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