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>
FastMCP defaults to DNS rebinding protection (allowed_hosts=localhost only),
which rejects requests from the Mac (192.168.178.82) to the Jetson
(192.168.178.103:8765). Security is already provided by Bearer token auth
in _TokenAuth middleware and UFW restricting port 8765 to trusted LAN IPs,
making host-header validation redundant in this deployment context.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
F-13 settings (leads_dir, synthesis_llm_*, synthesis_top_k,
synthesis_min_grounded_ratio, synthesis_gap_min_coverage) appeared twice
due to independent commits on F-13 and F-14 branches. Kept the second
(more complete) block; removed the first.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Documents MCP server setup for Claude Code (.mcp.json) and Claude Desktop
(claude_desktop_config.json), HTTP transport config, and available tools table.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Lead.__post_init__: raises ValueError on empty provenance list
- find_gaps: no-chunk path now carries topic-marker Provenance instead of []
- _update_index: docstring corrected (rebuilds, not append-only)
- test_model: test_lead_empty_provenance_raises covers the new invariant
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Replace 3-gram substring match with:
- _last_sentence(): only the last sentence before a citation is checked
(prevents a hallucinated paragraph grounding via a phrase at its end)
- _content_words(): stopwords removed from both claim and chunk before
n-gram comparison (prevents bypass via "the discrete conformal map")
- Content-5-gram: require 5 consecutive non-stopword tokens from last
sentence to appear in the chunk's content-word stream
- Claims with <5 content words in last sentence → ungrounded by default
Add adversarial tests: stopword-3-gram bypass → grounded=False;
legitimate content-5-gram → grounded=True.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add _detect_conflicts() using adversative keyword heuristic (but,
however, in contrast, …) between chunks of different bibkeys; results
populate CompileReport.conflicts and appear in wiki/log.md.
Also add CompileReport.quarantined field (used by Fix 2).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
_inject_cross_refs temporarily replaces backtick spans with null-byte
placeholders before injecting [[slug]] cross-refs, then restores them.
This prevents concept titles inside `code` from being rewritten.
Add tests for inline-code protection and full-list cross-ref injection.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
compile_concept now accepts chunks as a positional parameter; compile_all
retrieves chunks once and passes them directly, avoiding double-retrieve.
Also separates all_concepts (full list) from compile_concepts (filtered),
so cross-ref injection always uses the complete concept list regardless of
--concept filter (Fix 6 + Fix 8).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
_parse_claims now skips matches where bibkey contains spaces or starts
with "http", preventing Markdown hyperlinks like [text](https://...) from
being misidentified as citations. Add two tests.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Wrap llm.generate() in compile_concept with a broad try/except;
log a warning and return an empty ConceptPage (no crash) when the
LLM endpoint is unreachable. Add logging module import.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- mathpix.py + figures.py: wrap fitz page-loop in try/finally so
doc.close() is guaranteed even on exception (no file-handle leak)
- ingest.py: DELETE FROM formulas/figures WHERE paper_id before re-insert
so --rich re-ingest is idempotent (BIGSERIAL has no natural UNIQUE key;
ON CONFLICT DO NOTHING was a no-op)
Gate: 158 passed, ruff clean, mypy clean
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
