diff --git a/nomad/app/v1/routers/entries.py b/nomad/app/v1/routers/entries.py
index 69834042b44b59e44a43c0b0428c1baf4dd71273..8e9d07ee6af9510ed74ca58619517c4cf4bd157c 100644
--- a/nomad/app/v1/routers/entries.py
+++ b/nomad/app/v1/routers/entries.py
@@ -1126,12 +1126,10 @@ def edit(query: Query, user: User, mongo_update: Dict[str, Any] = None, re_index
with utils.timer(logger, 'edit elastic update executed', size=len(entry_ids)):
if re_index:
updated_metadata: List[datamodel.EntryMetadata] = []
- # TODO: Quick and dirty, should remove
- updated_entry_fields = {k: v for k, v in mongo_update.items() if not k.startswith('metadata__')}
for calc in proc.Calc.objects(calc_id__in=entry_ids):
entry_metadata = calc.mongo_metadata(calc.upload)
# Ensure that updated fields are marked as "set", even if they are cleared
- entry_metadata.m_update_from_dict(updated_entry_fields)
+ entry_metadata.m_update_from_dict(mongo_update)
# Add to list
updated_metadata.append(entry_metadata)
@@ -1220,11 +1218,7 @@ async def post_entry_metadata_edit(
verify_reference = None
if isinstance(quantity.type, metainfo.Reference):
verify_reference = quantity.type.target_section_def.section_cls
- # TODO: quick and dirty, we are anyway rewriting this soon
- if quantity.categories and datamodel.MongoMetadata.m_def in quantity.categories:
- mongo_key = 'metadata__%s' % quantity.name
- else:
- mongo_key = quantity.name
+ mongo_key = quantity.name
has_error = False
for action in quantity_actions:
action.success = True
diff --git a/nomad/datamodel/__init__.py b/nomad/datamodel/__init__.py
index 7c36b85df1825f57f9c51f89b7984afaecc157ef..2016d4fda2c360b898b7798212092189420bb4b7 100644
--- a/nomad/datamodel/__init__.py
+++ b/nomad/datamodel/__init__.py
@@ -54,11 +54,6 @@ The class :class:`Dataset` is used to represent datasets and their attributes.
.. autoclass:: nomad.datamodel.Dataset
:members:
-The class :class:`MongoMetadata` is used to tag metadata stored in mongodb.
-
-.. autoclass:: nomad.datamodel.MongoMetadata
- :members:
-
The class :class:`EntryMetadata` is used to represent all metadata about an entry.
.. autoclass:: nomad.datamodel.EntryMetadata
@@ -83,7 +78,7 @@ from nomad.metainfo import Environment
from .datamodel import (
Dataset, User, Author, EditableUserMetadata, UserProvidableMetadata, OasisMetadata,
- UploadMetadata, MongoUploadMetadata, MongoEntryMetadata, MongoSystemMetadata, MongoMetadata,
+ UploadMetadata, MongoUploadMetadata, MongoEntryMetadata, MongoSystemMetadata,
EntryMetadata, EntryArchive)
from .optimade import OptimadeEntry, Species
from .metainfo import m_env
diff --git a/nomad/datamodel/datamodel.py b/nomad/datamodel/datamodel.py
index 52858ded2d88340bfd9f84de4e64ff60d71bffc5..e9f102b68ed564e9ffd174b9279329005a4dd7ca 100644
--- a/nomad/datamodel/datamodel.py
+++ b/nomad/datamodel/datamodel.py
@@ -311,14 +311,6 @@ class MongoSystemMetadata(metainfo.MCategory):
pass
-class MongoMetadata(metainfo.MCategory):
- '''
- NOMAD entry quantities that are stored in mongodb on the entry level, in the metadata dict,
- and not necessarely in the archive.
