Merge branch 'develop' into dependabot/github_actions/github/codeql-action-4

Author: ofahimIQSS

conf/keycloak/builtin-users-spi/pom.xml

@@ -100,7 +100,7 @@
     </build>
 
     <properties>
-        <keycloak.version>26.3.2</keycloak.version>
+        <keycloak.version>26.3.4</keycloak.version>
         <java.version>17</java.version>
         <jakarta.persistence.version>3.2.0</jakarta.persistence.version>
         <mindrot.jbcrypt.version>0.4</mindrot.jbcrypt.version>

doc/release-notes/11695-change-api-get-storage-driver.md

@@ -0,0 +1,12 @@
+## Get Dataset/Dataverse Storage Driver API
+
+### Changed Json response - breaking change!
+
+The API for getting the Storage Driver info has been changed/extended.
+/api/datasets/{identifier}/storageDriver
+/api/admin/dataverse/{dataverse-alias}/storageDriver
+changed "message" to "name" and added "type" and "label"
+
+Also added query param for /api/admin/dataverse/{dataverse-alias}/storageDriver?getEffective=true to recurse the chain of parents to find the effective storageDriver
+
+See also [the guides](https://dataverse-guide--11664.org.readthedocs.build/en/11664/api/native-api.html#configure-a-dataset-to-store-all-new-files-in-a-specific-file-store), #11695, and #11664.

doc/release-notes/11710-get-available-dataverses-api.md

@@ -0,0 +1,5 @@
+### New API endpoint for retrieving a list of Dataverse Collections to which a given Dataset or Dataverse Collection may be linked
+
+-The end point also takes in a search term which currently must be part of the collections' names.
+-The user calling this API must have Link Dataset or Link Dataverse permission on the Dataverse Collections returned.
+-If the Collection has already been linked to the given Dataset or Collection, it will not be returned.

doc/release-notes/11822-faster-permission-indexing.md

@@ -0,0 +1 @@
+Permission reindexing, which occurs, e.g., after a user has been granted a role on a collection, has been made faster and less memory intensive in this release.

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

@@ -60,6 +60,10 @@ The current driver can be seen using::
 
     curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/$dataverse-alias/storageDriver
 
+Or to recurse the chain of parents to find the effective storageDriver::
+
+    curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/$dataverse-alias/storageDriver?getEffective=true
+
 (Note that for ``dataverse.files.store1.label=MyLabel``, ``store1`` will be returned.)
 
 and can be reset to the default store with::

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

@@ -13,6 +13,7 @@ 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/$dataverse-alias/links the Json response has changed breaking the backward compatibility of the API.
+- For GET /api/admin/dataverse/{dataverse-alias}/storageDriver and /api/datasets/{identifier}/storageDriver the driver name is no longer returned in data.message. This value is now returned in data.name.
 - For PUT /api/dataverses/$dataverse-alias/inputLevels custom input levels that had been previously set will no longer be deleted. To delete input levels send an empty list (deletes all), then send the new/modified list.
 - For GET /api/externalTools and /api/externalTools/{id} the responses are now formatted as JSON (previously the toolParameters and allowedApiCalls were a JSON object and array (respectively) that were serialized as JSON strings) and any configured "requirements" are included.
 

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

@@ -732,6 +732,50 @@ Note: you must have "Add Dataset" permission in the given collection to invoke t
 
 .. _featured-collections:
 
