rag_server: read_publication finds the shipped originals, falls back to honest chunk reassembly; get_dataset_code resolves notebooks under the published layout (WP3)

#1
by kuivi - opened

Fixes from running this server against the published dataset copy, cleared with Dmitrii
in July, then hardened by an adversarial review round (codex + an independent reviewer):

  • get_dataset_code: md_path in the registry names notebook_harvest/parsed/... and
    eqc_qa/notebooks_code/..., neither of which ships; both families are published under
    originals_md/notebooks/. With the fallback, 186 of 186 listed notebook ids resolve.
    The family md_path implies is searched first, so a basename repeated across families
    would resolve to its own copy.

  • read_publication: papers.jsonl records absolute paths from the build machine, so on
    any other deployment 0 of 12,411 md_paths resolve — while publications_md.tar.gz in
    this same dataset ships the verbatim originals for 11,209 of them. The same
    registry-vs-published-layout mismatch, the same fix: resolve
    /originals_md/publications_md/parsed_md//vlm/.md (or
    $PUBS_MD_ROOT) before anything else.

  • Only when no original exists anywhere (1,210 of 12,411) is the text reassembled from
    the publications collection's chunks — and the reply is honest about what that is:
    full_text=false, text_fidelity="reconstructed-lossy", every 2500-char loader cap
    marked in-line in the text (measured: 12.8% of corpus characters fall past that cap),
    registry metadata (authors/abstract/linked_products) merged back in, and a store
    failure reported as an error instead of masquerading as "not parsed yet". Ordering
    prefers an explicit chunk_index payload field (the newer content-hash chunkers) over
    the numeric chunk_id tail (the currently served corpus); chunks with neither sort
    last and are counted in order_uncertain. The chunk cap truncates a sorted TAIL,
    never holes in the middle; per-paper scroll results are cached so pagination does not
    re-move the paper once per page.

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