dataforge/engine/repair.py

"""Public repair engine for DataForge backend surfaces.

The engine is the stable boundary shared by CLI, Playground, MCP, and any
OpenEnv adapter that needs repair semantics. It keeps the core invariant in one
place: detect -> propose -> safety -> SMT verification -> journal/snapshot ->
atomic mutation -> byte-identical revert.
"""

from __future__ import annotations

import hashlib
import json
import os
from collections.abc import Callable, Iterator
from contextlib import contextmanager
from datetime import UTC, datetime
from pathlib import Path
from typing import Literal, cast

from pydantic import BaseModel, ConfigDict, Field

from dataforge.calibration import AbstentionPolicy, corrector_default_policy
from dataforge.detectors import run_all_detectors
from dataforge.detectors.base import Issue, Schema
from dataforge.observability import repair_stage_span
from dataforge.repair_contract import CONTRACT_VERSION
from dataforge.repairers import build_repairers
from dataforge.repairers.base import ProposedFix, RepairAttempt, RetryContext
from dataforge.safety import SafetyContext, SafetyFilter, SafetyResult, SafetyVerdict
from dataforge.schema_inference import (
    ConstraintReviewArtifact,
    infer_verification_schema,
    merge_schema_with_reviewed_constraints,
)
from dataforge.table import (
    Table,
    TableLike,
    cell_value,
    column_names,
    copy_table,
    row_count,
    set_cell_value,
    table_to_csv_bytes,
)
from dataforge.table import (
    read_csv as read_table_csv,
)
from dataforge.transactions.files import (
    SourceLockError,
    atomic_write_bytes,
    lock_path_for,
)
from dataforge.transactions.files import (
    source_path_lock as transaction_source_path_lock,
)
from dataforge.transactions.log import (
    append_applied_event,
    append_created_transaction,
    cache_dir_for,
    sha256_bytes,
    sha256_file,
    snapshot_path_for,
)
from dataforge.transactions.txn import CellFix, RepairTransaction, generate_txn_id
from dataforge.verifier import SMTVerifier, VerificationVerdict

RepairMode = Literal["dry_run", "apply"]
EscalationResolver = Callable[
    [ProposedFix, Schema | None, SafetyContext, SafetyFilter, SafetyResult],
    tuple[SafetyContext, SafetyResult],
]


class RepairEngineError(RuntimeError):
    """Base exception for public repair engine failures."""


class TransactionApplyError(RepairEngineError):
    """Raised when an apply transaction cannot be completed safely."""


class CandidateFix(BaseModel):
    """Stable public representation of a proposed cell repair."""

    row: int = Field(ge=0)
    column: str = Field(min_length=1)
    old_value: str
    new_value: str
    detector_id: str = Field(min_length=1)
    operation: Literal["update", "delete_row"] = "update"
    reason: str = Field(min_length=1)
    confidence: float = Field(ge=0.0, le=1.0)
    provenance: str = Field(min_length=1)

    model_config = ConfigDict(strict=True, extra="forbid", frozen=True)

    @classmethod
    def from_proposed(cls, proposed_fix: ProposedFix) -> CandidateFix:
        """Create a public candidate from an internal repair proposal."""
        fix = proposed_fix.fix
        return cls(
            row=fix.row,
            column=fix.column,
            old_value=fix.old_value,
            new_value=fix.new_value,
            detector_id=fix.detector_id,
            operation=fix.operation,
            reason=proposed_fix.reason,
            confidence=proposed_fix.confidence,
            provenance=proposed_fix.provenance,
        )


RootCauseCategory = Literal[
    "data_entry_error",
    "decimal_shift",
    "sentinel_null_encoding",
    "fd_conflict",
    "domain_violation",
    "duplicate_key_violation",
    "referential_break",
    "unknown",
]


class RootCause(BaseModel):
    """Public diagnosis attached to an issue before repair is applied."""

    row: int = Field(ge=0)
    column: str = Field(min_length=1)
    issue_type: str = Field(min_length=1)
    category: RootCauseCategory
    confidence: float = Field(ge=0.0, le=1.0)
    reason: str = Field(min_length=1)

    model_config = ConfigDict(strict=True, extra="forbid", frozen=True)


class CandidateRepair(CandidateFix):
    """Public repair candidate with verifier context."""

    verifier_reason: str = Field(min_length=1)


class VerifiedFix(CandidateRepair):
    """A candidate that passed safety and SMT verification."""


ProofStatus = Literal[
    "accepted",
    "rejected",
    "unknown",
    "denied",
    "escalated",
    "attempted_not_fixed",
    "not_run",
]


class ProofObligation(BaseModel):
    """Verifier/safety obligation emitted for a repair attempt."""

    obligation_id: str = Field(min_length=1)
    verifier: Literal["smt", "sql", "safety", "repairer"]
    status: ProofStatus
    reason: str = Field(min_length=1)
    unsat_core: tuple[str, ...] = Field(default_factory=tuple)

    model_config = ConfigDict(strict=True, extra="forbid", frozen=True)


class RepairFailure(BaseModel):
    """Machine-readable account of an issue that could not be repaired."""

    row: int = Field(ge=0)
    column: str = Field(min_length=1)
    issue_type: str = Field(min_length=1)
    status: str = Field(min_length=1)
    reason: str = Field(min_length=1)
    attempt_count: int = Field(ge=1)
    unsat_core: tuple[str, ...] = Field(default_factory=tuple)

    model_config = ConfigDict(strict=True, extra="forbid", frozen=True)

    @classmethod
    def from_attempts(cls, attempts: list[RepairAttempt]) -> RepairFailure:
        """Build a public failure record from one issue's attempt trace."""
        final = attempts[-1]
        issue = final.issue
        return cls(
            row=issue.row,
            column=issue.column,
            issue_type=issue.issue_type,
            status=final.status,
            reason=final.reason,
            attempt_count=len(attempts),
            unsat_core=tuple(final.unsat_core),
        )


class RepairReceipt(BaseModel):
    """Stable receipt for a dry-run or applied repair pipeline run."""

    schema_version: Literal["repair_receipt_v1"] = "repair_receipt_v1"
    receipt_version: Literal["repair_receipt_v1"] = "repair_receipt_v1"
    contract_version: str = CONTRACT_VERSION
    mode: RepairMode
    applied: bool
    reversible: bool
    source_path: str
    source_sha256: str = Field(pattern=r"^[0-9a-f]{64}$")
    post_sha256: str | None = Field(default=None, pattern=r"^[0-9a-f]{64}$")
    txn_id: str | None = None
    allowed_columns: list[str] = Field(default_factory=list)
    valid_rows: list[int] = Field(default_factory=list)
    safety_verdict: str = Field(default="allow", min_length=1)
    verifier_verdict: str = Field(default="not_run", min_length=1)
    candidate_provenance: list[str] = Field(default_factory=list)
    root_causes: list[RootCause] = Field(default_factory=list)
    candidate_repairs: list[CandidateRepair] = Field(default_factory=list)
    suggested_fixes: list[CandidateRepair] = Field(default_factory=list)
    proof_obligations: list[ProofObligation] = Field(default_factory=list)
    accepted_constraint_ids: list[str] = Field(default_factory=list)
    constraints_artifact_sha256: str | None = Field(default=None, pattern=r"^[0-9a-f]{64}$")
    patch_plan_sha256: str | None = Field(default=None, pattern=r"^[0-9a-f]{64}$")
    revert_command: str | None = None
    limitations: list[str] = Field(default_factory=list)
    abstentions: list[str] = Field(default_factory=list)
    failure_reasons: list[str] = Field(default_factory=list)
    issues_count: int = Field(ge=0)
    fixes_count: int = Field(ge=0)
    reason: str = Field(min_length=1)

    model_config = ConfigDict(strict=True, extra="forbid", frozen=True)


class RepairPipelineRequest(BaseModel):
    """Input contract for running the public repair pipeline."""

    source_path: Path
    mode: RepairMode = "dry_run"
    repair_schema: Schema | None = Field(default=None, alias="schema")
    allow_llm: bool = False
    model: str | None = None
    allow_pii: bool = False
    confirm_pii: bool = False
    confirm_escalations: bool = False
    interactive: bool = False
    create_dry_run_transaction: bool = False
    constraints: ConstraintReviewArtifact | None = None
    constraints_artifact_sha256: str | None = Field(default=None, pattern=r"^[0-9a-f]{64}$")
    corrector_policy: AbstentionPolicy | None = None

    model_config = ConfigDict(
        strict=True,
        arbitrary_types_allowed=True,
        extra="forbid",
        frozen=True,
        populate_by_name=True,
    )


class RepairPipelineResult(BaseModel):
    """Output contract for a public repair pipeline run."""

