Add connect_concepts_to_hdf5, add_group_and_return_child_group.

src/nomad_measurements/utils.py

@@ -39,6 +39,7 @@
     from structlog.stdlib import (
         BoundLogger,
     )
+from nomad_measurements.xrd.nx import connect_concepts_to_hdf5
 
 
 def get_reference(upload_id: str, entry_id: str) -> str:
@@ -200,6 +201,23 @@ def __init__(
         self._hdf5_datasets = collections.OrderedDict()
         self._hdf5_attributes = collections.OrderedDict()
 
+    def add_group_and_return_child_group(
+        self, child_group_name, parent_group=None, nxclass=None
+    ):
+        """Create group with name `child_group_name` under the parent_group"""
+
+        if (parts := child_group_name.split('[', 1)) and len(parts) > 1:
+            nxclass = parts[0]
+            grp_name_tmp = parts[1].split(']')[0]
+        else:
+            grp_name_tmp = child_group_name
+        parent_group.require_group(grp_name_tmp)
+        child_group = parent_group[grp_name_tmp]
+        if nxclass:
+            child_group.attrs['NX_class'] = 'NX' + nxclass.lower()
+
+        return child_group
+
     def add_dataset(  # noqa: PLR0913
         self,
         path: str,
@@ -236,10 +254,7 @@ def add_dataset(  # noqa: PLR0913
         dataset = dict(
             data=data,
             attrs={},
-            hdf5_path=(
-                f'/uploads/{self.archive.m_context.upload_id}/raw'
-                f'/{self.data_file}#{path}'
-            ),
+            hdf5_path=path,
             archive_path=archive_path,
             internal_reference=internal_reference,
         )
@@ -328,7 +343,13 @@ def _write_nx_file(self):
         """
         if self.data_file.endswith('.h5'):
             self.data_file = self.data_file.replace('.h5', '.nxs')
-        raise NotImplementedError('Method `write_nx_file` is not implemented.')
+
+        with self.archive.m_context.raw_file(self.data_file, 'rw') as h5_file:
+            h5 = h5py.File(h5_file.name, 'rw')
+            connect_concepts_to_hdf5(archive=self.archive, hdf5handler=self, h5_root=h5)
+            h5.close()
+
+        # raise NotImplementedError('Method `write_nx_file` is not implemented.')
         # TODO add archive data to `hdf5_data_dict` before creating the nexus file. Use
         # `populate_hdf5_data_dict` method for each quantity that is needed in .nxs
         # file. Create a NeXus file with the data in `hdf5_data_dict`.

src/nomad_measurements/xrd/nx.py

@@ -16,6 +16,18 @@
 # limitations under the License.
 #
 
+from typing import TYPE_CHECKING
+
+import copy
+from pynxtools.nomad.dataconverter import populate_nexus_subsection
+
+if TYPE_CHECKING:
+    from nomad.datamodel.datamodel import EntryArchive
+
+    from nomad_measurements.utils import HDF5Handler
+    import h5py as h5
+
+
 NEXUS_DATASET_PATHS = [
     '/ENTRY[entry]/experiment_result/intensity',
     '/ENTRY[entry]/experiment_result/two_theta',
@@ -37,3 +49,114 @@
     '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/ratio_k_alphatwo_k_alphaone',
     '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta',
 ]
+
+
+CONCEPT_MAP = {
+    '/ENTRY[entry]/method': 'archive.data.method',
+    '/ENTRY[entry]/measurement_type': 'archive.data.diffraction_method_name',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_axis': 'archive.data.results[0].scan_axis',
+    '/ENTRY[entry]/experiment_config/count_time': 'archive.data.results[0].count_time.magnitude',
+    'line': '',
+    '/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.magnitude',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_current/@units': 'archive.data.xrd_settings.source.xray_tube_current.units',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage': 'archive.data.xrd_settings.source.xray_tube_voltage.magnitude',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage/@units': 'archive.data.xrd_settings.source.xray_tube_voltage.units',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one': 'archive.data.xrd_settings.source.kalpha_one.magnitude',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one/@units': 'archive.data.xrd_settings.source.kalpha_one.units',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two': 'archive.data.xrd_settings.source.kalpha_two.magnitude',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two/@units': 'archive.data.xrd_settings.source.kalpha_two.units',
+    '/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.magnitude',
+    '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta/@units': 'archive.data.xrd_settings.source.kbeta.units',
+    '/ENTRY[entry]/@default': 'experiment_result',
+    '/ENTRY[entry]/experiment_result/@signal': 'intensity',
+    '/ENTRY[entry]/definition': 'NXxrd_pan',
+}
+
+
+def walk_through_object(parent_obj, attr_chain, default=None):
+    """
+    Walk though the object until reach the leaf.
+
+    Args:
+        parent_obj: This is a python obj.
+        attr_chain: Dot separated obj chain.
+        default: A value to be returned by default, if not data is found.
+    """
+    if parent_obj is None:
+        return
+    expected_parts = 2
+    if isinstance(attr_chain, str):
+        parts = attr_chain.split('.', 1)
+
+        if len(parts) == expected_parts:
+            child_nm, rest_part = parts
+            if '[' in child_nm:
+                child_nm, index = child_nm.split('[')
+                index = int(index[:-1])
+                # section always exists
+                child_obj = getattr(parent_obj, child_nm)[index]
+            else:
+                child_obj = getattr(parent_obj, child_nm, default)
+            return walk_through_object(child_obj, rest_part, default=default)
+        else:
+            return getattr(parent_obj, attr_chain, default)
+
+
+def connect_concepts_to_hdf5(
+    archive: 'EntryArchive', hdf5handler: HDF5Handler, h5_root: h5.Group
+):
+    """
+    Connect the concepts between `ELNXrayDiffraction` and `NXxrd_pan` schema.
+
+    Args:
+        template (Template): The pynxtools template, a inherited class from python dict.
+        archive (EntryArchive): Nomad archive contains secttions, subsections and
+            quantities.
+        scan_type (str): Name of the scan type such as line and RSM.
+    """
+
+    # General concepts
+    # ruff: noqa: E501
+    value = None
+    concept_map_tmp = copy.deepcopy(CONCEPT_MAP)
+    handled_keys = []
+    for key, archive_concept in concept_map_tmp.items():
+        if isinstance(archive_concept, str) and archive_concept.startswith('archive.'):
+            _, arch_attr = archive_concept.split('.', 1)
+            value = None
+            try:
+                value = walk_through_object(archive, arch_attr)
+            # Use multiple excepts to avoid catching all exceptions
+            except (AttributeError, IndexError, KeyError, ValueError):
+                pass
+
+        if value is not None:
+            key_parts = key.split('/')
+            if key[-1].startswith('@'):
+                # attr
+                key_parts = key_parts[:-2]
+                hdf5handler.add_attribute(
+                    path=key,
+                    data=value,
+                )
+            else:
+                key_parts = key_parts[:-1]
+                hdf5handler.add_dataset(
+                    path=key,
+                    data=value,
+                )
+
+            # Construct group
+            child_group = hdf5handler.add_group_and_return_child_group(
+                child_group_name=key_parts[0], parent_group=h5_root
+            )
+            for nx_concept in key_parts[1:]:
+                child_group = hdf5handler.add_group_and_return_child_group(
+                    child_group_name=nx_concept, parent_group=child_group
+                )
+            handled_keys.append(key)
+
+    for key in handled_keys:
+        _ = concept_map_tmp.pop(key, None)