scripts/report_defextra_status.py

from __future__ import annotations

# ruff: noqa: E402

import argparse
import csv
import re
import time
from pathlib import Path
from typing import Dict, Tuple

try:
    from scripts.defextra_markers import normalize_paper_id
except ModuleNotFoundError as exc:
    if exc.name != "scripts":
        raise
    import sys

    PROJECT_ROOT = Path(__file__).resolve().parent.parent
    if str(PROJECT_ROOT) not in sys.path:
        sys.path.insert(0, str(PROJECT_ROOT))
    from scripts.defextra_markers import normalize_paper_id


def _normalize_title(title: str) -> str:
    return " ".join((title or "").lower().split())


def _load_csv(path: Path) -> list[dict]:
    with path.open(encoding="utf-8", newline="") as handle:
        return list(csv.DictReader(handle))


def _parse_missing_report(path: Path) -> Tuple[list[str], list[str]]:
    missing_defs: list[str] = []
    missing_ctxs: list[str] = []
    if not path.exists():
        return missing_defs, missing_ctxs
    section = None
    for line in path.read_text(encoding="utf-8").splitlines():
        line = line.strip()
        if line.startswith("Missing definitions"):
            section = "def"
            continue
        if line.startswith("Missing contexts"):
            section = "ctx"
            continue
        if not line.startswith("-"):
            continue
        item = line[1:].strip()
        if section == "def":
            missing_defs.append(item)
        elif section == "ctx":
            missing_ctxs.append(item)
    return missing_defs, missing_ctxs


def _index_recent_pdfs(
    pdf_dir: Path,
    cutoff_ts: float,
) -> Dict[str, Path]:
    index: Dict[str, Path] = {}
    if not pdf_dir.exists():
        return index
    version_re = re.compile(r"^(?P<base>.+?)(v\d+)$", re.IGNORECASE)
    arxiv_re = re.compile(r"^(?P<base>\d{4}\.\d{4,5})v\d+$", re.IGNORECASE)
    pii_re = re.compile(r"(S\d{8,})", re.IGNORECASE)
    for suffix in ("*.pdf", "*.PDF"):
        for path in pdf_dir.rglob(suffix):
            try:
                if path.stat().st_mtime < cutoff_ts:
                    continue
            except OSError:
                continue
            stem = path.stem
            keys = {stem, stem.lower(), normalize_paper_id(stem)}
            if stem.startswith("paper_"):
                stripped = stem[len("paper_") :]
                keys.update(
                    {stripped, stripped.lower(), normalize_paper_id(stripped)},
                )
            if stem.endswith("_fixed") or stem.endswith("-fixed"):
                base = (
                    stem[: -len("_fixed")]
                    if stem.endswith("_fixed")
                    else stem[: -len("-fixed")]
                )
                if base:
                    keys.update({base, base.lower(), normalize_paper_id(base)})
            match = arxiv_re.match(stem)
            if match:
                base = match.group("base")
                keys.update({base, base.lower(), normalize_paper_id(base)})
            match = version_re.match(stem)
            if match:
                base = match.group("base")
                keys.update({base, base.lower(), normalize_paper_id(base)})
            pii_match = pii_re.search(stem)
            if pii_match:
                pii = pii_match.group(1)
                keys.update({pii, pii.lower(), normalize_paper_id(pii)})
            for key in keys:
                if key:
                    index.setdefault(key, path)
    return index


def main() -> None:
    parser = argparse.ArgumentParser(
        description="Report DefExtra hydration coverage and missing spans.",
    )
    parser.add_argument(
        "--legal-csv",
        type=Path,
        default=Path("results/paper_results/defextra_legal_tablefix.csv"),
        help="Legal CSV used for hydration.",
    )
    parser.add_argument(
        "--legal-report",
        type=Path,
        default=Path(
            "results/paper_results/defextra_legal_tablefix_report.txt",
        ),
        help="Report generated by prepare_defextra_legal.py.",
    )
    parser.add_argument(
        "--hydrated-csv",
        type=Path,
        default=Path(
            "results/paper_results/defextra_hydrated_tablefix_test.csv",
        ),
        help="Hydrated CSV from hydrate_defextra.py.",
    )
    parser.add_argument(
        "--pdf-dir",
        type=Path,
        default=Path("ManualPDFsGROBID/manual_pdfs/manual_pdfs"),
        help="Directory with user PDFs (used to tag recent downloads).",
    )
    parser.add_argument(
        "--recent-days",
        type=int,
        default=7,
        help="How many days count as 'recent' for PDF downloads.",
    )
    parser.add_argument(
        "--output",
        type=Path,
        default=None,
        help="Optional report output path.",
    )
    args = parser.parse_args()

    legal_rows = _load_csv(args.legal_csv)
    hydrated_rows = (
        _load_csv(args.hydrated_csv) if args.hydrated_csv.exists() else []
    )

    ref_ids = {
        row.get("paper_id", "") for row in legal_rows if row.get("paper_id")
    }
    hyd_ids = {
        row.get("paper_id", "") for row in hydrated_rows if row.get("paper_id")
    }
    missing_papers = sorted(ref_ids - hyd_ids)

    missing_defs, missing_ctxs = _parse_missing_report(args.legal_report)

    idx = {
        (row.get("paper_id", ""), row.get("concept", "")): row
        for row in legal_rows
    }

    implicit_defs = []
    implicit_ctxs = []
    for item in missing_defs:
        try:
            pid, concept = [p.strip() for p in item.split("|", 1)]
        except ValueError:
            continue
        row = idx.get((pid, concept))
        if (
            row
            and (row.get("definition_type") or "").strip().lower()
            == "implicit"
        ):
            implicit_defs.append(item)
    for item in missing_ctxs:
        try:
            pid, concept = [p.strip() for p in item.split("|", 1)]
        except ValueError:
            continue
        row = idx.get((pid, concept))
        if (
            row
            and (row.get("definition_type") or "").strip().lower()
            == "implicit"
        ):
            implicit_ctxs.append(item)

    cutoff_ts = time.time() - (args.recent_days * 86400)
    recent_index = _index_recent_pdfs(args.pdf_dir, cutoff_ts)

    recent_missing_defs = []
    recent_missing_ctxs = []
    recent_missing_papers = []

    for pid in missing_papers:
        if pid in recent_index or normalize_paper_id(pid) in recent_index:
            recent_missing_papers.append(pid)

    for item in missing_defs:
        try:
            pid, concept = [p.strip() for p in item.split("|", 1)]
        except ValueError:
            continue
        if pid in recent_index or normalize_paper_id(pid) in recent_index:
            recent_missing_defs.append(item)

    for item in missing_ctxs:
        try:
            pid, concept = [p.strip() for p in item.split("|", 1)]
        except ValueError:
            continue
        if pid in recent_index or normalize_paper_id(pid) in recent_index:
            recent_missing_ctxs.append(item)

    lines = []
    lines.append(f"Missing papers (no hydrated rows): {len(missing_papers)}")
    for pid in missing_papers:
        lines.append(f"- {pid}")
    lines.append("")
    lines.append(
        f"Missing definition spans marked implicit: {len(implicit_defs)}",
    )
    for item in implicit_defs:
        lines.append(f"- {item}")
    lines.append("")
    lines.append(
        f"Missing context spans marked implicit: {len(implicit_ctxs)}",
    )
    for item in implicit_ctxs:
        lines.append(f"- {item}")
    lines.append("")
    lines.append(
        f"Missing papers with recent PDFs (<= {args.recent_days} days): "
        f"{len(recent_missing_papers)}",
    )
    for pid in recent_missing_papers:
        lines.append(f"- {pid}")
    lines.append("")
    lines.append(
        f"Missing definition spans with recent PDFs (<= {args.recent_days} days): "
        f"{len(recent_missing_defs)}",
    )
    for item in recent_missing_defs:
        lines.append(f"- {item}")
    lines.append("")
    lines.append(
        f"Missing context spans with recent PDFs (<= {args.recent_days} days): "
        f"{len(recent_missing_ctxs)}",
    )
    for item in recent_missing_ctxs:
        lines.append(f"- {item}")
    lines.append("")

    output = "\n".join(lines) + "\n"
    if args.output is not None:
        args.output.parent.mkdir(parents=True, exist_ok=True)
        args.output.write_text(output, encoding="utf-8")
        print(f"Wrote report to {args.output}")
    else:
        print(output)


if __name__ == "__main__":
    main()