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from __future__ import annotations
import json
import click
from pathlib import Path
from slugify import slugify
from .extract import parse_markdown
DEFAULT_ALTS = [
{"vendor": "Vendor A", "catalog_number": "TBD"},
{"vendor": "Vendor B", "catalog_number": "TBD"},
]
@click.command()
@click.argument("protocol_md", type=click.Path(exists=True))
@click.option("--out", "out_path", type=click.Path(), help="Output JSON file")
def main(protocol_md, out_path):
proto = parse_markdown(Path(protocol_md).read_text(encoding="utf-8"))
items = []
for r in proto.reagents:
items.append({
"name": r.name,
"amount": r.amount,
"unit": r.unit,
"alternatives": DEFAULT_ALTS,
})
payload = {"protocol": slugify(proto.title), "items": items}
if out_path:
Path(out_path).write_text(json.dumps(payload, indent=2), encoding="utf-8")
else:
print(json.dumps(payload, indent=2))
if __name__ == "__main__":
main()
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