8000 Refix reference by RubelMozumder · Pull Request #604 · FAIRmat-NFDI/pynxtools · GitHub
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Refix reference #604

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Merged
merged 2 commits into from
Mar 27, 2025
Merged

Refix reference #604

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a88fea7
fix the Reference.
RubelMozumder Mar 27, 2025
226d85a
ruff.
RubelMozumder Mar 27, 2025
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42 changes: 26 additions & 16 deletions src/pynxtools/nomad/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -176,45 +176,55 @@ def get_entry_reference(archive, f_name):


class NexusIdentifiers(ArchiveSection):
NeXus_identifiers = SubSection(
Nexus_identifiers = SubSection(
section_def=AnchoredReference,
repeats=True,
description="These are the NOMAD references correspond to NeXus identifierNAME fields.",
)

def normalize(self, archive, logger):
# Consider multiple identifiers exists in the same group/section
def generate_anchored_reference_and_normalize(value, idname):
def generate_anchored_reference_and_normalize(
attr_obj, id_value, idname, is_full_storage=False
):
"""Generate anchored reference, connect to m quantities, and normalize."""
field_n = idname.split("__field")[0]
logger.info(f"Lab id {value} to be created")
nx_id = AnchoredReference(lab_id=value, name=field_n)
nx_id.m_set_section_attribute(
"m_nx_data_path",
self.m_get_quantity_attribute(idname, "m_nx_data_path"),
)
nx_id.m_set_section_attribute(
"m_nx_data_file",
self.m_get_quantity_attribute(idname, "m_nx_data_file"),
)
logger.info(f"Lab id {id_value} to be created")
nx_id = AnchoredReference(lab_id=id_value, name=field_n)
if not is_full_storage:
nx_data_path = attr_obj.m_get_quantity_attribute(
idname, "m_nx_data_path"
)
nx_data_file = attr_obj.m_get_quantity_attribute(
idname, "m_nx_data_file"
)
else:
nx_data_path = attr_obj.attributes.get("m_nx_data_path")
nx_data_file = attr_obj.attributes.get("m_nx_data_file")

nx_id.m_set_section_attribute("m_nx_data_path", nx_data_path)
nx_id.m_set_section_attribute("m_nx_data_file", nx_data_file)

self.Nexus_identifiers.append(nx_id)
nx_id.normalize(archive, logger)
self.NeXus_identifiers.append(nx_id)

identifiers = [
key
for key in self.__dict__.keys()
if key.startswith("identifier") and key.endswith("__field")
]
if identifiers:
self.NeXus_identifiers = []
self.Nexus_identifiers = []
for identifier in identifiers:
if not (val := getattr(self, identifier)):
continue
if isinstance(val, dict):
for idname, idobj in val.items():
generate_anchored_reference_and_normalize(idobj.value, idname)
generate_anchored_reference_and_normalize(
idobj, idobj.value, idname, True
)
else:
generate_anchored_reference_and_normalize(val, identifier)
generate_anchored_reference_and_normalize(self, val, identifier)
super().normalize(archive, logger)


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