mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-10 00:34:29 +00:00
63 lines
1.7 KiB
Python
63 lines
1.7 KiB
Python
from argparse import ArgumentParser
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from pathlib import Path
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from linkml_runtime.dumpers import yaml_dumper
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from nwb_linkml.generators.pydantic import NWBPydanticGenerator
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from nwb_linkml import io
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def generate_core_yaml(output_path:Path):
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core = io.load_nwb_core()
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built_schemas = core.build().schemas
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for schema in built_schemas:
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output_file = output_path / (schema.name + '.yaml')
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yaml_dumper.dump(schema, output_file)
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def generate_core_pydantic(yaml_path:Path, output_path:Path):
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for schema in yaml_path.glob('*.yaml'):
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python_name = schema.stem.replace('.', '_').replace('-', '_')
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pydantic_file = (output_path / python_name).with_suffix('.py')
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generator = NWBPydanticGenerator(
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str(schema),
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pydantic_version='2',
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emit_metadata=True,
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gen_classvars=True,
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gen_slots=True
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)
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gen_pydantic = generator.serialize()
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with open(pydantic_file, 'w') as pfile:
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pfile.write(gen_pydantic)
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def parser() -> ArgumentParser:
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parser = ArgumentParser('Generate NWB core schema')
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parser.add_argument(
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'--yaml',
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help="directory to export linkML schema to",
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type=Path,
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default=Path(__file__).parent.parent / 'nwb_linkml' / 'schema'
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)
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parser.add_argument(
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'--pydantic',
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help="directory to export pydantic models",
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type=Path,
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default=Path(__file__).parent.parent / 'nwb_linkml' / 'models'
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)
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return parser
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def main():
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args = parser().parse_args()
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args.yaml.mkdir(exist_ok=True)
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args.pydantic.mkdir(exist_ok=True)
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generate_core_yaml(args.yaml)
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generate_core_pydantic(args.yaml, args.pydantic)
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if __name__ == "__main__":
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main()
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