diff --git a/nomad/app/flask/api/upload.py b/nomad/app/flask/api/upload.py
index e0bf42a02060d447329496259242939805de0659..57679044798cb6ba265b41883f20b3d914442be3 100644
--- a/nomad/app/flask/api/upload.py
+++ b/nomad/app/flask/api/upload.py
@@ -93,7 +93,7 @@ calc_model = api.inherit('UploadCalculationProcessing', proc_model, {
'calc_id': fields.String,
'mainfile': fields.String,
'upload_id': fields.String,
- 'parser': fields.String,
+ 'parser_name': fields.String,
'metadata': fields.Raw(
attribute='_entry_metadata',
description='The repository metadata for this entry.')
diff --git a/nomad/app/v1/routers/uploads.py b/nomad/app/v1/routers/uploads.py
index d1e2b6b0ebd14d2899dbc664036c7fc73508464d..c6b6f4866745fbfbeeb868bf91756f2ce9f62d55 100644
--- a/nomad/app/v1/routers/uploads.py
+++ b/nomad/app/v1/routers/uploads.py
@@ -103,7 +103,7 @@ class EntryProcData(ProcData):
entry_id: str = Field()
mainfile: str = Field()
upload_id: str = Field()
- parser: str = Field()
+ parser_name: str = Field()
entry_metadata: Optional[dict] = Field()
@@ -130,7 +130,7 @@ class EntryProcDataPagination(Pagination):
def validate_order_by(cls, order_by): # pylint: disable=no-self-argument
if order_by is None:
return 'mainfile' # Default value
- assert order_by in ('mainfile', 'parser', 'process_status', 'current_process'), 'order_by must be a valid attribute'
+ assert order_by in ('mainfile', 'parser_name', 'process_status', 'current_process'), 'order_by must be a valid attribute'
return order_by
@validator('page_after_value')
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index ac6879d85c7c865c88c0b3620256864a4accb253..d314df10b98866b05f7ba484fafe489082ab702b 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -147,7 +147,7 @@ class Calc(Proc):
Attributes:
calc_id: the calc_id of this calc
- parser: the name of the parser used to process this calc
+ parser_name: the name of the parser used to process this calc
upload_id: the id of the upload used to create this calculation
mainfile: the mainfile (including path in upload) that was used to create this calc
@@ -156,7 +156,7 @@ class Calc(Proc):
calc_id = StringField(primary_key=True)
upload_id = StringField()
mainfile = StringField()
- parser = StringField()
+ parser_name = StringField()
metadata = DictField() # Stores user provided metadata and system metadata (not archive metadata)
@@ -164,9 +164,9 @@ class Calc(Proc):
'strict': False,
'indexes': [
'upload_id',
- 'parser',
+ 'parser_name',
('upload_id', 'mainfile'),
- ('upload_id', 'parser'),
+ ('upload_id', 'parser_name'),
('upload_id', 'process_status'),
('upload_id', 'metadata.nomad_version'),
'metadata.processed',
@@ -186,7 +186,7 @@ class Calc(Proc):
self._entry_metadata: datamodel.EntryMetadata = None
@classmethod
- def get(cls, id):
+ def get(cls, id) -> 'Calc':
return cls.get_by_id(id, 'calc_id')
@property
@@ -299,11 +299,11 @@ class Calc(Proc):
entry_metadata.published = upload.published
entry_metadata.with_embargo = (upload.embargo_length > 0)
# Entry metadata
- if self.parser is not None:
- entry_metadata.parser_name = self.parser
- parser = parser_dict[self.parser]
+ entry_metadata.parser_name = self.parser_name
+ if self.parser_name is not None:
+ parser = parser_dict[self.parser_name]
if parser.domain:
- entry_metadata.domain = parser_dict[self.parser].domain
+ entry_metadata.domain = parser.domain
entry_metadata.calc_id = self.calc_id
entry_metadata.mainfile = self.mainfile
@@ -436,13 +436,13 @@ class Calc(Proc):
logger.warn('no parser matches during re-process, not updating the entry')
self.warnings = ['no matching parser found during processing']
else:
- parser_changed = self.parser != parser.name and parser_dict[self.parser].name != parser.name
+ parser_changed = self.parser_name != parser.name and parser_dict[self.parser_name].name != parser.name
if reparse_if_parser_unchanged and not parser_changed:
should_parse = True
elif reparse_if_parser_changed and parser_changed:
should_parse = True
- if should_parse and self.parser != parser.name:
- if parser_dict[self.parser].name == parser.name:
+ if should_parse and self.parser_name != parser.name:
+ if parser_dict[self.parser_name].name == parser.name:
logger.info(
'parser renamed, using new parser name',
parser=parser.name)
@@ -450,7 +450,7 @@ class Calc(Proc):
logger.info(
'different parser matches during re-process, use new parser',
parser=parser.name)
