docs/defextra_hydration.md

# DefExtra hydration

## Overview

This dataset cannot ship excerpts. We ship markers only. Users supply PDFs and run hydration to reconstruct the definitions and contexts.

See [`README.md`](../README.md) for the high‑level overview and examples.

## Requirements

- Python 3.10+
- A running GROBID server (default: `http://localhost:8070`).

  Example Docker run:

  ```bash
  docker run --rm -p 8070:8070 grobid/grobid:0.8.0
  ```

- Python packages used by scripts:
  - `grobid-client-python`, `lxml`, `pdfplumber`, `pdfminer.six`, `PyPDF2`, `pyarrow`

## UV usage

This repo ships a `pyproject.toml`, so you can run:

```bash
uv run python scripts/hydrate_defextra.py ...
```

## Getting PDFs

See `docs/get_pdfs.md` for sources and a helper script that lists required PDFs.

## Quickstart (run GROBID)

1) Place your PDFs in `pdfs/`.
2) Hydrate (runs GROBID unless `--skip-grobid`):

```bash
uv run python scripts/hydrate_defextra.py \
  --legal-csv data/defextra_legal.csv \
  --pdf-dir pdfs \
  --grobid-out grobid_out \
  --output-csv defextra_hydrated.csv \
  --report defextra_hydrated_report.txt \
  --require-complete
```

## Quickstart (skip GROBID, use existing TEI)

If you already have TEI XML files (e.g., produced by your own GROBID run), point
`--grobid-out` to that TEI folder and add `--skip-grobid`:

```bash
uv run python scripts/hydrate_defextra.py \
  --legal-csv data/defextra_legal.csv \
  --pdf-dir pdfs \
  --grobid-out /path/to/tei_xml_dir \
  --output-csv defextra_hydrated.csv \
  --report defextra_hydrated_report.txt \
  --require-complete \
  --skip-grobid
```

## File naming expectations

- Preferred: `<paper_id>.pdf` (the `paper_id` in the CSV).
- DOI/arXiv/PII aliases are supported for common cases.
- Hash IDs are often Semantic Scholar IDs; many PDFs can be downloaded from there.

## GROBID configuration

- By default, `scripts/pdf_to_grobid.py` generates a temporary config that points to `http://localhost:8070`.
- Use `--grobid-config config.json` to override the URL/timeout/batch size.

## Hash mismatch behavior

- The legal CSV includes hash markers to verify that the PDF content matches the paper version.
- Default: **skip** PDFs with hash mismatches and report them.
- Optional: `--allow-pdf-hash-mismatch` to continue anyway (use only after manual inspection).

## Interpretation of warnings

- `Error initializing GROBID client` or `GROBID server ... does not appear up and running`:
  GROBID is not reachable. Start the server (or Docker) or pass `--grobid-config` with the correct URL. If you already have TEI files, rerun with `--skip-grobid`.

- `Processing failed ... [BAD_INPUT_DATA] ... error code: 139` or `pdfalto` errors:
  GROBID could not parse a PDF (often a damaged or unusual file). Hydration may still succeed via PDF text fallback, but TEI will be missing. Try a different PDF version.

- `Warning: PDF hash markers did not match ... skipping PDF`:
  The PDF content differs from the expected version. Replace the PDF with the correct version or rerun with `--allow-pdf-hash-mismatch` and manually inspect outputs.

- `Warning: PDF text extraction failed ...`:
  The PDF text fallback failed (pdfplumber/pdfminer/PyPDF2). Hydration then relies on TEI only. Try a different PDF or a different extraction backend.

- `incorrect startxref pointer` or similar PDF syntax warnings:
  The PDF appears malformed. Often recoverable, but if hydration fails, obtain a clean copy.

- Summary lines:
  - `Missing TEI for N papers`: GROBID output missing for those PDFs.
  - `Missing definition spans` / `Missing context spans`: nothing matched after TEI + hash + anchor + PDF fallback.
  - `Hydrated from PDF fallback`: spans were reconstructed from PDF text (not TEI).

## Legal CSV schema (marker columns)

- `definition_char_start`, `definition_char_end`: exact TEI substring span (optional).
- `definition_match`: `exact`/`hash`/`missing` indicating how the TEI span was found.
- `definition_hash64`, `definition_sha256`, `definition_token_count`: full span hash.
- `definition_head_*`, `definition_mid_*`, `definition_tail_*`: anchor hashes (window size 12).
- `definition_head_alt_*`, `definition_mid_alt_*`, `definition_tail_alt_*`: anchor hashes (window size 6).
- Same fields exist for `context_*`.
- `definition_preserve_linebreaks`, `context_preserve_linebreaks`:
  keep line breaks when present in the manual copy (tables).
- `definition_preserve_hyphenation`, `context_preserve_hyphenation`:
  preserve line-break hyphenation when present.
- `definition_has_bracket_citation`, `context_has_bracket_citation`:
  whether the manual copy included `[12]`‑style citations.
- `definition_has_paren_citation`, `context_has_paren_citation`:
  whether the manual copy included `(Author, 2019)`‑style citations.
- `definition_has_letter_digit`, `context_has_letter_digit`:
  whether the manual copy contained letter‑digit runs like `bias4`.
- `definition_end_punct`, `context_end_punct`:
  trailing punctuation marker captured from the manual copy.

