Optionally collect full-text snippets to deepen evidence beyond abstracts.

This skill is intentionally conservative: in many survey runs, abstract/snippet mode is enough and avoids heavy downloads.

Inputs

papers/core_set.csv (expects paper_id, title, and ideally pdf_url/arxiv_id/url)
Optional: outline/mapping.tsv (to prioritize mapped papers)

Outputs

papers/fulltext_index.jsonl (one record per attempted paper)
Side artifacts:

papers/pdfs/<paper_id>.pdf (cached downloads)

papers/fulltext/<paper_id>.txt (extracted text)

Decision: evidence mode

queries.md can set evidence_mode: "abstract" | "fulltext".

abstract (default template): do not download; write an index that clearly records skipping.

fulltext: download PDFs (when possible) and extract text to papers/fulltext/.

Local PDFs Mode

When you cannot/should not download PDFs (restricted network, rate limits, no permission), provide PDFs manually and run in “local PDFs only” mode.

PDF naming convention: papers/pdfs/<paper_id>.pdf where <paper_id> matches papers/core_set.csv.
Set - evidence_mode: "fulltext" in queries.md.
Run: python .codex/skills/pdf-text-extractor/scripts/run.py --workspace <ws> --local-pdfs-only

If PDFs are missing, the script writes a to-do list:

output/MISSING_PDFS.md (human-readable summary)
papers/missing_pdfs.csv (machine-readable list)

Workflow (heuristic)

Read papers/core_set.csv.
If outline/mapping.tsv exists, prioritize mapped papers first.
For each selected paper (fulltext mode):

resolve pdf_url (use pdf_url, else derive from arxiv_id/url when possible)

download to papers/pdfs/<paper_id>.pdf if missing
extract a reasonable prefix of text to papers/fulltext/<paper_id>.txt
append/update a JSONL record in papers/fulltext_index.jsonl with status + stats
Never overwrite existing extracted text unless explicitly requested (delete the .txt to re-extract).

Quality checklist

papers/fulltext_index.jsonl exists and is non-empty. If evidence_mode: "fulltext": at least a small but non-trivial subset has extracted text (strict mode blocks if extraction coverage is near-zero). If evidence_mode: "abstract": the index records clearly reflect skip status (no downloads attempted).

Script

Quick Start

python .codex/skills/pdf-text-extractor/scripts/run.py --help
python .codex/skills/pdf-text-extractor/scripts/run.py --workspace <workspace_dir>

All Options

--max-papers <n>: cap number of papers processed (can be overridden by queries.md)
--max-pages <n>: extract at most N pages per PDF
--min-chars <n>: minimum extracted chars to count as OK
--sleep <sec>: delay between downloads
--local-pdfs-only: do not download; only use papers/pdfs/<paper_id>.pdf if present
queries.md supports: evidence_mode, fulltext_max_papers, fulltext_max_pages, fulltext_min_chars

Examples

Abstract mode (no downloads):

Set - evidence_mode: "abstract" in queries.md, then run the script (it will emit papers/fulltext_index.jsonl with skip statuses)

Fulltext mode with local PDFs only:

Set - evidence_mode: "fulltext" in queries.md, put PDFs under papers/pdfs/, then run: python .codex/skills/pdf-text-extractor/scripts/run.py --workspace <ws> --local-pdfs-only

Fulltext mode with smaller budget:

python .codex/skills/pdf-text-extractor/scripts/run.py --workspace <ws> --max-papers 20 --max-pages 4 --min-chars 1200

Notes

Downloads are cached under papers/pdfs/; extracted text is cached under papers/fulltext/.
The script does not overwrite existing extracted text unless you delete the .txt file.

Troubleshooting

Issue: no PDFs are available to download

Fix:

Use evidence_mode: abstract (default) or provide local PDFs under papers/pdfs/ and rerun with --local-pdfs-only.

Issue: extracted text is empty/garbled