task.py

__all__ = [
    "ENV_NAME",
    "TASK_DATASET_NAME",
    "GradablePaperQAEnvironment",
    "LitQATaskDataset",
    "LitQAv2TaskDataset",
    "LitQAv2TaskSplit",
]

import logging
import re
from abc import ABC
from collections.abc import Awaitable, Callable, Sequence
from copy import deepcopy
from enum import StrEnum
from typing import TYPE_CHECKING, Any, Self, assert_never

from aviary.core import (
    TASK_DATASET_REGISTRY,
    Frame,
    Messages,
    TaskDataset,
    ToolRequestMessage,
    ToolResponseMessage,
)
from aviary.env import ENV_REGISTRY

from paperqa.types import DocDetails

from .search import SearchIndex, maybe_get_manifest

try:
    from ldp.alg import ComputeTrajectoryMetricsMixin
except ImportError:

    class ComputeTrajectoryMetricsMixin:  # type: ignore[no-redef]
        """Placeholder for when ldp isn't installed."""


from paperqa.docs import Docs
from paperqa.litqa import (
    DEFAULT_EVAL_MODEL_NAME,
    DEFAULT_LABBENCH_HF_HUB_NAME,
    DEFAULT_REWARD_DISTRIBUTION,
    LitQAEvaluation,
    read_litqa_v2_from_hub,
)
from paperqa.llms import EmbeddingModel, LiteLLMModel, LLMModel
from paperqa.types import PQASession

from .env import POPULATE_FROM_SETTINGS, PaperQAEnvironment
from .models import QueryRequest
from .tools import GenerateAnswer

if TYPE_CHECKING:
    from ldp.data_structures import Trajectory

logger = logging.getLogger(__name__)


class GradablePaperQAEnvironment(PaperQAEnvironment):
    """Extended environment that can grade answers."""

    def __init__(
        self,
        query: QueryRequest,
        docs: Docs,
        llm_model: LiteLLMModel | None = POPULATE_FROM_SETTINGS,
        summary_llm_model: LiteLLMModel | None = POPULATE_FROM_SETTINGS,
        embedding_model: EmbeddingModel | None = POPULATE_FROM_SETTINGS,
        evaluation_from_answer: (
            Callable[[PQASession | str], Awaitable[LitQAEvaluation]] | None
        ) = None,
        sources: str | list[str] | None = None,
        rewards: Sequence[float] = DEFAULT_REWARD_DISTRIBUTION,
        evaluation_callback: Callable[[LitQAEvaluation], Awaitable] | None = None,
        **env_kwargs,
    ):
        super().__init__(
            query, docs, llm_model, summary_llm_model, embedding_model, **env_kwargs
        )
        self._evaluation_from_answer = evaluation_from_answer
        # Enables checking an Index has the right DOI(s)
        self.sources: list[str] | None = (
            [sources] if isinstance(sources, str) else sources
        )
        self._evaluation_callback = evaluation_callback
        self._rewards = rewards

    async def validate_sources(
        self, manifest_or_index: dict[str, DocDetails] | SearchIndex | None = None
    ) -> None:
        """Validate the sources can be found in the input manifest or index."""
        if not self.sources:
            return
        if manifest_or_index is None:  # Let's try to load in the manifest
            manifest_or_index = await maybe_get_manifest(
                filename=await self._query.settings.agent.index.finalize_manifest_file()
            )
        if isinstance(manifest_or_index, SearchIndex):
            entity: str = "index"
            file_names: set[str] = {k for k in await manifest_or_index.index_files if k}
            lowercased_dois: set[str] = set()
        else:
            entity = "manifest"
            file_names = {k for k in manifest_or_index if k}
            lowercased_dois = {
                v["doi"].lower() for v in manifest_or_index.values() if v["doi"]
            }
        if not file_names:  # File names being empty means something's wrong
            logger.warning(
                f"Can't validate sources {self.sources} without a correctly specified"
                f" {entity}."
            )
            return
        not_found = [
            s
            for s in self.sources
            if s not in file_names and s.lower() not in lowercased_dois
        ]
        if not_found:
            raise ValueError(
                f"Sources {not_found} of {self.sources} not found in the {entity},"
                f" the corresponding query was {self._query.query!r}."
            )

