Example for nomad-oasis-with-plugins not working when uploading the test file.

[KatiGithub]

At the end of this documentation, there is a link to download the pre-made nomad-oasis-with-plugins.zip file. After executing all the required permission changes, the nomad_oasis_worker container threw out this error:

`ERROR nomad.search 2024-01-04T16:13:49 could not create entry index doc

• exception: Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/base.py", line 862, in proc_task
  rv = unwrapped_func(proc, *args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1006, in process_entry
  self._process_entry_local()
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1081, in _process_entry_local
  entry.archiving()
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1259, in archiving
  assert self._parser_results.metadata == self._entry_metadata
  AssertionError

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/elasticsearch_extension.py", line 955, in index_entries
  entry_index_doc = entry_type.create_index_doc(entry)
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/elasticsearch_extension.py", line 276, in create_index_doc
  result = root.m_to_dict(**kwargs)
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2261, in m_to_dict
  return {key: value for key, value in items()}
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2261, in
  return {key: value for key, value in items()}
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2255, in items
  yield name, sub_section.m_to_dict(**kwargs)
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2261, in m_to_dict
  return {key: value for key, value in items()}
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2261, in
  return {key: value for key, value in items()}
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2205, in items
  yield name, serialize_quantity(quantity, False, True, path)
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2100, in serialize_quantity
  return [serialize(item, f"{path}/{index}") for index, item in enumerate(target_value)]
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2100, in
  return [serialize(item, f"{path}/{index}") for index, item in enumerate(target_value)]
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 2085, in serialize_and_transform
  return transform(quantity, self, serialize_before_transform(value, path_override), path_override)
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/metainfo.py", line 1982, in serialize_reference
  value = value.m_resolved()
  AttributeError: 'NoneType' object has no attribute 'm_resolved'

• exception_hash: gY1U9XsiH-wv4BGWyv76ccQvjNzW

• nomad.commit:

• nomad.deployment: oasis

• nomad.entry_id: None

• nomad.search.n_entries: 1

• nomad.service: unknown nomad service

• nomad.version: 1.2.1
  ERROR nomad.search 2024-01-04T16:13:49 failed to bulk index entries

• exception: Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/base.py", line 862, in proc_task
  rv = unwrapped_func(proc, *args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1006, in process_entry
  self._process_entry_local()
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1081, in _process_entry_local
  entry.archiving()
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1259, in archiving
  assert self._parser_results.metadata == self._entry_metadata
  AssertionError

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/nomad/utils/init.py", line 265, in timer
  yield kwargs
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/elasticsearch_extension.py", line 975, in index_entries
  indexing_result = entry_index.bulk(
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/elasticsearch_extension.py", line 472, in wrapper
  return self.__elasticsearch_operation(name, *args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/elasticsearch_extension.py", line 455, in __elasticsearch_operation
  results = getattr(self.elastic_client, name)(*args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/elasticsearch/client/utils.py", line 347, in _wrapped
  return func(*args, params=params, headers=headers, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/elasticsearch/client/init.py", line 469, in bulk
  raise ValueError("Empty value passed for a required argument 'body'.")
  ValueError: Empty value passed for a required argument 'body'.

• exception_hash: debgmyE3ak8qT0DkWIZty94yc6OZ

• nomad.commit:

• nomad.deployment: oasis

• nomad.search.exec_time: 5.888938903808594e-05

• nomad.search.n_actions: 0

• nomad.search.n_entries: 1

• nomad.search.size: 2

• nomad.service: unknown nomad service

• nomad.version: 1.2.1
  ERROR nomad.processing 2024-01-04T16:13:49 could not index archive after processing failure

• exception: Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/base.py", line 862, in proc_task
  rv = unwrapped_func(proc, *args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1006, in process_entry
  self._process_entry_local()
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1081, in _process_entry_local
  entry.archiving()
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1259, in archiving
  assert self._parser_results.metadata == self._entry_metadata
  AssertionError

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/nomad/processing/data.py", line 1152, in _on_fail
  indexing_errors = search.index(self._parser_results)
  File "/usr/local/lib/python3.9/site-packages/nomad/search.py", line 181, in index
  errors = index_entries(entries, refresh=refresh or update_materials)
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/elasticsearch_extension.py", line 975, in index_entries
  indexing_result = entry_index.bulk(
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/elasticsearch_extension.py", line 472, in wrapper
  return self.__elasticsearch_operation(name, *args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/nomad/metainfo/elasticsearch_extension.py", line 455, in __elasticsearch_operation
  results = getattr(self.elastic_client, name)(*args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/elasticsearch/client/utils.py", line 347, in _wrapped
  return func(*args, params=params, headers=headers, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/elasticsearch/client/init.py", line 469, in bulk
  raise ValueError("Empty value passed for a required argument 'body'.")
  ValueError: Empty value passed for a required argument 'body'.`

There was no changes made from the original version except for removal of the image lines in docker-compose.plugins.yaml.

Edit:

Forgot to mention but the GUI shows that the file FAILED to process and I couldn't show the log of the upload because of this:

[lauri-codes]

Hi @KatiGithub,

Sorry for the late response. Are you still experiencing this problem? I could help you debug the issue. Maybe you can try redoing the installation with the updated documentation and without touching any of the files. If that does not run successfully, we already have some clues on where to start.