zotero-mcp-code

name	zotero-mcp-code
description	Search Zotero library using code execution for efficient multi-strategy searches without crash risks. Use this skill when the user needs comprehensive Zotero searches with automatic deduplication and ranking.

Zotero MCP Code Execution Skill

Search your Zotero library using code execution for safe, efficient, comprehensive searches.

🎯 Core Concept

Instead of calling MCP tools directly (which loads all results into context and risks crashes), write Python code that:

1. Fetches large datasets (50-100+ items per strategy)
2. Filters and ranks in code execution environment
3. Returns only top N results to context

Benefits:

• ✅ No crash risk (large data stays in code)
• ✅ Automatic multi-strategy search
• ✅ Automatic deduplication
• ✅ Automatic ranking
• ✅ One function call instead of 5-10

⚠️ Critical Notes

Multi-Term Searches

Zotero treats multi-word queries as AND conditions!

❌ Wrong: comprehensive_search("Atyal Atayal 泰雅族") → finds 0 results (needs ALL terms) ✅ Right: Search each term separately and merge results (see Pattern 6 below)

When to use multi-term OR search:

• Multiple spellings (Atayal, Atyal)
• Multiple languages (Atayal, 泰雅族)
• Synonyms (skill transfer, transfer of learning)

Semantic Search Status

Semantic search is now working correctly (fixed 2025-01-08). However, you may see 404 error messages in output from the semantic search engine itself - these can be ignored as our wrapper handles them correctly.

🚀 Basic Usage

For 90% of Zotero searches, use this simple pattern:

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths

from zotero_lib import SearchOrchestrator, format_results

# Single comprehensive search
orchestrator = SearchOrchestrator()
results = orchestrator.comprehensive_search(
    "user's query here",
    max_results=20,  # Return top 20 most relevant
    use_semantic=True  # Semantic search now works correctly
)

# Format and display
print(format_results(results, include_abstracts=True))

This automatically:

• Performs semantic search (vector similarity)
• Performs keyword search (qmode="everything" + "titleCreatorYear")
• Performs tag-based search
• Fetches 100+ items total
• Deduplicates results
• Ranks by relevance
• Returns only top 20 to context

📋 Common Patterns

Pattern 1: Simple Search (Most Common)

User asks: "Find papers about embodied cognition"

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import SearchOrchestrator, format_results

orchestrator = SearchOrchestrator()
results = orchestrator.comprehensive_search("embodied cognition", max_results=20)
print(format_results(results))

Pattern 2: Filtered Search

User asks: "Find recent journal articles about machine learning"

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import ZoteroLibrary, SearchOrchestrator, format_results

library = ZoteroLibrary()
orchestrator = SearchOrchestrator(library)

# Fetch broadly (safe - filtering happens in code)
items = library.search_items("machine learning", limit=100)

# Filter in code
filtered = orchestrator.filter_by_criteria(
    items,
    item_types=["journalArticle"],
    date_range=(2020, 2025)
)

print(format_results(filtered[:15]))

Pattern 3: Author Search

User asks: "What papers do I have by Kahneman?"

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import ZoteroLibrary, format_results

library = ZoteroLibrary()
results = library.search_items(
    "Kahneman",
    qmode="titleCreatorYear",
    limit=50
)

# Sort by date
sorted_results = sorted(results, key=lambda x: x.date, reverse=True)
print(format_results(sorted_results))

Pattern 4: Tag-Based Search

User asks: "Show me papers tagged with 'learning' and 'cognition'"

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import ZoteroLibrary, format_results

library = ZoteroLibrary()
results = library.search_by_tag(["learning", "cognition"], limit=50)
print(format_results(results[:20]))

Pattern 5: Recent Papers

User asks: "What did I recently add?"

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import ZoteroLibrary, format_results

library = ZoteroLibrary()
results = library.get_recent(limit=20)
print(format_results(results))

Pattern 6: Multi-Term OR Search (Multiple Spellings/Languages)

User asks: "Find papers about Atyal or 泰雅族" (alternate spellings/languages)

IMPORTANT: Zotero treats multi-word queries as AND conditions. For OR searches, search each term separately and merge.

