From 5bee735ef84e3ef362a10709f9c82cb2a52bcb3a Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Fri, 16 Apr 2021 14:55:19 +0200
Subject: [PATCH] Added support for latest optimade features.
---
= | 7 +++++++
nomad/app/optimade/filterparser.py | 4 +++-
nomad/datamodel/optimade.py | 1 +
tests/app/flask/utils.py | 4 +++-
tests/app/test_optimade.py | 6 ++++--
5 files changed, 18 insertions(+), 4 deletions(-)
create mode 100644 =
diff --git a/= b/=
new file mode 100644
index 0000000000..9b92bcf0f4
--- /dev/null
+++ b/=
@@ -0,0 +1,7 @@
+============================= test session starts ==============================
+platform darwin -- Python 3.7.7, pytest-3.10.0, py-1.10.0, pluggy-0.13.1 -- /Users/markus/Documents/Projects/nomad-fairdi/.pyenv/bin/python
+cachedir: .pytest_cache
+rootdir: /Users/markus/Documents/Projects/nomad-fairdi/tests, inifile: pytest.ini
+plugins: celery-4.4.7, cov-2.7.1, timeout-1.4.2
+collecting ...
+========================= no tests ran in 0.01 seconds =========================
diff --git a/nomad/app/optimade/filterparser.py b/nomad/app/optimade/filterparser.py
index f233403361..2cab798bd6 100644
--- a/nomad/app/optimade/filterparser.py
+++ b/nomad/app/optimade/filterparser.py
@@ -17,7 +17,7 @@
#
from typing import Dict
-from elasticsearch_dsl import Q
+from elasticsearch_dsl import Q, Date
from cachetools import cached
from optimade.filterparser import LarkParser
@@ -49,6 +49,8 @@ def _get_transformer(nomad_properties, without_prefix):
quantities['id'] = Quantity('id', es_field='calc_id')
quantities['immutable_id'] = Quantity('immutable_id', es_field='calc_id')
+ quantities['last_modified'] = Quantity(
+ 'last_modified', es_field='upload_time', elastic_mapping_type=Date)
quantities['elements'].length_quantity = quantities['nelements']
quantities['elements'].has_only_quantity = Quantity(name='only_atoms')
diff --git a/nomad/datamodel/optimade.py b/nomad/datamodel/optimade.py
index b617069a14..b42b5e0b9a 100644
--- a/nomad/datamodel/optimade.py
+++ b/nomad/datamodel/optimade.py
@@ -240,6 +240,7 @@ class OptimadeEntry(MSection):
species_at_sites = Quantity(
type=str, shape=['nsites'],
links=optimade_links('h.6.2.12'),
+ a_search=Search(),
a_optimade=Optimade(query=False, entry=True, sortable=False, type='list'), description='''
Name of the species at each site (where values for sites are specified with the same
order of the cartesian_site_positions property). The properties of the species are
diff --git a/tests/app/flask/utils.py b/tests/app/flask/utils.py
index 3e20e664ef..02268e90f3 100644
--- a/tests/app/flask/utils.py
+++ b/tests/app/flask/utils.py
@@ -18,6 +18,7 @@
from typing import List
import numpy as np
+import datetime
from nomad import processing, files
from nomad.datamodel import EntryMetadata, MongoMetadata, EntryArchive
@@ -102,7 +103,8 @@ class Upload():
entry_metadata.m_update(
domain='dft', upload_id=self.upload_id, calc_id='test_calc_id_%d' % id,
- mainfile='test_mainfile', published=True, processed=True, with_embargo=False)
+ mainfile='test_mainfile', published=True, processed=True, with_embargo=False,
+ upload_time=datetime.datetime.now())
entry_metadata.apply_domain_metadata(archive)
diff --git a/tests/app/test_optimade.py b/tests/app/test_optimade.py
index 77eea728df..b684da761e 100644
--- a/tests/app/test_optimade.py
+++ b/tests/app/test_optimade.py
@@ -60,7 +60,7 @@ def example_structures(elastic_infra, mongo_infra, raw_files_infra):
upload.create_test_structure(1, 2, 1, [], 0)
upload.create_test_structure(2, 2, 1, ['C'], 0)
upload.create_test_structure(3, 2, 1, [], 1)
- upload.create_test_structure(4, 1, 1, [], 0)
+ upload.create_test_structure(4, 1, 1, [], 0, metadata=dict(upload_time='1978-04-08T10:10:00Z'))
upload.create_upload_files()
search.refresh()
@@ -126,7 +126,9 @@ def example_structures(elastic_infra, mongo_infra, raw_files_infra):
('nelements LENGTH = 1', -1),
('LENGTH nelements = 1', -1),
('chemical_formula_anonymous starts with "A"', -1),
- ('elements HAS ONY "H", "O"', -1)
+ ('elements HAS ONY "H", "O"', -1),
+ ('last_modified >= "2009-02-01T20:07:00Z"', 3),
+ ('species_at_sites HAS "C"', 1)
])
def test_optimade_parser(example_structures, query, results):
if results >= 0:
--
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