ToolUniverse Tool Creator

Create new scientific tools for the ToolUniverse framework following established best practices.

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Table of Contents

1. Critical Knowledge
2. Core Concepts
3. Implementation Guide
4. Testing Strategy
5. Common Patterns
6. Troubleshooting
7. Reference

---

Critical Knowledge

Top 7 Mistakes (90% of Failures)

1. Missing default_config.py Entry - Tools silently won't load
2. Non-nullable Mutually Exclusive Parameters - Validation errors (NEW #1 issue in 2026)
3. Fake test_examples - Tests fail, agents get bad examples
4. Single-level Testing - Misses registration bugs
5. Skipping test_new_tools.py - Misses schema/API issues
6. Tool Names > 55 chars - Breaks MCP compatibility
7. Raising Exceptions - Should return error dicts instead

Most Common (2026): Mistake #2 affects 60% of new tools. Always make mutually exclusive parameters nullable: {"type": ["string", "null"]}

Tool Creator vs SDK User

SDK User (Using)	Tool Creator (Building)
tu.tools.ToolName()	@register_tool() + JSON
Handle responses	Design schemas
One-level usage	Three-step registration

---

Core Concepts

Two-Stage Architecture

Stage 1: Tool Class              Stage 2: Wrappers (Auto-Generated)
Python Implementation            From JSON Configs
       ↓                                  ↓
@register_tool("MyTool")         MyAPI_list_items()
class MyTool(BaseTool):          MyAPI_search()
    def run(arguments):          MyAPI_get_details()

Key Points:

• One class handles multiple operations
• JSON defines individual tool wrappers
• Users call wrappers, which route to class
• Need BOTH for tools to work

Three-Step Registration

Step 1: Class Registration

@register_tool("MyAPITool")  # Decorator registers class
class MyAPITool(BaseTool):
    pass

Step 2: Config Registration ⚠️ MOST COMMONLY MISSED

# In src/tooluniverse/default_config.py
TOOLS_CONFIGS = {
    "my_category": os.path.join(current_dir, "data", "my_category_tools.json"),
}

Step 3: Wrapper Generation (Automatic)

tu = ToolUniverse()
tu.load_tools()  # Auto-generates wrappers in tools/

Verification Script:

import sys
sys.path.insert(0, 'src')

# Step 1: Check class registered
from tooluniverse.tool_registry import get_tool_registry
import tooluniverse.your_tool_module
registry = get_tool_registry()
assert "YourToolClass" in registry, "❌ Step 1 FAILED"
print("✅ Step 1: Class registered")

# Step 2: Check config registered
from tooluniverse.default_config import TOOLS_CONFIGS
assert "your_category" in TOOLS_CONFIGS, "❌ Step 2 FAILED"
print("✅ Step 2: Config registered")

# Step 3: Check wrappers generated
from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()
assert hasattr(tu.tools, 'YourCategory_operation1'), "❌ Step 3 FAILED"
print("✅ Step 3: Wrappers generated")
print(f"✅ All steps complete!")

Standard Response Format

All tools must return:

{
  "status": "success" | "error",
  "data": {...},        // On success
  "error": "message"    // On failure
}

Why: Consistent error handling, composability, user expectations

---

Implementation Guide

File Structure

Required Files:

• src/tooluniverse/my_api_tool.py - Implementation
• src/tooluniverse/data/my_api_tools.json - Tool definitions
• tests/unit/test_my_api_tool.py - Tests
• examples/my_api_examples.py - Usage examples

Auto-Generated (don't create manually):

• src/tooluniverse/tools/MyAPI_*.py - Wrappers

Pattern 1: Multi-Operation Tool (Recommended)

Python Class:

from typing import Dict, Any
from tooluniverse.tool import BaseTool
from tooluniverse.tool_utils import register_tool
import requests

@register_tool("MyAPITool")
class MyAPITool(BaseTool):
    """Tool for MyAPI database."""
    
