Fix bug in upload_calculation for CalcJobs with local codes

This code path was not tested at all and so the remaining occurrence of
`get_folder_list` which is part of the old repository interface that was
removed in `v1.0.0` went unnoticed.

The fix was forced to write files to temporary files and flush them
instead of using a filelike object, because `Transport.put` only accepts
absolute filepaths for the moment.

aiida/backends/tests/engine/test_calc_job.py

@@ -10,6 +10,7 @@
 """Test for the `CalcJob` process sub class."""
 from copy import deepcopy
 from functools import partial
+import os
 from unittest.mock import patch
 
 import pytest
@@ -38,9 +39,11 @@ class TestCalcJob(AiidaTestCase):
     @classmethod
     def setUpClass(cls, *args, **kwargs):
         super().setUpClass(*args, **kwargs)
+        import aiida
+        files = [os.path.join(os.path.dirname(aiida.__file__), os.pardir, '.ci', 'add.sh')]
         cls.computer.configure()  # pylint: disable=no-member
         cls.remote_code = orm.Code(remote_computer_exec=(cls.computer, '/bin/true')).store()
-        cls.local_code = orm.Code(local_executable='true', files=['/bin/true']).store()
+        cls.local_code = orm.Code(local_executable='add.sh', files=files).store()
         cls.inputs = {
             'x': orm.Int(1),
             'y': orm.Int(2),
@@ -213,3 +216,18 @@ def test_exception_presubmit(self):
             launch.run(ArithmeticAddCalculation, code=self.remote_code, **self.inputs)
 
         self.assertIn('exception occurred in presubmit call', str(context.exception))
+
+    def test_run_local_code(self):
+        """Run a dry-run with local code."""
+        inputs = deepcopy(self.inputs)
+        inputs['code'] = self.local_code
+        inputs['metadata']['computer'] = self.computer
+        inputs['metadata']['dry_run'] = True
+
+        # The following will run `upload_calculation` which will test that uploading files works correctly
+        _, node = launch.run_get_node(ArithmeticAddCalculation, **inputs)
+        uploaded_files = os.listdir(node.dry_run_info['folder'])
+
+        # Since the repository will only contain files on the top-level due to `Code.set_files` we only check those
+        for filename in self.local_code.list_object_names():
+            self.assertTrue(filename in uploaded_files)

aiida/engine/daemon/execmanager.py

@@ -47,7 +47,7 @@ def upload_calculation(node, transport, calc_info, folder, inputs=None, dry_run=
     link_label = 'remote_folder'
     if node.get_outgoing(RemoteData, link_label_filter=link_label).first():
         execlogger.warning('CalcJobNode<{}> already has a `{}` output: skipping upload'.format(node.pk, link_label))
-        return calc_info, script_filename
+        return calc_info
 
     computer = node.computer
 
@@ -139,8 +139,14 @@ def upload_calculation(node, transport, calc_info, folder, inputs=None, dry_run=
     for code in input_codes:
         if code.is_local():
             # Note: this will possibly overwrite files
-            for f in code.get_folder_list():
-                transport.put(code.get_abs_path(f), f)
+            for f in code.list_object_names():
+                # Note, once #2579 is implemented, use the `node.open` method instead of the named temporary file in
+                # combination with the new `Transport.put_object_from_filelike`
+                # Since the content of the node could potentially be binary, we read the raw bytes and pass them on
+                with NamedTemporaryFile(mode='wb+') as handle:
+                    handle.write(code.get_object_content(f, mode='rb'))
+                    handle.flush()
+                    transport.put(handle.name, f)
             transport.chmod(code.get_local_executable(), 0o755)  # rwxr-xr-x
 
     # In a dry_run, the working directory is the raw input folder, which will already contain these resources
@@ -192,7 +198,6 @@ def find_data_node(inputs, uuid):
             with NamedTemporaryFile(mode='wb+') as handle:
                 handle.write(data_node.get_object_content(filename, mode='rb'))
                 handle.flush()
-                handle.seek(0)
                 transport.put(handle.name, target)
 
     if dry_run: