Research-Stack/5-Applications/scripts/SCIENCEHUB_README.md

ScienceHub MCP — Sovereign Research Surface

What It Is

An MCP server that lets your LLM say "I need " and automatically:

1. Searches your local corpus (Zotero + PDFs)
2. If missing, fetches from arXiv
3. Ingests into Zotero + local storage
4. Returns a structured report

Installation

Requirements

• Python 3.11+
• mcp SDK: pip install mcp
• pdftotext + pdfinfo (from poppler-utils)
• SQLite (built-in)

MCP Client Config (Claude Desktop)

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "sciencehub": {
      "command": "python3",
      "args": [
        "/home/allaun/Documents/Research Stack/scripts/sciencehub_mcp.py"
      ]
    }
  }
}

MCP Client Config (Cline / Continue)

Add to your .vscode/mcp-settings.json or Cline MCP settings:

{
  "mcpServers": [
    {
      "name": "sciencehub",
      "command": "python3",
      "args": [
        "/home/allaun/Documents/Research Stack/scripts/sciencehub_mcp.py"
      ]
    }
  ]
}

Tools

need — The "I need X" pipeline

Input: {"query": "I need attention mechanism survey", "auto_ingest": true}

What happens:

• Searches local Zotero library + PDF corpus
• If found locally → returns hit list, no fetch
• If missing → searches arXiv, downloads PDF, ingests to Zotero, reports back

search_local — Query your corpus

Input: {"query": "burgers turbulence", "limit": 10}

Searches:

• zotero_items (titles, DOIs, URLs, extras)
• local_pdfs (filenames, arXiv IDs, DOIs)
• arxiv_meta (cached abstracts)

fetch_arxiv — Direct download by ID

Input: {"arxiv_id": "1706.03762", "ingest": true}

Downloads to ~/Downloads/data/Downloads_from_internet/Deep Research/alphaXiv_PDFs_2026_04/ and creates a Zotero item.

review_paper — Quick PDF review

Input: {"path": "/path/to/paper.pdf"}

Runs pdfinfo + pdftotext -l 1 and returns metadata + first-page excerpt.

corpus_report — Library stats

Returns counts of Zotero items, local PDFs, completed/failed needs.

CLI Mode (no MCP client needed)

cd "/home/allaun/Documents/Research Stack"

# Stats
python3 scripts/sciencehub_mcp.py --report

# Search local corpus
python3 scripts/sciencehub_mcp.py --search "burgers turbulence"

# Full "I need" pipeline (dry-run with --no-ingest)
python3 scripts/sciencehub_mcp.py "I need attention mechanism survey"

# Review a specific PDF
python3 scripts/sciencehub_mcp.py --review /path/to/paper.pdf

# Fetch by arXiv ID
python3 scripts/sciencehub_mcp.py --fetch 1706.03762

Companion Scripts

Ingest Watcher (ingest_watcher.py)

Monitors directories for new PDFs, auto-ingests them into Zotero.

# Dry run
python3 scripts/ingest_watcher.py --once --dry-run

# Actual ingest
python3 scripts/ingest_watcher.py --once

# Daemon mode
python3 scripts/ingest_watcher.py --daemon --interval 60

Review Agent (review_agent.py)

Generates structured reviews for ingested papers.

# Review one paper
python3 scripts/review_agent.py --paper /path/to/paper.pdf

# Batch review 5 unreviewed papers
python3 scripts/review_agent.py --batch 5

# Daemon mode (loops every 5 min)
python3 scripts/review_agent.py --daemon --interval 300

Architecture

┌─────────────────────────────────────────┐
│  LLM (Claude / Cline / Continue)        │
│  says: "I need <topic>"                  │
└──────────────────┬──────────────────────┘
                   │  MCP stdio
┌──────────────────▼──────────────────────┐
│  sciencehub_mcp.py                      │
│  ├── ScienceHub.need(query)             │
│  │   ├── CorpusIndex.search(query)      │
│  │   └── if miss → ArxivClient.search() │
│  │       └── ArxivClient.download()      │
│  │           └── ZoteroWriter.add_preprint()│
│  └── review_paper → pdfinfo + pdftotext │
└─────────────────────────────────────────┘

Data Flow

• Zotero DB: ~/Zotero/zotero.sqlite (read + write)
• Index DB: ~/Research Stack/data/substrate_index.db (read + write)
• PDF Archive: ~/Downloads/data/Downloads_from_internet/Deep Research/alphaXiv_PDFs_2026_04/
• Watcher Log: ~/Research Stack/data/ingest_watcher.log

Safety

• Zotero DB is backed up automatically before every write (zotero.sqlite.backup.YYYYMMDD_HHMMSS)
• On any write failure, backup is restored automatically
• arXiv downloads are validated (must be > 1KB)
• Duplicate authors are deduplicated (unique constraint handled)

Troubleshooting

Problem	Fix
"arXiv search failed"	Check internet; script uses https://export.arxiv.org
"Zotero ingest failed"	Check Zotero is closed (no lock on DB)
"No text" in review	PDF may be scanned/image; needs OCR
MCP not connecting	Verify pip install mcp and Python path
Ollama review hangs	Switch to stub mode: set OLLAMA_MODEL env or pass --stub