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import SearchOrchestrator, format_results

orchestrator = SearchOrchestrator()

# Search each term separately
all_results = {}
for term in ['Atayal', '泰雅族']:
    results = orchestrator.comprehensive_search(term, max_results=50, use_semantic=True)
    for item in results:
        all_results[item.key] = item  # Deduplicate by key

# Re-rank combined results
ranked = orchestrator._rank_items(list(all_results.values()), 'Atayal 泰雅族')

# Optional: Filter for specific content
filtered = [item for item in ranked
            if any(term in (item.title + item.abstract).lower()
                   for term in ['atyal', 'atayal', '泰雅'])]

print(format_results(filtered[:25], include_abstracts=True))

Pattern 7: Multi-Topic AND Search

User asks: "Find papers about both cognition and learning"

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import SearchOrchestrator, format_results

orchestrator = SearchOrchestrator()

# Search both topics
results1 = orchestrator.comprehensive_search("cognition", max_results=30)
results2 = orchestrator.comprehensive_search("learning", max_results=30)

# Find intersection
keys1 = {item.key for item in results1}
keys2 = {item.key for item in results2}
common_keys = keys1 & keys2

if common_keys:
    common_items = [item for item in results1 if item.key in common_keys]
    print("Papers about both topics:")
    print(format_results(common_items))
else:
    print("No papers found on both topics.")
    print("\nCognition results:")
    print(format_results(results1[:10]))
    print("\nLearning results:")
    print(format_results(results2[:10]))

🔧 Advanced Usage

Custom Filtering Logic

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import ZoteroLibrary, SearchOrchestrator, format_results

library = ZoteroLibrary()
orchestrator = SearchOrchestrator(library)

# Fetch large dataset
items = library.search_items("neural networks", limit=100)

# Custom filtering
recent_with_doi = [
    item for item in items
    if item.doi and item.date and int(item.date[:4]) >= 2020
]

print(format_results(recent_with_doi[:15]))

Multi-Angle Custom Search

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import ZoteroLibrary, SearchOrchestrator, format_results

library = ZoteroLibrary()
orchestrator = SearchOrchestrator(library)

all_results = set()

# Multiple search angles
queries = [
    "skill transfer",
    "transfer of learning",
    "generalization of skills"
]

for query in queries:
    results = library.search_items(query, limit=30)
    all_results.update(results)

# Rank combined results
ranked = orchestrator._rank_items(list(all_results), "skill transfer")
print(format_results(ranked[:20]))

Iterative Refinement

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import ZoteroLibrary, SearchOrchestrator, format_results

library = ZoteroLibrary()
orchestrator = SearchOrchestrator(library)

# Initial search
initial = library.search_items("memory", limit=50)

# Analyze tags
tag_freq = {}
for item in initial:
    for tag in item.tags:
        tag_freq[tag] = tag_freq.get(tag, 0) + 1

# Find most common tag
if tag_freq:
    most_common_tag = max(tag_freq, key=tag_freq.get)

    # Refine search
    refined = orchestrator.filter_by_criteria(
        initial,
        required_tags=[most_common_tag]
    )

    print(f"Papers with most common tag '{most_common_tag}':")
    print(format_results(refined))

📚 API Reference

SearchOrchestrator

Main class for automated searching.

comprehensive_search(query, max_results=20, use_semantic=True, use_keyword=True, use_tags=True, search_limit_per_strategy=50)

Performs multi-strategy search with automatic deduplication and ranking.

Parameters:

• query (str): Search query
• max_results (int): Maximum results to return (default: 20)
• use_semantic (bool): Use semantic search (default: True)
• use_keyword (bool): Use keyword search (default: True)
• use_tags (bool): Use tag search (default: True)
• search_limit_per_strategy (int): Items to fetch per strategy (default: 50)

Returns: List of ZoteroItem objects

filter_by_criteria(items, item_types=None, date_range=None, required_tags=None, excluded_tags=None)

Filter items by various criteria.

Parameters:

• items (list): Items to filter
• item_types (list): Allowed item types (e.g., ["journalArticle"])
• date_range (tuple): (min_year, max_year)
• required_tags (list): Tags that must be present
• excluded_tags (list): Tags that must not be present

Returns: Filtered list of ZoteroItem objects

ZoteroLibrary

Low-level interface to Zotero.

search_items(query, qmode="titleCreatorYear", item_type="-attachment", limit=100, tag=None)

Basic keyword search.

semantic_search(query, limit=100, search_type="hybrid")

Semantic/vector search.

search_by_tag(tags, item_type="-attachment", limit=100)

Search by tags.

get_recent(limit=50)

Get recently added items.

get_tags()

Get all tags in library.

format_results(items, include_abstracts=True, max_abstract_length=300)

Format items as markdown.