    BASE_URL = "https://api.example.com/v1"
    
    def __init__(self, tool_config):
        super().__init__(tool_config)
        self.parameter = tool_config.get("parameter", {})
        self.required = self.parameter.get("required", [])
    
    def run(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
        """Route to operation handler."""
        operation = arguments.get("operation")
        
        if not operation:
            return {"status": "error", "error": "Missing: operation"}
        
        if operation == "list_items":
            return self._list_items(arguments)
        elif operation == "search":
            return self._search(arguments)
        else:
            return {"status": "error", "error": f"Unknown: {operation}"}
    
    def _list_items(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
        """List items with pagination."""
        try:
            params = {}
            if "limit" in arguments:
                params["limit"] = arguments["limit"]
            
            response = requests.get(
                f"{self.BASE_URL}/items",
                params=params,
                timeout=30
            )
            response.raise_for_status()
            
            data = response.json()
            return {
                "status": "success",
                "data": data.get("items", []),
                "total": data.get("total", 0)
            }
        except requests.exceptions.Timeout:
            return {"status": "error", "error": "Timeout after 30s"}
        except requests.exceptions.HTTPError as e:
            return {"status": "error", "error": f"HTTP {e.response.status_code}"}
        except Exception as e:
            return {"status": "error", "error": str(e)}
    
    def _search(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
        """Search items by query."""
        query = arguments.get("query")
        if not query:
            return {"status": "error", "error": "Missing: query"}
        
        try:
            response = requests.get(
                f"{self.BASE_URL}/search",
                params={"q": query},
                timeout=30
            )
            response.raise_for_status()
            
            data = response.json()
            return {
                "status": "success",
                "results": data.get("results", []),
                "count": data.get("count", 0)
            }
        except requests.exceptions.RequestException as e:
            return {"status": "error", "error": f"API failed: {str(e)}"}

JSON Configuration:

[
  {
    "name": "MyAPI_list_items",
    "class": "MyAPITool",
    "description": "List items from database with pagination. Returns item IDs and names. Supports filtering by status and type. Example: limit=10 returns first 10 items.",
    "parameter": {
      "type": "object",
      "required": ["operation"],
      "properties": {
        "operation": {
          "const": "list_items",
          "description": "Operation type (fixed)"
        },
        "limit": {
          "type": "integer",
          "description": "Max results (1-100)",
          "minimum": 1,
          "maximum": 100
        }
      }
    },
    "return": {
      "type": "object",
      "properties": {
        "status": {"type": "string", "enum": ["success", "error"]},
        "data": {"type": "array"},
        "total": {"type": "integer"},
        "error": {"type": "string"}
      },
      "required": ["status"]
    },
    "test_examples": [
      {
        "operation": "list_items",
        "limit": 10
      }
    ]
  }
]

Pattern 2: Async Polling (Job-Based APIs)

import time

def _submit_job(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
    """Submit job and poll for results."""
    try:
        # Submit
        submit_response = requests.post(
            f"{self.BASE_URL}/jobs/submit",
            json={"data": arguments.get("data")},
            timeout=30
        )
        submit_response.raise_for_status()
        job_id = submit_response.json().get("job_id")
        
        # Poll
        for attempt in range(60):  # 2 min max
            status_response = requests.get(
                f"{self.BASE_URL}/jobs/{job_id}/status",
                timeout=30
            )
            status_response.raise_for_status()
            
            result = status_response.json()
            if result.get("status") == "completed":
                return {
                    "status": "success",
                    "data": result.get("results"),
                    "job_id": job_id
                }
            elif result.get("status") == "failed":
                return {
                    "status": "error",
                    "error": result.get("error"),
                    "job_id": job_id
                }
            
            time.sleep(2)  # Poll every 2s
        
        return {"status": "error", "error": "Timeout after 2 min"}
    except requests.exceptions.RequestException as e:
        return {"status": "error", "error": str(e)}

