paper-fulltext-harvest

# Paper Full-text Harvest

Pipeline for downloading academic paper full-text at scale. Handles the three classes of sources that exist in 2026:

1. **Publisher TDM APIs** (Elsevier / Wiley / Springer) — for paywalled content where the institution has a subscription
2. **OA aggregators** (Unpaywall / OpenAlex / Crossref) — for Open Access copies regardless of publisher
3. **Browser fallback** (logged-in user profile) — for paywalled publishers without a TDM API (ACS / RSC / IEEE / AIP / IOP / APS / T&F / many CN journals)

The publisher router (`auto_paper_download/publishers.py`) recognises **25 DOI
prefixes** across 19 families, each annotated with the right downstream path
(TDM client / OA aggregator / browser fallback) and a support tier. The router is
shared with the standalone [`auto-paper-harvester`](https://github.com/jxtse/auto-paper-harvester)
CLI — see [`SUPPORTED_PUBLISHERS.md`](https://github.com/jxtse/auto-paper-harvester/blob/main/docs/SUPPORTED_PUBLISHERS.md)
there for the full per-publisher table.

## Decision tree

```
Have a DOI list?
├── DOIs from Elsevier (10.1016, 10.1006, 10.1011)
│   └── Use ElsevierClient (TDM XML API)             → §1
├── DOIs from Wiley (10.1002, 10.1111)
│   └── Use WileyClient (TDM PDF API)                → §1
├── DOIs from Springer/Nature (10.1007, 10.1038, 10.1186, 10.1147)
│   ├── OA papers → SpringerClient OA API            → §1
│   └── Subscription papers → fall through to OA/browser
├── Browser-only publishers without TDM API
│   (10.1021 ACS, 10.1039 RSC, 10.1126 Science, 10.1109 IEEE,
│    10.1063 AIP, 10.1088/10.1143 IOP, 10.1103 APS, 10.1146 Annual Reviews,
│    10.1080 T&F, 10.1116 AVS, 10.1149 ECS, 10.1364 Optica, 10.3938 KPS)
│   ├── Try OA first via Unpaywall/OpenAlex          → §2
│   └── Last resort: browser fallback                → §3
├── OA-leaning publishers (10.1073 PNAS, 10.3762 Beilstein)
│   └── OpenAlex/Unpaywall usually works             → §2
└── Mixed list (typical case)
    └── Use the orchestrated CLI (handles all of the above) → §0
```

## §0. Quick start (orchestrated CLI)

For a typical mixed list of DOIs from Web of Science / Scopus export:

```bash
# Setup once
cp scripts/.env.example .env
# Edit .env to fill API keys (see §4 "Configuration")

# Run
python -m auto_paper_download \
    --savedrecs your_export.xls \
    --output-dir ./downloads/ \
    --delay 2.0
```

The CLI:
- Parses DOIs from WoS savedrecs (or pass multiple `--savedrecs`)
- Routes each DOI to the right client by prefix
- Handles rate limiting + retries
- Per-publisher success summary at end

For **resume-safe Elsevier bulk** (the most common large run, e.g. 5000+ Elsevier DOIs):

```bash
python scripts/redownload_elsevier.py \
    --excel papers.xlsx \
    --output-dir ./elsevier_xml/ \
    --resume \
    --long-pause-every 200 \
    --long-pause-sec 300
```

## §1. Publisher TDM APIs

Read `references/tdm-apis.md` for full per-publisher details.

**Quick reference:**

| Publisher | API | Auth env var | Output | Rate limit |
|---|---|---|---|---|
| **Elsevier** | `api.elsevier.com/content/article/doi/{DOI}?view=FULL` | `ELSEVIER_API_KEY` + `ELSEVIER_INSTTOKEN` | XML (full-text) | ~5 req/sec |
| **Wiley** | `api.wiley.com/onlinelibrary/tdm/v1/articles/{DOI}` | `WILEY_TDM_TOKEN` | PDF | 3 req/sec hard cap |
| **Springer (OA)** | `api.springernature.com/openaccess/json` | `SPRINGER_API_KEY` | JSON+text | 1 req/sec free |
| **Crossref TDM** | URL from `link[]` field with `intended-application: text-mining` | `CR_CLICKTHROUGH_TOKEN` | varies | varies |

**Critical:** All TDM APIs require **institutional IP allowlisting** — must run from the institution's network or VPN. Test with one DOI before bulk runs.

**Instantiate clients directly:**

```python
from auto_paper_download.clients import ElsevierClient, WileyClient

elsevier = ElsevierClient()  # reads env vars
xml_path = elsevier.download_structured_full_text(
    doi="10.1016/j.ces.2025.123003",
    article_dir=Path("downloads/10.1016_j.ces.2025.123003"),
)

wiley = WileyClient()
pdf_path = wiley.download_pdf(
    doi="10.1002/anie.202500001",
    article_dir=Path("downloads/10.1002_anie.202500001"),
)
```

## §2. OA fallback (Unpaywall / OpenAlex / Crossref)

For papers that may have OA copies regardless of publisher.

```python
from auto_paper_download.clients import UnpaywallClient, OpenAlexClient, CrossrefClient

# Unpaywall: best OA PDF URL
up = UnpaywallClient()
pdf_path = up.download_pdf(doi=doi, article_dir=Path("downloads/.."))

# OpenAlex: alternative OA source
oa = OpenAlexClient()
pdf_path = oa.download_pdf(doi=doi, article_dir=Path("downloads/.."))

# Crossref: tries to find publisher PDF link
cr = CrossrefClient()
pdf_path = cr.download_pdf(doi=doi, article_dir=Path("downloads/.."))
```

**Always validate downloaded PDFs:** First 4 bytes must be `%PDF` and file size > 50KB. The clients in this skill do this automatically.

Expected hit rate for OA fallback: 40-60% on a generic chemistry/biology list. Recent papers (>2023) have higher OA rates.

## §3. Browser fallback (paywalled, no TDM)

For publishers where API isn't available but the user has institutional
Cloudflare/SSO access via browser cookies. **Slowest path — only use after
exhausting §1–§2**.

### Two routes — pick one

| | Route A: OpenClaw `browser` tool | Route B: `auto-paper-harvester` v0.2+ CLI |
|---|---|---|
| **What** | Drive the user's running Chrome via the agent's `browser` capability with `profile="user"` | Standalone CLI with built-in Playwright `launch_persistent_context` |
| **Setup** | None — reuses whatever Chrome the user is logged into | `pip install 'auto-paper-download[browser]' && playwright install chromium` |
| **Cookies** | User's existing daily-driver Chrome cookies (zero re-login) | Dedicated isolated profile; user logs into SSO once on first run |
| **Selectors** | Per-publisher CSS in `references/browser-fallback.md` (ACS / Wiley / RSC / T&F / Nature / AIP / CN journals) | Per-family select