            urls = s3io.generateTemporaryS3UploadUrls(dataset.getGlobalIdForFileStorageAsString(), storageIdentifier, fileSize);
 
         } catch (IOException io) {
             logger.warning(io.getMessage());

src/main/java/edu/harvard/iq/dataverse/api/Datasets.java

@@ -2798,7 +2798,7 @@ public Response getMPUploadUrls(@Context ContainerRequestContext crc, @PathParam
             String storageIdentifier = null;
             try {
                 storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation());
-                response = s3io.generateTemporaryS3UploadUrls(dataset.getGlobalId().asString(), storageIdentifier, fileSize);
+                response = s3io.generateTemporaryS3UploadUrls(dataset.getGlobalIdForFileStorageAsString(), storageIdentifier, fileSize);
 
             } catch (IOException io) {
                 logger.warning(io.getMessage());