code/spec_rag/dataset.py

from __future__ import annotations

from dataclasses import dataclass
from typing import Iterable, List, Optional

from .prompt import format_chat_example, format_molt5_prompt


@dataclass
class RAGExample:
    spectrum_id: str
    spectrum_token: str
    context_smiles: List[str]
    target_smiles: Optional[str]

    def as_molt5(self) -> dict:
        return {
            "spectrum_id": self.spectrum_id,
            "input_text": format_molt5_prompt(
                self.spectrum_token, self.context_smiles, self.target_smiles
            ),
            "target_text": self.target_smiles or "",
        }

    def as_chat(self) -> dict:
        return {
            "spectrum_id": self.spectrum_id,
            "messages": format_chat_example(
                self.spectrum_token, self.context_smiles, self.target_smiles
            ),
        }


def build_examples(
    spectrum_ids: Iterable[str],
    spectrum_token: str,
    contexts: List[List[str]],
    targets: Optional[List[str]] = None,
) -> List[RAGExample]:
    examples: List[RAGExample] = []
    for i, sid in enumerate(spectrum_ids):
        target = targets[i] if targets is not None else None
        examples.append(
            RAGExample(
                spectrum_id=str(sid),
                spectrum_token=spectrum_token,
                context_smiles=contexts[i],
                target_smiles=target,
            )
        )
    return examples