Merge pull request IQSS#10979 from GlobalDataverseCommunityConsortium/IQSS-10975

IQSS 10975 - fix file replace

Author: ofahimIQSS

Diff for: doc/release-notes/10975-fix-file-replace-via-api

@@ -0,0 +1,3 @@
+A bug that caused replacing files via API when file PIDs were enabled has been fixed.
+
+ For testing purposes, the FAKE PID provider can now be used with file PIDs enabled. (The FAKE provider is not recommended for any production use.)

Diff for: src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDatasetVersionCommand.java

@@ -230,7 +230,8 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
                     if (!theDataset.getOrCreateEditVersion().equals(fmd.getDatasetVersion())) {
                         fmd = FileMetadataUtil.getFmdForFileInEditVersion(fmd, theDataset.getOrCreateEditVersion());
                     }
-                } 
+                }
+                fmd.setDataFile(ctxt.em().merge(fmd.getDataFile()));
                 fmd = ctxt.em().merge(fmd);
 
                 // There are two datafile cases as well - the file has been released, so we're
@@ -241,20 +242,23 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
                     ctxt.engine().submit(new DeleteDataFileCommand(fmd.getDataFile(), getRequest()));
                     // and remove the file from the dataset's list
                     theDataset.getFiles().remove(fmd.getDataFile());
+                    ctxt.em().remove(fmd.getDataFile());
+                    ctxt.em().remove(fmd);
                 } else {
-                    // if we aren't removing the file, we need to explicitly remove the fmd from the
-                    // context and then remove it from the datafile's list
                     ctxt.em().remove(fmd);
+                    // if we aren't removing the file, we need to remove it from the datafile's list
                     FileMetadataUtil.removeFileMetadataFromList(fmd.getDataFile().getFileMetadatas(), fmd);
                 }
-                // In either case, to fully remove the fmd, we have to remove any other possible
+                // In either case, we've removed from the  context 
+                // And, to fully remove the fmd, we have to remove any other possible
                 // references
                 // From the datasetversion
                 FileMetadataUtil.removeFileMetadataFromList(theDataset.getOrCreateEditVersion().getFileMetadatas(), fmd);
                 // and from the list associated with each category
                 for (DataFileCategory cat : theDataset.getCategories()) {
                     FileMetadataUtil.removeFileMetadataFromList(cat.getFileMetadatas(), fmd);
                 }
+
             }
             for(FileMetadata fmd: theDataset.getOrCreateEditVersion().getFileMetadatas()) {
                 logger.fine("FMD: " + fmd.getId() + " for file: " + fmd.getDataFile().getId() + "is in final draft version");    

Diff for: src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/fake/FakeDOIProvider.java

@@ -44,8 +44,11 @@ public List<String> getProviderInformation() {
     }
 
     @Override
-    public String createIdentifier(DvObject dvo) throws Throwable {
-        return "fakeIdentifier";
+    public String createIdentifier(DvObject dvObject) throws Throwable {
+        if(dvObject.getIdentifier() == null || dvObject.getIdentifier().isEmpty() ){
+            dvObject = generatePid(dvObject);
+        }
+        return dvObject.getIdentifier();
     }
 
     @Override