feat(grobid): R-A reference backfill + native arm64 GROBID on Jetson
Enable roadmap R-A (GROBID reference extraction) end-to-end and run it against local Jetson infra instead of a Mac/Rosetta emulation. Backfill: - Add scripts/ra_grobid_backfill.py: references-only, idempotent citation backfill (dry-run default). Deliberately not ingest_paper(source_path=pdf), which re-OCRs and replaces the DQ-3-clean .txt chunks; this touches only the citations table (ON CONFLICT DO NOTHING). 7 tests. - Make extract_references timeout configurable (large theses exceed the 60s default, especially against a slower GROBID). Jetson infra: - Bump grobid/grobid 0.8.2 -> 0.9.0-crf. The -crf tag is the only GROBID variant published as an arm64 multi-arch manifest; every 0.8.x tag and the full deep-learning image are amd64-only, which is why GROBID never ran on the aarch64 Jetson. Enable the 4g memory cap + init/ulimits per GROBID docs. - Add docs/infra/grobid-jetson.md runbook: arm64 image rationale, the two host prerequisites (docker-group membership + the Compose v2 CLI plugin, both missing on the Jetson), service-scoped deploy, and the GET /api/isalive check. Verified live 2026-06-17: native arm64 pull, isalive=true, end-to-end extract_references on lutz-2024-thesis.pdf = 116 refs (101 with DOI/arXiv). docs(audit): mark R-A core done (citing coverage 27/29 -> 29/29; edges 920 -> 1022). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This commit is contained in:
Tarik Moussa
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scripts/__init__.py
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scripts/__init__.py
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"""Operational one-off scripts (importable for tests)."""
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scripts/ra_grobid_backfill.py
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scripts/ra_grobid_backfill.py
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"""R-A — GROBID reference backfill (references-only, idempotent).
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Adds GROBID-parsed citations to the live corpus **without** re-chunking the body,
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so the DQ-3-verified-clean ``.txt`` chunks are preserved. Complements the DQ-1
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Semantic-Scholar supplement with references the APIs lack (notably the two
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TU-Berlin ``depositonce`` theses, which neither OpenAlex nor S2 indexes).
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Why references-only instead of ``ingest_paper(source_path=pdf)``
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----------------------------------------------------------------
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The PDF branch of :func:`codex.ingest.ingest_paper` runs Nougat OCR and then
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``DELETE FROM chunks`` + re-INSERT — it would replace the clean ``.txt`` chunks
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(DQ-3) with unmeasured PDF-OCR text and additionally requires the Nougat server.
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This backfill touches only the ``citations`` table (``ON CONFLICT DO NOTHING``),
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so it is safe, idempotent, and needs only a reachable GROBID server.
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Prerequisite
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------------
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A reachable GROBID server. The corpus' ``GROBID_URL`` points at the Jetson
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(``http://192.168.178.103:8070``). GROBID now runs natively on that aarch64 host
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via the multi-arch CRF-only image (``grobid/grobid:0.9.0-crf``) — see
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``docs/infra/grobid-jetson.md`` for the deploy + docker-permission fix and the
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``GET /api/isalive`` check. (The old ``grobid/grobid:0.8.2`` pin was amd64-only,
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which is why GROBID never came up; pass ``--grobid-url`` to override the default.)
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Use the SSH DB tunnel for ``DATABASE_URL`` as documented in
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``docs/audit/DATA-QUALITY-2026-06-15.md``.
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Usage
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-----
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# dry run (no writes) over the two zero-edge theses
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PYTHONPATH=. python scripts/ra_grobid_backfill.py --zero-edge-only
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# write every paper's GROBID-parsed refs to the live DB
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PYTHONPATH=. python scripts/ra_grobid_backfill.py --write
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Default is **dry-run**; pass ``--write`` to mutate the live DB.
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"""
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from __future__ import annotations
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import argparse
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import logging
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from pathlib import Path
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import psycopg
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import psycopg.rows
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from codex.config import get_settings
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from codex.db import get_conn
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from codex.models import Citation
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from codex.parsing.grobid import extract_references
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logger = logging.getLogger(__name__)
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DEFAULT_PDF_DIR = "/Users/tarikmoussa/Desktop/ConformalLabpp/papers"
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def _normalize_cited_id(doi: str = "", arxiv_id: str = "") -> str | None:
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"""Normalize a GROBID-extracted reference id to the corpus' canonical form.
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DOIs → bare, lower-cased (strip ``https://doi.org/`` / ``http://`` / ``doi:``),
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matching ``papers.id`` and ``codex.sources.openalex._normalize_doi`` (DQ-5).
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arXiv ids → strip a leading ``arXiv:`` prefix, leaving the bare id
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(``2305.10988``, ``math/0603097``). DOI takes precedence when both exist.
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Kept self-contained rather than reusing ``ingest._norm_cited_id`` because it
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additionally strips the ``arXiv:`` prefix (which GROBID can emit but that
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helper leaves untouched), and to avoid importing a private cross-module name.
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"""
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doi = (doi or "").strip()
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if doi:
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s = doi.lower()
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for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):
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if s.startswith(prefix):
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return s[len(prefix) :]
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return s
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arx = (arxiv_id or "").strip()
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if arx:
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return arx[len("arxiv:") :].strip() if arx.lower().startswith("arxiv:") else arx
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return None
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def build_grobid_citations(
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paper_id: str,
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pdf_path: str | Path,
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grobid_url: str | None = None,
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timeout: float = 60.0,
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) -> list[Citation]:
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"""Extract a paper's references via GROBID and return normalized Citations.
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``citing_id`` is the canonical ``paper_id``; ``cited_id`` is normalized.
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Self-citations and within-paper duplicates are dropped. Refs with neither a
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DOI nor an arXiv id are skipped (they cannot join the graph).
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"""
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refs = extract_references(str(pdf_path), grobid_url=grobid_url, timeout=timeout)
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seen: set[str] = set()
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citations: list[Citation] = []
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for ref in refs:
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cited = _normalize_cited_id(ref.get("doi", ""), ref.get("arxiv_id", ""))
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if not cited or cited == paper_id or cited in seen:
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continue
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seen.add(cited)
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citations.append(Citation(citing_id=paper_id, cited_id=cited))
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return citations
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def _coverage(conn: psycopg.Connection[psycopg.rows.DictRow]) -> tuple[int, int, int]:
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"""Return (n_papers, n_papers_with_out_edges, n_citations) from the live DB."""
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row = conn.execute(
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"""
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SELECT (SELECT count(*) FROM papers) AS papers,
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(SELECT count(DISTINCT citing_id) FROM citations) AS citing,
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(SELECT count(*) FROM citations) AS edges
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"""
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).fetchone()
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assert row is not None
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return int(row["papers"]), int(row["citing"]), int(row["edges"])
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def main(argv: list[str] | None = None) -> int:
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parser = argparse.ArgumentParser(description=__doc__)
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parser.add_argument("--pdf-dir", default=DEFAULT_PDF_DIR, help="directory of source PDFs")
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parser.add_argument("--grobid-url", default=None, help="override Settings().grobid_url")
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parser.add_argument("--only", default=None, help="restrict to a single paper id")
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parser.add_argument(
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"--zero-edge-only",
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action="store_true",
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help="only papers with 0 out-edges (the R-A primary targets)",
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)
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parser.add_argument("--limit", type=int, default=None, help="cap number of papers")
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parser.add_argument(
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"--timeout",
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type=float,
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default=300.0,
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help="GROBID HTTP timeout (s); theses can need >60s, esp. emulated",
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)
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parser.add_argument(
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"--write", action="store_true", help="WRITE to the live DB (default: dry-run)"
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)
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args = parser.parse_args(argv)
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logging.basicConfig(level=logging.INFO, format="%(levelname)s %(message)s")
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grobid_url = args.grobid_url or get_settings().grobid_url
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pdf_dir = Path(args.pdf_dir)
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pdfs = {p.stem: p for p in pdf_dir.glob("*.pdf")}
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with get_conn() as conn:
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rows = conn.execute(
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"""
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SELECT p.id, p.source_path,
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(SELECT count(*) FROM citations ci WHERE ci.citing_id = p.id) AS out_edges
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FROM papers p
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ORDER BY out_edges, p.id
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"""
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).fetchall()
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targets: list[tuple[str, Path]] = []
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for r in rows:
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if args.only and r["id"] != args.only:
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continue
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if args.zero_edge_only and r["out_edges"] != 0:
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continue
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stem = Path(r["source_path"]).stem if r["source_path"] else None
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pdf = pdfs.get(stem) if stem else None
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if pdf is None:
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logger.warning("no PDF for %s (stem=%s) — skipping", r["id"], stem)
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continue
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targets.append((r["id"], pdf))
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if args.limit is not None:
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targets = targets[: args.limit]
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logger.info(
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"GROBID=%s | papers to process=%d | mode=%s",
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grobid_url,
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len(targets),
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"WRITE" if args.write else "DRY-RUN",
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)
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all_citations: list[Citation] = []
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for paper_id, pdf in targets:
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try:
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cits = build_grobid_citations(
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paper_id, pdf, grobid_url=grobid_url, timeout=args.timeout
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)
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except Exception as exc:
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logger.warning("GROBID extraction failed for %s (%s): %s", paper_id, pdf.name, exc)
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continue
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logger.info("%-38s %3d refs (%s)", paper_id, len(cits), pdf.name)
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all_citations.extend(cits)
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logger.info("total candidate citations: %d", len(all_citations))
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if not args.write:
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logger.info("DRY-RUN — no rows written. Re-run with --write to apply.")
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return 0
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before = _coverage(conn)
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with conn.cursor() as cur:
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cur.executemany(
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"""
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INSERT INTO citations (citing_id, cited_id, context)
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VALUES (%s, %s, %s)
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ON CONFLICT (citing_id, cited_id) DO NOTHING
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""",
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[(c.citing_id, c.cited_id, c.context) for c in all_citations],
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)
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conn.commit()
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after = _coverage(conn)
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logger.info(
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"coverage papers=%d citing %d->%d edges %d->%d (+%d)",
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after[0],
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before[1],
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after[1],
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before[2],
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after[2],
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after[2] - before[2],
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)
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return 0
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if __name__ == "__main__":
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raise SystemExit(main())
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