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Clean up schema.py
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@RubelMozumder
RubelMozumder committed Sep 11, 2024
1 parent a12420c commit 23de8a0
Showing 1 changed file with 56 additions and 138 deletions.
194 changes: 56 additions & 138 deletions src/pynxtools/nomad/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,13 @@
# limitations under the License.
#

import json
import os
import os.path
import pickle
import re
import sys

# noinspection PyPep8Naming
import xml.etree.ElementTree as ET
from typing import Any, Dict, List, Optional, Union
Expand All @@ -30,14 +33,37 @@
from nomad import utils
from nomad.datamodel import EntryArchive, EntryData, EntryMetadata
from nomad.datamodel.metainfo.basesections import (
BaseSection, Component, CompositeSystem, CompositeSystemReference,
Entity, EntityReference, Instrument)
BaseSection,
Component,
CompositeSystem,
Entity,
EntityReference,
Instrument,
)
from nomad.datamodel.metainfo.eln import BasicEln
from nomad.metainfo import (Attribute, Bytes, Datetime, Definition, MEnum,
Package, Quantity, Section, SubSection)
from nomad.metainfo.data_type import (Bytes, Datatype, Datetime, Number,
m_bool, m_complex128, m_float64,
m_int, m_int64, m_str)
from nomad.metainfo import (
Attribute,
Bytes,
Datetime,
Definition,
MEnum,
Package,
Quantity,
Section,
SubSection,
)
from nomad.metainfo.data_type import (
Bytes,
Datatype,
Datetime,
Number,
m_bool,
m_complex128,
m_float64,
m_int,
m_int64,
m_str,
)
from nomad.utils import get_logger, strip
from toposort import toposort_flatten
except ImportError as exc:
Expand All @@ -46,8 +72,7 @@
) from exc

from pynxtools import get_definitions_url
from pynxtools.definitions.dev_tools.utils.nxdl_utils import \
get_nexus_definitions_path
from pynxtools.definitions.dev_tools.utils.nxdl_utils import get_nexus_definitions_path

# __URL_REGEXP from
# https://stackoverflow.com/questions/3809401/what-is-a-good-regular-expression-to-match-a-url
Expand All @@ -68,7 +93,6 @@

__BASESECTIONS_MAP: Dict[str, Any] = {
"NXfabrication": [Instrument],
# "NXsample": CompositeSystemReference,
"NXsample": [CompositeSystem],
"NXsample_component": [Component],
"NXidentifier": [EntityReference],
Expand Down Expand Up @@ -595,7 +619,9 @@ def __create_class_section(xml_node: ET.Element) -> Section:

if "extends" in xml_attrs:
nx_base_sec = __to_section(xml_attrs["extends"])
class_section.base_sections = [nx_base_sec] + [cls.m_def for cls in nomad_base_sec_cls]
class_section.base_sections = [nx_base_sec] + [
cls.m_def for cls in nomad_base_sec_cls
]

__add_common_properties(xml_node, class_section)

Expand Down Expand Up @@ -731,9 +757,6 @@ def __create_package_from_nxdl_directories(nexus_section: Section) -> Package:

nexus_metainfo_package: Optional[Package] = None # pylint: disable=C0103

import pickle
import traceback


def save_nexus_schema(suf):
nexus_metainfo_package
Expand Down Expand Up @@ -810,51 +833,48 @@ def init_nexus_metainfo():
init_nexus_metainfo()


# Appending the normalize method from a function
def normalize_nxfabrication(self, archive, logger):
current_cls =__section_definitions["NXfabrication"].section_cls
"""Normalizer for NXfabrication section."""
current_cls = __section_definitions["NXfabrication"].section_cls
super(current_cls, self).normalize(archive, logger)
self.lab_id = "Hello"


def normalize_nxsample_component(self, archive, logger):
"""Normalizer for NXsample_component section."""
current_cls = __section_definitions["NXsample_component"].section_cls
if self.name__field:
self.name = self.name__field
if self.mass__field:
self.mass = self.mass__field
#we may want to add normalisation for mass_fraction (calculating from components)
# we may want to add normalisation for mass_fraction (calculating from components)
super(current_cls, self).normalize(archive, logger)


def normalize_nxsample(self, archive, logger):
"""Normalizer for NXsample section."""
current_cls = __section_definitions["NXsample"].section_cls
if self.name__field:
self.name = self.name__field
#one could also copy local ids to nxidentifier for search purposes
# one could also copy local ids to nxidentifier for search purposes
super(current_cls, self).normalize(archive, logger)


def normalize_nxidentifier(self, archive, logger):
"""Normalizer for NXidentifier section."""

def create_Entity(lab_id, archive, f_name):
#entity = section.m_def
#new_archive = EntryArchive()

#entity=Entity()
#entity.lab_id=lab_id
entity=BasicEln()
entity.lab_id=lab_id
entity.entity=Entity()
entity.entity.lab_id=lab_id



