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 for the high‑level overview and examples.

Requirements

• Python 3.10+

• A running GROBID server (default: http://localhost:8070).

  Example Docker run:

  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:

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):

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:

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 for concrete mismatch types with short excerpts.