+List Dataverse Collections to Which a Given Dataset or Dataverse Collection May Be Linked
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The user may provide a search term to limit the list of Dataverse Collections returned. The search term will be compared to the name of the Dataverse Collections.
+The response is a JSON array of the ids, aliases, and names of the Dataverse collections to which a given Dataset or Dataverse Collection may be linked:
+
+For a given Dataverse Collection:
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export OBJECT_TYPE=dataverse
+  export ID=collectionAlias
+  export SEARCH_TERM=searchOn
+
+  curl -H "X-Dataverse-key:$API_TOKEN" -X GET "$SERVER_URL/api/dataverses/$ID/$OBJECT_TYPE/linkingDataverses?searchTerm=$SEARCH_TERM" 
+
+The fully expanded example above (without environment variables) looks like this:
+
+.. code-block:: bash
+
+  curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X GET "https://demo.dataverse.org/api/dataverses/collectionAlias/dataverse/linkingDataverses?searchTerm=searchOn" 
+
+For a given Dataset:
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export OBJECT_TYPE=dataset
+  export PERSISTENT_IDENTIFIER=doi:10.5072/FK2/J8SJZB
+  export SEARCH_TERM=searchOn
+
+  curl -H "X-Dataverse-key:$API_TOKEN" -X GET "$SERVER_URL/api/dataverses/:persistentId/$OBJECT_TYPE/linkingDataverses?searchTerm=SEARCH_TERM&persistentId=$PERSISTENT_IDENTIFIER" 
+
+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 GET "https://demo.dataverse.org/api/dataverses/:persistentId/dataset/linkingDataverses?searchTerm=searchOn&persistentId=doi:10.5072/FK2/J8SJZB" 
+
+You may also add an optional "alreadyLinked=true" parameter to return collections which are already linked to the given Dataset or Dataverse Collection.
+
 List Featured Collections for a Dataverse Collection
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

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

@@ -9,6 +9,7 @@
 import jakarta.persistence.Id;
 import jakarta.persistence.Index;
 import jakarta.persistence.JoinColumn;
+import jakarta.persistence.NamedNativeQuery;
 import jakarta.persistence.NamedQueries;
 import jakarta.persistence.NamedQuery;
 import jakarta.persistence.OneToOne;
@@ -35,6 +36,18 @@
     @NamedQuery(name = "DatasetLinkingDataverse.findIdsByLinkingDataverseId",
                query = "SELECT o.dataset.id FROM DatasetLinkingDataverse AS o WHERE o.linkingDataverse.id = :linkingDataverseId")
 })
+
+    @NamedNativeQuery(
+        name = "DatasetLinkingDataverse.findByDatasetIdAndLinkingDataverseName",
+        query = """
+                select o.linkingDataverse_id  from DatasetLinkingDataverse as o  
+                LEFT JOIN dataverse dv ON dv.id = o.linkingDataverse_id 
+                WHERE o.dataset_id =? AND ((LOWER(dv.name) LIKE ? and ((SUBSTRING(LOWER(dv.name),0,(LENGTH(dv.name)-9)) LIKE ?)
+                or (SUBSTRING(LOWER(dv.name),0,(LENGTH(dv.name)-9)) LIKE ?))) 
+                or (LOWER(dv.name) NOT LIKE ? and ((LOWER(dv.name) LIKE ?)
+                or (LOWER(dv.name) LIKE ?))))""" 
+    )
+
 public class DatasetLinkingDataverse implements Serializable {
     private static final long serialVersionUID = 1L;
     @Id

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

@@ -5,6 +5,7 @@
  */
 package edu.harvard.iq.dataverse;
 
+import jakarta.ejb.EJB;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Logger;
@@ -13,7 +14,6 @@
 import jakarta.persistence.EntityManager;
 import jakarta.persistence.NoResultException;
 import jakarta.persistence.PersistenceContext;
-import jakarta.persistence.Query;
 import jakarta.persistence.TypedQuery;
 
 /**
@@ -28,6 +28,9 @@ public class DatasetLinkingServiceBean implements java.io.Serializable {
     @PersistenceContext(unitName = "VDCNet-ejbPU")
     private EntityManager em;
 