    receipt: RepairReceipt
    issues: list[Issue]
    fixes: list[VerifiedFix]
    failures: list[RepairFailure] = Field(default_factory=list)
    transaction: RepairTransaction | None = None

    model_config = ConfigDict(
        strict=True, arbitrary_types_allowed=True, extra="forbid", frozen=True
    )


def _atomic_write_bytes(path: Path, payload: bytes) -> None:
    """Write bytes to ``path`` through an atomic same-directory replacement."""
    atomic_write_bytes(path, payload)


def read_csv(path: Path) -> Table:
    """Read a CSV using conservative string-preserving defaults."""
    return read_table_csv(path)


def _csv_bytes_after_fixes(path: Path, fixes: list[CellFix]) -> bytes:
    """Validate fixes against a CSV and return the mutated CSV bytes."""
    df = read_csv(path)
    for fix in fixes:
        if fix.operation != "update":
            raise ValueError(f"Unsupported repair operation '{fix.operation}' for row {fix.row}.")
        if fix.column not in column_names(df):
            raise ValueError(f"Column '{fix.column}' not found in '{path}'.")
        if fix.row < 0 or fix.row >= row_count(df):
            raise ValueError(f"Row {fix.row} is out of bounds for '{path}'.")

        current_value = cell_value(df, fix.row, fix.column)
        if current_value != fix.old_value:
            raise ValueError(
                f"Refusing to apply stale fix for row {fix.row}, column '{fix.column}': "
                f"expected '{fix.old_value}', found '{current_value}'."
            )
        set_cell_value(df, fix.row, fix.column, fix.new_value)

    return table_to_csv_bytes(df)


def apply_fixes_to_csv(path: Path, fixes: list[CellFix]) -> str:
    """Atomically apply ordered cell fixes to a CSV and return post-state SHA-256."""
    payload = _csv_bytes_after_fixes(path, fixes)
    _atomic_write_bytes(path, payload)
    return hashlib.sha256(payload).hexdigest()


def _lock_path_for(source_path: Path) -> Path:
    """Return the filesystem lock path for a source file."""
    return lock_path_for(source_path)


@contextmanager
def source_path_lock(
    source_path: Path,
    *,
    timeout_seconds: float = 5.0,
    stale_after_seconds: float = 300.0,
) -> Iterator[None]:
    """Acquire an exclusive lock for a source path using an atomic lock file."""
    try:
        with transaction_source_path_lock(
            source_path,
            timeout_seconds=timeout_seconds,
            stale_after_seconds=stale_after_seconds,
        ):
            yield
    except SourceLockError as exc:
        raise TransactionApplyError(str(exc)) from exc


def _write_snapshot_once(snapshot_path: Path, source_bytes: bytes) -> None:
    """Write an immutable snapshot and fail if the transaction id already exists."""
    snapshot_path.parent.mkdir(parents=True, exist_ok=True)
    try:
        with snapshot_path.open("xb") as handle:
            handle.write(source_bytes)
            handle.flush()
            os.fsync(handle.fileno())
    except FileExistsError as exc:
        raise TransactionApplyError(
            f"Transaction snapshot already exists: {snapshot_path}"
        ) from exc


def create_repair_transaction(
    path: Path,
    fixes: list[ProposedFix],
    source_bytes: bytes,
    *,
    txn_id: str | None = None,
) -> tuple[RepairTransaction, Path]:
    """Create an unapplied transaction journal and immutable source snapshot."""
    resolved_path = path.resolve()
    transaction_id = txn_id or generate_txn_id()
    snapshot_path = snapshot_path_for(resolved_path, transaction_id)
    _write_snapshot_once(snapshot_path, source_bytes)

    transaction = RepairTransaction(
        txn_id=transaction_id,
        created_at=datetime.now(UTC),
        source_path=str(resolved_path),
        source_sha256=sha256_bytes(source_bytes),
        source_snapshot_path=str(snapshot_path.resolve()),
        fixes=[proposal.fix for proposal in fixes],
        applied=False,
    )
    try:
        log_path = append_created_transaction(transaction)
    except Exception:
        snapshot_path.unlink(missing_ok=True)
        raise
    return transaction, log_path