#new_archive.data=entity
import json
entity = BasicEln()
entity.lab_id = lab_id
entity.entity = Entity()
entity.entity.lab_id = lab_id

with archive.m_context.raw_file(f_name, "w") as f_obj:
json.dump({"data": entity.m_to_dict(with_meta=True,include_derived=True)}, f_obj, indent=4)
json.dump(
{"data": entity.m_to_dict(with_meta=True, include_derived=True)},
f_obj,
indent=4,
)
archive.m_context.process_updated_raw_file(f_name)

def get_entry_reference(archive, f_name):
Expand All @@ -866,15 +886,12 @@ def get_entry_reference(archive, f_name):

return f"/entries/{entry_id}/archive#/data"




current_cls = __section_definitions["NXidentifier"].section_cls
#super(current_cls, self).normalize(archive, logger)
# super(current_cls, self).normalize(archive, logger)
if self.identifier__field:
logger.info(f"{self.identifier__field} - identifier received")
self.lab_id = self.identifier__field # + "__occurrence"
EntityReference.normalize(self,archive,logger)
EntityReference.normalize(self, archive, logger)
if not self.reference:
logger.info(f"{self.lab_id} to be created")

Expand All @@ -884,62 +901,6 @@ def get_entry_reference(archive, f_name):
logger.info(f"{self.reference} - referenced directly")




#self.reference = "Registered NOMAD Entry not found"
# new_archive = EntryArchive()
# entry_metadata = new_archive.metadata
# if entry_metadata is None:
# entry_metadata = new_archive.m_create(EntryMetadata)

# entry_id=('{:%dd}' % utils.default_hash_len).format(0)
# entry_metadata.m_update(
# entry_id=entry_id,
# upload_id=archive.metadata.upload_id,
# mainfile=archive.metadata.mainfile,
# entry_hash=entry_id,
# domain='nexus',
# entry_create_time=datetime.utcnow(),
# processed=True,
# parser_name='parsers/internal',
# )

# if new_archive.data is None:
# new_archive.data=EntryData()
# #new_archive.m_create(EntryData)
# new_archive.data.entity=Entity()
# new_archive.data.entity.lab_id=self.lab_id
# new_archive.metadata=EntryMetadata()
# if new_archive.metadata.entry_type is None:
# new_archive.metadata.entry_type = "Entity"
# new_archive.metadata.domain = "nexus"
# new_archive.normalize(new_archive,logger)
# logger.info(f"New Entry for {self.lab_id}: " + str(new_archive.m_to_dict()))
# new_archive.save()



# TODO. NXsample_component -> CompositeSystem
# Write a normalize function for NXsample_component

# If the lab_id exists somewhere in NOMAD, we make a reference to the data section in another entry that contains this lab_id

# self.reference = CompositeSystemReference(lab_id=123456789)

# # If the lab_id does not exist somewhere else in NOMAD, we make a new Entry for the sample and reference its data section here.
# if not self.reference:
# new_sample_archive = EntryArchive()

# # Not working
# new_sample_archive.add_section(self)

# # Make a reference to the new entry
# self.lab_id = archive_lab_id
# super(__section_definitions["NXsample"].section_cls, self).normalize(
# archive, logger
# )


__NORMALIZER_MAP: Dict[str, Any] = {
"NXfabrication": normalize_nxfabrication,
"NXsample": normalize_nxsample,
Expand All @@ -952,51 +913,8 @@ def get_entry_reference(archive, f_name):
if nx_name == "NXobject":
continue

# nomad_base_sec_cls = __BASESECTIONS_MAP.get(nx_name, BaseSection)
normalize_func = __NORMALIZER_MAP.get(nx_name)

# Append the normalize method from a function
if normalize_func:
section.section_cls.normalize = normalize_func

# if nomad_base_sec_cls is not None:
# if section.base_sections and isinstance(section.base_sections, list):
# # section.base_sections.append(nomad_base_sec_cls.m_def)
# section.base_sections = section.base_sections[::-1]
# else:
# section.base_sections = [nomad_base_sec_cls.m_def]
# nomad_base_sec_cls.m_def.init_metainfo()
# section.init_metainfo()

#################################################
# Approach B: Using a new class
# class NxNomad_Instrument(Instrument):
# test_attr = Quantity(
# type=str,
# description="A reference to a NOMAD `Instrument` entry.",
# )
# def normalize(self, archive, logger):
# logger.info(f" ###### : from : ##, {type(self)}")
# super(NxNomad_Instrument, self).normalize(archive, logger)
# archive.results.eln.test_attr = "Hello"
# self.test_attr = "Hello"

# __BASESECTIONS_MAP: Dict[str, Any] = {
# "NXfabrication": NxNomad_Instrument,
# # "NXobject": BaseSection,
# }

# # Handling nomad BaseSection and other inherited Section from BaseSection
# for nx_name, section in __section_definitions.items():
# if nx_name == "NXobject":
# continue

# nomad_base_sec_cls = __BASESECTIONS_MAP.get(nx_name, BaseSection)

# if nomad_base_sec_cls is not None:
# if section.base_sections and isinstance(section.base_sections, list):
# section.base_sections.append(nomad_base_sec_cls.m_def)
# section.base_sections = section.base_sections[::-1]
# else:
# section.base_sections = [nomad_base_sec_cls.m_def]
# nomad_base_sec_cls.m_def.init_metainfo()
# section.init_metainfo()

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