include root-dataset and sub-dataset in UUID-set

This commit fixes a bug in which sub-dataset entries
in the tree-version-list and in the uuid-set would
not be added, if the dataset was a sub-dataset.

The changed code correctly re-uses the top-level
nodes that already contain the sub-dataset when
adding the super-dataset instead of cresting new,
empty top level nodes, it also adds the sub-dataset
explicitly.

datalad_metalad/add.py

@@ -60,7 +60,10 @@
 from dataladmetadatamodel.metadatapath import MetadataPath
 from dataladmetadatamodel.metadatarootrecord import MetadataRootRecord
 from dataladmetadatamodel.uuidset import UUIDSet
-from dataladmetadatamodel.versionlist import TreeVersionList
+from dataladmetadatamodel.versionlist import (
+    TreeVersionList,
+    VersionList,
+)
 from dataladmetadatamodel.mapper.gitmapper.objectreference import flush_object_references
 from dataladmetadatamodel.mapper.gitmapper.utils import locked_backend
 
@@ -472,16 +475,17 @@ def add_finite_set(metadata_objects: List[JSONType],
                 tvl_us_cache=tvl_us_cache,
                 mrr_cache=mrr_cache)
 
-            error_result = check_dataset_ids(
-                metadata_store,
-                UUID(dataset_id),
-                add_parameter)
+            if not un_versioned_path:
+                error_result = check_dataset_ids(
+                    metadata_store,
+                    UUID(dataset_id),
+                    add_parameter)
 
-            if error_result:
-                if not allow_id_mismatch:
-                    yield error_result
-                    continue
-                lgr.warning(error_result["message"])
+                if error_result:
+                    if not allow_id_mismatch:
+                        yield error_result
+                        continue
+                    lgr.warning(error_result["message"])
 
             # If the key "path" is present in the metadata
             # dictionary, we assume that the metadata-dictionary describes
@@ -710,6 +714,22 @@ def _get_top_nodes(realm: Path,
             f"dataset id {ap.dataset_id} at path {ap.dataset_path}, but "
             f"the id of the stored dataset is {mrr.dataset_identifier}")
 
+    # Ensure that the UUID of the newly added dataset is in the UUID set. The
+    # auto_create above will only automatically create elements for the values
+    # in `dataset_id` and `primary_data_version`.
+    if ap.dataset_id not in uuid_set.uuids():
+        uuid_version_list = VersionList()
+        uuid_set.set_version_list(ap.dataset_id, uuid_version_list)
+    else:
+        uuid_version_list = uuid_set.get_version_list(ap.dataset_id)
+
+    if ap.dataset_version not in uuid_version_list.versions():
+        uuid_version_list.set_versioned_element(
+            ap.dataset_version,
+            str(time.time()),
+            ap.unversioned_path,
+            mrr)
+
     return tree_version_list, uuid_set, mrr