Merge branch 'develop' into 11733-api-get-file-citation-format

Author: sekmiller

doc/release-notes/12258-publish-submit-contains-files.md

@@ -0,0 +1,2 @@
+## Bug: Publish and Submit for review must contain files
+When `requireFilesToPublishDataset` is set on a Dataverse a Dataset must contain files to be published or submitted for review. This fix make sure the dataset version contains files, and not just the dataset. It also adds this check to the `Submit for Review` functionality.

doc/release-notes/7956-show_original_file_format.md

@@ -0,0 +1,2 @@
+This release changes the display behavior of the file, dataset and collection ("dataverse") pages for tabular files. They will show the original file name and information, and will allow editing of the original file name. The ingested *.tab version is still available from the download menu. 
+ 

doc/release-notes/8013-history-of-access-request-available-via-api.md

@@ -0,0 +1,8 @@
+### Feature: Extend List File Access Requests API ###
+
+Added ability to get access request history via the `/datafile/{id}/listRequests` API. The API returns a list of users/groups where the request for access is waiting for an accept or reject. Already accepted or rejected requests are not returned.
+
+By adding the flag 'includeHistory=true' all of the requests will be returned. Pagination is also implemented in this feature. Adding a start page parameter and max list size (`&start=0` and `&per_page=20`) can limit the amount of data being returned.
+
+See https://guides.dataverse.org/en/latest/api/dataaccess.html#list-file-access-requests
+

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

@@ -10,7 +10,11 @@ This API changelog is experimental and we would love feedback on its usefulness.
 v6.11
 -----
 
-- 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.
+- The following API will now return ``403`` if the ``requireFilesToPublishDataset`` flag is set and the dataset version contains 0 files.
+
+  - **/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. The unused ``wd`` property has been dropped.
 
 v6.10
 -----

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

@@ -460,7 +460,22 @@ This method returns a list of Authenticated Users who have requested access to t
 
 A curl example using an ``id``::
 
-    curl -H "X-Dataverse-key:$API_TOKEN" -X GET http://$SERVER/api/access/datafile/{id}/listRequests
+    curl -H "X-Dataverse-key:$API_TOKEN" -X GET $SERVER/api/access/datafile/{id}/listRequests
+
+Query parameters have been added to retrieve the historical list of "created", "granted", and "rejected" requests:
+
+* `includeHistory` When `true` this will force the return of all requests and not just the "created" ones.
+* `start` For pagination, use this to request a specific page.
+* `per_page` For pagination, use this to limit the number of items in each paged list.
+
+.. note:: Pagination is only available when `includeHistory` is `true`
+
+If requesting a page beyond the last page this API will return a 404 "There are no access requests for this file:..."
+If requesting a page before page 1 or requesting the number of items to be 0 or less this API will ignore these parameters and return the entire list.
+
+A curl example using an ``id``::
+
+    curl -H "X-Dataverse-key:$API_TOKEN" -X GET "$SERVER/api/access/datafile/{id}/listRequests?includeHistory=true&start=1&per_page=20"
 
 User Has Requested Access to a File:
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -471,7 +486,7 @@ This method returns true or false depending on whether or not the calling user h
 
 A curl example using an ``id``::
 
-    curl -H "X-Dataverse-key:$API_TOKEN" -X GET "http://$SERVER/api/access/datafile/{id}/userFileAccessRequested"
+    curl -H "X-Dataverse-key:$API_TOKEN" -X GET "$SERVER/api/access/datafile/{id}/userFileAccessRequested"
 
 
 Get User Permissions on a File:

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

@@ -1299,7 +1299,7 @@ The following attributes are supported:
 * ``description`` Description
 * ``affiliation`` Affiliation
 * ``filePIDsEnabled`` ("true" or "false") Restricted to use by superusers and only when the :ref:`:AllowEnablingFilePIDsPerCollection <:AllowEnablingFilePIDsPerCollection>` setting is true. Enables or disables registration of file-level PIDs in datasets within the collection (overriding the instance-wide setting).
-* ``requireFilesToPublishDataset`` ("true" or "false") Restricted to use by superusers. Defines if Dataset needs files in order to be published.  If not set the determination will be made through inheritance by checking the owners of this collection. Publishing by a superusers will not be blocked.
+* ``requireFilesToPublishDataset`` ("true" or "false") Restricted to use by superusers. Defines if Dataset version needs files in order to be published or submitted for review.  If not set the determination will be made through inheritance by checking the owners of this collection. Publishing by a superusers will not be blocked.
 * ``allowedDatasetTypes`` Restricted to use by superusers. By default "dataset" is implied. Pass a comma-separated list of dataset types (e.g. "dataset,software"). You cannot unset this attribute so if you want to delete a dataset type, set ``allowedDatasetTypes`` to a dataset type you won't be deleting. See also :ref:`dataset-types`.
 
 See also :ref:`update-dataverse-api`.