- self.parser = parser.name # Parser changed or renamed
+ self.parser_name = parser.name # Parser changed or renamed
# 2. Either parse the entry, or preserve it as it is.
if should_parse:
@@ -533,10 +533,10 @@ class Calc(Proc):
def parsing(self):
''' The process step that encapsulates all parsing related actions. '''
self.set_process_step('parsing')
- context = dict(parser=self.parser, step=self.parser)
+ context = dict(parser=self.parser_name, step=self.parser_name)
logger = self.get_logger(**context)
- parser = parser_dict[self.parser]
- self._entry_metadata.parser_name = self.parser
+ parser = parser_dict[self.parser_name]
+ self._entry_metadata.parser_name = self.parser_name
with utils.timer(logger, 'parser executed', input_size=self.mainfile_file.size):
if not config.process_reuse_parser:
@@ -567,7 +567,7 @@ class Calc(Proc):
information in section_encyclopedia as well as the DFT domain metadata.
"""
try:
- logger = self.get_logger(parser=self.parser, step=self.parser)
+ logger = self.get_logger(parser=self.parser_name, step=self.parser_name)
# Open the archive of the phonon calculation.
upload_files = StagingUploadFiles(self.upload_id)
@@ -652,7 +652,7 @@ class Calc(Proc):
datamodel.EntryArchive.metadata, self._entry_metadata)
for normalizer in normalizers:
- if normalizer.domain is not None and normalizer.domain != parser_dict[self.parser].domain:
+ if normalizer.domain is not None and normalizer.domain != parser_dict[self.parser_name].domain:
continue
normalizer_name = normalizer.__name__
@@ -1342,8 +1342,8 @@ class Upload(Proc):
if entry.process_running:
count_already_processing += 1
# Ensure that we update the parser if in staging
- if not self.published and parser.name != entry.parser:
- entry.parser = parser.name
+ if not self.published and parser.name != entry.parser_name:
+ entry.parser_name = parser.name
entry.save()
matched_entries.add(calc_id)
except KeyError:
@@ -1352,7 +1352,7 @@ class Upload(Proc):
entry = Calc.create(
calc_id=calc_id,
mainfile=filename,
- parser=parser.name,
+ parser_name=parser.name,
worker_hostname=self.worker_hostname,
upload_id=self.upload_id)
entry.save()
@@ -1428,7 +1428,7 @@ class Upload(Proc):
