diff --git a/nomad/config.py b/nomad/config.py
index 43bd47d4ec096d06da3d21b42824e18f1880f1b9..8a4537107ef247dd2534950f21addacd924babdc 100644
--- a/nomad/config.py
+++ b/nomad/config.py
@@ -211,6 +211,7 @@ datacite = NomadConfig(
version = '0.7.6'
commit = gitinfo.commit
release = 'devel'
+default_domain = 'dft'
service = 'unknown nomad service'
auxfile_cutoff = 100
parser_matching_size = 9128
diff --git a/nomad/datamodel/base.py b/nomad/datamodel/base.py
index c6a00d80dd49292c1d219a4d69ff5942a11b53bc..75918c6c0c4166904ac17381e955b0bfe4cbd8a8 100644
--- a/nomad/datamodel/base.py
+++ b/nomad/datamodel/base.py
@@ -388,7 +388,9 @@ class Domain:
quantity = domain_quantities.get(quantity_name, None)
if quantity is None:
- domain_quantities[quantity_name] = DomainQuantity()
+ quantity = DomainQuantity()
+ quantity.domain = name
+ domain_quantities[quantity_name] = quantity
# add all domain quantities
for quantity_name, quantity in domain_quantities.items():
diff --git a/nomad/normalizing/normalizer.py b/nomad/normalizing/normalizer.py
index bbd76b3fd57082ecba4d54e816f900c7e6ba5b05..2ca1efbf906e3479aa0aa5080537f5006b494e78 100644
--- a/nomad/normalizing/normalizer.py
+++ b/nomad/normalizing/normalizer.py
@@ -18,12 +18,6 @@ from typing import List
from nomad.parsing import AbstractParserBackend
from nomad.utils import get_logger
-s_system = 'section_system'
-s_scc = 'section_single_configuration_calculation'
-s_frame_sequence = 'section_frame_sequence'
-r_scc_to_system = 'single_configuration_calculation_to_system_ref'
-r_frame_sequence_local_frames = 'frame_sequence_local_frames_ref'
-
class Normalizer(metaclass=ABCMeta):
"""
@@ -34,7 +28,7 @@ class Normalizer(metaclass=ABCMeta):
backend: The backend used to read and write data from and to.
"""
- domain = 'DFT'
+ domain = 'dft'
""" The domain this normalizer should be used in. Default for all normalizer is 'DFT'. """
def __init__(self, backend: AbstractParserBackend) -> None:
@@ -93,50 +87,40 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
Attempt to find a single section_system that is representative for the
entry. The selection depends on the type of calculation.
"""
- system_idx = None
-
# Try to find a frame sequence, only first found is considered
try:
- frame_seqs = self._backend[s_frame_sequence]
- frame_seq = frame_seqs[0]
- sampling_method_idx = frame_seq["frame_sequence_to_sampling_ref"]
- sec_sampling_method = self._backend["section_sampling_method"][sampling_method_idx]
- sampling_method = sec_sampling_method["sampling_method"]
- frames = frame_seq["frame_sequence_local_frames_ref"]
- if sampling_method == "molecular_dynamics":
+ frame_seq = self._backend['section_frame_sequence'][0]
+ sampling_method_idx = frame_seq['frame_sequence_to_sampling_ref']
+ sec_sampling_method = self._backend['section_sampling_method'][sampling_method_idx]
+ sampling_method = sec_sampling_method['sampling_method']
+ frames = frame_seq['frame_sequence_local_frames_ref']
+ if sampling_method == 'molecular_dynamics':
scc_idx = frames[0]
else:
scc_idx = frames[-1]
- scc = self._backend[s_scc][scc_idx]
- system_idx = scc["single_configuration_calculation_to_system_ref"]
+ scc = self._backend['section_single_configuration_calculation'][scc_idx]
+ return scc['single_configuration_calculation_to_system_ref']
except Exception:
- frame_seqs = []
+ pass
# If no frame sequences detected, try to find scc
- if len(frame_seqs) == 0:
- try:
- sccs = self._backend[s_scc]
- scc = sccs[-1]
- system_idx = scc["single_configuration_calculation_to_system_ref"]
- except Exception:
- sccs = []
-
- # If no sccs exist, try to find systems
- if len(sccs) == 0:
- try:
- systems = self._backend.get_sections(s_system)
- system_idx = systems[-1]
- except Exception:
- sccs = []
-
- if system_idx is None:
- self.logger.error('no "representative" section system found')
- else:
- self.logger.info(
- 'chose "representative" system for normalization',
- )
+ try:
+ sccs = self._backend['section_single_configuration_calculation']
+ scc = sccs[-1]
+ return scc['single_configuration_calculation_to_system_ref']
+ except Exception:
+ pass
+
+ # If no sccs exist, try to find systems
+ try:
+ systems = self._backend.get_sections('section_system')
+ return systems[-1]
+ except Exception:
+ pass
+
+ self.logger.error('no "representative" section system found')
- return system_idx
+ return None
def __normalize_system(self, g_index, representative, logger=None) -> bool:
try:
@@ -157,11 +141,12 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
def normalize(self, logger=None) -> None:
super().normalize(logger)
- all_systems = self._backend.get_sections(s_system)
+ all_systems = self._backend.get_sections('section_system')
# Process representative system first
representative_system_idx = self.__representative_system()
if representative_system_idx is not None:
+ self.logger.info('chose "representative" section system')
self.__normalize_system(representative_system_idx, True, logger)
# All the rest if requested
diff --git a/nomad/search.py b/nomad/search.py
index 9be8df3abb8d98fa396524044318a8232bee78be..5714f84801a47bae8dccbb8e7538c958850fce60 100644
--- a/nomad/search.py
+++ b/nomad/search.py
@@ -286,7 +286,7 @@ class SearchRequest:
There is also scrolling for quantities to go through all quantity values. There is no
paging for aggregations.
