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FAIRmat-NFDI · Dec 20, 2024 · ae97d7c · ae97d7c
1 parent 17fdf24
commit ae97d7c
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Showing 3 changed files with 41 additions and 23 deletions.
diff --git a/src/nomad_measurements/utils.py b/src/nomad_measurements/utils.py
@@ -351,8 +351,9 @@ def write_file(self):
                     nexus file. Creating h5 file instead."""
                 )
                 if self.archive.m_context.raw_path_exists(self.data_file):
-                    os.remove(os.path.join(self.archive.m_context.raw_path(),
-                              self.data_file))
+                    os.remove(
+                        os.path.join(self.archive.m_context.raw_path(), self.data_file)
+                    )
                 self._write_hdf5_file()
         else:
             self._write_hdf5_file()
@@ -519,9 +520,7 @@ def walk_through_object(parent_obj, attr_chain):
 
             return child_obj
 
-    def populate_nx_dataset_and_attribute(
-        self, attr_dict: dict, dataset_dict: dict
-    ):
+    def populate_nx_dataset_and_attribute(self, attr_dict: dict, dataset_dict: dict):
         """Construct datasets and attributes for nexus and populate."""
 
         for nx_path, arch_path in CONCEPT_MAP.items():

diff --git a/src/nomad_measurements/xrd/nx.py b/src/nomad_measurements/xrd/nx.py
@@ -45,13 +45,28 @@
     '/ENTRY[entry]/method': 'archive.data.method',
     '/ENTRY[entry]/measurement_type': 'archive.data.diffraction_method_name',
     '/ENTRY[entry]/experiment_result/@signal': 'intensity',
-    '/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_axis': 'archive.data.results[0].scan_axis',
-    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_material': 'archive.data.xrd_settings.source.xray_tube_material',
-    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_current': 'archive.data.xrd_settings.source.xray_tube_current',
-    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage': 'archive.data.xrd_settings.source.xray_tube_voltage',
-    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one': 'archive.data.xrd_settings.source.kalpha_one',
-    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two': 'archive.data.xrd_settings.source.kalpha_two',
-    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/ratio_k_alphatwo_k_alphaone': 'archive.data.xrd_settings.source.ratio_kalphatwo_kalphaone',
-    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta': 'archive.data.xrd_settings.source.kbeta',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_axis': (
+        'archive.data.results[0].scan_axis'
+    ),
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_material': (
+        'archive.data.xrd_settings.source.xray_tube_material'
+    ),
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_current': (
+        'archive.data.xrd_settings.source.xray_tube_current'
+    ),
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage': (
+        'archive.data.xrd_settings.source.xray_tube_voltage'
+    ),
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one': (
+        'archive.data.xrd_settings.source.kalpha_one'
+    ),
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two': (
+        'archive.data.xrd_settings.source.kalpha_two'
+    ),
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/ratio_k_alphatwo_k_alphaone': (
+        'archive.data.xrd_settings.source.ratio_kalphatwo_kalphaone'
+    ),
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta': (
+        'archive.data.xrd_settings.source.kbeta'
+    ),
 }
-
diff --git a/src/nomad_measurements/xrd/schema.py b/src/nomad_measurements/xrd/schema.py
@@ -15,6 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+
 from typing import (
     TYPE_CHECKING,
     Any,
@@ -73,9 +74,9 @@
 from nomad_measurements.utils import (
     HDF5Handler,
     get_bounding_range_2d,
-    merge_sections,
     get_entry_id_from_file_name,
-    get_reference
+    get_reference,
+    merge_sections,
 )
 from nomad_measurements.xrd.nx import NEXUS_DATASET_PATHS
 
@@ -1142,7 +1143,7 @@ class ELNXRayDiffraction(XRayDiffraction, EntryData):
     nexus_results = Quantity(
         type=ArchiveSection,
         description='Reference to the NeXus entry.',
-        a_eln = ELNAnnotation(component=ELNComponentEnum.ReferenceEditQuantity)
+        a_eln=ELNAnnotation(component=ELNComponentEnum.ReferenceEditQuantity),
     )
 
     def get_read_write_functions(self) -> tuple[Callable, Callable]:
@@ -1308,12 +1309,15 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger'):
                 if self.hdf5_handler.data_file != self.auxiliary_file:
                     self.auxiliary_file = self.hdf5_handler.data_file
 
-        if (archive.m_context.raw_path_exists(self.auxiliary_file) and
-            self.auxiliary_file.endswith('.nxs')):
-            nx_entry_id = get_entry_id_from_file_name(archive=archive,
-                                                      file_name=self.auxiliary_file)
-            ref_to_nx_entry_data = get_reference(archive.metadata.upload_id,
-                                                 nx_entry_id)
+        if archive.m_context.raw_path_exists(
+            self.auxiliary_file
+        ) and self.auxiliary_file.endswith('.nxs'):
+            nx_entry_id = get_entry_id_from_file_name(
+                archive=archive, file_name=self.auxiliary_file
+            )
+            ref_to_nx_entry_data = get_reference(
+                archive.metadata.upload_id, nx_entry_id
+            )
             self.nexus_results = f'{ref_to_nx_entry_data}'
 
         super().normalize(archive, logger)