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

@@ -135,7 +135,7 @@ public DataCitation(FileMetadata fm, boolean direct) {
         getCommonValuesFrom(dsv);
 
         // file Title for direct File citation
-        fileTitle = fm.getLabel();
+        fileTitle = fm.getLabelForOriginal();
         DataFile df = fm.getDataFile();
 
         // File description

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

@@ -247,11 +247,31 @@ public String toUri() {
     inverseJoinColumns = @JoinColumn(name = "authenticated_user_id"))
     private List<AuthenticatedUser> fileAccessRequesters;
 
-    
-    public List<FileAccessRequest> getFileAccessRequests(){
-        return fileAccessRequests;
+    public List<FileAccessRequest> getFileAccessRequests() {
+        return getFileAccessRequests(0, 0);
     }
-    
+
+    /**
+     * Get Requests with pagination option
+     * @param numResultsPerPageRequested
+     * @param paginationStart starts at 1
+     * @return
+     */
+    public List<FileAccessRequest> getFileAccessRequests(int numResultsPerPageRequested, int paginationStart) {
+        if (numResultsPerPageRequested < 1 || paginationStart < 1) {
+            return fileAccessRequests;
+        } else {
+            int startIndex = (paginationStart - 1) * numResultsPerPageRequested;
+            int endIndex = startIndex + numResultsPerPageRequested;
+            if (startIndex >= fileAccessRequests.size()) {
+                return List.of();
+            } else if (endIndex > fileAccessRequests.size()) {
+                endIndex = fileAccessRequests.size();
+            }
+            return fileAccessRequests.subList(startIndex, endIndex);
+        }
+    }
+
     public List<FileAccessRequest> getFileAccessRequests(FileAccessRequest.RequestState state){
         return fileAccessRequests.stream().filter(far -> far.getState() == state).collect(Collectors.toList());
     }
@@ -527,6 +547,11 @@ public Long getOriginalFileSize() {
         return null;
     }
 
+    public String getFriendlyOriginalFileSize() {
+        Long size = (getOriginalFileSize()==null) ? filesize : getOriginalFileSize();
+        return getFriendlySize(size);
+    }
+    
     public String getOriginalFileName() {
         if (isTabularData()) {
             DataTable dataTable = getDataTable();
@@ -539,7 +564,7 @@ public String getOriginalFileName() {
     }
 
 
-    private String getDerivedOriginalFileName() {
+    public String getDerivedOriginalFileName() {
         FileMetadata fm = getFileMetadata();
         String filename = fm.getLabel();
         String originalExtension = FileUtil.generateOriginalExtension(getOriginalFileFormat());
@@ -689,8 +714,12 @@ public void setFilesize(long filesize) {
      * @return 
      */
     public String getFriendlySize() {
-        if (filesize != null) {
-            return FileSizeChecker.bytesToHumanReadable(filesize);
+        return getFriendlySize(filesize);
+    }
+    
+    private String getFriendlySize(Long size) {
+        if (size != null) {
+            return FileSizeChecker.bytesToHumanReadable(size);
         } else {
             return BundleUtil.getStringFromBundle("file.sizeNotAvailable");
         }
@@ -849,6 +878,15 @@ public void addFileAccessRequest(FileAccessRequest request) {
         this.fileAccessRequests.add(request);
     }
 
+    public List<FileAccessRequest> getAccessRequestsForAssignee(RoleAssignee roleAssignee) {
+        if (this.fileAccessRequests == null) {
+            return null;
+        }
+
+        return this.fileAccessRequests.stream()
+                .filter(fileAccessRequest -> fileAccessRequest.getRequester().equals(roleAssignee)).toList();
+    }
+
     public FileAccessRequest getAccessRequestForAssignee(RoleAssignee roleAssignee) {
         if (this.fileAccessRequests == null) {
             return null;

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

@@ -835,6 +835,18 @@ public String getReminderString(Dataset dataset, boolean canPublishDataset, bool
 
         String reminderString;
 
+        if (dataset.getOwner().getEffectiveRequiresFilesToPublishDataset()) {
+            List<FileMetadata> files = dataset.getLatestVersion().getFileMetadatas();
+            if (files.size() < 1) {
+                if (canPublishDataset) {
+                    reminderString = BundleUtil.getStringFromBundle("dataset.mayNotPublish.FilesRequired");
+                } else {
+                    reminderString = BundleUtil.getStringFromBundle("dataset.mayNotSubmitForReview.FilesRequired");
+                }
+                return reminderString;
+            }
+        }
+
         if (canPublishDataset) {
             reminderString = BundleUtil.getStringFromBundle("dataset.message.publish.warning");
         } else {

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

@@ -4,6 +4,7 @@
 import java.util.Date;
 
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
+import edu.harvard.iq.dataverse.util.BundleUtil;
 import jakarta.persistence.Column;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EnumType;
@@ -143,6 +144,20 @@ public String getStateLabel() {
         }
         return null; 
     }
+
+    // For use by UI to allow for internationalization
+    public String getStateLabelNationalized() {
+        if(isStateCreated()) {
+            return BundleUtil.getStringFromBundle("permission.fileAccess.created");
+        }
+        if(isStateGranted()) {
+            return BundleUtil.getStringFromBundle("permission.fileAccess.granted");
+        }
+        if(isStateRejected()) {
+            return BundleUtil.getStringFromBundle("permission.fileAccess.rejected");
+        }
+        return null;
+    }
 
     public void setStateCreated() {
         this.requestState = RequestState.CREATED;
@@ -197,4 +212,4 @@ public boolean equals(Object object) {
     }
 
 
-}
+}