'''
- def __init__(self, domain: str, query=None):
+ def __init__(self, domain: str = config.default_domain, query=None):
self._domain = domain
self._query = query
self._search = Search(index=config.elastic.index_name)
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index 3b44218f19f2594c3457f5ed4530c5005ad77bc7..4ace9feecd4340bcd253ad1b0205870bd2e9ea6f 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -20,7 +20,7 @@ import json
import re
import shutil
-from nomad import utils, infrastructure, config, datamodel
+from nomad import utils, infrastructure, config
from nomad.files import UploadFiles, StagingUploadFiles, PublicUploadFiles
from nomad.processing import Upload, Calc
from nomad.processing.base import task as task_decorator, FAILURE, SUCCESS
@@ -106,6 +106,10 @@ def assert_processing(upload: Upload, published: bool = False):
with upload_files.raw_file(path) as f:
f.read()
+ # check some domain metadata
+ assert calc.metadata['n_atoms'] > 0
+ assert len(calc.metadata['atoms']) > 0
+
assert upload.get_calc(calc.calc_id).metadata is not None
@@ -378,14 +382,14 @@ def test_malicious_parser_task_failure(proc_infra, failure, test_user):
assert len(calc.errors) == 1
-def test_ems_data(proc_infra, test_user, monkeypatch):
- monkeypatch.setattr('nomad.config.domain', 'ems')
- monkeypatch.setattr('nomad.datamodel.Domain.instance', datamodel.Domain.instances['ems'])
- monkeypatch.setattr('nomad.datamodel.CalcWithMetadata', datamodel.Domain.instance.domain_entry_class)
+def test_ems_data(proc_infra, test_user):
+
upload = run_processing(('test_ems_upload', 'tests/data/proc/example_ems.zip'), test_user)
- additional_keys = ['method', 'experiment_location', 'experiment_time', 'formula', 'chemical']
+ additional_keys = [
+ 'ems.method', 'ems.experiment_location', 'ems.experiment_time', 'ems.formula',
+ 'ems.chemical']
assert upload.total_calcs == 1
assert len(upload.calcs) == 1
diff --git a/tests/test_search.py b/tests/test_search.py
index 1f7691dcc18492751de36a186760fcebb067baa8..9b1f2d0e29c9209c72bf1c6391282911b0c25d03 100644
--- a/tests/test_search.py
+++ b/tests/test_search.py
@@ -151,18 +151,18 @@ def test_search_totals(elastic, example_search_data):
def test_search_exclude(elastic, example_search_data):
for item in SearchRequest().execute_paginated()['results']:
- assert 'atoms' in item
+ assert 'dft.atoms' in item
- for item in SearchRequest().exclude('atoms').execute_paginated()['results']:
- assert 'atoms' not in item
+ for item in SearchRequest().exclude('dft.atoms').execute_paginated()['results']:
+ assert 'dft.atoms' not in item
def test_search_include(elastic, example_search_data):
for item in SearchRequest().execute_paginated()['results']:
- assert 'atoms' in item
+ assert 'dft.atoms' in item
for item in SearchRequest().include('calc_id').execute_paginated()['results']:
- assert 'atoms' not in item
+ assert 'dft.atoms' not in item
assert 'calc_id' in item
@@ -236,7 +236,6 @@ def assert_search_upload(upload: datamodel.UploadWithMetadata, additional_keys:
assert key in hit
for key in additional_keys:
- print(hit.keys())
assert key in hit
assert hit[key] != config.services.unavailable_value