## Legal CSV columns (full)

| Column | Description |
| --- | --- |
| `paper_id` | Paper identifier (often a Semantic Scholar ID, DOI, or arXiv ID). |
| `paper_title` | Paper title. |
| `paper_doi` | DOI (if available). |
| `paper_arxiv` | arXiv ID or URL (if available). |
| `concept` | Term / concept being defined. |
| `definition_type` | Definition type (e.g., explicit / implicit). |
| `source_file` | Source JSON filename used during curation. |
| `is_out_of_domain` | Boolean flag for out‑of‑domain papers. |
| `definition_preserve_linebreaks` | Whether line breaks should be preserved in the definition. |
| `context_preserve_linebreaks` | Whether line breaks should be preserved in the context. |
| `definition_preserve_hyphenation` | Whether hyphenation should be preserved in the definition. |
| `context_preserve_hyphenation` | Whether hyphenation should be preserved in the context. |
| `definition_has_bracket_citation` | Definition contains bracket‑style citations (e.g., `[12]`). |
| `definition_has_paren_citation` | Definition contains parenthetical citations (e.g., `(Smith, 2020)`). |
| `definition_has_letter_digit` | Definition contains letter–digit patterns (e.g., `bias4`). |
| `context_has_bracket_citation` | Context contains bracket‑style citations. |
| `context_has_paren_citation` | Context contains parenthetical citations. |
| `context_has_letter_digit` | Context contains letter–digit patterns. |
| `definition_end_punct` | Expected trailing punctuation for definition. |
| `context_end_punct` | Expected trailing punctuation for context. |
| `marker_version` | Marker format version. |
| `hash_version` | Hashing scheme version. |
| `definition_char_start` | Character start offset (TEI) for definition (if available). |
| `definition_char_end` | Character end offset (TEI) for definition (if available). |
| `definition_match` | Debug marker: reference string used to compute definition hashes. |
| `definition_hash64` | 64‑bit hash of definition token sequence. |
| `definition_sha256` | SHA‑256 hash of definition token sequence. |
| `definition_token_count` | Token count for definition span. |
| `definition_head_hash64` | Head‑anchor 64‑bit hash for definition. |
| `definition_head_sha256` | Head‑anchor SHA‑256 hash for definition. |
| `definition_head_token_count` | Head‑anchor token count for definition. |
| `definition_mid_hash64` | Mid‑anchor 64‑bit hash for definition. |
| `definition_mid_sha256` | Mid‑anchor SHA‑256 hash for definition. |
| `definition_mid_token_count` | Mid‑anchor token count for definition. |
| `definition_tail_hash64` | Tail‑anchor 64‑bit hash for definition. |
| `definition_tail_sha256` | Tail‑anchor SHA‑256 hash for definition. |
| `definition_tail_token_count` | Tail‑anchor token count for definition. |
| `definition_head_alt_hash64` | Alternate head‑anchor 64‑bit hash for definition. |
| `definition_head_alt_sha256` | Alternate head‑anchor SHA‑256 hash for definition. |
| `definition_head_alt_token_count` | Alternate head‑anchor token count for definition. |
| `definition_mid_alt_hash64` | Alternate mid‑anchor 64‑bit hash for definition. |
| `definition_mid_alt_sha256` | Alternate mid‑anchor SHA‑256 hash for definition. |
| `definition_mid_alt_token_count` | Alternate mid‑anchor token count for definition. |
| `definition_tail_alt_hash64` | Alternate tail‑anchor 64‑bit hash for definition. |
| `definition_tail_alt_sha256` | Alternate tail‑anchor SHA‑256 hash for definition. |
| `definition_tail_alt_token_count` | Alternate tail‑anchor token count for definition. |
| `context_char_start` | Character start offset (TEI) for context (if available). |
| `context_char_end` | Character end offset (TEI) for context (if available). |
| `context_match` | Debug marker: reference string used to compute context hashes. |
| `context_hash64` | 64‑bit hash of context token sequence. |
| `context_sha256` | SHA‑256 hash of context token sequence. |
| `context_token_count` | Token count for context span. |
| `context_head_hash64` | Head‑anchor 64‑bit hash for context. |
| `context_head_sha256` | Head‑anchor SHA‑256 hash for context. |
| `context_head_token_count` | Head‑anchor token count for context. |
| `context_mid_hash64` | Mid‑anchor 64‑bit hash for context. |
| `context_mid_sha256` | Mid‑anchor SHA‑256 hash for context. |
| `context_mid_token_count` | Mid‑anchor token count for context. |
| `context_tail_hash64` | Tail‑anchor 64‑bit hash for context. |
| `context_tail_sha256` | Tail‑anchor SHA‑256 hash for context. |
| `context_tail_token_count` | Tail‑anchor token count for context. |
| `context_head_alt_hash64` | Alternate head‑anchor 64‑bit hash for context. |
| `context_head_alt_sha256` | Alternate head‑anchor SHA‑256 hash for context. |
| `context_head_alt_token_count` | Alternate head‑anchor token count for context. |
| `context_mid_alt_hash64` | Alternate mid‑anchor 64‑bit hash for context. |
| `context_mid_alt_sha256` | Alternate mid‑anchor SHA‑256 hash for context. |
| `context_mid_alt_token_count` | Alternate mid‑anchor token count for context. |
| `context_tail_alt_hash64` | Alternate tail‑anchor 64‑bit hash for context. |
| `context_tail_alt_sha256` | Alternate tail‑anchor SHA‑256 hash for context. |
| `context_tail_alt_token_count` | Alternate tail‑anchor token count for context. |

## Notes

- Small mismatches are expected due to PDF/GROBID text normalization.
- Missing exact TEI spans do **not** block hydration; hash/anchor markers are used as fallback.
- Exact TEI spans are validated against stored hashes; if they do not match, citation‑stripped hash/anchor matching is used instead.
- See [`docs/mismatch_examples.md`](mismatch_examples.md) for concrete mismatch types with short excerpts.