def apply_transaction(
    path: Path,
    fixes: list[ProposedFix],
    source_bytes: bytes,
    *,
    txn_id: str | None = None,
) -> str:
    """Journal, snapshot, atomically apply fixes, and restore bytes on failure."""
    resolved_path = path.resolve()
    with source_path_lock(resolved_path):
        current_bytes = resolved_path.read_bytes()
        if current_bytes != source_bytes:
            raise TransactionApplyError(
                "Refusing to apply repairs because the source file changed after detection."
            )

        with repair_stage_span("transaction_create", fixes_count=len(fixes)):
            transaction, log_path = create_repair_transaction(
                resolved_path,
                fixes,
                source_bytes,
                txn_id=txn_id,
            )
        try:
            with repair_stage_span("transaction_apply", fixes_count=len(fixes)):
                post_sha256 = apply_fixes_to_csv(
                    resolved_path,
                    [proposal.fix for proposal in fixes],
                )
                append_applied_event(log_path, transaction.txn_id, post_sha256=post_sha256)
        except Exception as exc:
            _atomic_write_bytes(resolved_path, source_bytes)
            if sha256_file(resolved_path) != transaction.source_sha256:
                raise TransactionApplyError(
                    "Apply failed and the source file could not be restored to original bytes."
                ) from exc
            raise

    return transaction.txn_id


def _build_retry_context(issue: Issue, attempts: list[RepairAttempt]) -> RetryContext:
    """Build retry hints from previous failed attempts."""
    rejected_values = frozenset(
        attempt.fix.fix.new_value
        for attempt in attempts
        if attempt.fix is not None and attempt.status in {"denied", "rejected", "unknown"}
    )
    hints: list[str] = []
    for attempt in attempts:
        hints.append(attempt.reason)
        hints.extend(attempt.unsat_core)
    return RetryContext(
        issue=issue,
        previous_attempts=tuple(attempts),
        rejected_values=rejected_values,
        hints=tuple(hints),
    )


def propose_repairs(
    issues: list[Issue],
    path: Path,
    working_df: TableLike,
    schema: Schema | None,
    *,
    allow_llm: bool,
    model: str | None,
    allow_pii: bool,
    confirm_pii: bool,
    confirm_escalations: bool,
    interactive: bool,
    escalation_resolver: EscalationResolver | None = None,
    verification_schema: Schema | None = None,
) -> tuple[list[ProposedFix], list[list[RepairAttempt]]]:
    """Run repairers and gates issue-by-issue against a working dataframe.

    ``verification_schema`` is the inferred, advisory safety net used only when
    no authoritative ``schema`` is present. It gates *untrusted* (LLM-originated)
    corrections so they are checked against inferred type/domain/regex/FD rather
    than structurally auto-accepted. Deterministic fixes are correct by
    construction and are never second-guessed by it, which keeps schema-less
    deterministic runs byte-identical.
    """
    with repair_stage_span("propose", step="repairers_build", allow_llm=allow_llm):
        repairers = build_repairers(
            cache_dir=cache_dir_for(path),
            allow_llm=allow_llm,
            model=model,
        )
    safety_filter = SafetyFilter()
    verifier = SMTVerifier()
    safety_context = SafetyContext(
        allow_pii=allow_pii,
        confirm_pii=confirm_pii,
        confirm_escalations=confirm_escalations,
    )

    accepted_fixes: list[ProposedFix] = []
    attempt_groups: list[list[RepairAttempt]] = []

    for issue in issues:
        attempts: list[RepairAttempt] = []
        repairer = repairers.get(issue.issue_type)
        if repairer is None:
            attempts.append(
                RepairAttempt(
                    issue=issue,
                    attempt_number=1,
                    status="attempted_not_fixed",
                    reason="No repairer is registered for this issue type.",
                )
            )
            attempt_groups.append(attempts)
            continue

        accepted = False
        retry_context = RetryContext(issue=issue)
        for attempt_number in range(1, 4):
            candidate = repairer.propose(issue, working_df, schema, retry_context=retry_context)
            if candidate is None:
                attempts.append(
                    RepairAttempt(
                        issue=issue,
                        attempt_number=attempt_number,
                        status="attempted_not_fixed",
                        reason="No repair proposal was available for this issue.",
                    )
                )
                break

