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from __future__ import annotations |
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from typing import List, Optional |
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from pydantic import BaseModel, Field, ValidationError, model_validator |
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class Reagent(BaseModel): |
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name: str |
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amount: Optional[float] = Field(default=None, description="Numeric amount if known") |
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unit: Optional[str] = Field(default=None, description="Unit for amount, e.g., µL, mg, mM") |
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vendor: Optional[str] = None |
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catalog_number: Optional[str] = None |
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class Step(BaseModel): |
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number: int |
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description: str |
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duration_minutes: Optional[float] = None |
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temperature_c: Optional[float] = None |
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hazards: List[str] = [] |
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class Protocol(BaseModel): |
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title: str |
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sources: List[str] |
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equipment: List[str] = [] |
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reagents: List[Reagent] = [] |
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steps: List[Step] |
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safety_notes: List[str] = [] |
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ruo_disclaimer: str |
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@model_validator(mode="after") |
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def check_steps_sequential(self): |
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nums = [s.number for s in self.steps] |
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if nums != list(range(1, len(nums) + 1)): |
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raise ValueError("Steps must be sequential starting at 1") |
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return self |
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def validate_protocol(proto: Protocol) -> None: |
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"""Raises ValidationError if invalid.""" |
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if not proto.ruo_disclaimer.lower().startswith("research use only"): |
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raise ValidationError([{"loc":("ruo_disclaimer",), "msg":"Missing RUO disclaimer"}], Protocol) |
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