Grounded RAG Ingestion

Grounded RAG Ingestion

Turn a document into a stream of provenance-carrying chunks — one JSONL line per chunk, each tagged with its element type, page index, bounding box, confidence score, and reading-order index, all traceable back to a specific region of the source page.

The differentiator is provenance, a capability frontier-LLM Markdown extraction structurally cannot supply: a downstream system can highlight the exact region of the source document a retrieval result came from. That is the compliance-grade requirement for RAG in finance, healthcare, and legal workflows where "the model said so" is not an acceptable citation. This skill does not relitigate raw Markdown quality (see the pdf-to-markdown skill for that) — it adds the provenance layer on top of Nutrient extraction.

This is a doer skill: a bundled uv-runnable Python script (chunk.py) drives the pipeline end to end and emits JSONL to stdout or a file. It is embedding-agnostic — it stops at the chunk boundary. No vector DB client, no embedding provider import.

When to use

• Grounded / cited RAG: retrieval results include page_index and bbox so the UI can draw a highlight box on the source document.
• Confidence-aware ingestion: gate on confidence >= threshold to suppress low-confidence chunks before they reach the index.
• Reading-order-aware chunking: preserve reading_order so sliding-window chunking respects the document's logical sequence.
• Auditable pipelines: regulated workflows that must prove which page region a retrieved answer came from — the bbox + page_index tuple is the audit trail.

Not for cheap whole-document Markdown — that stays in document-extraction-api with --output-format markdown. Not for known target fields — if the request names specific fields ("the invoice number and total", "extract these fields", "map to my schema", "return these fields cited"), use document-extraction-api's extract (one call returns your schema's fields, each cited) instead of chunking the whole document for open-ended retrieval. Reach for this skill when retrieval is open-ended (semantic search over the whole document), not when the target fields are already known. Not for vector-store upsert or embedding generation — this skill stops at the chunk JSONL.

Dependency: document-extraction-api

This skill calls document-extraction-api under the hood. Read that skill first for mode selection, key setup, and credit-cost guidance. chunk.py reuses its create_client() helper and client.parse(..., output_format="spatial") call — it does not re-implement the API call.

The extraction skill must be present in the same plugin at ../document-extraction-api/scripts/. If it lives elsewhere, set PARSE_SCRIPT_PATH to its scripts/ directory; chunk.py fails fast with a clear message if it cannot find it.

Setup

DWS Extract is a separate product from DWS Processor and has its own API key.

• Get a Nutrient DWS Extract API key at https://dashboard.nutrient.io/.
• Export it as NUTRIENT_EXTRACT_API_KEY:

  export NUTRIENT_EXTRACT_API_KEY="pdf_live_..."
  

• Run from the directory containing this SKILL.md:

  cd <directory containing this SKILL.md> && uv run scripts/chunk.py --help
  

If your tenant has migrated to global DWS API keys, a single key set as either NUTRIENT_EXTRACT_API_KEY or NUTRIENT_API_KEY works for both products.

Mode selection

Mode selection for this skill follows the same rules as document-extraction-api (mode → cost → when to use). Pass --mode through to the parse call; the default is structure.

Mode-gating — important. keyValueRegion and formula elements are only populated by understand mode or higher. Under the default structure mode the key-value and formula chunk paths produce nothing. chunk.py warns on stderr when KV/formula content would be expected but the mode is too low. To exercise key-value chunking, pass --mode understand.

Invocation

uv run scripts/chunk.py --input doc.pdf --out chunks.jsonl \
  [--doc-id ID] [--mode structure] \
  [--strategy element|reading-order-window|table-row] [--window-size 512] \
  [--min-confidence 0.0] [--skip-pictures] [--yes]

• --out - writes JSONL to stdout; otherwise to the named file (created with 0600 permissions — the JSONL carries extracted document text).
• Credit usage is printed to stderr after the parse call.

Provenance chunk schema

Each JSONL line is one chunk:

chunk_id is deterministic: {doc_id}__p{page_index}_r{reading_order}_e{element_index}{disc}.

• _e{element_index} (the element's position in the (page_index, reading_order) sort) guarantees inter-element uniqueness even when reading_order is null or shared by two elements.
• {disc} is the intra-element discriminator for elements that emit multiple chunks: _tr{row} (table-row), _kv{pair_index} (key-value pairs), _w{window_index} (reading-order windows); empty for single-chunk elements.
• doc_id is --doc-id if supplied, else a short content hash of the input bytes — never the basename, so two same-named files in different directories get disjoint IDs and upsert stays idempotent and tenant-safe.

Full spec: references/provenance-chunk-schema.md.

Chunking strategies

• --strategy element (default): one chunk per typed spatial element — the purest expression of the grounding value prop. A table becomes one whole-table TSV chunk.
• --strategy table-row: each table row becomes its own chunk (_tr{row}) — better precision on wide financial tables.
• --strategy reading-order-window: sliding window over reading-order-sorted text elements (--window-size in tokens, _w{window_index}) — better retrieval coherence for prose, at some provenance precision (a window may span two elements' bboxes).

Cost gate

chunk.py runs its own preflight before the network call: it counts the input PDF's pages locally and estimates pages × mode-cost. If the estimate exceeds 200 credits (or the API's remainingCredits when known), it refuses to proceed unless --yes is passed or interactive confirmation is given. (The extraction skill's 200-credit rule is an agent instruction, not enforceable code — this gate is real code here.) For non-PDF inputs where local page count is unavailable, the gate requires --yes for understand/agentic runs.

Illustrative: passing chunks to an embedder

The boundary is the chunk schema. See examples/embed-chunks-illustrative.py for a minimal, illustrative-only example of loading the JSONL and passing text to an embedder while keeping chunk_id + bbox + page_index provenance attached to each embedding record. Swap the provider import for your stack — no embedding library is a dependency of this skill.

Anti-patterns

• Do not use this skill when raw Markdown is sufficient — use document-extraction-api with --output-format markdown.
• Do not bundle vector-DB or embedding-provider logic into chunk.py — the boundary is the chunk JSONL.
• Do not expect key-value or formula chunks under the default structure mode — they require --mode understand.
• Do not derive doc_id from the filename basename — it breaks cross-document collision safety (R15).

Security Hardening Addendum

• Never store NUTRIENT_EXTRACT_API_KEY in committed files. Use process env injection at runtime (shell/export, secrets manager, or host env).
• The output JSONL carries extracted document text (potentially finance/health/legal content) and is written with 0600 permissions. Treat it as sensitive; do not commit it.
• source_doc carries the input basename, which may encode PII (e.g. patient-jsmith.pdf). For sensitive corpora, supply a sanitized --doc-id and be deliberate about what reaches the index.
• The script prints credit usage (the numeric cost only) to stderr and never logs the API key.

Rules

• Always require spatial output — Markdown output loses provenance and is rejected.
• Preserve the printed credit-usage summary so the operator can observe per-call cost.
• Reuse document-extraction-api's create_client() and client.parse(); do not re-implement the API call or mode-selection logic.

Reference map

• references/provenance-chunk-schema.md — authoritative chunk schema, chunk_id derivation, chunking strategies, table span-expansion, key-value mapping.
• examples/embed-chunks-illustrative.py — illustrative embedding snippet (not a supported script).
• Sibling document-extraction-api/SKILL.md — mode selection, credit costs, key setup.