- '''
- pass
-
-
class DomainMetadata(metainfo.MCategory):
''' NOMAD entry quantities that are determined by the uploaded data. '''
pass
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 4fccacbc35f99ac519765b7f59faf64f22d35cff..b1e4ddd671885b3f3dd521e40ec5d1928e1dc6ee 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -62,9 +62,6 @@ section_workflow = datamodel.EntryArchive.workflow.name
section_results = datamodel.EntryArchive.results.name
-_old_mongo_metadata = tuple(
- quantity.name for quantity in datamodel.MongoMetadata.m_def.definitions)
-
_mongo_upload_metadata = tuple(
quantity.name for quantity in MongoUploadMetadata.m_def.definitions)
_mongo_entry_metadata = tuple(
@@ -174,8 +171,6 @@ class Calc(Proc):
references: user provided references (URLs) for this entry
coauthors: a user provided list of co-authors
datasets: a list of user curated datasets this entry belongs to
-
- metadata: the metadata record wit calc and user metadata, see :class:`EntryMetadata`
'''
upload_id = StringField()
calc_id = StringField(primary_key=True)
@@ -196,8 +191,6 @@ class Calc(Proc):
shared_with = ListField(StringField(), default=None)
datasets = ListField(StringField(), default=None)
- metadata = DictField() # Stores user provided metadata and system metadata (not archive metadata)
-
meta: Any = {
'strict': False,
'indexes': [
@@ -251,7 +244,7 @@ class Calc(Proc):
def _initialize_metadata_for_processing(self):
'''
Initializes self._entry_metadata and self._parser_results in preparation for processing.
- Existing values in self.metadata are loaded first, then generated system values are
+ Existing values in mongo are loaded first, then generated system values are
applied.
'''
self._entry_metadata = EntryMetadata()
@@ -333,7 +326,6 @@ class Calc(Proc):
and applies the values to `entry_metadata`.
'''
assert upload.upload_id == self.upload_id, 'Could not apply metadata: upload_id mismatch'
- entry_metadata.m_update_from_dict(self.metadata) # TODO: Flatten?
# Upload metadata
for field in _mongo_upload_metadata:
setattr(entry_metadata, field, getattr(upload, field))
@@ -357,10 +349,6 @@ class Calc(Proc):
for field in _mongo_entry_metadata_except_system_fields:
setattr(self, field, entry_metadata_dict.get(field))
- self.metadata = entry_metadata.m_to_dict(
- include_defaults=True,
- categories=[datamodel.MongoMetadata]) # TODO use embedded doc? Flatten?
-
def set_mongo_entry_metadata(self, *args, **kwargs):
'''
Sets the entry level metadata in mongo. Expects either a positional argument
@@ -375,8 +363,6 @@ class Calc(Proc):
for key, value in kwargs.items():
if key in _mongo_entry_metadata_except_system_fields:
setattr(self, key, value)
- elif key in _old_mongo_metadata:
- self.metadata[key] = value
else:
assert False, f'Cannot set metadata field: {key}'
@@ -1365,7 +1351,7 @@ class Upload(Proc):
with utils.timer(logger, 'calcs processing called'):
# process call calcs
Calc.process_all(
- Calc.process_calc, dict(upload_id=self.upload_id), exclude=['metadata'],
+ Calc.process_calc, dict(upload_id=self.upload_id),
process_kwargs=dict(reprocess_settings=settings))
logger.info('completed to trigger process of all calcs')
@@ -1764,7 +1750,7 @@ class Upload(Proc):
'upload.embargo_length',
'entries')
required_keys_entry_level = (
- '_id', 'upload_id', 'mainfile', 'parser_name', 'process_status', 'entry_create_time', 'metadata')
+ '_id', 'upload_id', 'mainfile', 'parser_name', 'process_status', 'entry_create_time')
required_keys_datasets = (
'dataset_id', 'dataset_name', 'user_id')
@@ -1864,7 +1850,7 @@ class Upload(Proc):
# Instantiate an entry object from the json, and validate it
entry_keys_to_copy = list(_mongo_entry_metadata)
entry_keys_to_copy.extend((
- 'upload_id', 'metadata', 'errors', 'warnings',
+ 'upload_id', 'errors', 'warnings',
'last_status_message', 'current_process', 'current_process_step',
'complete_time', 'worker_hostname', 'celery_task_id'))
try: