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.