⚙️ Configuration

Default Parameters

Good defaults for most searches:

orchestrator.comprehensive_search(
    query,
    max_results=20,              # Top 20 results
    search_limit_per_strategy=50 # Fetch 50 per strategy
)

Adjusting Search Depth

For quick searches (fewer results, faster):

results = orchestrator.comprehensive_search(
    query,
    max_results=10,
    search_limit_per_strategy=20
)

For thorough searches (more comprehensive):

results = orchestrator.comprehensive_search(
    query,
    max_results=30,
    search_limit_per_strategy=100
)

🔍 How It Works

Behind the Scenes

When you call comprehensive_search("embodied cognition", max_results=20):

1. Semantic Search (if enabled):

   • Searches "embodied cognition" (hybrid mode) → 50 items
   • Searches "embodied cognition" (vector mode) → 50 items

2. Keyword Search (if enabled):

   • Searches with qmode="everything" → 50 items
   • Searches with qmode="titleCreatorYear" → 50 items

3. Tag Search (if enabled):

   • Extracts words from query
   • Finds matching tags in library
   • Searches by matching tags → 50 items

4. Processing:

   • Combines all results (~250 items)
   • Deduplicates using item keys (~120 unique)
   • Ranks by relevance score
   • Returns top 20

5. Context:

   • Only the final 20 items go to LLM context
   • All processing happens in code execution environment

Why This Is Better

Old Approach (Direct MCP):

# 5+ function calls, all results to context
results1 = zotero_semantic_search("query", limit=10)  # Crash risk if > 15
results2 = zotero_search_items("query", limit=10)
# ... manual deduplication, no ranking
# All items (50+) load into context

New Approach (Code Execution):

# 1 function call, only top results to context
results = orchestrator.comprehensive_search("query", max_results=20)
# Fetches 250+ items, processes in code, returns top 20

🛠️ Error Handling

Always handle potential errors:

import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import SearchOrchestrator, format_results

orchestrator = SearchOrchestrator()

try:
    results = orchestrator.comprehensive_search("query", max_results=20)

    if results:
        print(format_results(results))
    else:
        print("No results found. Try a broader search term.")

except Exception as e:
    print(f"Search failed: {e}")
    print("Please check your Zotero MCP configuration.")

📖 Examples

See /Users/niyaro/Documents/Code/zotero-code-execution/examples.py for 8 complete working examples.

🎓 Quick Reference

Task	Code
Basic search	orchestrator.comprehensive_search(query, max_results=20)
Filter by type	orchestrator.filter_by_criteria(items, item_types=["journalArticle"])
Filter by date	orchestrator.filter_by_criteria(items, date_range=(2020, 2025))
Search author	library.search_items(author, qmode="titleCreatorYear", limit=50)
Search by tag	library.search_by_tag([tags], limit=50)
Recent items	library.get_recent(limit=20)
Format output	format_results(items, include_abstracts=True)

💡 Tips

1. Start simple: Use comprehensive_search() for most queries
2. Adjust depth: Use search_limit_per_strategy to control thoroughness
3. Filter after: Fetch broadly, filter in code
4. Custom logic: Use Python for complex filtering
5. Check errors: Always wrap in try/except

📁 Documentation

• Quick Start: /Users/niyaro/Documents/Code/zotero-code-execution/QUICK_START.md
• Full Docs: /Users/niyaro/Documents/Code/zotero-code-execution/README.md
• Examples: /Users/niyaro/Documents/Code/zotero-code-execution/examples.py
• Status: /Users/niyaro/Documents/Code/zotero-code-execution/HONEST_STATUS.md

⚠️ Important Notes

• This uses code execution, not direct MCP calls
• Large datasets are processed in code, keeping context small
• Semantic search may not be available (falls back to keyword)
• Results are automatically deduplicated and ranked
• Safe to use large limits (100+) because filtering happens in code

🔄 Migration from zotero-mcp

Old pattern:

# Multiple manual MCP calls
results1 = zotero_semantic_search("query", limit=10)
results2 = zotero_search_items("query", limit=10)
# Manual deduplication...

New pattern:

# One function call with code execution
import sys
sys.path.append('/Users/niyaro/Documents/Code/zotero-code-execution')
import setup_paths
from zotero_lib import SearchOrchestrator, format_results

orchestrator = SearchOrchestrator()
results = orchestrator.comprehensive_search("query", max_results=20)
print(format_results(results))

---

Remember: This skill uses code execution to safely handle large searches. The implementation is in /Users/niyaro/Documents/Code/zotero-code-execution/.