diff --git a/README.md b/README.md
index 9be6726e08f8f776ccb9443659b98f25fb55d122..726bf268719163c240dc7b5f9ce4ad5c11416f66 100644
--- a/README.md
+++ b/README.md
@@ -46,6 +46,9 @@ contributing, and API reference.
Omitted versions are plain bugfix releases with only minor changes and fixes.
+### v0.10.6
+- support for NOMAD fields in optimade
+
### v0.10.4
- new "basic" parser to cover codes without proper parser
- removed old nomad-coe parser dependencies
diff --git a/nomad/app/optimade/common.py b/nomad/app/optimade/common.py
new file mode 100644
index 0000000000000000000000000000000000000000..224c98ea6291654d9121694861300c54c7012d6d
--- /dev/null
+++ b/nomad/app/optimade/common.py
@@ -0,0 +1,40 @@
+#
+# 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.
+#
+from typing import Tuple, Generator
+
+from nomad.metainfo.search_extension import Search
+from nomad.search import search_quantities
+
+
+def provider_specific_fields() -> Generator[Tuple[str, Search], None, None]:
+ for search_quantity in search_quantities.values():
+ nmd_name = search_quantity.qualified_name
+ nmd_name_split = nmd_name.split('.')
+
+ if len(nmd_name_split) == 1:
+ # plain metadata
+ pass
+ elif not nmd_name_split[0] in ['dft', 'encyclopedia']:
+ # other domains fields that do not make sense in the optimade context
+ continue
+ elif len(nmd_name_split) > 2 and nmd_name_split[1] == 'optimade':
+ # these are already in optimade
+ continue
+
+ opt_name = nmd_name.replace('.', '_')
+ yield opt_name, search_quantity
diff --git a/nomad/app/optimade/elasticsearch.py b/nomad/app/optimade/elasticsearch.py
index 18604840d04d33a8762ad10ff64090a8f311faa6..c543ead4cb3cdf0fbc4820ff472ee84d96197f6c 100644
--- a/nomad/app/optimade/elasticsearch.py
+++ b/nomad/app/optimade/elasticsearch.py
@@ -1,30 +1,89 @@
-from typing import Tuple, List, Union, Dict, Set, Any
+from typing import Optional, Tuple, List, Union, Dict, Set, Any
from fastapi import HTTPException
+from pydantic import create_model
from elasticsearch_dsl import Search, Q
+from datetime import datetime
+import numpy as np
from optimade.filterparser import LarkParser
from optimade.server.entry_collections import EntryCollection
from optimade.server.query_params import EntryListingQueryParams, SingleEntryQueryParams
from optimade.server.exceptions import BadRequest
from optimade.server.mappers import StructureMapper
-from optimade.models import StructureResource
+from optimade.models import StructureResource, StructureResourceAttributes
+from optimade.models.utils import OptimadeField, SupportLevel
+from optimade.server.schemas import ENTRY_INFO_SCHEMAS
-from nomad import datamodel, files, search, utils
+from nomad import datamodel, files, search, utils, metainfo
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
+from .common import provider_specific_fields
logger = utils.get_logger(__name__)
+float64 = np.dtype('float64')
+
+
+class StructureResourceAttributesByAlias(StructureResourceAttributes):
+ def dict(self, *args, **kwargs):
+ kwargs['by_alias'] = True
+ return super().dict(*args, **kwargs)
+
+
+def create_nomad_structure_resource_attributes_cls():
+ fields: Dict[str, Tuple[type, OptimadeField]] = {}
+
+ for name, search_quantity in provider_specific_fields():
+ quantity = search_quantity.definition
+
+ pydantic_type: type
+ if not quantity.is_scalar:
+ pydantic_type = list
+ elif quantity.type in [str, int, float, bool]:
+ pydantic_type = quantity.type if quantity.type != float64 else float
+ elif quantity.type == metainfo.Datetime:
+ pydantic_type = datetime
+ elif isinstance(quantity.type, metainfo.MEnum):
+ pydantic_type = str
+ elif isinstance(quantity.type, metainfo.Reference):
+ continue
+ else:
+ raise NotImplementedError('Search quantity type not support in optimade API')
+
+ field = Optional[pydantic_type], OptimadeField(
+ None,
+ alias=f'_nmd_{name}',
+ sortable=False,
+ description=quantity.description if quantity.description else 'Not available. Will be added soon.',
+ support=SupportLevel.OPTIONAL,
+ queryable=SupportLevel.OPTIONAL)
+
+ fields[f'nmd_{name}'] = field
+
