🧪 Additional tests for upload_calculation

src/aiida/engine/daemon/execmanager.py

@@ -333,8 +333,6 @@ def _copy_remote_files(logger, node, computer, transport, remote_copy_list, remo
 def _copy_local_files(logger, node, transport, inputs, local_copy_list):
     """Perform the copy instructions of the ``local_copy_list``."""
 
-    # The transport class can only copy files directly from the file system, so the files in the source node's repo
-    # have to first be copied to a temporary directory on disk.
     for uuid, filename, target in local_copy_list:
         logger.debug(f'[submission of calculation {node.uuid}] copying local file/folder to {target}')
 
@@ -347,21 +345,37 @@ def _copy_local_files(logger, node, transport, inputs, local_copy_list):
             logger.warning(f'failed to load Node<{uuid}> specified in the `local_copy_list`')
             continue
 
+        # The transport class can only copy files directly from the file system, so the files in the source node's repo
+        # have to first be copied to a temporary directory on disk.
         with TemporaryDirectory() as tmpdir:
             dirpath = pathlib.Path(tmpdir)
 
             # If no explicit source filename is defined, we assume the top-level directory
             filename_source = filename or '.'
-            filename_target = target or ''
+            filename_target = target or '.'
+
+            file_type_source = data_node.base.repository.get_object(filename_source).file_type
+
+            # The logic below takes care of an edge case where the source is a file but the target is a directory. In
+            # this case, the v2.5.1 implementation would raise an `IsADirectoryError` exception, because it would try
+            # to open the directory in the sandbox folder as a file when writing the contents.
+            if file_type_source == FileType.FILE and target and transport.isdir(target):
+                raise IsADirectoryError
+
+            # In case the source filename is specified and it is a directory that already exists in the remote, we
+            # want to avoid nested directories in the target path to replicate the behavior of v2.5.1. This is done by
+            # setting the target filename to '.', which means the contents of the node will be copied in the top level
+            # of the temporary directory, whose contents are then copied into the target directory.
+            if filename and transport.isdir(filename):
+                filename_target = '.'
 
-            # Make the target filepath absolute and create any intermediate directories if they don't yet exist
             filepath_target = (dirpath / filename_target).resolve().absolute()
             filepath_target.parent.mkdir(parents=True, exist_ok=True)
 
-            if data_node.base.repository.get_object(filename_source).file_type == FileType.DIRECTORY:
+            if file_type_source == FileType.DIRECTORY:
                 # If the source object is a directory, we copy its entire contents
                 data_node.base.repository.copy_tree(filepath_target, filename_source)
-                transport.put(f'{dirpath}/*', target or '.')
+                transport.put(f'{dirpath}/*', target or '.', overwrite=True)
             else:
                 # Otherwise, simply copy the file
                 with filepath_target.open('wb') as handle:

src/aiida/transports/plugins/local.py

@@ -354,7 +354,7 @@ def puttree(self, localpath, remotepath, *args, **kwargs):
 
         the_destination = os.path.join(self.curdir, remotepath)
 
-        shutil.copytree(localpath, the_destination, symlinks=not dereference)
+        shutil.copytree(localpath, the_destination, symlinks=not dereference, dirs_exist_ok=overwrite)
 
     def rmtree(self, path):
         """Remove tree as rm -r would do

src/aiida/transports/plugins/ssh.py

@@ -929,7 +929,7 @@ def puttree(self, localpath, remotepath, callback=None, dereference=True, overwr
             self.mkdir(remotepath)  # and make a directory at its place
         else:  # remotepath exists already: copy the folder inside of it!
             remotepath = os.path.join(remotepath, os.path.split(localpath)[1])
-            self.mkdir(remotepath)  # create a nested folder
+            self.makedirs(remotepath, ignore_existing=overwrite)  # create a nested folder
 
         for this_source in os.walk(localpath):
             # Get the relative path