zotero-paper-reader

name	zotero-paper-reader
description	Read and analyze academic papers from Zotero library. Use when the user requests to read, access, or analyze a paper by title, author, or topic from their Zotero library. Automatically searches Zotero, converts PDFs to markdown, and provides analysis.
allowed-tools	Bash(python:*), Bash(pymupdf:*), Read, WebSearch

Zotero Paper Reader

Read and analyze academic papers directly from the Zotero library.

When to Use

• "Read this paper from Zotero"
• "Find and read [paper title]"
• "Access [author name] paper"
• "Get the paper about [topic]"
• "Convert [paper] from Zotero to markdown"

Workflow

Step 1: Search Zotero Library

Search for the paper using SQLite:

sqlite3 ~/Zotero/zotero.sqlite "
SELECT
    items.key,
    itemDataValues.value as title,
    itemTypes.typeName
FROM items
JOIN itemData ON items.itemID = itemData.itemID
JOIN itemDataValues ON itemData.valueID = itemDataValues.valueID
JOIN fields ON itemData.fieldID = fields.fieldID
JOIN itemTypes ON items.itemTypeID = itemTypes.itemTypeID
WHERE fields.fieldName = 'title'
    AND itemDataValues.value LIKE '%关键词%'
ORDER BY items.dateAdded DESC
LIMIT 10;
"

Step 2: Get PDF Attachment

sqlite3 ~/Zotero/zotero.sqlite "
SELECT
    itemAttachments.key,
    itemAttachments.path
FROM itemAttachments
WHERE parentItemID = (
    SELECT itemID FROM items WHERE key = 'ITEM_KEY'
)
AND contentType = 'application/pdf';
"

Step 3: Convert PDF to Markdown

Use PyMuPDF to extract text:

import fitz  # PyMuPDF

def pdf_to_markdown(pdf_path, output_path):
    """Convert PDF to Markdown"""
    doc = fitz.open(pdf_path)
    markdown_content = []

    for page_num, page in enumerate(doc, 1):
        text = page.get_text()
        markdown_content.append(f"## Page {page_num}\n\n{text}\n\n")

    with open(output_path, 'w', encoding='utf-8') as f:
        f.write(''.join(markdown_content))

    doc.close()
    return output_path

# Usage
pdf_to_markdown("~/Zotero/storage/ABC123/paper.pdf", "paper.md")

Step 4: Read and Analyze

Read the converted markdown file:

# For large papers, read in sections
with open("paper.md", 'r', encoding='utf-8') as f:
    lines = f.readlines()

# Read abstract and introduction (first 300-500 lines)
content = ''.join(lines[:500])

Provide the user with:

1. Paper metadata (title, authors, publication year)
2. Brief summary of the abstract
3. Main findings or sections of interest
4. Offer to read specific sections

PDF Processing Tools

Install PyMuPDF

pip install pymupdf

Extract Text Only

import fitz
doc = fitz.open("paper.pdf")
for page in doc:
    print(page.get_text())

Extract with Formatting

import fitz
doc = fitz.open("paper.pdf")
for page in doc:
    blocks = page.get_text("dict")["blocks"]
    for block in blocks:
        if "lines" in block:
            for line in block["lines"]:
                for span in line["spans"]:
                    print(span["text"])

Extract Images

import fitz
doc = fitz.open("paper.pdf")
for page_num, page in enumerate(doc):
    images = page.get_images()
    for img_index, img in enumerate(images):
        xref = img[0]
        base_image = doc.extract_image(xref)
        with open(f"image_{page_num}_{img_index}.png", "wb") as f:
            f.write(base_image["image"])

Example Usage

User request: "Read the paper 'Attention Is All You Need' from my Zotero library"

1. Search: Find paper by title
2. Get attachment: Find PDF path
3. Convert: Extract text to markdown
4. Analyze: Summarize key findings
5. Report: Provide structured summary

Notes

• For large papers (>40k tokens), read in sections
• PyMuPDF handles most PDF formats well
• Some scanned PDFs may require OCR (use pytesseract)
• Complex layouts (multi-column) may need additional processing