API Key Configuration

Tools can specify API key requirements in JSON config:

required_api_keys - Tool won't load without these:

{
  "name": "NVIDIA_ESMFold_predict",
  "required_api_keys": ["NVIDIA_API_KEY"],
  ...
}

optional_api_keys - Tool loads and works without keys, but with reduced performance:

{
  "name": "PubMed_search_articles",
  "optional_api_keys": ["NCBI_API_KEY"],
  "description": "Search PubMed. Rate limits: 3 req/sec without key, 10 req/sec with NCBI_API_KEY.",
  ...
}

When to use optional_api_keys:

• APIs with rate limits that improve with a key (NCBI: 3→10 req/sec, Semantic Scholar: 1→100 req/sec)
• APIs that work anonymously but have better quotas with authentication
• Tools that should always be available, even for users without API keys

Implementation pattern for optional keys:

def __init__(self, tool_config):
    super().__init__(tool_config)
    # Read from environment variable only (not as parameter)
    self.api_key = os.environ.get("NCBI_API_KEY", "")

def run(self, arguments):
    # Adjust behavior based on key availability
    has_key = bool(self.api_key)
    rate_limit = 0.1 if has_key else 0.4  # Faster with key
    ...

Key rules:

• ❌ Don't add api_key as a tool parameter for optional keys
• ✅ Read optional keys from environment variables only
• ✅ Include rate limit info in tool description
• ✅ Tool must work (with degraded performance) when key is missing

JSON Best Practices

Tool Naming (≤55 chars for MCP):

• Template: {API}_{action}_{target}
• ✅ Good: FDA_get_drug_info (20 chars)
• ❌ Bad: FDA_get_detailed_drug_information_with_history (55+ chars)

Description (150-250 chars, high-context):

{
  "description": "Search database for items. Returns up to 100 results with scores. Supports wildcards (* ?) and Boolean operators (AND, OR, NOT). Example: 'protein AND membrane' finds membrane proteins."
}

Include: What it returns, data source, use case, input format, example

test_examples (MUST be real):

{
  "test_examples": [
    {
      "operation": "search",
      "query": "protein",     // ✅ Real, common term
      "limit": 10
    }
  ]
}

❌ Don't use: "id": "XXXXX", "placeholder": "example_123"
✅ Do use: Real IDs from actual API documentation

JSON Config Conventions

• The "type" field in JSON must match the Python class name from @register_tool
• Include return_schema to define tool output structure (not just return)
• Put example inputs in test_examples only; avoid examples blocks inside parameter/return_schema — they bloat configs and drift from reality
• For large allow-lists, document values in description and enforce in Python (avoid giant schema enum)
• Auto-discovery: tools placed in src/tooluniverse/ are auto-discovered; no __init__.py modification needed
• Optional: implement validate_parameters(arguments) for custom validation

For the full implementation plan, maintenance checklist, and large API expansion guidance, see references/implementation-guide.md

---

Testing Strategy

Final Validation with test_new_tools.py (MANDATORY)

All new tools MUST pass scripts/test_new_tools.py before submission.

This script tests tools using their test_examples from JSON configs and validates responses against return_schema.

# Test your specific tools
python scripts/test_new_tools.py your_tool_name

# Test with verbose output
python scripts/test_new_tools.py your_tool_name -v

# Test all tools (for full validation)
python scripts/test_new_tools.py

# Stop on first failure
python scripts/test_new_tools.py your_tool_name --fail-fast

What it validates:

• Tool execution succeeds (no exceptions)
• Response matches return_schema (if defined)
• 404 errors tracked separately (indicates bad test_examples)
• Tools with missing API keys are skipped gracefully

Common failures and fixes:

Failure	Cause	Fix
404 ERROR	Invalid ID in test_examples	Use real IDs from API docs
Schema Mismatch	Response doesn't match return_schema	Update schema or fix response format
Exception	Code bug or missing dependency	Check error message, fix implementation

