validate_data.py

#!/usr/bin/env python3
"""Validate the bundled BEND-BCI Space tables and their paper provenance.

The local checks run in the standalone Hugging Face Space.  Passing
``--canonical-root`` additionally compares every manuscript-facing summary
against ``paper/results`` in the main benchmark repository.
"""

from __future__ import annotations

import argparse
import hashlib
import json
from pathlib import Path
from typing import Iterable

import numpy as np
import pandas as pd


DATASETS = {
    "monkey",
    "allen_neuropixels",
    "speech",
    "mc_pacman",
    "ratinabox",
}
CONSISTENCY_DATASETS = DATASETS - {"mc_pacman"}
LATENT_COORDINATE_SPACE = "per_session_whitened_reference_aligned_3d"
FIGURE5_TARGET_SESSION = "sub-C_ses-CO-20150716_behavior+ecephys"

# Coverage is defined in manuscript v7 Supplementary Table 2.
EXPECTED_COVERAGE = {
    "clean_prediction_summary.csv": (115, 112),
    "robustness_summary.csv": (115, 112),
    "scalability_summary.csv": (115, 112),
    "consistency_summary.csv": (54, 46),
    "neuron_shap_summary.csv": (105, 105),
    "trial_shapley_summary.csv": (81, 81),
    "trial_shapley_retrain_summary.csv": (99, 99),
}

REQUIRED_COLUMNS = {
    "clean_prediction_summary.csv": {
        "model", "dataset", "status", "metric", "score", "decoder",
    },
    "robustness_summary.csv": {
        "model", "dataset", "status", "metric", "noise_levels", "scores",
        "raw_auc",
    },
    "scalability_summary.csv": {
        "model", "dataset", "status", "training_time_sec",
        "inference_time_sec", "peak_ram_gb", "peak_vram_gb",
    },
    "consistency_summary.csv": {
        "model", "dataset", "is_active_model", "mean_r2", "n_sessions",
        "sessions", "latent_dim", "scoring_modes", "normalizations",
    },
    "neuron_shap_summary.csv": {
        "model", "dataset", "is_active_model", "auc", "spearman_corr",
        "shap_mean_value", "shap_min_value", "shap_max_value",
        "shap_fraction_positive", "shap_fraction_negative",
    },
    "trial_shapley_summary.csv": {
        "model", "dataset", "is_active_model", "analysis", "perturbation_auc",
        "rotation_angle_deg", "rotation_subspace_dim_spec",
        "trial_selection_mode", "converged", "shapley_mean_value",
        "shapley_min_value", "shapley_max_value",
        "shapley_fraction_positive", "shapley_fraction_negative",
    },
    "trial_shapley_retrain_summary.csv": {
        "analysis", "model", "is_active_model", "condition", "metric", "score",
    },
    "trial_historical_trajectories.csv": {
        "model", "target_session", "trial_index", "trial_id",
        "direction_index", "direction_label", "time_index", "target_x",
        "target_y", "current_only_x", "current_only_y",
        "historical_selected_x", "historical_selected_y", "current_only_r2",
        "historical_selected_r2",
    },
    "latent_samples.csv": {
        "model", "dataset", "session", "session_label", "x", "y", "z",
        "condition", "trial_index", "time_index", "eval_time_index",
        "coordinate_space", "reference_session", "alignment", "landmark_type",
        "n_alignment_landmarks", "is_reference", "session_order",
    },
    "latent_trajectories.csv": {
        "model", "dataset", "session", "session_label", "x", "y", "z",
        "condition", "time_index", "eval_time_index", "n_points",
        "coordinate_space", "reference_session", "alignment", "landmark_type",
        "n_alignment_landmarks", "is_reference", "session_order",
    },
}

UNIQUE_KEYS = {
    "clean_prediction_summary.csv": ["model", "dataset"],
    "robustness_summary.csv": ["model", "dataset"],
    "scalability_summary.csv": ["model", "dataset"],
    "consistency_summary.csv": ["model", "dataset"],
    "neuron_shap_summary.csv": ["model", "dataset"],
    "trial_shapley_summary.csv": ["model", "dataset"],
    "trial_shapley_retrain_summary.csv": ["analysis", "model", "condition"],
}

CANONICAL_NAMES = {
    "clean_prediction_summary.csv": "metrics_summary.csv",
    "robustness_summary.csv": "robustness_summary.csv",
    "scalability_summary.csv": "scalability_summary.csv",
    "consistency_summary.csv": "consistency_summary.csv",
    "neuron_shap_summary.csv": "neuron_shap_summary.csv",
    "trial_shapley_summary.csv": "trial_shapley_summary.csv",
    "trial_shapley_retrain_summary.csv": "trial_shapley_retrain_summary.csv",
}


class ValidationError(RuntimeError):
    """Raised when Space data violates its manuscript-facing contract."""


