made the "includeFiles" option true by default, cleaned up the ".find…

…Deep()" logic. #9763

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

@@ -676,11 +676,11 @@ public Timestamp getCitationDate() {
         Timestamp citationDate = null;
         //Only calculate if this dataset doesn't use an alternate date field for publication date
         if (citationDateDatasetFieldType == null) {
-            List<DatasetVersion> versions = this.versions;
+            //List<DatasetVersion> versions = this.versions;
             // TODo - is this ever not version 1.0 (or draft if not published yet)
-            DatasetVersion oldest = versions.get(versions.size() - 1);
+            //DatasetVersion oldest = versions.get(versions.size() - 1);
             citationDate = super.getPublicationDate();
-            if (oldest.isPublished()) {
+            /*if (oldest.isPublished()) {
                 List<FileMetadata> fms = oldest.getFileMetadatas();
                 for (FileMetadata fm : fms) {
                     Embargo embargo = fm.getDataFile().getEmbargo();
@@ -691,7 +691,7 @@ public Timestamp getCitationDate() {
                         }
                     }
                 }
-            }
+            }*/
         }
         return citationDate;
     }

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

@@ -194,6 +194,7 @@ public DatasetVersion findDeep(Object pk) {
             .setHint("eclipselink.left-join-fetch", "o.fileMetadatas.datasetVersion")
             .setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.releaseUser")
             .setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.creator")
+            .setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.dataFileTags")
             .getSingleResult();
     }
 

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

@@ -467,19 +467,13 @@ public Response useDefaultCitationDate(@Context ContainerRequestContext crc, @Pa
     @AuthRequired
     @Path("{id}/versions")
     public Response listVersions(@Context ContainerRequestContext crc, @PathParam("id") String id, @QueryParam("includeFiles") Boolean includeFiles, @QueryParam("limit") Integer limit, @QueryParam("offset") Integer offset) {
-        // @todo:  when full versions list - including files - is requested, consider 
-        // using datasetservice.findDeep() (needs testing on "monstrous" datasets 
-        // with a lot of versions!)
 
         return response( req -> {
             Dataset dataset = findDatasetOrDie(id); 
-            if (includeFiles == null ? false : includeFiles) {
-                dataset = datasetService.findDeep(dataset.getId());
-            } 
-            //return ok( execCommand( new ListVersionsCommand(req, findDatasetOrDie(id), offset, limit) )
-            return ok( execCommand( new ListVersionsCommand(req, dataset, offset, limit) )
+
+            return ok( execCommand( new ListVersionsCommand(req, dataset, offset, limit, (includeFiles == null ? true : includeFiles)) )
                                 .stream()
-                                .map( d -> json(d, includeFiles == null ? false : includeFiles) )
+                                .map( d -> json(d, includeFiles == null ? true : includeFiles) )
                                 .collect(toJsonArray()));
         }, getRequestUser(crc));
     }
@@ -491,8 +485,15 @@ public Response getVersion(@Context ContainerRequestContext crc, @PathParam("id"
         return response( req -> {
             // @todo: consider using DatasetVersionServiceBean.findDeep() here 
             DatasetVersion dsv = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers);
-            return (dsv == null || dsv.getId() == null) ? notFound("Dataset version not found")
-                    : ok(json(dsv, includeFiles == null ? false : includeFiles));
+
+            if (dsv == null || dsv.getId() == null) {
+                return notFound("Dataset version not found");
+            }
+
+            if (includeFiles == null ? true : includeFiles) {
+                dsv = datasetversionService.findDeep(dsv.getId());
+            }
+            return ok(json(dsv, includeFiles == null ? true : includeFiles));
         }, getRequestUser(crc));
     }
 
@@ -512,23 +513,6 @@ public Response getVersionFiles(@Context ContainerRequestContext crc, @PathParam
         }, getRequestUser(crc));
     }
 
-    //@todo: remember to delete this! (for experiments only!)
-    @GET
-    @AuthRequired
-    @Path("{id}/versions/{versionId}/files2")
-    public Response getVersionFiles2(@Context ContainerRequestContext crc, @PathParam("id") String datasetId, @PathParam("versionId") Long versionId, @QueryParam("limit") Integer limit, @QueryParam("offset") Integer offset, @QueryParam("orderCriteria") String orderCriteria, @Context UriInfo uriInfo, @Context HttpHeaders headers) {
-        return response( req -> {
-            //DatasetVersion datasetVersion = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers);
-            DatasetVersionServiceBean.FileMetadatasOrderCriteria fileMetadatasOrderCriteria;
-            try {
-                fileMetadatasOrderCriteria = orderCriteria != null ? DatasetVersionServiceBean.FileMetadatasOrderCriteria.valueOf(orderCriteria) : DatasetVersionServiceBean.FileMetadatasOrderCriteria.NameAZ;
-            } catch (IllegalArgumentException e) {
-                return error(Response.Status.BAD_REQUEST, "Invalid order criteria: " + orderCriteria);
-            }
-            return ok(jsonFileMetadatas(datasetversionService.getFileMetadatasByDbId(versionId, limit, offset, fileMetadatasOrderCriteria)));
-        }, getRequestUser(crc));
-    }
-
     @GET
     @AuthRequired
     @Path("{id}/dirindex")

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ListVersionsCommand.java

@@ -14,6 +14,7 @@
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
+import edu.harvard.iq.dataverse.engine.command.exception.CommandExecutionException;
 import java.util.LinkedList;
 import java.util.List;
 
@@ -28,31 +29,45 @@ public class ListVersionsCommand extends AbstractCommand<List<DatasetVersion>> {
     private final Dataset ds;
     private final Integer limit; 
     private final Integer offset;
+    private final Boolean deepLookup; 
 
     public ListVersionsCommand(DataverseRequest aRequest, Dataset aDataset) {
         this(aRequest, aDataset, null, null);
     }
-
+    
     public ListVersionsCommand(DataverseRequest aRequest, Dataset aDataset, Integer offset, Integer limit) {
+        this(aRequest, aDataset, null, null, false);
+    }
+
+    public ListVersionsCommand(DataverseRequest aRequest, Dataset aDataset, Integer offset, Integer limit, boolean deepLookup) {
         super(aRequest, aDataset);
         ds = aDataset;
         this.offset = offset; 
         this.limit = limit; 
+        this.deepLookup = deepLookup; 
     }
 
     @Override
     public List<DatasetVersion> execute(CommandContext ctxt) throws CommandException {
 
         boolean includeUnpublished = ctxt.permissions().request(getRequest()).on(ds).has(Permission.EditDataset);
 
-        if (offset == null && limit == null) {
-            // @todo: this fragment can be dropped, and the service-based method below 
-            // can be used for both cases.
-            // @todo: on the other hand, consider using datasetservice.findDeep()
-            // when a full list of versions is requested. 
+        if (offset == null && limit == null) { 
+
             List<DatasetVersion> outputList = new LinkedList<>();
             for (DatasetVersion dsv : ds.getVersions()) {
                 if (dsv.isReleased() || includeUnpublished) {
+                    if (deepLookup) {
+                        // @todo: when "deep"/extended lookup is requested, and 
+                        // we call .findDeep() to look up each version again, 
+                        // there is probably a more economical way to obtain the 
+                        // numeric ids of the versions, by a direct single query,
+                        // rather than go through ds.getVersions() like we are now. 
+                        dsv = ctxt.datasetVersion().findDeep(dsv.getId());
+                        if (dsv == null) {
+                            throw new CommandExecutionException("Failed to look up full list of dataset versions", this);
+                        }
+                    }
                     outputList.add(dsv);
                 }
             }