            preferred = safety_filter.choose_preferred([candidate], schema, safety_context)
            safety_result = safety_filter.evaluate(preferred, schema, safety_context)
            if (
                safety_result.verdict == SafetyVerdict.ESCALATE
                and interactive
                and escalation_resolver is not None
            ):
                safety_context, safety_result = escalation_resolver(
                    preferred,
                    schema,
                    safety_context,
                    safety_filter,
                    safety_result,
                )

            if safety_result.verdict == SafetyVerdict.DENY:
                attempts.append(
                    RepairAttempt(
                        issue=issue,
                        attempt_number=attempt_number,
                        fix=preferred,
                        status="denied",
                        reason=safety_result.reason,
                    )
                )
                retry_context = _build_retry_context(issue, attempts)
                continue

            if safety_result.verdict == SafetyVerdict.ESCALATE:
                attempts.append(
                    RepairAttempt(
                        issue=issue,
                        attempt_number=attempt_number,
                        fix=preferred,
                        status="escalated",
                        reason=safety_result.reason,
                    )
                )
                break

            with repair_stage_span(
                "smt_verify",
                issue_type=issue.issue_type,
                row=issue.row,
            ):
                guard_schema = (
                    verification_schema
                    if (schema is None and preferred.provenance != "deterministic")
                    else None
                )
                verifier_result = verifier.verify(
                    working_df,
                    [preferred],
                    schema,
                    verification_schema=guard_schema,
                )
            if verifier_result.verdict == VerificationVerdict.ACCEPT:
                accepted_fixes.append(preferred)
                set_cell_value(
                    working_df,
                    preferred.fix.row,
                    preferred.fix.column,
                    preferred.fix.new_value,
                )
                attempts.append(
                    RepairAttempt(
                        issue=issue,
                        attempt_number=attempt_number,
                        fix=preferred,
                        status="accepted",
                        reason=verifier_result.reason,
                    )
                )
                accepted = True
                break

            attempts.append(
                RepairAttempt(
                    issue=issue,
                    attempt_number=attempt_number,
                    fix=preferred,
                    status=(
                        "rejected"
                        if verifier_result.verdict == VerificationVerdict.REJECT
                        else "unknown"
                    ),
                    reason=verifier_result.reason,
                    unsat_core=verifier_result.unsat_core,
                )
            )
            retry_context = _build_retry_context(issue, attempts)

        if (
            not accepted
            and attempts
            and attempts[-1].status not in {"attempted_not_fixed", "escalated"}
        ):
            last_reason = attempts[-1].reason
            attempts[-1] = attempts[-1].model_copy(
                update={
                    "status": "attempted_not_fixed",
                    "reason": (
                        f"Issue was attempted but not fixed after {len(attempts)} attempt(s). "
                        f"Last failure: {last_reason}"
                    ),
                }
            )
        attempt_groups.append(attempts)

    return accepted_fixes, attempt_groups


_LLM_PROVENANCE = frozenset({"llm_live", "llm_cache"})


def _partition_auto_apply(
    fixes: list[ProposedFix],
    policy: AbstentionPolicy,
) -> tuple[list[ProposedFix], list[ProposedFix]]:
    """Split verified fixes into auto-apply vs review (suggestion) by policy.

    Deterministic fixes are correct by construction and always auto-apply.
    LLM-origin fixes auto-apply only when their calibrated confidence clears the
    per-class threshold; otherwise they are held as reviewable suggestions. With
    the default propose-not-apply policy, every LLM fix becomes a suggestion.
    """
    auto: list[ProposedFix] = []
    suggested: list[ProposedFix] = []
    for fix in fixes:
        deterministic = fix.provenance not in _LLM_PROVENANCE
        if deterministic or policy.action_for(fix.fix.detector_id, fix.confidence) == "auto_apply":
            auto.append(fix)
        else:
            suggested.append(fix)
    return auto, suggested


def _escalated_llm_suggestions(
    attempt_groups: list[list[RepairAttempt]],
) -> list[ProposedFix]:
    """Collect LLM proposals blocked by the unconfirmed-LLM-write escalation.

    These passed the repairer but were not auto-applied because the safety
    constitution requires explicit confirmation for LLM writes. They are surfaced
    as suggestions so the value is visible without being silently applied.
    """
    suggestions: list[ProposedFix] = []
    for attempts in attempt_groups:
        for attempt in attempts:
            if (
                attempt.fix is not None
                and attempt.fix.provenance in _LLM_PROVENANCE
                and attempt.status == "escalated"
            ):
                suggestions.append(attempt.fix)
    return suggestions


def _suggestion_candidates(fixes: list[ProposedFix]) -> list[CandidateRepair]:
    """Build public suggestion payloads for corrector fixes held for review."""
    return [
        CandidateRepair(
            **CandidateFix.from_proposed(fix).model_dump(),
            verifier_reason=(
                "Held for human review: LLM-origin correction not auto-applied by "
                "default (calibrated abstention / unconfirmed LLM write)."
            ),
        )
        for fix in fixes
    ]


def _verified_fixes(
    fixes: list[ProposedFix],
    attempt_groups: list[list[RepairAttempt]],
) -> list[VerifiedFix]:
    """Build public verified fix payloads using accepted attempt reasons."""
    accepted_reasons: dict[tuple[int, str, str], str] = {}
    for attempts in attempt_groups:
        for attempt in attempts:
            if attempt.status == "accepted" and attempt.fix is not None:
                fix = attempt.fix.fix
                accepted_reasons[(fix.row, fix.column, fix.new_value)] = attempt.reason

    return [
        VerifiedFix(
            **CandidateFix.from_proposed(fix).model_dump(),
            verifier_reason=accepted_reasons.get(
                (fix.fix.row, fix.fix.column, fix.fix.new_value),
                "Accepted by verifier.",
            ),
        )
        for fix in fixes
    ]


def _candidate_repairs(attempt_groups: list[list[RepairAttempt]]) -> list[CandidateRepair]:
    """Build public candidate payloads for every emitted repair proposal."""
    candidates: list[CandidateRepair] = []
    for attempts in attempt_groups:
        for attempt in attempts:
            if attempt.fix is None:
                continue
            candidates.append(
                CandidateRepair(
                    **CandidateFix.from_proposed(attempt.fix).model_dump(),
                    verifier_reason=attempt.reason,
                )
            )
    return candidates


def _failed_attempts(attempt_groups: list[list[RepairAttempt]]) -> list[RepairFailure]:
    """Return failures for issue groups whose final status was not accepted."""
    return [
        RepairFailure.from_attempts(attempts)
        for attempts in attempt_groups
        if attempts and attempts[-1].status != "accepted"
    ]


def _root_cause_category(issue: Issue, attempts: list[RepairAttempt]) -> RootCauseCategory:
    """Classify the likely repair cause from deterministic issue evidence."""
    del attempts
    issue_type = issue.issue_type.lower()
    actual = str(issue.actual or "").strip().lower()
    expected = str(issue.expected or "").strip().lower()
    sentinel_values = {"", "na", "n/a", "null", "none", "nan", "nil", "-", "unknown"}

    if issue_type == "decimal_shift":
        return "decimal_shift"
    if issue_type in {"fd_violation", "functional_dependency"} or "fd" in issue_type:
        return "fd_conflict"
    if "domain" in issue_type or "accepted" in issue_type or "regex" in issue_type:
        return "domain_violation"
    if "duplicate" in issue_type or "unique" in issue_type or "key" in issue_type:
        return "duplicate_key_violation"
    if "relationship" in issue_type or "referential" in issue_type:
        return "referential_break"
    if actual in sentinel_values or expected in sentinel_values:
        return "sentinel_null_encoding"
    if issue_type in {"type_mismatch", "outlier"}:
        return "data_entry_error"
    return "unknown"


def _root_causes(
    issues: list[Issue],
    attempt_groups: list[list[RepairAttempt]],
) -> list[RootCause]:
    """Create one public root-cause diagnosis per detected issue."""
    diagnoses: list[RootCause] = []
    for issue, attempts in zip(issues, attempt_groups, strict=False):
        category = _root_cause_category(issue, attempts)
        final_reason = attempts[-1].reason if attempts else issue.reason
        diagnoses.append(
            RootCause(
                row=issue.row,
                column=issue.column,
                issue_type=issue.issue_type,
                category=category,
                confidence=issue.confidence,
                reason=final_reason if category == "unknown" else issue.reason,
            )
        )
    return diagnoses


def _proof_obligations(attempt_groups: list[list[RepairAttempt]]) -> list[ProofObligation]:
    """Expose every safety/verifier obligation evaluated during repair."""
    obligations: list[ProofObligation] = []
    for attempts in attempt_groups:
        for attempt in attempts:
            issue = attempt.issue
            if attempt.status in {"denied", "escalated"}:
                verifier: Literal["smt", "sql", "safety", "repairer"] = "safety"
            elif attempt.status == "attempted_not_fixed" and attempt.fix is None:
                verifier = "repairer"
            else:
                verifier = "smt"
            status: ProofStatus = (
                cast(ProofStatus, attempt.status)
                if attempt.status
                in {
                    "accepted",
                    "rejected",
                    "unknown",
                    "denied",
                    "escalated",
                    "attempted_not_fixed",
                }
                else "not_run"
            )
            obligations.append(
                ProofObligation(
                    obligation_id=(
                        f"{verifier}::{issue.issue_type}::{issue.row}::"
                        f"{issue.column}::attempt::{attempt.attempt_number}"
                    ),
                    verifier=verifier,
                    status=status,
                    reason=attempt.reason,
                    unsat_core=tuple(attempt.unsat_core),
                )
            )
    return obligations


def _receipt_limitations(
    request: RepairPipelineRequest,
    failures: list[RepairFailure],
    batch_safety: SafetyResult,
    txn_id: str | None,
) -> list[str]:
    """Describe honest limits for the exact receipt payload."""
    limitations: list[str] = []
    if request.mode == "dry_run":
        limitations.append("Dry run only; no source data was mutated.")
    if txn_id is None:
        limitations.append("No reversible transaction id exists for this run.")
    if failures:
        limitations.append("Some issues abstained or failed repair; see failure_reasons.")
    if batch_safety.verdict != SafetyVerdict.ALLOW:
        limitations.append(batch_safety.reason)
    if request.allow_llm:
        limitations.append(
            "LLM-originated candidates remain subordinate to safety and verifier gates."
        )
    return limitations


def _patch_plan_sha256(source_sha256: str, fixes: list[ProposedFix]) -> str | None:
    """Return a stable hash for the ordered local patch plan."""
    if not fixes:
        return None
    payload = {
        "source_sha256": source_sha256,
        "fixes": [
            {
                "row": fix.fix.row,
                "column": fix.fix.column,
                "old_value": fix.fix.old_value,
                "new_value": fix.fix.new_value,
                "operation": fix.fix.operation,
                "detector_id": fix.fix.detector_id,
                "provenance": fix.provenance,
            }
            for fix in fixes
        ],
    }
    canonical = json.dumps(payload, sort_keys=True, separators=(",", ":")).encode("utf-8")
    return hashlib.sha256(canonical).hexdigest()


def _receipt_verifier_verdict(
    fixes: list[ProposedFix],
    failures: list[RepairFailure],
) -> str:
    """Summarize verifier outcomes for the public repair receipt."""
    statuses = {failure.status for failure in failures}
    if "unknown" in statuses:
        return "unknown"
    if "rejected" in statuses:
        return "reject"
    if fixes:
        return "accept"
    return "not_run"


def run_repair_pipeline(request: RepairPipelineRequest) -> RepairPipelineResult:
    """Run the public repair pipeline from detection through optional apply."""
    source_path = request.source_path.resolve()
    source_bytes = source_path.read_bytes()
    source_sha256 = sha256_bytes(source_bytes)
    effective_schema, accepted_constraint_ids = merge_schema_with_reviewed_constraints(
        request.repair_schema,
        request.constraints,
        source_sha256=source_sha256,
    )
    df = read_csv(source_path)
    with repair_stage_span("detect", row_count=row_count(df)):
        issues = run_all_detectors(df, effective_schema)
    # Inferred, advisory safety net for untrusted corrections when no
    # authoritative schema exists. Never drives repairs or raises issues; only
    # gates LLM-originated values in propose_repairs.
    verification_schema = infer_verification_schema(df) if effective_schema is None else None
    with repair_stage_span("propose", issue_count=len(issues)):
        accepted_fixes, attempt_groups = propose_repairs(
            issues,
            source_path,
            copy_table(df),
            effective_schema,
            allow_llm=request.allow_llm,
            model=request.model,
            allow_pii=request.allow_pii,
            confirm_pii=request.confirm_pii,
            confirm_escalations=request.confirm_escalations,
            interactive=request.interactive,
            verification_schema=verification_schema,
        )

    # Route LLM-origin corrections: auto-apply only when a calibrated per-class
    # threshold is cleared; otherwise (and by default) hold them as suggestions.
    # Fixes blocked by the unconfirmed-LLM-write escalation also become
    # suggestions. Deterministic fixes are unaffected -> allow_llm=False runs
    # stay byte-identical.
    corrector_policy = request.corrector_policy or corrector_default_policy()
    accepted_fixes, policy_suggestions = _partition_auto_apply(accepted_fixes, corrector_policy)
    suggested_fixes = policy_suggestions + _escalated_llm_suggestions(attempt_groups)

    with repair_stage_span("safety_gate", fixes_count=len(accepted_fixes)):
        batch_safety = SafetyFilter().evaluate_batch(
            accepted_fixes,
            SafetyContext(confirm_escalations=request.confirm_escalations),
        )
    failures = _failed_attempts(attempt_groups)
    transaction: RepairTransaction | None = None
    txn_id: str | None = None
    post_sha256: str | None = None
    applied = False
    reason = "No accepted fixes were produced."

    if batch_safety.verdict != SafetyVerdict.ALLOW:
        accepted_fixes = []
        reason = batch_safety.reason
    elif request.mode == "apply" and accepted_fixes:
        txn_id = apply_transaction(source_path, accepted_fixes, source_bytes)
        post_sha256 = sha256_file(source_path)
        applied = True
        reason = f"Applied {len(accepted_fixes)} fix(es)."
    elif request.create_dry_run_transaction:
        transaction, _log_path = create_repair_transaction(
            source_path, accepted_fixes, source_bytes
        )
        txn_id = transaction.txn_id
        reason = (
            "Dry run completed without mutating the source file."
            if accepted_fixes
            else "No accepted fixes were produced."
        )
    elif accepted_fixes:
        reason = "Dry run completed without mutating the source file."

    if txn_id is not None and transaction is None:
        # Replaying the log is unnecessary for the public contract here; this
        # minimal receipt is intentionally enough for API callers.
        transaction = None

    verified_fixes = _verified_fixes(accepted_fixes, attempt_groups)
    candidate_repairs = _candidate_repairs(attempt_groups)
    suggestion_candidates = _suggestion_candidates(suggested_fixes)
    proof_obligations = _proof_obligations(attempt_groups)
    root_causes = _root_causes(issues, attempt_groups)
    limitations = _receipt_limitations(request, failures, batch_safety, txn_id)
    patch_plan_sha256 = _patch_plan_sha256(source_sha256, accepted_fixes)
    with repair_stage_span(
        "receipt",
        issues_count=len(issues),
        fixes_count=len(accepted_fixes),
        applied=applied,
    ):
        receipt = RepairReceipt(
            mode=request.mode,
            applied=applied,
            reversible=True,
            source_path=str(source_path),
            source_sha256=source_sha256,
            post_sha256=post_sha256,
            txn_id=txn_id,
            allowed_columns=column_names(df),
            valid_rows=list(range(row_count(df))),
            safety_verdict=batch_safety.verdict.value,
            verifier_verdict=_receipt_verifier_verdict(accepted_fixes, failures),
            candidate_provenance=sorted({fix.provenance for fix in accepted_fixes}),
            root_causes=root_causes,
            candidate_repairs=candidate_repairs,
            suggested_fixes=suggestion_candidates,
            proof_obligations=proof_obligations,
            accepted_constraint_ids=accepted_constraint_ids,
            constraints_artifact_sha256=request.constraints_artifact_sha256,
            patch_plan_sha256=patch_plan_sha256,
            revert_command=f"dataforge revert {txn_id}" if txn_id is not None else None,
            limitations=limitations,
            abstentions=[failure.reason for failure in failures],
            failure_reasons=[failure.reason for failure in failures],
            issues_count=len(issues),
            fixes_count=len(accepted_fixes),
            reason=reason,
        )
    return RepairPipelineResult(
        receipt=receipt,
        issues=issues,
        fixes=verified_fixes,
        failures=failures,
        transaction=transaction,
    )