def _sha256(path: Path) -> str:
    digest = hashlib.sha256()
    with path.open("rb") as handle:
        for chunk in iter(lambda: handle.read(1024 * 1024), b""):
            digest.update(chunk)
    return digest.hexdigest()


def _active_mask(frame: pd.DataFrame) -> pd.Series:
    if "status" in frame.columns:
        return frame["status"].fillna("").eq("present")
    if "is_active_model" in frame.columns:
        return frame["is_active_model"].astype(str).str.lower().eq("true")
    return pd.Series(True, index=frame.index)


def _require(condition: bool, message: str, errors: list[str]) -> None:
    if not condition:
        errors.append(message)


def _same_values(left: pd.DataFrame, right: pd.DataFrame) -> None:
    pd.testing.assert_frame_equal(
        left.reset_index(drop=True),
        right.reset_index(drop=True),
        check_dtype=False,
        check_exact=True,
        check_categorical=False,
    )


def _validate_latent_cell(
    frame: pd.DataFrame,
    *,
    table_label: str,
    model: str,
    dataset: str,
    sessions: list[str],
    landmark_type: str,
    errors: list[str],
) -> None:
    """Validate reference/alignment metadata for one method-dataset cell."""
    cell = frame[
        frame["model"].astype(str).eq(model)
        & frame["dataset"].astype(str).eq(dataset)
    ]
    for session_order, session in enumerate(sessions):
        session_rows = cell[cell["session"].astype(str).eq(session)]
        if session_rows.empty:
            errors.append(f"{table_label}: missing {model}/{dataset}/{session}")
            continue

        expected_reference = "true" if session_order == 0 else "false"
        observed_reference = set(
            session_rows["is_reference"].dropna().astype(str).str.lower()
        )
        _require(
            observed_reference == {expected_reference},
            f"{table_label}: {model}/{dataset}/{session} is_reference "
            f"values {sorted(observed_reference)}",
            errors,
        )
        expected_alignment = "identity" if session_order == 0 else "proper_similarity_procrustes"
        observed_alignment = set(session_rows["alignment"].dropna().astype(str))
        _require(
            observed_alignment == {expected_alignment},
            f"{table_label}: {model}/{dataset}/{session} alignment "
            f"values {sorted(observed_alignment)}",
            errors,
        )
        observed_reference_sessions = set(
            session_rows["reference_session"].dropna().astype(str)
        )
        _require(
            observed_reference_sessions == {sessions[0]},
            f"{table_label}: {model}/{dataset}/{session} reference metadata "
            f"{sorted(observed_reference_sessions)}",
            errors,
        )
        observed_landmarks = set(session_rows["landmark_type"].dropna().astype(str))
        _require(
            observed_landmarks == {landmark_type},
            f"{table_label}: {model}/{dataset}/{session} landmarks "
            f"{sorted(observed_landmarks)}",
            errors,
        )
        orders = pd.to_numeric(session_rows["session_order"], errors="coerce")
        _require(
            orders.notna().all()
            and np.isfinite(orders.to_numpy()).all()
            and orders.eq(session_order).all(),
            f"{table_label}: {model}/{dataset}/{session} has invalid session_order",
            errors,
        )
        landmark_counts = pd.to_numeric(
            session_rows["n_alignment_landmarks"], errors="coerce"
        )
        _require(
            landmark_counts.notna().all()
            and np.isfinite(landmark_counts.to_numpy()).all()
            and landmark_counts.ge(3).all(),
            f"{table_label}: {model}/{dataset}/{session} has invalid landmark count",
            errors,
        )


def validate_local(data_dir: Path) -> dict[str, pd.DataFrame]:
    """Validate schemas, coverage, uniqueness, and fixed analysis conventions."""

    frames: dict[str, pd.DataFrame] = {}
    errors: list[str] = []

    for name, columns in REQUIRED_COLUMNS.items():
        path = data_dir / name
        if not path.exists():
            errors.append(f"missing required table: {path}")
            continue
        frame = pd.read_csv(path)
        missing = sorted(columns - set(frame.columns))
        _require(not missing, f"{name}: missing columns {missing}", errors)
        if missing:
            continue
        frames[name] = frame

    manifest_path = data_dir / "release_manifest.json"
    if not manifest_path.exists():
        errors.append(f"missing release manifest: {manifest_path}")
    else:
        try:
            manifest = json.loads(manifest_path.read_text(encoding="utf-8"))
        except (json.JSONDecodeError, OSError) as exc:
            errors.append(f"invalid release manifest: {exc}")
            manifest = {}
        if not isinstance(manifest, dict):
            errors.append("invalid release manifest: top-level value must be an object")
            manifest = {}
        raw_manifest_spaces = manifest.get("latent_coordinate_spaces", [])
        if not isinstance(raw_manifest_spaces, list):
            errors.append("release manifest: latent_coordinate_spaces must be a list")
            raw_manifest_spaces = []
        elif not all(isinstance(value, str) for value in raw_manifest_spaces):
            errors.append("release manifest: coordinate-space values must be strings")
            raw_manifest_spaces = []
        manifest_spaces = set(raw_manifest_spaces)
        _require(
            manifest_spaces == {LATENT_COORDINATE_SPACE},
            f"release manifest: coordinate spaces {sorted(manifest_spaces)}",
            errors,
        )
        manifest_tables = manifest.get("tables", {})
        if not isinstance(manifest_tables, dict):
            errors.append("release manifest: tables must be an object")
            manifest_tables = {}
        for name in REQUIRED_COLUMNS:
            entry = manifest_tables.get(name)
            if not isinstance(entry, dict):
                errors.append(f"release manifest: missing table entry {name}")
                continue
            path = data_dir / name
            if not path.exists():
                continue
            expected_hash = entry.get("sha256")
            actual_hash = _sha256(path)
            _require(
                expected_hash == actual_hash,
                f"release manifest: SHA-256 mismatch for {name}",
                errors,
            )
            if name in frames:
                _require(
                    entry.get("rows") == len(frames[name]),
                    f"release manifest: row-count mismatch for {name}",
                    errors,
                )

    for name, (n_rows, n_active) in EXPECTED_COVERAGE.items():
        if name not in frames:
            continue
        frame = frames[name]
        _require(len(frame) == n_rows, f"{name}: expected {n_rows} rows, found {len(frame)}", errors)
        active = int(_active_mask(frame).sum())
        _require(active == n_active, f"{name}: expected {n_active} available rows, found {active}", errors)

    for name, keys in UNIQUE_KEYS.items():
        if name not in frames or not set(keys).issubset(frames[name].columns):
            continue
        duplicates = frames[name].duplicated(keys, keep=False)
        _require(not duplicates.any(), f"{name}: duplicate keys for {keys}", errors)

    for name in ("clean_prediction_summary.csv", "robustness_summary.csv", "scalability_summary.csv"):
        if name in frames:
            observed = set(frames[name]["dataset"].dropna().astype(str))
            _require(observed == DATASETS, f"{name}: dataset set is {sorted(observed)}", errors)

    if "clean_prediction_summary.csv" in frames:
        prediction = frames["clean_prediction_summary.csv"]
        _require(prediction["model"].nunique() == 23, "prediction: expected 23 methods", errors)
        metrics = set(prediction.loc[_active_mask(prediction), "metric"].dropna())
        _require(metrics == {"accuracy", "r2"}, f"prediction: unexpected metrics {sorted(metrics)}", errors)

    if "consistency_summary.csv" in frames:
        consistency = frames["consistency_summary.csv"]
        active = consistency.loc[_active_mask(consistency)]
        observed = set(active["dataset"].dropna().astype(str))
        _require(observed == CONSISTENCY_DATASETS, f"consistency: dataset set is {sorted(observed)}", errors)
        norms = set(active["normalizations"].dropna().astype(str))
        _require(norms == {"per_session_whitening"}, f"consistency: unexpected normalization {sorted(norms)}", errors)

    if "neuron_shap_summary.csv" in frames:
        feature = frames["neuron_shap_summary.csv"]
        allen = feature[feature["dataset"].eq("allen_neuropixels")]
        _require(not allen.empty and allen["spearman_corr"].notna().all(), "feature attribution: Allen Spearman values missing", errors)
        other = feature[~feature["dataset"].eq("allen_neuropixels")]
        _require(other["auc"].notna().all(), "feature attribution: ROC-AUC values missing", errors)
        _require(feature["shap_min_value"].lt(0).any(), "feature attribution: signed negative values absent", errors)

    if "trial_shapley_summary.csv" in frames:
        trial = frames["trial_shapley_summary.csv"]
        _require(set(trial["analysis"].dropna()) == {"subspace_rotation"}, "trial valuation: noncanonical analysis", errors)
        angles = set(pd.to_numeric(trial["rotation_angle_deg"], errors="coerce").dropna())
        _require(angles == {75.0}, f"trial valuation: rotation angles {sorted(angles)}", errors)
        dims = set(trial["rotation_subspace_dim_spec"].dropna().astype(str))
        _require(dims == {"full"}, f"trial valuation: subspace specs {sorted(dims)}", errors)
        modes = set(trial["trial_selection_mode"].dropna().astype(str))
        _require(modes == {"random"}, f"trial valuation: selection modes {sorted(modes)}", errors)
        _require(trial["perturbation_auc"].notna().all(), "trial valuation: detection AUC missing", errors)
        _require(trial["shapley_min_value"].lt(0).any(), "trial valuation: signed negative values absent", errors)

    if "trial_shapley_retrain_summary.csv" in frames:
        retrain = frames["trial_shapley_retrain_summary.csv"]
        expected = {
            "within_session_cleaning": {"mixed_full", "data_shapley", "oracle"},
            "cross_session_old_trial_selection": {
                "target_only", "all_sessions", "oldonly_dshap_negative_removal",
            },
        }
        observed = {
            analysis: set(group["condition"].dropna().astype(str))
            for analysis, group in retrain.groupby("analysis")
        }
        _require(observed == expected, f"trial retraining: conditions {observed}", errors)

    if "trial_historical_trajectories.csv" in frames:
        historical = frames["trial_historical_trajectories.csv"]
        _require(
            len(historical) == 135 * 35,
            "historical trajectories: expected 135 trials × 35 time bins",
            errors,
        )
        keys = ["trial_index", "time_index"]
        _require(
            not historical.duplicated(keys, keep=False).any(),
            f"historical trajectories: duplicate keys for {keys}",
            errors,
        )
        _require(
            set(historical["model"].dropna().astype(str)) == {"rnn"},
            "historical trajectories: expected the Figure 5e RNN example",
            errors,
        )
        _require(
            set(historical["target_session"].dropna().astype(str))
            == {FIGURE5_TARGET_SESSION},
            "historical trajectories: unexpected target session",
            errors,
        )
        _require(
            historical["trial_index"].nunique() == 135
            and historical["trial_id"].nunique() == 135,
            "historical trajectories: expected 135 held-out trials and trial IDs",
            errors,
        )
        time_counts = historical.groupby("trial_index")["time_index"].nunique()
        _require(
            len(time_counts) == 135 and time_counts.eq(35).all(),
            "historical trajectories: every trial must contain 35 time bins",
            errors,
        )
        direction_indices = pd.to_numeric(
            historical["direction_index"], errors="coerce"
        )
        _require(
            direction_indices.notna().all()
            and set(direction_indices.astype(int)) == set(range(8)),
            "historical trajectories: expected all eight reach directions",
            errors,
        )
        for column in (
            "target_x",
            "target_y",
            "current_only_x",
            "current_only_y",
            "historical_selected_x",
            "historical_selected_y",
            "current_only_r2",
            "historical_selected_r2",
        ):
            values = pd.to_numeric(historical[column], errors="coerce")
            _require(
                values.notna().all() and np.isfinite(values.to_numpy()).all(),
                f"historical trajectories: non-finite {column} values",
                errors,
            )
        _require(
            historical["current_only_r2"].nunique() == 1
            and historical["historical_selected_r2"].nunique() == 1,
            "historical trajectories: expected one R² value per condition",
            errors,
        )

    for name in ("latent_samples.csv", "latent_trajectories.csv"):
        if name not in frames:
            continue
        latent = frames[name]
        observed = set(latent["dataset"].dropna().astype(str))
        _require(observed.issubset(CONSISTENCY_DATASETS), f"{name}: unsupported datasets {sorted(observed - CONSISTENCY_DATASETS)}", errors)
        for column in ("x", "y", "z"):
            values = pd.to_numeric(latent[column], errors="coerce")
            _require(
                values.notna().all() and np.isfinite(values.to_numpy()).all(),
                f"{name}: non-finite {column} values",
                errors,
            )
        for column in (
            "coordinate_space",
            "reference_session",
            "alignment",
            "landmark_type",
            "n_alignment_landmarks",
            "is_reference",
            "session_order",
        ):
            _require(
                latent[column].notna().all(),
                f"{name}: missing {column} values",
                errors,
            )
        spaces = set(latent["coordinate_space"].dropna().astype(str))
        _require(
            spaces == {LATENT_COORDINATE_SPACE},
            f"{name}: coordinate spaces {sorted(spaces)}",
            errors,
        )

    if {
        "consistency_summary.csv", "latent_samples.csv", "latent_trajectories.csv"
    }.issubset(frames):
        consistency = frames["consistency_summary.csv"]
        consistency = consistency.loc[_active_mask(consistency)].copy()
        samples = frames["latent_samples.csv"]
        trajectories = frames["latent_trajectories.csv"]
        expected_sample_sessions: set[tuple[str, str, str]] = set()
        expected_trajectory_sessions: set[tuple[str, str, str]] = set()
        for row in consistency.itertuples(index=False):
            sessions = (
                []
                if pd.isna(row.sessions)
                else [item.strip() for item in str(row.sessions).split(";") if item.strip()]
            )
            if not sessions:
                errors.append(f"consistency: {row.model}/{row.dataset} has no sessions")
                continue
            try:
                expected_n_sessions = int(row.n_sessions)
            except (TypeError, ValueError):
                expected_n_sessions = -1
            _require(
                len(sessions) == expected_n_sessions,
                f"consistency: {row.model}/{row.dataset} lists {len(sessions)} "
                f"sessions but n_sessions={row.n_sessions}",
                errors,
            )
            expected_sample_sessions.update(
                (str(row.model), str(row.dataset), session) for session in sessions
            )
            if str(row.dataset) != "ratinabox":
                expected_trajectory_sessions.update(
                    (str(row.model), str(row.dataset), session) for session in sessions
                )
            _validate_latent_cell(
                samples,
                table_label="latent samples",
                model=str(row.model),
                dataset=str(row.dataset),
                sessions=sessions,
                landmark_type=str(row.scoring_modes),
                errors=errors,
            )
            if str(row.dataset) != "ratinabox":
                _validate_latent_cell(
                    trajectories,
                    table_label="latent trajectories",
                    model=str(row.model),
                    dataset=str(row.dataset),
                    sessions=sessions,
                    landmark_type=str(row.scoring_modes),
                    errors=errors,
                )

        observed_sample_sessions = set(
            samples[["model", "dataset", "session"]].astype(str).itertuples(index=False, name=None)
        )
        observed_trajectory_sessions = set(
            trajectories[["model", "dataset", "session"]].astype(str).itertuples(index=False, name=None)
        )
        _require(
            observed_sample_sessions == expected_sample_sessions,
            "latent samples: active consistency session coverage differs",
            errors,
        )
        _require(
            observed_trajectory_sessions == expected_trajectory_sessions,
            "latent trajectories: applicable consistency session coverage differs",
            errors,
        )
        _require(
            len(observed_sample_sessions) == 173,
            f"latent samples: expected 173 sessions, found {len(observed_sample_sessions)}",
            errors,
        )

    if errors:
        raise ValidationError("\n".join(f"- {item}" for item in errors))
    return frames


def validate_canonical(data_dir: Path, canonical_root: Path) -> None:
    """Require Space summaries to equal the current paper result tables."""

    results_dir = canonical_root / "paper" / "results"
    errors: list[str] = []
    for dashboard_name, paper_name in CANONICAL_NAMES.items():
        dashboard_path = data_dir / dashboard_name
        paper_path = results_dir / paper_name
        if not dashboard_path.exists():
            errors.append(f"missing dashboard table: {dashboard_path}")
            continue
        if not paper_path.exists():
            errors.append(f"missing canonical table: {paper_path}")
            continue
        try:
            _same_values(pd.read_csv(dashboard_path), pd.read_csv(paper_path))
        except AssertionError as exc:
            first_line = str(exc).splitlines()[0] if str(exc) else "values differ"
            errors.append(f"{dashboard_name} != {paper_name}: {first_line}")
    if errors:
        raise ValidationError("\n".join(f"- {item}" for item in errors))


def build_parser() -> argparse.ArgumentParser:
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument("--data-dir", type=Path, default=Path(__file__).resolve().parent / "data")
    parser.add_argument(
        "--canonical-root",
        type=Path,
        help="Main benchmark repository root; enables exact paper/results comparisons.",
    )
    return parser


def main(argv: Iterable[str] | None = None) -> int:
    args = build_parser().parse_args(argv)
    frames = validate_local(args.data_dir)
    if args.canonical_root is not None:
        validate_canonical(args.data_dir, args.canonical_root.resolve())
    print(f"Validated {len(frames)} BEND-BCI Space tables in {args.data_dir}")
    if args.canonical_root is not None:
        print("Canonical paper/results comparison passed")
    return 0


if __name__ == "__main__":
    raise SystemExit(main())