Zotero Tagging

Zotero Tagging Skill (Claude Code)

Automatically tag Zotero items with timestamp tags after search results or bibliography generation. Credentials stored securely in macOS Keychain.

When to Use This Skill

Use this skill when:

• User has generated a bibliography using the Zotero MCP skill
• User wants to tag search results for later retrieval
• User needs to organize Zotero items by search session
• User asks to "tag these items" or "add tags to the bibliography"

Core Philosophy

Tag search results for traceability. After generating bibliographies or search results:

• Automatically extract item keys from the output
• Tag all items with a timestamp tag format: Zotero-MCP-Results-YYYY-MM-DD-HHMM
• Enable easy re-finding of these exact items in Zotero later
• Track which searches generated which bibliographies

Prerequisites

Before using this skill, ensure:

1. Credentials are set up - User must run setup_credentials.py once to store:

   • Zotero Library ID
   • Zotero API Key (with write access)

2. Python environment - Virtual environment with dependencies installed:

   • pyzotero - Zotero web API client
   • keyring - macOS Keychain integration

3. Zotero Web API Access - User needs:

   • API key from https://www.zotero.org/settings/keys/new
   • Write access enabled on the API key

Security Model

All credentials stored in macOS Keychain:

• ✓ Encrypted by macOS system
• ✓ No plain text files
• ✓ No passwords in code
• ✓ System-managed authentication
• ✓ Viewable/manageable in Keychain Access.app

Service name: zotero-tag-automation

Workflow

Step 1: Check Setup

Before tagging, verify credentials are configured:

cd /Users/niyaro/Documents/Code/zotero-tag-automation
source venv/bin/activate
python -c "import keyring; print('Library ID:', keyring.get_password('zotero-tag-automation', 'library_id'))"

If credentials not found, guide user to run:

python setup_credentials.py

Step 2: Extract Item Keys

From a bibliography markdown file, extract all Zotero item keys:

# Extract keys from bibliography file
grep -o 'zotero://select/library/items/[A-Z0-9]*' bibliography.md | \
  sed 's/.*items\///' | \
  sort -u > /tmp/item_keys.txt

# Show extracted keys
cat /tmp/item_keys.txt

Step 3: Tag Items

Run the tagging script with extracted keys:

cd /Users/niyaro/Documents/Code/zotero-tag-automation
source venv/bin/activate
python tag_items.py $(cat /tmp/item_keys.txt)

Output format:

Tagging 23 items with: Zotero-MCP-Results-2025-10-25-1417

[1/23] ✓ W44VF3CG
[2/23] ✓ M4G5W339
...

Summary:
  Successful: 23/23
  Failed: 0/23
  Tag: Zotero-MCP-Results-2025-10-25-1417

Step 4: Confirm and Report

After tagging, report to user:

• Total items tagged
• Tag name used
• Any errors encountered
• How to find these items in Zotero (search by tag)

Common Usage Patterns

Pattern 1: After Bibliography Generation

User request: "Find papers on X and create a bibliography"

Workflow:

1. Use Zotero MCP skill to search and generate bibliography
2. Save bibliography to file (e.g., /Users/niyaro/Desktop/bibliography.md)
3. Ask user: "Would you like me to tag all 23 items for easy retrieval later?"
4. If yes:
   • Extract item keys from bibliography
   • Run tagging script
   • Report tag name and success count

Pattern 2: Tag Existing Bibliography File

User request: "Tag all the items from bibliography.md"

Workflow:

1. Check file exists
2. Extract item keys
3. Run tagging script
4. Report results

Pattern 3: Tag Specific Items

User request: "Tag items W44VF3CG and M4G5W339"

Workflow:

python tag_items.py W44VF3CG M4G5W339

Pattern 4: First-Time Setup

User request: "Set up Zotero tagging"

Workflow:

1. Guide user to get API key from Zotero
2. Run setup script:

   cd /Users/niyaro/Documents/Code/zotero-tag-automation
   source venv/bin/activate
   python setup_credentials.py
   

3. Verify credentials stored successfully
4. Explain usage

Error Handling

Credentials Not Found

Error: "Credentials not found in Keychain"

Solution:

python setup_credentials.py

Guide user through entering:

• Library ID (from Zotero settings)
• API Key (from https://www.zotero.org/settings/keys/new with write access)

API Key Permissions Error

Error: "403 Forbidden" or "Write access denied"

Solution:

• API key needs write access enabled
• Create new API key at https://www.zotero.org/settings/keys/new
• Check both:
  • ✓ Allow library access
  • ✓ Allow write access
• Re-run setup with new key

Item Not Found

Error: "404 Not Found" for specific item

Possible causes:

• Item key is invalid
• Item was deleted from Zotero
• Library ID mismatch

Solution:

• Verify item exists in Zotero
• Check Library ID in Keychain is correct

Version Conflict

Error: "PreConditionFailed" or version conflict

Solution:

• Item was modified elsewhere
• Script will skip and continue with next items
• Re-run script to retry failed items

Tag Format

Format: Zotero-MCP-Results-YYYY-MM-DD-HHMM

Examples:

• Zotero-MCP-Results-2025-10-25-1417
• Zotero-MCP-Results-2025-10-26-0930

Benefits:

• Sortable by date/time
• Clearly indicates source (MCP search)
• Unique per search session
• Easy to search in Zotero

Integration with Zotero MCP Skill

This skill complements the Zotero MCP skill:

1. Zotero MCP Skill - Search and generate bibliographies
2. Zotero Tagging Skill - Tag the items from those bibliographies

Recommended workflow:

User: "Find papers on Indigenous language certification"
  ↓
Use Zotero MCP Skill → Generate bibliography → Save to file
  ↓
Ask: "Tag these 23 items for later retrieval?"
  ↓
Use Zotero Tagging Skill → Extract keys → Tag items → Report success

File Locations

Script location: /Users/niyaro/Documents/Code/zotero-tag-automation/

Key files:

• setup_credentials.py - One-time credential setup
• tag_items.py - Reusable tagging script
• venv/ - Python virtual environment
• README.md - User documentation

Credentials location: macOS Keychain (service: zotero-tag-automation)

Important Notes

• Claude Code only - This skill is designed for Claude Code environment
• Requires setup - User must run setup_credentials.py once before first use
• Write access required - API key must have write permissions
• Web API only - Uses Zotero web API, not local API (local API is read-only)
• No plain text credentials - All credentials encrypted in macOS Keychain
• Timestamps are local - Tags use system time in YYYY-MM-DD-HHMM format

Quick Reference Commands

Setup (one-time):

cd /Users/niyaro/Documents/Code/zotero-tag-automation
python3 -m venv venv
source venv/bin/activate
pip install pyzotero keyring
python setup_credentials.py

Tag from bibliography:

source venv/bin/activate
grep -o 'items/[A-Z0-9]*' bibliography.md | sed 's/items\///' | xargs python tag_items.py

Tag specific items:

source venv/bin/activate
python tag_items.py W44VF3CG M4G5W339 IQBVNCGF

Check credentials:

security find-generic-password -s "zotero-tag-automation" -a "library_id"

Remember: Always activate the virtual environment (source venv/bin/activate) before running Python scripts.