Consolidates the session's loose ends: Jetson offline (blocker), R-F accent re-clean pending, 5 feature branches unmerged to main (+ merge order), tmux-on-Jetson infra TODO, and documented known limits.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The Mac->Jetson SSH tunnel dropped repeatedly during multi-minute live writes (re-ingest, embed loops, sweeps), aborting them partway. Document the fix: run long ops on the Jetson inside tmux (DB is localhost, no tunnel; survives SSH drops), use autossh for interactive tunnels, and optionally make backfill writes per-item resilient.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Polish _clean_title for R-F: strip accent/escape macros (backslash-quote o to o, backslash-amp), convert tilde ties to spaces, and truncate at a word boundary so stored section titles read cleanly (mobius invariance, colin de verdiere). Tests added; ruff + mypy clean.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Add quality.section_label(title, content): for section-aware .tex ingest, keep the controlled bucket (intro/theorem/proof/abstract/bibliography) when the real \section heading maps to one, else store the cleaned title verbatim (e.g. 'preliminaries', 'rigidity') instead of collapsing to 'body'. Math papers title most sections descriptively, so R-C's vocab-only mapping left ~90% as 'body'; this lifts the section signal toward near-full. .pdf/.txt/run_quality_pass keep content-based classify_section unchanged. Safe because the section column is write-only (no consumer filters on the vocab).
New _clean_title (strip LaTeX/numbering, lower-case, truncate). Tests: section_label bucket/verbatim/fallback paths + _clean_title; .tex ingest stores a descriptive heading as its title. Full suite 377 passed; ruff + mypy clean.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Add graph.citing_coverage() (papers with >=1 out-edge / total) and a graph_min_citing_coverage setting (default 0.8). codex graph report now surfaces 'Citing coverage: N/M papers with out-edges (P%)' in text and JSON, and warns when the share is below threshold -- low citing coverage starves PageRank/coupling even when the paper count looks healthy (the DQ-1 sub-item). Separate from the existing total-count graph_min_corpus_size warning.
Tests: citing_coverage unit tests + CLI tests (line shown, warning fires/suppressed, JSON field). Full suite green; ruff + mypy clean. Live: graph report shows 29/29 (100%), no warning.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
OpenAlex returns arXiv works under the arXiv DOI (10.48550/arXiv.<id>); _normalize_doi (DQ-5) left it as 10.48550/arxiv.<id>, but the corpus keys arXiv papers on the BARE id (2305.10988 / math/0603097). So re-ingesting an arXiv paper by its bare id missed INSERT ... ON CONFLICT (id) and tripped papers_openalex_id_key — the arXiv half of DQ-5, explicitly deferred there and surfaced again driving the R-C .tex re-ingest.
Add _canonical_id() (normalize DOI, then strip the 10.48550/arxiv. prefix) and use it in _map_paper. Regression tests (modern + legacy arXiv DOI, regular DOI unchanged, fetch_paper bare id). Confirmed live: re-ingesting 2305.10988 now UPDATEs in place. Full suite 370 passed; ruff + mypy clean.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Old arXiv submissions (e.g. legacy math/* papers) are served as a bare gzipped .tex rather than a .tar.gz, which tarfile.open rejected with 'invalid header'. Fall back to gunzipping the body directly when the tar parse fails, so R-C covers those papers too (recovers math/0001176 + math/0306167). Adds a regression test.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Flatten multi-file arXiv LaTeX (\input/\include) in arxiv.fetch_source so the full body is assembled rather than just the primary file's include skeleton, and add section-aware chunking (tex.chunk_sections) so .tex chunks never span a \section boundary and are labelled by their real heading. The ingest .tex path now produces (section, chunk) pairs, quality-gated together so labels stay aligned; the stored 'section' column gains genuine signal instead of mostly 'body' (serves DQ-3 fidelity + audit R-12).
Adds scripts/rc_tex_reingest.py to re-ingest arXiv papers from .tex (dry-run by default; replaces chunks). Tests: flatten_inputs, chunk_sections, multi-file fetch_source, section-label ingest, is_arxiv_id. Full suite 365 passed; ruff + mypy clean.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
GROBID is only needed during reference extraction (ra_grobid_backfill.py),
not for normal corpus operations (search, embeddings, wiki). Idle it still
holds ~3.5GB on the 8GB Jetson, so keep it stopped by default.
- infra/docker-compose.yml: grobid restart unless-stopped -> "no" (no auto-start
on boot; db keeps unless-stopped). Start/stop papers-grobid around an R-A run.
- docs/infra/grobid-jetson.md: add "Run on-demand" section with the start/stop
workflow, and record the refextract head-to-head evaluation on the Jetson that
led to keeping GROBID: far worse DOI recall on this math corpus (lutz thesis
101 usable IDs vs refextract 2) and slower per PDF despite a smaller footprint.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Add crossref.fetch_references(doi), which parses message.reference[].DOI into Citations (DOI-less book/unstructured refs are skipped — they cannot join the graph). Wire it as the third leg of the ingest citation fallback chain: OpenAlex-empty -> S2 -> Crossref, for DOI papers only (Crossref's works endpoint is DOI-keyed). Cited DOIs are normalized to the canonical bare lower-case form via _norm_cited_id.
As a fallback it fires only when OpenAlex and S2 both return no references, so it adds a forward-looking third source without changing the already-covered corpus.
Tests: fetch_references unit tests (DOI edges / unstructured skipped / no refs / 404) and ingest tests for both fallback directions. Full suite 361 passed; ruff + mypy clean. Live-validated: 33/40/24 refs for Springer/ACM/Wiley DOIs.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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>
wiki/index.md is regenerated by `codex wiki compile` from wiki/concepts.yaml
(the tracked source), so the generated index should not be version-controlled.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
GROBID extracts a cited DOI verbatim from PDF reference text, so it can be mixed-case, a https://doi.org/ URL, or doi:-prefixed. The PDF citation branch inserted it unchanged, while every other path (S2 supplement, OpenAlex, papers.id itself) uses the bare lower-cased DOI. Once R-A runs GROBID reference extraction over arXiv PDFs, those un-normalized cited-ids would never equal a bare-lowercase papers.id/cited_id — dangling the cross-citations and splitting one reference into case-/URL-variant graph nodes.
Extend _norm_cited_id to strip https://doi.org//http://doi.org//doi: prefixes and lower-case (mirroring openalex._normalize_doi), making it the single canonical cited-id normalizer, and route the GROBID branch through it. arXiv ids and S2 paperIds still pass through untouched.
Add test_ingest_pdf_grobid_citations_normalize_doi covering mixed-case, URL-form, and doi:-prefixed DOIs plus an arXiv-only ref.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Clarify that DQ-3's 'VERIFIED CLEAN' covers the ingest pipeline (txt -> chunks)
only — it treats the .txt as ground truth. The upstream PDF/source -> .txt
extraction (done outside codex-py) is unmeasured and shown to be lossy (DQ-3's
dropped chunks were garbled OCR tables already present in the .txt). Add DQ-6 to
measure that layer; 36 source PDFs are available. Note R-A/R-C (re-ingest from
PDF/.tex) would largely sidestep it.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
openalex._map_paper set Paper.id from the raw `doi` field, which OpenAlex
returns as a full URL (https://doi.org/10.x). The canonical papers.id (M-1
migration) is the bare, lower-cased DOI, so re-ingesting a DOI paper missed
ON CONFLICT (id) and tripped the separate papers_openalex_id_key constraint
(UniqueViolation).
Fix: _normalize_doi() strips https://doi.org//http://doi.org//doi: and
lower-cases; applied in the DOI branch of _map_paper only (W-id fallback
untouched). Also un-breaks _s2_id_for/Crossref recovery, which the URL form
silently defeated. Corrected the _SAMPLE_WORK fixture to the URL form (the bare
fixture hid the bug) + added _normalize_doi and re-ingest idempotency regression
tests.
Live verification: re-ingest of 10.1007/s00454-019-00132-8 (previously crashed)
now UPDATEs in place — single row, added_at unchanged, no stray row, citations
45->45. Unblocks roadmap R-A/R-C. Full suite 348 green.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Re-ran chunk_text + is_quality_chunk on all 29 source .txt files vs stored
chunks. Coverage 109-114% everywhere (the >100% is the 64/512-word overlap, i.e.
full retention); stored==kept for every paper. Only 18 chunks dropped corpus-wide,
all low_alpha = garbled OCR tables in 2 scanned-book sources (0-387-29555-0_13,
depositonce-5415) — no real math content lost. Head/tail aligned (no truncation).
Closes the data-quality assessment axis: DQ-1 (citations), DQ-2 (metadata),
DQ-3 (fidelity), DQ-4 (retrieval) all resolved. DQ-5 (re-ingest idempotency)
remains, tracked separately.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Three papers lacked abstracts and 1911.00966 was fully degraded (OpenAlex 404
-> empty `Paper(id, title="")` stub). Recovery sources verified, then wired in:
- arxiv.fetch_metadata: resolve an arXiv id to a Paper via the Atom export API
(authoritative for preprints). Used as an ingest fallback on OpenAlex 404,
replacing the empty stub.
- crossref.py (new): fetch_abstract(doi), JATS-stripped, Crossref Polite Pool.
- semanticscholar.fetch_abstract: fetch just the abstract field.
- ingest.py: _recover_abstract() supplements an empty abstract from S2 then
Crossref *before* embedding, so the paper gets a real (non-zero) vector.
Live DB backfill: 1911.00966 fully recovered from arXiv (bibkey
PinkallSpringborn2019, 384-char abstract, its 10 chunks now visible to chunk
search); 10.1007/s00454-019-00132-8 abstract from S2 (1186 chars). Book chapter
10.1007/978-3-642-17413-1_7 has no abstract in OpenAlex/S2/Crossref -> documented
limit. Corpus now has 1 paper without an abstract.
Also documented DQ-5 (not fixed): ingest_paper is not idempotent for DOI papers
(openalex returns full-URL id vs the bare canonical id) -> re-ingest trips
papers_openalex_id_key. Blocks roadmap R-A/R-C; needs a careful _map_paper fix.
Tests: arxiv/crossref/s2 fetchers + ingest recovery paths (342 passing).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
12/29 papers had zero citations: OpenAlex indexes arXiv preprints and theses
without a parsed reference list (verified referenced_works_count=0 server-side
for all 11 with an openalex_id). Not an ingest bug — a source-coverage limit.
- ingest.py: when OpenAlex returns no references, fall back to a Semantic
Scholar reference supplement (_s2_reference_supplement); citing_id rewritten
to canonical papers.id, DOI cited-ids lowercased. Removed a now-redundant
discarded S2 probe in the OpenAlex-404 arXiv branch.
- semanticscholar.py: fix TypeError on S2's HTTP-200 {"data": null} no-refs
responses (.get("data", []) returns None when the key is present-but-null).
- tests: regression test for the OpenAlex-empty -> S2 path.
- Live DB backfilled idempotently: +330 citations (590->920), zero-out-edge
papers 12->2, citing coverage 17->27/29. Only the 2 TU-Berlin depositonce
theses remain (no references in any source).
- docs: DATA-QUALITY-2026-06-15.md — DQ-1 resolution, DQ-4 result, and a
free-source acquisition roadmap (R-A..R-E).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
`codex search paper` crashed on the live DB with "operator does not exist:
vector <-> double precision[]". The pgvector `<->` operator needs its RHS
typed as vector; peer call sites (mcp_server.py, wiki.py) cast but the CLI
did not. Mocked unit tests never exercise real pgvector, so it went unseen.
Add the cast to both `<->` occurrences and a regression guard asserting the
SQL contains `::vector`.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Second audit axis (data, not code): is the information in the DB actually good?
Baseline scan of the live 29-paper corpus + four open investigation items
prepared self-contained for a cold session.
- Good: chunks 0/1507 fail the F-16 re-gate, healthy sizing, 0 dups.
- DQ-1 (HIGH): 12/29 papers have zero citations; 11 of them have an openalex_id,
so OpenAlex returned empty referenced_works (source-coverage limit, not a bug)
— propose an S2 references supplement.
- DQ-2 (MED): 3 papers no abstract; 1911.00966 fully metadata-less (OpenAlex 404).
- DQ-3 (MED): chunk-vs-source fidelity not yet verified.
- DQ-4 (MED): retrieval relevance not yet measured.
Includes connection steps, exact ids, priorities, and a reproduce appendix.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The C-7 re-ingest hit M-1 live: TRUNCATE succeeded, then ingest failed on the
missing chunks.section column (schema.sql never applied to the live DB). Adding
the column then failed with 'must be owner' — the app user 'researcher' has DML
+ TRUNCATE but not DDL on the postgres-owned core tables. M-1's fix therefore
needs a privileged migration role, not just an idempotent schema. Records the
unblock and the helper's new preflight.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- Part D synthesis: C-11 HIGH (lead-ID collision → silent overwrite), R-8 MED, D-4 LOW.
- Part E wiki-rest: R-9 MED (cross-ref injection corrupts LaTeX math), C-12/C-13/R-10/R-11 LOW.
- Part F embed/quality/models: C-14/R-12 LOW + C-7 corroboration. Cleanest modules.
- Part G cli/config: C-15 MED (embedding_dim vs hardcoded vector(1024)), R-13/S-4/R-14/D-5 LOW.
Executive summary: 45 findings total (8 HIGH, 11 MED, 26 LOW). Five root themes;
dominant one is un-normalized identity (C-1/C-7/C-10/M-1). Whole repo reviewed.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Closes request (a) — the second pass over loop-1 §8 open items:
- Part A grounding guard: C-4 (HIGH, zero-claim pages bypass quarantine),
C-5/R-1 MED, C-6/R-2/R-3 LOW.
- Part B sources/: C-7 (HIGH, papers.id stored in OpenAlex URL form vs the
bare-ID contract), T-3 MED, R-4/R-5/C-9 LOW.
- Part C parsing/: C-10 MED (formulas/figures key on filename not paper.id),
R-6/R-7 LOW — all latent (live corpus is .txt).
Running tally: 30 findings, 7 HIGH. Common root: un-normalized identity.
Parts D-G (synthesis/wiki/embed/cli) still open.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Audit of main @5dfa6e4: 4 HIGH (S-1 secret-in-tree, M-1 missing migration
path, C-1 unpropagated ID-mismatch fix in discover.py, D-1 stale ADR-F15
validation, T-1 untested resolution SQL) plus MED/LOW findings. Findings
only; remediation planning deferred to the next loop phase.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- .gitignore: ignore .env.* (keep .env.example) so local DB-credential
profiles like .env.jetson-ingest can never be staged (audit S-1).
- ingest_all.sh: batch-ingest helper writing to the Jetson DB via SSH tunnel.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Committed code predated the line-length=100 ruff config; this brings the
five drifted files into compliance. No logic change.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Fixes preprint/journal duplicate problem: arXiv papers were ingested
under their preprint OpenAlex ID, but corpus citations reference the
published-version OpenAlex ID → those citations were invisible in the
graph (appeared as dangling).
Changes:
- infra/schema.sql: CREATE TABLE paper_identifiers (paper_id, openalex_id)
with UNIQUE index; seeded from papers.openalex_id on migration
- codex/graph.py: build_citation_graph LEFT JOINs paper_identifiers as
a second resolution path: COALESCE(p.id, pi.paper_id, c.cited_id)
- codex/ingest.py: every ingest inserts openalex_id into paper_identifiers
(ON CONFLICT DO NOTHING) — aliases can be added manually alongside
Live DB: 35 rows seeded + 4 published-version aliases added:
math/0503219 → W2163787581 (DCG 2007)
math/0306167 → W2136126748 (Commun Analysis Geom 2004)
math/0203250 → W1567166970 (Trans AMS 2003)
1005.2698 → W1511400044 (Geom & Topol 2015)
Effect: dangling 574→570; Bobenko+Springborn 2007 now IN-KB rank 9.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
build_citation_graph now does:
SELECT c.citing_id, COALESCE(p.id, c.cited_id) AS cited_id
FROM citations c
LEFT JOIN papers p ON p.openalex_id = c.cited_id
Before: cited_id (OpenAlex IDs) never matched papers.id (DOIs) →
13 cross-citations between ingested papers were invisible in graph.
After: in-KB papers use their canonical DOI key; dangling references
keep their raw OpenAlex ID unchanged.
Test: test_cross_citation_uses_doi_when_in_kb (42 passed).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
D-04: add _make_bibkey(paper) — ConcatSurnames+Year, ≤3 authors full list,
>3 authors FirstEtAlYear. Applied in ingest_paper when paper.bibkey is
None. ON CONFLICT now fills NULL bibkeys via COALESCE(papers.bibkey,
EXCLUDED.bibkey) while preserving manually-set values.
D-05b: add codex/__main__.py so `python -m codex` dispatches to the CLI.
D-05c: fix test_ingest.py:75 — rename var to raw_api_citations (the raw
OpenAlex payload with citing_id=openalex_id) and add regression
assertion: citing_id written to DB must equal paper.id (DOI), not
paper.openalex_id.
D-05a (proxy): add TestEntryPoint.test_python_m_codex_help — runs
`sys.executable -m codex --help` via subprocess, covering the
non-uv-run entry path. 253 tests green, ruff+mypy clean.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Closes audit N-02: docs/adr/ADR-F13-synthesis-engine.md was missing,
blocking R-34. Documents spike result (GO, Opus APPROVE 2 passes),
four-stage lead taxonomy, grounding discipline, three-level
zero-fact-leak invariant, and falsification-gate in _parse_conjecture_output.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Two bugs exposed during first batch ingest run after D-03 fix:
1. `.txt` files were silently skipped ("Unbekannter Dateityp") — added
plain-text read path alongside .tex and .pdf.
2. After D-03, OpenAlex resolves arXiv IDs → paper.id uses the DOI
(https://doi.org/…) but fetch_citations emits citing_id=openalex_id
(https://openalex.org/W…). FK constraint citations_citing_id_fkey
→ papers.id violated. Fix: rewrite citing_id to paper.id after
fetching from OpenAlex.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
