Merge pull request #65 from FAIRmat-NFDI/61-add-tests-for-xrd-parser

Add tests for xrd parser

nomad.yaml

@@ -4,7 +4,7 @@ normalize:
     - MetainfoNormalizer
 plugins:
   include: 
-    - nomad_measurements.xrd
+    - parsers/nomad_measurements/xrd
   options:
     parsers/nomad_measurements/xrd:
       python_package: nomad_measurements.xrd

src/nomad_measurements/utils.py

@@ -15,6 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+import os.path
 from typing import (
     TYPE_CHECKING,
     Any,
@@ -49,10 +50,12 @@ def create_archive(
     ) -> str:
     import json
     from nomad.datamodel.context import ClientContext
+    entity_entry = entity.m_to_dict(with_root_def=True)
     if isinstance(archive.m_context, ClientContext):
-        return None
+        with open(file_name, 'w') as outfile:
+            json.dump({"data": entity_entry}, outfile, indent=4)
+        return os.path.abspath(file_name)
     if not archive.m_context.raw_path_exists(file_name):
-        entity_entry = entity.m_to_dict(with_root_def=True)
         with archive.m_context.raw_file(file_name, 'w') as outfile:
             json.dump({"data": entity_entry}, outfile)
         archive.m_context.process_updated_raw_file(file_name)

tests/data/XRD-918-16_10.xrdml

@@ -9,7 +9,7 @@
 		<entry>Batch program=C:\PANalytical\Data Collector\Programs\BBHD-FASS_4-70_step01_40s_Omar_6 samples.xrdmp, Identifier={D0DF481D-C866-435E-BCBB-469939A807AC}</entry>
 	</comment>
 	<sample type="To be analyzed">
-		<id>918-16</id>
+		<id></id>
 		<name></name>
 		<preparedBy></preparedBy>
 	</sample>

tests/test_parser.py

@@ -0,0 +1,56 @@
+#
+# 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 os
+import pytest
+
+from nomad.client import parse, normalize_all
+
+@pytest.fixture(params=[
+    'XRD-918-16_10.xrdml',
+    'm54313_om2th_10.xrdml',
+    '23-012-AG_2thomegascan_long.brml',
+    'Omega-2Theta_scan_high_temperature.rasx',
+    'RSM_111_sdd=350.rasx',
+    'TwoTheta_scan_powder.rasx',
+])
+def parsed_archive(request):
+    '''
+    Sets up data for testing and cleans up after the test.
+    '''
+    rel_file = os.path.join('tests', 'data', request.param)
+    file_archive = parse(rel_file)[0]
+    measurement = os.path.join(
+        'tests', 'data', '.'.join(request.param.split('.')[:-1]) + '.archive.json'
+    )
+    assert file_archive.data.measurement.m_proxy_value == os.path.abspath(measurement)
+    measurement_archive = parse(measurement)[0]
+
+    yield measurement_archive
+
+    if os.path.exists(measurement):
+        os.remove(measurement)
+
+def test_normalize_all(parsed_archive):
+    normalize_all(parsed_archive)
+    print(parsed_archive.data)
+    assert parsed_archive.data.xrd_settings.source.xray_tube_material == 'Cu'
+    assert parsed_archive.data.results[0].source_peak_wavelength.magnitude \
+        == pytest.approx(1.540598, 1e-2)
+    assert parsed_archive.results.properties.structural.diffraction_pattern[0]\
+        .incident_beam_wavelength.magnitude * 1e10 \
+        == pytest.approx(1.540598, 1e-2)

tests/test_utils.py

@@ -1,10 +1,16 @@
+import numpy as np
+
 from nomad.datamodel.metainfo.basesections import (
     Component,
     CompositeSystem,
     PureSubstanceComponent,
     PureSubstanceSection,
 )
-from nomad_measurements.utils import merge_sections
+from nomad.units import ureg
+from nomad_measurements.utils import(
+    merge_sections,
+    to_pint_quantity,
+)
 
 def test_merge_sections():
     component_1 = Component(
@@ -49,5 +55,13 @@ def test_merge_sections():
     merge_sections(system_3, system_2)
     assert system_3.components[0].name == 'Cu'
 
+def test_to_pint_quantity():
+    assert to_pint_quantity(1, 'mA') == 1 * ureg.mA
+    assert str(to_pint_quantity(np.asarray([1., 2.]), 'm')) \
+        == str(np.asarray([1., 2.]) * ureg.m)
+    assert str(to_pint_quantity(np.asarray([1., 2.]), '')) \
+        == str(np.asarray([1., 2.]))
+    assert to_pint_quantity('Copper', '') == 'Copper'
+
 if __name__ == '__main__':
     test_merge_sections()