+    @EJB
+    DataverseServiceBean dataverseService;
+    
 
 
     public List<Dataset> findLinkedDatasets(Long dataverseId) {
@@ -41,13 +44,42 @@ public List<Dataset> findLinkedDatasets(Long dataverseId) {
     }
 
     public List<Dataverse> findLinkingDataverses(Long datasetId) {
+        return findLinkingDataverses(datasetId, "");
+    }
+    
+    public List<Dataverse> findLinkingDataverses(Long datasetId, String searchTerm) {
         List<Dataverse> retList = new ArrayList<>();
-        TypedQuery<DatasetLinkingDataverse> typedQuery = em.createNamedQuery("DatasetLinkingDataverse.findByDatasetId", DatasetLinkingDataverse.class)
-            .setParameter("datasetId", datasetId);
-        for (DatasetLinkingDataverse datasetLinkingDataverse : typedQuery.getResultList()) {
-            retList.add(datasetLinkingDataverse.getLinkingDataverse());
+        if (searchTerm == null || searchTerm.isEmpty()) {
+            TypedQuery<DatasetLinkingDataverse> typedQuery = em.createNamedQuery("DatasetLinkingDataverse.findByDatasetId", DatasetLinkingDataverse.class)
+                    .setParameter("datasetId", datasetId);
+            for (DatasetLinkingDataverse datasetLinkingDataverse : typedQuery.getResultList()) {
+                retList.add(datasetLinkingDataverse.getLinkingDataverse());
+            }
+            return retList;
+
+        } else {
+
+            String pattern = searchTerm.toLowerCase();
+
+            String pattern1 = pattern + "%";
+            String pattern2 = "% " + pattern + "%";
+
+            // Adjust the queries for very short, 1 and 2-character patterns:
+            if (pattern.length() == 1) {
+                pattern1 = pattern;
+                pattern2 = pattern + " %";
+            }
+            TypedQuery<Long> typedQuery
+                    = em.createNamedQuery("DatasetLinkingDataverse.findByDatasetIdAndLinkingDataverseName", Long.class)
+                            .setParameter(1, datasetId).setParameter(2, "%dataverse").setParameter(3, pattern1)
+                            .setParameter(4, pattern2).setParameter(5, "%dataverse").setParameter(6, pattern1).setParameter(7, pattern2);
+
+            for (Long id : typedQuery.getResultList()) {
+                retList.add(dataverseService.find(id));
+            }
+            return retList;
         }
-        return retList;
+
     }
 
     public void save(DatasetLinkingDataverse datasetLinkingDataverse) {

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

@@ -13,6 +13,7 @@
 import jakarta.persistence.Id;
 import jakarta.persistence.Index;
 import jakarta.persistence.JoinColumn;
+import jakarta.persistence.NamedNativeQuery;
 import jakarta.persistence.NamedQueries;
 import jakarta.persistence.NamedQuery;
 import jakarta.persistence.OneToOne;
@@ -39,6 +40,16 @@
     @NamedQuery(name = "DataverseLinkingDataverse.findIdsByLinkingDataverseId",
                query = "SELECT o.dataverse.id FROM DataverseLinkingDataverse AS o WHERE o.linkingDataverse.id = :linkingDataverseId")
 })
+    @NamedNativeQuery(
+        name = "DataverseLinkingDataverse.findByDataverseIdAndLinkingDataverseName",
+        query = """
+                select o.linkingDataverse_id  from DataverseLinkingDataverse as o  
+                LEFT JOIN dataverse dv ON dv.id = o.linkingDataverse_id 
+                WHERE o.dataverse_id =? AND ((LOWER(dv.name) LIKE ? and ((SUBSTRING(LOWER(dv.name),0,(LENGTH(dv.name)-9)) LIKE ?)
+                or (SUBSTRING(LOWER(dv.name),0,(LENGTH(dv.name)-9)) LIKE ?))) 
+                or (LOWER(dv.name) NOT LIKE ? and ((LOWER(dv.name) LIKE ?)
+                or (LOWER(dv.name) LIKE ?))))""" 
+    )
 public class DataverseLinkingDataverse implements Serializable {
     private static final long serialVersionUID = 1L;
     @Id