+ return create_model(
+ 'NomadStructureResourceAttributes',
+ __base__=StructureResourceAttributesByAlias,
+ **fields)
+
+
+NomadStructureResourceAttributes = create_nomad_structure_resource_attributes_cls()
+
+
+class NomadStructureResource(StructureResource):
+ attributes: NomadStructureResourceAttributes # type: ignore
+
+
+ENTRY_INFO_SCHEMAS['structures'] = NomadStructureResource.schema
class StructureCollection(EntryCollection):
def __init__(self):
super().__init__(
- resource_cls=StructureResource,
+ resource_cls=NomadStructureResource,
resource_mapper=StructureMapper,
transformer=get_transformer(nomad_properties='dft', without_prefix=False))
diff --git a/nomad/app/optimade/filterparser.py b/nomad/app/optimade/filterparser.py
index 2cab798bd620d5b17be2408a66e594cb483084b6..b0e43155ae05bd8f53c8bb8ac7062323fc1f6f00 100644
--- a/nomad/app/optimade/filterparser.py
+++ b/nomad/app/optimade/filterparser.py
@@ -25,7 +25,7 @@ from optimade.filtertransformers.elasticsearch import (
Quantity, ElasticTransformer as OPTElasticTransformer)
from optimade.models import CHEMICAL_SYMBOLS, ATOMIC_NUMBERS
-from nomad.search import search_quantities
+from .common import provider_specific_fields
_parser = LarkParser(version=(0, 10, 1))
@@ -58,14 +58,7 @@ def _get_transformer(nomad_properties, without_prefix):
quantities['elements_ratios'].nested_quantity = quantities['elements_ratios']
if nomad_properties is not None:
- for search_quantity in search_quantities.values():
- name = search_quantity.name
- if '.' in name:
- if name.startswith(nomad_properties):
- name = name[len(nomad_properties) + 1:]
- else:
- continue
-
+ for name, search_quantity in provider_specific_fields():
names = ['_nmd_' + name]
if without_prefix:
names.append(name)
diff --git a/tests/app/test_optimade.py b/tests/app/test_optimade.py
index b684da761e52964e212c0580d59d637da434de3b..3afdcc5eccbe8b97ba32c5862b7d0809a0992af6 100644
--- a/tests/app/test_optimade.py
+++ b/tests/app/test_optimade.py
@@ -22,6 +22,7 @@ import pytest
from nomad.processing import Upload
from nomad import search
from nomad.app.optimade import parse_filter
+from nomad.app.optimade.common import provider_specific_fields
from tests.conftest import clear_elastic, clear_raw_files
@@ -128,7 +129,9 @@ def example_structures(elastic_infra, mongo_infra, raw_files_infra):
('chemical_formula_anonymous starts with "A"', -1),
('elements HAS ONY "H", "O"', -1),
('last_modified >= "2009-02-01T20:07:00Z"', 3),
- ('species_at_sites HAS "C"', 1)
+ ('species_at_sites HAS "C"', 1),
+ ('_nmd_dft_system = "molecule / cluster"', 3),
+ ('_nmd_encyclopedia_material_formula = "H20"', 0)
])
def test_optimade_parser(example_structures, query, results):
if results >= 0:
@@ -280,6 +283,15 @@ def test_structure_endpoint(client, example_structures):
assert len(attr.get('dimension_types')) == 3
+def test_nmd_properties_info(client):
+ rv = client.get('/optimade/info/structures')
+ assert rv.status_code == 200
+ data = rv.json()
+ assert '_nmd_dft_system' in data['data']['properties']
+ assert '_nmd_encyclopedia_material_formula' in data['data']['properties']
+ assert '_nmd_atoms' in data['data']['properties']
+
+
def test_nmd_properties(client, example_structures):
rv = client.get('/optimade/structures/%s' % 'test_calc_id_1?response_fields=_nmd_atoms,_nmd_dft_system,_nmd_doesnotexist')
assert rv.status_code == 200
@@ -290,3 +302,16 @@ def test_nmd_properties(client, example_structures):
assert attr.get('_nmd_atoms') == ['H', 'O']
assert '_nmd_dft_system' in attr
assert '_nmd_doesnotexist' not in attr
+
+
+def test_nmd_properties_include_all(client, example_structures):
+ all_fields = [f'_nmd_{name}' for name, _ in provider_specific_fields()]
+ rv = client.get(f'/optimade/structures/test_calc_id_1?response_fields={",".join(all_fields)}')
+ assert rv.status_code == 200
+ data = rv.json()
+ assert data.get('data') is not None
+ attr = data['data'].get('attributes')
+ assert attr is not None
+ assert attr.get('_nmd_atoms') == ['H', 'O']
+ assert '_nmd_dft_system' in attr
+ assert '_nmd_encyclopedia_material_formula' in attr