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from __future__ import annotations
import re
import json
import click
from pathlib import Path
from markdown_it import MarkdownIt
from .schema import Protocol, Step, Reagent, validate_protocol
md = MarkdownIt()
RUO_PREFIX = "Research Use Only (RUO)."
def parse_markdown(md_text: str) -> Protocol:
# Very light parser for the example template
title_match = re.search(r"^#\s+(.+)$", md_text, re.M)
title = title_match.group(1).strip() if title_match else "Untitled Protocol"
sources = re.findall(r"^\*\*Sources\*\*:([^\n]+)$", md_text, re.M)
sources = [s.strip() for s in ",".join(sources).split(",") if s.strip()] or []
equipment_section = re.search(r"## Equipment\n([\s\S]*?)\n##", md_text)
equipment = []
if equipment_section:
equipment = [l.strip("- ") for l in equipment_section.group(1).splitlines() if l.strip().startswith("-")]
reagents_section = re.search(r"## Reagents[\s\S]*?\n([\s\S]*?)\n##", md_text)
reagents = []
if reagents_section:
for l in reagents_section.group(1).splitlines():
if l.strip().startswith("-"):
name = l.strip("- ").strip()
reagents.append(Reagent(name=name))
# Steps
steps = []
for i, m in enumerate(re.finditer(r"^\d+\.\s+(.+)$", md_text, re.M), start=1):
steps.append(Step(number=i, description=m.group(1).strip()))
# Safety
safety = []
safety_sec = re.search(r"## Safety notes\n([\s\S]*?)\n##|$", md_text)
if safety_sec:
for l in safety_sec.group(1).splitlines():
if l.strip().startswith("-"):
safety.append(l.strip("- ").strip())
disclaimer = "Research Use Only (RUO). Not for use in diagnostic procedures or patient care."
return Protocol(
title=title,
sources=sources,
equipment=equipment,
reagents=reagents,
steps=steps,
safety_notes=safety,
ruo_disclaimer=disclaimer,
)
@click.command()
@click.argument("path", type=click.Path(exists=True))
@click.option("--validate", "do_validate", is_flag=True, help="Validate after parsing")
@click.option("--json-out", "json_out", is_flag=True, help="Print JSON to stdout")
def main(path, do_validate, json_out):
text = Path(path).read_text(encoding="utf-8")
proto = parse_markdown(text)
if do_validate:
validate_protocol(proto)
if json_out:
click.echo(proto.model_dump_json(indent=2))
if __name__ == "__main__":
main()
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