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Implementation skeleton for YAML IVAS/APSuite parser
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| # | ||
| # 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. | ||
| # | ||
| """Wrapping multiple parsers for vendor files with NOMAD Oasis/ELN/YAML metadata.""" | ||
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| import pathlib | ||
| from typing import Any, Dict | ||
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| import flatdict as fd | ||
| import yaml | ||
| from ase.data import chemical_symbols | ||
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| from pynxtools_apm.concepts.mapping_functors_pint import add_specific_metadata_pint | ||
| from pynxtools_apm.configurations.cameca_cfg import APM_CAMECA_TO_NEXUS | ||
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| class NxApmNomadOasisCamecaParser: | ||
| """Parse manually collected content from an IVAS / AP Suite YAML.""" | ||
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| def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False): | ||
| """Construct class""" | ||
| print(f"Extracting data from IVAS/APSuite file: {file_path}") | ||
| if pathlib.Path(file_path).name.endswith(".cameca"): | ||
| self.file_path = file_path | ||
| self.entry_id = entry_id if entry_id > 0 else 1 | ||
| self.verbose = verbose | ||
| try: | ||
| with open(self.file_path, "r", encoding="utf-8") as stream: | ||
| self.yml = fd.FlatDict(yaml.safe_load(stream), delimiter="/") | ||
| if self.verbose: | ||
| for key, val in self.yml.items(): | ||
| print(f"key: {key}, value: {val}") | ||
| except (FileNotFoundError, IOError): | ||
| print(f"File {self.file_path} not found !") | ||
| self.apsuite = fd.FlatDict({}, delimiter="/") | ||
| return | ||
|
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| def parse_ranging_definitions(self, template: dict) -> dict: | ||
| """Interpret human-readable ELN input to generate consistent composition table.""" | ||
| src = "sample/composition" | ||
| if src in self.yml: | ||
| if isinstance(self.yml[src], list): | ||
| dct: Dict[Any, Any] = {} # IMPLEMENT ME! | ||
| prfx = f"/ENTRY[entry{self.entry_id}]/sample/chemical_composition" | ||
| ion_id = 1 | ||
| for symbol in chemical_symbols[1::]: | ||
| # ase convention is that chemical_symbols[0] == "X" | ||
| # to enable using ordinal number for indexing | ||
| if symbol in dct: | ||
| if isinstance(dct[symbol], tuple) and len(dct[symbol]) == 2: | ||
| trg = f"{prfx}/ionID[ion{ion_id}]" | ||
| template[f"{trg}/chemical_symbol"] = symbol | ||
| template[f"{trg}/composition"] = dct[symbol][0] | ||
| if dct[symbol][1] is not None: | ||
| template[f"{trg}/composition_error"] = dct[symbol][1] | ||
| ion_id += 1 | ||
| return template | ||
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| def parse(self, template: dict) -> dict: | ||
| """Copy data from self into template the appdef instance.""" | ||
| self.parse_ranging_definitions(template) | ||
| identifier = [self.entry_id] | ||
| add_specific_metadata_pint( | ||
| APM_CAMECA_TO_NEXUS, self.apsuite, identifier, template | ||
| ) | ||
| return template |