diff --git a/nomad/app_fastapi/optimade/elasticsearch.py b/nomad/app_fastapi/optimade/elasticsearch.py
index 881119e35b2b75b065be0f83cfa51ab4aaab1012..df868611aa98ea1f67fd7450d8d35d9b73111d45 100644
--- a/nomad/app_fastapi/optimade/elasticsearch.py
+++ b/nomad/app_fastapi/optimade/elasticsearch.py
@@ -22,7 +22,9 @@ from optimade.models import StructureResource
from nomad import config, datamodel, files, search, utils
-from nomad.normalizing.optimade import optimade_chemical_formula_reduced
+from nomad.normalizing.optimade import (
+ optimade_chemical_formula_reduced, optimade_chemical_formula_anonymous,
+ optimade_chemical_formula_hill)
from .filterparser import _get_transformer as get_transformer
@@ -113,14 +115,12 @@ class ElasticsearchStructureCollection(EntryCollection):
if nresults_now > 1:
raise HTTPException(
status_code=404,
- detail=f"Instead of a single entry, {nresults_now} entries were found",
- )
+ detail=f'Instead of a single entry, {nresults_now} entries were found')
results = results[0] if results else None
return results, data_returned, more_data_available, all_fields - fields
def _check_aliases(self, aliases):
- """ Check that aliases do not clash with mongo keywords. """
pass
def _es_to_optimade_result(
@@ -161,9 +161,14 @@ class ElasticsearchStructureCollection(EntryCollection):
if include('last_modified'):
attrs['last_modified'] = entry.last_processing if entry.last_processing is not None else entry.upload_time
+ # TODO this should be removed, once all data is reprocessed with the right normalization
attrs['chemical_formula_reduced'] = optimade_chemical_formula_reduced(
attrs['chemical_formula_reduced'])
-
+ attrs['chemical_formula_anonymous'] = optimade_chemical_formula_anonymous(
+ attrs['chemical_formula_reduced'])
+ attrs['chemical_formula_hill'] = optimade_chemical_formula_hill(
+ attrs['chemical_formula_hill'])
+ attrs['chemical_formula_descriptive'] = attrs['chemical_formula_hill']
dimension_types = attrs['dimension_types']
if isinstance(dimension_types, int):
attrs['dimension_types'] = [1] * dimension_types + [0] * (3 - dimension_types)
diff --git a/nomad/normalizing/optimade.py b/nomad/normalizing/optimade.py
index 201dcc1dbd9fcb106062cec5b5c6defd7c8d0282..99c35af589547ccc0b2eb9bc0e381745e2dc225e 100644
--- a/nomad/normalizing/optimade.py
+++ b/nomad/normalizing/optimade.py
@@ -23,6 +23,7 @@ import ase.data
import ase.formula
from string import ascii_uppercase
import pint.quantity
+from collections import OrderedDict
from nomad.normalizing.normalizer import SystemBasedNormalizer
from nomad.units import ureg
@@ -50,6 +51,43 @@ def optimade_chemical_formula_reduced(formula: str):
return formula
+def optimade_chemical_formula_anonymous(formula: str):
+ if formula is None:
+ return formula
+
+ try:
+ ase_formula = ase.formula.Formula(formula).count()
+ result_formula = ''
+ for index, element_count in enumerate(reversed(sorted(ase_formula.values()))):
+ result_formula += ascii_uppercase[index]
+ if element_count > 1:
+ result_formula += str(element_count)
+
+ return result_formula
+ except Exception:
+ return formula
+
+
+def optimade_chemical_formula_hill(formula: str):
+ if formula is None:
+ return formula
+
+ try:
+ ase_formula = ase.formula.Formula(formula).count()