# calculations. TODO: This should be replaced by a more
# extensive mechanism that supports more complex dependencies
# between calculations.
- phonon_calculations = Calc.objects(upload_id=self.upload_id, parser="parsers/phonopy")
+ phonon_calculations = Calc.objects(upload_id=self.upload_id, parser_name="parsers/phonopy")
for calc in phonon_calculations:
calc.process_phonon()
@@ -1586,7 +1586,7 @@ class Upload(Proc):
metadata__nomad_version__ne=config.meta.version)
@property
- def calcs(self):
+ def calcs(self) -> Iterable[Calc]:
''' All successfully processed calculations. '''
return Calc.objects(upload_id=self.upload_id, process_status=ProcessStatus.SUCCESS)
@@ -1810,7 +1810,7 @@ class Upload(Proc):
'upload.embargo_length',
'entries')
required_keys_entry_level = (
- '_id', 'upload_id', 'mainfile', 'parser', 'process_status', 'create_time', 'metadata')
+ '_id', 'upload_id', 'mainfile', 'parser_name', 'process_status', 'create_time', 'metadata')
required_keys_entry_metadata = (
'upload_time', 'calc_hash')
required_keys_datasets = (
@@ -1913,7 +1913,7 @@ class Upload(Proc):
# Instantiate an entry object from the json, and validate it
entry_keys_to_copy = (
- 'upload_id', 'mainfile', 'parser', 'metadata', 'errors', 'warnings',
+ 'upload_id', 'mainfile', 'parser_name', 'metadata', 'errors', 'warnings',
'last_status_message', 'current_process', 'current_process_step',
'create_time', 'complete_time', 'worker_hostname', 'celery_task_id')
try:
diff --git a/tests/app/v1/routers/test_uploads.py b/tests/app/v1/routers/test_uploads.py
index 8a62bdff3fc0ddc9b9864f6bf989a0ee53c0a59d..5e5cd165d7e28bd6984093ade13ae85d1e66f266 100644
--- a/tests/app/v1/routers/test_uploads.py
+++ b/tests/app/v1/routers/test_uploads.py
@@ -557,13 +557,13 @@ def test_get_upload(
id='pag-out-of-rage-page_after_value'),
pytest.param(
dict(
- query_args={'page_size': 1, 'order_by': 'parser'},
+ query_args={'page_size': 1, 'order_by': 'parser_name'},
expected_data_len=1,
expected_response={'processing_successful': 2, 'processing_failed': 0},
expected_pagination={
- 'total': 2, 'page': 1, 'page_after_value': None, 'next_page_after_value': '0', 'order_by': 'parser',
+ 'total': 2, 'page': 1, 'page_after_value': None, 'next_page_after_value': '0', 'order_by': 'parser_name',
'page_url': Any, 'next_page_url': Any, 'prev_page_url': None, 'first_page_url': Any}),
- id='pag-order_by-parser'),
+ id='pag-order_by-parser_name'),
pytest.param(
dict(
query_args={'page_size': 1, 'order_by': 'calc_id'},
diff --git a/tests/normalizing/test_encyclopedia.py b/tests/normalizing/test_encyclopedia.py
index 6977ddb1d2241b49123db6d5c7fe6255a2383095..fd573c0fc5dd21a322f981d5864097ca20c9b3ee 100644
--- a/tests/normalizing/test_encyclopedia.py
+++ b/tests/normalizing/test_encyclopedia.py
@@ -509,10 +509,10 @@ def test_phonon(test_user, proc_infra):
# Read the resulting archive
upload_id = upload.upload_id
- calcs = upload.calcs()
+ calcs = upload.calcs
phonon_id = None
for calc in calcs:
- if calc.parser == "parsers/phonopy":
+ if calc.parser_name == "parsers/phonopy":
phonon_id = calc.calc_id
break
upload_file = UploadFiles.get(upload_id)
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index 8b1cb97afc827519a7be76b2c237d3bfdfd52c6a..0138402aafbfa2b220882c43b898838611c70b8f 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -92,7 +92,7 @@ def assert_processing(upload: Upload, published: bool = False, process='process_
assert isinstance(upload_files, StagingUploadFiles)
for calc in Calc.objects(upload_id=upload.upload_id):
- assert calc.parser is not None
+ assert calc.parser_name is not None
assert calc.mainfile is not None
assert calc.process_status == ProcessStatus.SUCCESS
diff --git a/tests/utils.py b/tests/utils.py
index ba293947a7efa4e1715eb72657ad1c1024462c36..8013d6f395478c31cff1c01d5088c68f486590b0 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -189,7 +189,7 @@ class ExampleData:
calc_id=entry_metadata.calc_id,
upload_id=entry_metadata.upload_id,
mainfile=entry_metadata.mainfile,
- parser='parsers/vasp',
+ parser_name='parsers/vasp',
process_status=proc.ProcessStatus.SUCCESS)
upload_dict = self.uploads.get(entry_metadata.upload_id)
if upload_dict: