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from __future__ import annotations
# ruff: noqa: E402
import argparse
import csv
import os
import shutil
import sys
import re
from pathlib import Path
try:
from scripts.defextra_markers import (
doi_suffix,
normalize_arxiv,
normalize_doi,
normalize_paper_id,
)
from scripts.defextra_pdf_aliases import candidate_pdf_aliases
except ModuleNotFoundError as exc:
if exc.name != "scripts":
raise
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 (
doi_suffix,
normalize_arxiv,
normalize_doi,
normalize_paper_id,
)
from scripts.defextra_pdf_aliases import candidate_pdf_aliases
def _build_pdf_index(
source_dirs: list[Path],
*,
skip_dir: Path | None = None,
) -> dict[str, Path]:
index: dict[str, Path] = {}
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 source_dir in source_dirs:
if not source_dir.exists():
continue
for suffix in ("*.pdf", "*.PDF"):
for path in source_dir.rglob(suffix):
if skip_dir is not None:
try:
path_abs = path.resolve()
except (OSError, RuntimeError):
path_abs = path.absolute()
if skip_dir == path_abs or skip_dir in path_abs.parents:
continue
stem = path.stem
for key in {stem, stem.lower()}:
index.setdefault(key, path)
if stem.startswith("paper_"):
stripped = stem[len("paper_") :]
if stripped:
index.setdefault(stripped, path)
index.setdefault(stripped.lower(), path)
if stem.endswith("_fixed") or stem.endswith("-fixed"):
base = (
stem[: -len("_fixed")]
if stem.endswith("_fixed")
else stem[: -len("-fixed")]
)
if base:
index[base] = path
index[base.lower()] = path
if base.startswith("paper_"):
stripped_base = base[len("paper_") :]
if stripped_base:
index[stripped_base] = path
index[stripped_base.lower()] = path
match = arxiv_re.match(stem)
if match:
base = match.group("base")
index.setdefault(base, path)
index.setdefault(base.lower(), path)
match = version_re.match(stem)
if match:
base = match.group("base")
index.setdefault(base, path)
index.setdefault(base.lower(), path)
pii_match = pii_re.search(stem)
if pii_match:
pii = pii_match.group(1)
index.setdefault(pii, path)
index.setdefault(pii.lower(), path)
return index
def _candidate_ids(paper_id: str, doi: str, arxiv: str) -> list[str]:
candidates = []
if paper_id:
candidates.append(paper_id)
candidates.append(normalize_paper_id(paper_id))
if doi:
norm_doi = normalize_doi(doi)
candidates.append(norm_doi)
candidates.append(doi_suffix(norm_doi))
if arxiv:
norm_arxiv = normalize_arxiv(arxiv)
candidates.append(norm_arxiv)
ordered: list[str] = []
seen = set()
for item in candidates:
value = (item or "").strip()
if not value:
continue
if value not in seen:
seen.add(value)
ordered.append(value)
for alias in candidate_pdf_aliases(paper_id, doi, arxiv):
value = (alias or "").strip()
if not value:
continue
if value not in seen:
seen.add(value)
ordered.append(value)
return ordered
def _normalize_title(title: str) -> str:
return " ".join(title.lower().split())
def main() -> None:
parser = argparse.ArgumentParser(
description="Build a test-only PDF folder for DefExtra hydration.",
)
parser.add_argument(
"--legal-csv",
type=Path,
default=Path("results/paper_results/defextra_legal.csv"),
help="Legal DefExtra CSV with paper_ids.",
)
parser.add_argument(
"--source-dir",
action="append",
type=Path,
default=[
Path("ManualPDFsGROBID"),
Path("ManualPDFsGROBID/manual_pdfs/manual_pdfs"),
],
help="Source PDF directory (can be repeated).",
)
parser.add_argument(
"--output-dir",
type=Path,
default=Path("ManualPDFsGROBID/test_pdfs"),
help="Output directory for test PDFs.",
)
parser.add_argument(
"--mode",
choices=("symlink", "copy"),
default="symlink",
help="Whether to symlink or copy PDFs into the output dir.",
)
parser.add_argument(
"--report",
type=Path,
default=None,
help="Optional report file listing missing PDFs.",
)
args = parser.parse_args()
if not args.legal_csv.exists():
raise SystemExit(f"Legal CSV not found: {args.legal_csv}")
pdf_index = _build_pdf_index(
args.source_dir,
skip_dir=args.output_dir.resolve(),
)
args.output_dir.mkdir(parents=True, exist_ok=True)
missing: list[str] = []
matched = 0
seen_ids: set[str] = set()
with args.legal_csv.open("r", encoding="utf-8", newline="") as handle:
reader = csv.DictReader(handle)
rows = list(reader)
title_to_candidates: dict[str, list[str]] = {}
for row in rows:
title = _normalize_title(row.get("paper_title") or "")
if not title:
continue
paper_id = (row.get("paper_id") or "").strip()
doi = (row.get("paper_doi") or "").strip()
arxiv = (row.get("paper_arxiv") or "").strip()
candidates = _candidate_ids(paper_id, doi, arxiv)
if candidates:
title_to_candidates.setdefault(title, []).extend(candidates)
for row in rows:
paper_id = (row.get("paper_id") or "").strip()
if not paper_id or paper_id in seen_ids:
continue
seen_ids.add(paper_id)
doi = (row.get("paper_doi") or "").strip()
arxiv = (row.get("paper_arxiv") or "").strip()
title_key = _normalize_title(row.get("paper_title") or "")
path = None
for candidate in _candidate_ids(paper_id, doi, arxiv):
key = candidate.lower()
path = pdf_index.get(key) or pdf_index.get(f"paper_{key}")
if path is not None:
break
if path is None and title_key in title_to_candidates:
for candidate in title_to_candidates[title_key]:
key = candidate.lower()
path = pdf_index.get(key) or pdf_index.get(f"paper_{key}")
if path is not None:
break
if path is None:
missing.append(paper_id)
continue
dest_id = normalize_paper_id(paper_id) or paper_id
dest = args.output_dir / f"{dest_id}.pdf"
if dest.is_symlink():
try:
current = dest.resolve(strict=True)
except (OSError, RuntimeError):
current = None
if current is None or current != path.resolve():
dest.unlink()
else:
matched += 1
continue
elif dest.exists():
matched += 1
continue
if args.mode == "copy":
shutil.copy2(path, dest)
else:
# Relative symlink keeps the test folder portable.
rel = Path(os.path.relpath(path, start=dest.parent))
dest.symlink_to(rel)
matched += 1
print(f"Matched PDFs: {matched}")
print(f"Missing PDFs: {len(missing)}")
if missing:
print("Missing IDs (first 20):", ", ".join(missing[:20]))
if args.report is not None:
args.report.parent.mkdir(parents=True, exist_ok=True)
args.report.write_text("\n".join(missing) + "\n", encoding="utf-8")
print(f"Wrote report to {args.report}")
if __name__ == "__main__":
main()
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