    async def step(
        self, action: ToolRequestMessage
    ) -> tuple[Messages, float, bool, bool]:
        messages, reward, done, truncated = await super().step(action)
        if not done or not self._evaluation_from_answer:
            return messages, reward, done, truncated
        valid_answers, failed_answer_messages = [], []
        for m in messages:
            if (
                not isinstance(m, ToolResponseMessage)
                or m.name != GenerateAnswer.gen_answer.__name__
            ):
                continue  # Filter out non-answer messages (in case parallel tool calls)
            if answer := GenerateAnswer.extract_answer_from_message(content=m.content):
                valid_answers.append(answer)
            else:
                failed_answer_messages.append(m)
        if not valid_answers:  # No answer, so no positive reward
            return messages, reward, done, truncated
        if len(valid_answers) != 1:
            raise NotImplementedError(
                f"Expected just one answer message, got more than one in {messages}."
            )
        answer = valid_answers[0]
        if failed_answer_messages:
            logger.warning(
                "More than one answer detected, discarding failed answer messages"
                f" {failed_answer_messages}, continuing with answer {answer}."
            )
        # Okay, so we have one answer that was not a failed answer. Let's evaluate it
        evaluation = await self._evaluation_from_answer(answer)
        if evaluation_callback := self._evaluation_callback:
            await evaluation_callback(evaluation)
        return messages, reward + self._rewards[evaluation.value], done, truncated

    def export_frame(self) -> Frame:
        raise NotImplementedError("Didn't yet need to export a frame.")

    def __deepcopy__(self, memo) -> Self:
        copy_state = deepcopy(self.state, memo)
        # We don't know the side effects of deep copying a litellm.Router,
        # so we force a shallow copy of these LiteLLMModels
        env_model_kwargs: dict[str, Any] = {
            name: model if model is None else type(model)(**model.model_dump())
            for name, model in (
                ("llm_model", self._llm_model),
                ("summary_llm_model", self._summary_llm_model),
                ("embedding_model", self._embedding_model),
            )
        }
        copy_self = type(self)(
            query=deepcopy(self._query, memo),  # deepcopy for _docs_name
            docs=copy_state.docs,
            evaluation_from_answer=self._evaluation_from_answer,
            sources=self.sources,
            rewards=self._rewards,
            evaluation_callback=self._evaluation_callback,
            **env_model_kwargs,
        )
        copy_self.state = copy_state
        # Because we shallow copied the LiteLLMModels, we need to re-make the
        # tool functions within the tools
        copy_self.tools = copy_self.make_tools()
        return copy_self


ENV_NAME = "paperqa-local"
ENV_REGISTRY[ENV_NAME] = (
    GradablePaperQAEnvironment.__module__,
    GradablePaperQAEnvironment.__name__,
)


class LitQATaskDataset(
    TaskDataset[GradablePaperQAEnvironment], ComputeTrajectoryMetricsMixin, ABC
):
    """
    Abstract base class for a task dataset of LitQA v1 or v2 questions.

    This is an ABC because it's non-specific to a LitQA version.
    Examples include LitQA v1, v2, or a test stub version of LitQA.
    """

    def __init__(
        self,
        base_query: QueryRequest | dict | None = None,
        base_docs: Docs | dict | None = None,
        rewards: Sequence[float] = DEFAULT_REWARD_DISTRIBUTION,
        eval_model: LLMModel | str = DEFAULT_EVAL_MODEL_NAME,
        **env_kwargs,
    ):
        if base_query is None:
            base_query = QueryRequest()
        if isinstance(base_query, dict):
            base_query = QueryRequest(**base_query)
        self._base_query = base_query
        if base_docs is None:
            base_docs = Docs()
        if isinstance(base_docs, dict):
            base_docs = Docs(**base_docs)
        self._base_docs = base_docs
        self._rewards = rewards
        self._env_kwargs = env_kwargs
        self._eval_model = eval_model

