From ca4332e0190b8fab0e74edf0a22ffdaaea5ba37b Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Fri, 12 Apr 2024 01:23:08 +0200
Subject: [PATCH] Small fixes
---
nomad/app/optimade/filterparser.py | 10 +++++++++-
nomad/normalizing/results.py | 6 +++++-
.../example.archive.json | 2 +-
tests/metainfo/test_metainfo.py | 4 ++--
tests/metainfo/test_quantities.py | 8 +++-----
tests/normalizing/test_properties.py | 2 +-
6 files changed, 21 insertions(+), 11 deletions(-)
diff --git a/nomad/app/optimade/filterparser.py b/nomad/app/optimade/filterparser.py
index 9f51b6dc83..ca85b236e5 100644
--- a/nomad/app/optimade/filterparser.py
+++ b/nomad/app/optimade/filterparser.py
@@ -123,7 +123,15 @@ class ElasticTransformer(OPTElasticTransformer):
if quantity.elastic_mapping_type == 'text':
query_type = 'match'
- elif quantity.elastic_mapping_type in ['keyword', 'integer', 'float', 'bool']:
+ elif quantity.elastic_mapping_type in [
+ 'keyword',
+ 'short',
+ 'integer',
+ 'long',
+ 'float',
+ 'double',
+ 'bool',
+ ]:
query_type = 'term'
else:
raise NotImplementedError('Quantity has unsupported ES field type')
diff --git a/nomad/normalizing/results.py b/nomad/normalizing/results.py
index a301e1838e..936e915834 100644
--- a/nomad/normalizing/results.py
+++ b/nomad/normalizing/results.py
@@ -1059,7 +1059,11 @@ class ResultsNormalizer(Normalizer):
msd.diffusion_constant_error_type = (
diffusion_constant.error_type
)
- msd.diffusion_constant_errors = diffusion_constant.errors
+ msd.diffusion_constant_errors = (
+ diffusion_constant.errors
+ if isinstance(diffusion_constant.errors, list)
+ else [diffusion_constant.errors]
+ )
md = self.get_md_provenance(
msd_workflow.m_parent.m_parent.m_parent
diff --git a/tests/data/plugins/perovskite_solar_cell_database/example.archive.json b/tests/data/plugins/perovskite_solar_cell_database/example.archive.json
index 59f744665d..39767f81bc 100644
--- a/tests/data/plugins/perovskite_solar_cell_database/example.archive.json
+++ b/tests/data/plugins/perovskite_solar_cell_database/example.archive.json
@@ -73,7 +73,7 @@
"composition_leadfree": false,
"additives_compounds": "Cl",
"band_gap": 1.6,
- "band_gap_graded": false,
+ "band_gap_graded": "false",
"band_gap_estimation_basis": "Composition",
"storage_time_until_next_deposition_step": "Unknown",
"storage_atmosphere": "Unknown"
diff --git a/tests/metainfo/test_metainfo.py b/tests/metainfo/test_metainfo.py
index 4a2d3224f8..565c469441 100644
--- a/tests/metainfo/test_metainfo.py
+++ b/tests/metainfo/test_metainfo.py
@@ -650,7 +650,7 @@ class TestM1:
def test_pd_dataframe_quantity(self):
class TestSection(MSection):
- test_quantity = Quantity(type=np.dtype('int32'))
+ test_quantity = Quantity(type=np.dtype('int32'), shape=['*', '*'])
test_section = TestSection()
test_section.test_quantity = pd.DataFrame([[1, 2]])
@@ -790,7 +790,7 @@ class TestM1:
def test_validate_dimension(self):
system = System()
system.atom_labels = ['H']
- system.atom_positions = []
+ system.atom_positions = [[]]
assert len(system.m_validate()) > 0
def test_multiple_sub_sections(self):
diff --git a/tests/metainfo/test_quantities.py b/tests/metainfo/test_quantities.py
index 422a855e42..3e57b2386d 100644
--- a/tests/metainfo/test_quantities.py
+++ b/tests/metainfo/test_quantities.py
@@ -159,7 +159,7 @@ def test_normalization_string(def_type, orig_value, normalized_value):
+ [
pytest.param(
int,
- 'm',
+ 'inch',
[],
100 * units('m'),
100 * units('m'),
@@ -299,8 +299,8 @@ def test_complex_number(unit, quantity_type, value, shape):
'im': [[1, 2, 3], [4, 5, 6]],
}, # no shape checking anyway
np.array([[1, 2, 3], [4, 5, 6]]) + 1j * np.array([[1, 2, 3], [4, 5, 6]]),
- ['*'],
- id='complex-full',
+ ['*', '*'],
+ id='complex-full-2nd',
),
],
)
@@ -327,8 +327,6 @@ def test_complex_number_dict(unit, quantity_type, value, result, shape):
'quantity_type,value',
[
pytest.param(np.complex128, np.int64(1), id='downcast-from-int-128'),
- pytest.param(np.complex64, {'re': 1}, id='downcast-from-int-64'),
- pytest.param(np.complex64, {'re': 1.25}, id='downcast-from-float-64'),
pytest.param(np.complex128, {'re': [1.25, 1], 'im': 1}, id='mismatch-shape'),
pytest.param(np.complex128, {}, id='empty-dict'),
],
diff --git a/tests/normalizing/test_properties.py b/tests/normalizing/test_properties.py
index 80a3b4a80d..ad82111b39 100644
--- a/tests/normalizing/test_properties.py
+++ b/tests/normalizing/test_properties.py
@@ -495,7 +495,7 @@ def test_msds(molecular_dynamics):
2.1,
)
assert msd.diffusion_constant_error_type == 'Pearson correlation coefficient'
- assert np.array_equal(msd.diffusion_constant_errors, 0.98)
+ assert np.array_equal(msd.diffusion_constant_errors, [0.98])
@pytest.mark.skipif(simulationworkflowschema is None, reason=SCHEMA_IMPORT_ERROR)
--
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