- R-9 (MED): _inject_cross_refs now protects LaTeX math spans ($…$, $$…$$,
\(…\), \[…\]) like inline code, so a concept name inside a formula is no longer
rewritten to a [[slug]] link and corrupting the LaTeX. Regression test added.
- C-13 (LOW): mark ungrounded claims on the raw body BEFORE injecting cross-refs
(render then inject), so a concept name inside a claim cannot stop the ⚠ regex
from matching.
- C-12 (LOW): _try_embed_formulas is now a true no-op — it previously issued a
per-concept information_schema round-trip that did nothing.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
M-1: schema.sql could not be re-applied (leading CREATE TABLE/INDEX lacked
IF NOT EXISTS), apply_schema was never called, and the live migration just
failed on a missing chunks.section column. Fixes:
- schema.sql: all CREATE TABLE/INDEX now use IF NOT EXISTS — the whole file is
re-applyable as a no-op.
- codex migrate: new CLI command that applies schema.sql. Connects via
MIGRATION_DATABASE_URL (falls back to DATABASE_URL) and catches
InsufficientPrivilege with guidance — because the app role is DML-only and
core tables are owned by 'postgres' (the privilege dimension found during the
live migration incident).
- config: migration_database_url (optional privileged connection).
- db: apply_schema docstring corrected (idempotency now true) + privilege note.
- T-2: static test that schema.sql is fully idempotent; migrate privilege-error
test.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
extract_formulas/extract_figures derive paper_id from Path(pdf_path).stem, which
need not equal papers.id (and won't, given canonical ids). Inserting that stem
violated the formulas/figures -> papers(id) FK on rich (.pdf) ingest. The DELETE
already used paper.id; the INSERTs now do too.
Strengthened the rich-ingest test: the fake formula/figure carry a filename-stem
paper_id distinct from papers.id, and the test asserts the inserted rows are
keyed on papers.id.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
openalex.fetch_paper fills paper.id from OpenAlex's URL-form doi/id
(e.g. https://doi.org/10.48550/arxiv.math/0603097), and ingest upserted that as
papers.id. Live DB confirmed 35/36 ids were URL-form — breaking bare-id lookups
(graph related / discover citing / search by id) and leaving cited_id matching
to rely solely on openalex_id.
ingest now sets paper.id to the caller-supplied id (the arXiv id / DOI the CLI
and ingest scripts use); OpenAlex's work id is retained as openalex_id and in
paper_identifiers. Regression test: fetch_paper returns a URL-form id, papers.id
upsert uses the bare caller id.
T-3: the OpenAlex test fixture used a bare 'doi' (not the URL form the API
emits) and never asserted paper.id, which masked this. Fixture now uses the URL
form and the test pins fetch_paper's mapping.
NOTE: existing rows keep their URL-form ids until re-ingested — run ingest_all.sh
to migrate the 36-paper corpus (chosen migration path).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- D-2 config.py: graph_cite_boost_alpha described the OLD inverted formula
(score = dense * (1 + alpha*pr)); the code divides distance. Document the
actual boosted_distance = distance / (1 + alpha*pr).
- D-4 synthesis.py: write_leads claimed an 'append-only' INDEX.md that keeps
previously-recorded ids; _update_index actually rebuilds from on-disk glob.
Docstring now matches the implementation.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
discover.py compared the raw OpenAlex cited_id against papers.id (a DOI/arXiv
id), so an ingested paper cited by its OpenAlex id was mis-reported as a
discovery lead. graph.py already resolved this via papers.openalex_id, but the
fix was never propagated — two 'dangling' implementations disagreed.
Extract the resolution into one shared constant RESOLVED_CITATIONS_SQL in
graph.py; build_citation_graph and all four discover.py queries
(discovery_leads / citing_papers / cited_by / cocited_papers) now go through it,
so the 'what counts as ingested' rule cannot drift again.
Live-DB validated: before, 13 ingested papers leaked into discovery_leads;
after, the real discovery_leads() returns 0 ingested papers among its leads.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Each stage (find_connections/gaps/improvements/propose_conjectures) numbered its
leads from seq=1, so connection L-0001, gap L-0001 and improvement L-0001 all
resolved to grounded/L-0001.md. The CLI concatenates them
(connections + gaps + improvements) and write_leads writes in order, so later
kinds silently overwrote earlier ones — survivors = max(per-kind count), not the
sum. Reproduced: 4 distinct leads -> 2 files.
_make_lead_id now takes the kind and emits L-C-/L-G-/L-I-/L-X- prefixes, keeping
same-seq ids distinct across stages. Regression tests cover the format and the
no-collision invariant.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
compile_all's quarantine gate was guarded by `total_claims > 0`, so a page
with no parseable citations — including the LLM-outage case where
compile_concept returns an empty page — fell through to the publish branch and
was written to wiki/ + marked compiled. Such a page carries zero grounding
evidence.
Now: total_claims == 0 (or grounding_rate below threshold) quarantines and does
NOT update the compile-state, so a transient LLM failure retries next run
instead of freezing an empty/uncited page as 'compiled'. Empty bodies are
recorded but not written as draft files.
Regression test reproduces the exact bypass (uncited LLM output -> quarantined,
not published).
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>
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>
- 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>
- Implement all CLI commands as specified in F-07: ingest, search, and discover subcommands (leads, citing, cited-by, cocited), and provenance subcommands (scan, add-link, links, bib).
- Add ask command stub that exits with code 1 (not yet implemented).
- Implement comprehensive tests with mocked dependencies (no real DB/API calls).
Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
Review-Gate finding: GROBID emits type="arXiv" (camel-case), not "arxiv".
XPath literal match silently returned empty strings for all real responses.
Fix: iterate idno elements and compare .lower() == "arxiv".
Test fixture updated to reflect real GROBID output (type="arXiv").
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Bare Typer() with no commands raised RuntimeError at runtime.
Callback makes the entry point callable without exposing F-07 logic.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Review-Gate finding: pyproject.toml [project.scripts] referenced
codex.cli:app which was absent; uv run codex raised ModuleNotFoundError.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