    def _make_gradable_environment(
        self,
        ideal: str,
        distractors: str | list[str],
        question: str,
        use_unsure: bool = True,
        sources: str | list[str] | None = None,
    ) -> GradablePaperQAEnvironment:
        qa_prompt, evaluation_from_answer = LitQAEvaluation.from_question(
            ideal=ideal,
            distractors=distractors,
            question=question,
            use_unsure=use_unsure,
            eval_model=self._eval_model,
        )
        query = self._base_query.model_copy()
        query.query = qa_prompt
        return GradablePaperQAEnvironment(
            query=query,
            docs=self._base_docs.model_copy(),
            evaluation_from_answer=evaluation_from_answer,
            sources=sources,
            rewards=self._rewards,
            **self._env_kwargs,
        )

    def compute_trajectory_metrics(
        self, trajectories: "Sequence[Trajectory]"
    ) -> dict[str, list[float]]:
        total_paper_count: list[float] = []
        relevant_paper_count: list[float] = []
        evidence_count: list[float] = []
        for t in trajectories:
            split_answers = [
                split_answers
                for split_answers in (
                    re.split(
                        pattern=GenerateAnswer.ANSWER_SPLIT_REGEX_PATTERN,
                        string=obs.content,
                    )
                    for obs in t.steps[-1].next_observation
                    if (
                        isinstance(obs, ToolResponseMessage)
                        and obs.name == GenerateAnswer.TOOL_FN_NAME
                    )
                )
                # Filter for places where the regex split succeeded
                if len(split_answers) >= 4  # noqa: PLR2004
            ]
            for i, metric_list in enumerate(
                (total_paper_count, relevant_paper_count, evidence_count),
                start=1,  # Regex extraction of status starts after answer
            ):
                metric_list.append(  # Use mean to allow for multiple answers
                    sum(int(sa[i]) for sa in split_answers) / len(split_answers)
                    if split_answers  # Avoid div0 (when no answer was made)
                    else 0
                )
        return super().compute_trajectory_metrics(trajectories) | {
            "total_paper_count": total_paper_count,
            "relevant_paper_count": relevant_paper_count,
            "evidence_count": evidence_count,
            "correct": [
                int(t.steps[-1].reward == self._rewards[0]) for t in trajectories
            ],
            "correct_unsure": [
                int(t.steps[-1].reward in {self._rewards[0], self._rewards[1]})
                for t in trajectories
            ],
        }


class LitQAv2TaskSplit(StrEnum):
    TRAIN = "train"
    EVAL = "eval"


class LitQAv2TaskDataset(LitQATaskDataset):
    """Task dataset of LitQA v2 questions."""

    def __init__(
        self,
        *args,
        labbench_dataset: str = DEFAULT_LABBENCH_HF_HUB_NAME,
        split: str | LitQAv2TaskSplit = LitQAv2TaskSplit.EVAL,
        **kwargs,
    ):
        super().__init__(*args, **kwargs)
        train_df, eval_df = read_litqa_v2_from_hub(labbench_dataset)
        split = LitQAv2TaskSplit(split)
        if split == LitQAv2TaskSplit.TRAIN:
            self.data = train_df
        elif split == LitQAv2TaskSplit.EVAL:
            self.data = eval_df
        else:
            assert_never(split)

    def get_new_env_by_idx(self, idx: int) -> GradablePaperQAEnvironment:
        sources = []
        for s in self.data.iloc[idx].sources:
            try:
                (doi,) = (
                    s.split(substr, maxsplit=1)[1]
                    for substr in DocDetails.DOI_URL_FORMATS
                    if substr in s
                )
            except ValueError as exc:
                raise NotImplementedError(
                    f"Didn't handle DOI extraction from source {s!r}."
                ) from exc
            sources.append(doi)
        return self._make_gradable_environment(
            ideal=self.data.iloc[idx].ideal,
            distractors=self.data.iloc[idx].distractors,
            question=self.data.iloc[idx].question,
            sources=sources,
        )

    def __len__(self) -> int:
        return len(self.data)


TASK_DATASET_NAME = "litqa-v2"
TASK_DATASET_REGISTRY[TASK_DATASET_NAME] = (
    LitQAv2TaskDataset.__module__,
    LitQAv2TaskDataset.__name__,
)