+ result: Dict[str, int] = OrderedDict()
+ if 'C' in ase_formula:
+ for symbol in 'CH':
+ if symbol in ase_formula:
+ result[symbol] = ase_formula.pop(symbol)
+ for symbol, n in sorted(ase_formula.items()):
+ result[symbol] = n
+ return ''.join([
+ symbol + (str(n) if n > 1 else '')
+ for symbol, n in result.items()])
+ except Exception:
+ return formula
+
+
class OptimadeNormalizer(SystemBasedNormalizer):
'''
@@ -113,14 +151,11 @@ class OptimadeNormalizer(SystemBasedNormalizer):
# formulas
optimade.chemical_formula_reduced = optimade_chemical_formula_reduced(
get_value(section_system.chemical_composition_reduced))
- optimade.chemical_formula_hill = get_value(section_system.chemical_composition_bulk_reduced)
+ optimade.chemical_formula_hill = optimade_chemical_formula_hill(
+ get_value(section_system.chemical_composition))
optimade.chemical_formula_descriptive = optimade.chemical_formula_hill
- optimade.chemical_formula_anonymous = ''
- for i in range(len(optimade.elements)):
- part = '%s' % ascii_uppercase[i % len(ascii_uppercase)]
- if atom_counts[optimade.elements[i]] > 1:
- part += str(atom_counts[optimade.elements[i]])
- optimade.chemical_formula_anonymous += part
+ optimade.chemical_formula_anonymous = optimade_chemical_formula_anonymous(
+ optimade.chemical_formula_reduced)
# sites
optimade.nsites = len(nomad_species)
diff --git a/tests/app_fastapi/test_optimade.py b/tests/app_fastapi/test_optimade.py
index a13696ad1ab631d516527d9a12db4dcc54222467..07a4c7a7531ae97d032f320a942c3bf7e84f4eea 100644
--- a/tests/app_fastapi/test_optimade.py
+++ b/tests/app_fastapi/test_optimade.py
@@ -112,7 +112,7 @@ def example_structures(elastic_infra, mongo_infra, raw_files_infra):
('NOT chemical_formula_descriptive ENDS WITH "1"', 4),
('chemical_formula_descriptive CONTAINS "C" AND NOT chemical_formula_descriptive STARTS WITH "O"', 1),
('NOT chemical_formula_anonymous STARTS WITH "A"', 0),
- ('chemical_formula_anonymous CONTAINS "AB2" AND chemical_formula_anonymous ENDS WITH "C"', 1),
+ ('chemical_formula_anonymous CONTAINS "A2B" AND chemical_formula_anonymous ENDS WITH "C"', 1),
('nsites >=3 AND elements LENGTH = 2', 2),
('elements LENGTH = 2', 3),
('elements LENGTH 2', 3),
diff --git a/tests/normalizing/test_optimade.py b/tests/normalizing/test_optimade.py
new file mode 100644
index 0000000000000000000000000000000000000000..7fe9e5b55ab3f7fd3d692c4adb493c50afa0f1b9
--- /dev/null
+++ b/tests/normalizing/test_optimade.py
@@ -0,0 +1,41 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import pytest
+from nomad.normalizing import optimade
+
+
+@pytest.mark.parametrize('formula, expected', [
+ ('NaClHC', 'CHClNa'), ('NaClH2', 'ClH2Na')
+])
+def test_chemical_formula_hill(formula, expected):
+ assert optimade.optimade_chemical_formula_hill(formula) == expected
+
+
+@pytest.mark.parametrize('formula, expected', [
+ ('Na3Cl2H', 'A3B2C'), ('NaNaNaClClHH', 'A3B2C2')
+])
+def test_chemical_formula_anonymous(formula, expected):
+ assert optimade.optimade_chemical_formula_anonymous(formula) == expected
+
+
+@pytest.mark.parametrize('formula, expected', [
+ ('Na3Cl2H', 'Cl2HNa3'), ('NaNaNaClClHH', 'Cl2H2Na3')
+])
+def test_chemical_formula_reduced(formula, expected):
+ assert optimade.optimade_chemical_formula_reduced(formula) == expected