Merge pull request #16931 from mvdbeek/skip_datatype_change

[23.1] Skip change_datatype things if we're not actually changing the extension
galaxyproject · Oct 26, 2023 · 3e1d866 · 3e1d866
2 parents 1dd28f6 + d7beda0
commit 3e1d866
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 8 deletions.
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
@@ -590,13 +590,14 @@ def get_datatype_by_extension(self, ext):
         return self.datatypes_by_extension.get(ext, None)
 
     def change_datatype(self, data, ext):
-        data.extension = ext
-        # call init_meta and copy metadata from itself.  The datatype
-        # being converted *to* will handle any metadata copying and
-        # initialization.
-        if data.has_data():
-            data.set_size()
-            data.init_meta(copy_from=data)
+        if data.extension != ext:
+            data.extension = ext
+            # call init_meta and copy metadata from itself.  The datatype
+            # being converted *to* will handle any metadata copying and
+            # initialization.
+            if data.has_data():
+                data.set_size()
+                data.init_meta(copy_from=data)
         return data
 
     def load_datatype_converters(self, toolbox, use_cached=False):

diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py
@@ -604,7 +604,16 @@ def wrap(self, value, session):
         if isinstance(value, int):
             return session.query(galaxy.model.MetadataFile).get(value)
         else:
-            return session.query(galaxy.model.MetadataFile).filter_by(uuid=value).one()
+            wrapped_value = session.query(galaxy.model.MetadataFile).filter_by(uuid=value).one_or_none()
+            if wrapped_value:
+                return wrapped_value
+            else:
+                # If we've simultaneously copied the  dataset and we've changed the datatype on the
+                # copy we may not have committed the MetadataFile yet, so we need to commit the session.
+                # TODO: It would be great if we can avoid the commit in the future.
+                with transaction(session):
+                    session.commit()
+            return session.query(galaxy.model.MetadataFile).filter_by(uuid=value).one_or_none()
 
     def make_copy(self, value, target_context: MetadataCollection, source_context):
         session = target_context._object_session(target_context.parent)