---

Two-Level Testing (MANDATORY)

Level 1: Direct Class Testing

import json
from tooluniverse.your_tool_module import YourToolClass

def test_direct_class():
    """Test implementation logic."""
    with open("src/tooluniverse/data/your_tools.json") as f:
        tools = json.load(f)
        config = next(t for t in tools if t["name"] == "YourTool_operation1")
    
    tool = YourToolClass(config)
    result = tool.run({"operation": "operation1", "param": "value"})
    
    assert result["status"] == "success"
    assert "data" in result

Level 2: ToolUniverse Interface Testing

import pytest
from tooluniverse import ToolUniverse

class TestYourTools:
    @pytest.fixture
    def tu(self):
        tu = ToolUniverse()
        tu.load_tools()  # CRITICAL
        return tu
    
    def test_tools_load(self, tu):
        """Verify registration."""
        assert hasattr(tu.tools, 'YourTool_operation1')
    
    def test_execution(self, tu):
        """Test via ToolUniverse (how users call it)."""
        result = tu.tools.YourTool_operation1(**{
            "operation": "operation1",
            "param": "value"
        })
        assert result["status"] == "success"
    
    def test_error_handling(self, tu):
        """Test missing params."""
        result = tu.tools.YourTool_operation1(**{
            "operation": "operation1"
            # Missing required param
        })
        assert result["status"] == "error"

Level 3: Real API Testing

def test_real_api():
    """Verify actual API integration."""
    tu = ToolUniverse()
    tu.load_tools()
    
    result = tu.tools.YourTool_operation1(**{
        "operation": "operation1",
        "param": "real_value_from_docs"
    })
    
    if result["status"] == "success":
        assert "data" in result
        print("✅ Real API works")
    else:
        print(f"⚠️  API error (may be down): {result['error']}")

Why Both Levels:

• Level 1: Tests implementation, catches code bugs
• Level 2: Tests registration, catches config bugs
• Level 3: Tests integration, catches API issues

---

Systematic Testing for Multiple New Tools

When creating multiple tools at once (e.g., 5-15 tools for an API), use this systematic approach:

Step 1: Sample Testing (Quick validation)

# Test 1-2 tools per API to catch common issues
python scripts/test_new_tools.py MyAPI_get_item -v
python scripts/test_new_tools.py MyAPI_search -v

Step 2: Identify Patterns

Group errors by type:

• Parameter validation errors: "None is not of type 'integer'" → Make parameters nullable
• API errors: 404, 400 → Fix test_examples with real IDs
• Schema errors: "Data: None" → Check return format
• Wrong parameter names: "unexpected keyword" → Verify against config

Step 3: Fix Systematically

Fix all tools with same issue together:

# Fix all nullable parameter issues in JSON
# Then regenerate once:
python -m tooluniverse.generate_tools

Step 4: Verify All

Test all tools comprehensively:

# Test entire tool set
python scripts/test_new_tools.py MyAPI -v

# Verify count
python3 << 'EOF'
from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()
my_tools = [t for t in dir(tu.tools) if t.startswith('MyAPI_')]
print(f"✅ {len(my_tools)} MyAPI tools loaded")
EOF

Step 5: Verify Parameter Names

Before testing, verify parameter names match the config:

import json
with open('src/tooluniverse/data/myapi_tools.json') as f:
    tools = json.load(f)
    for tool in tools:
        print(f"{tool['name']}: {list(tool['parameter']['properties'].keys())}")

Don't assume parameter names like query, id, taxon - always verify!

Step 6: Data Structure Verification

Test understanding of return data structure:

result = tu.tools.MyAPI_get_item(id="123")

# For object data
if isinstance(result.get('data'), dict):
    print("✅ Returns single object")
    value = result['data'].get('field')

# For array data
elif isinstance(result.get('data'), list):
    print("✅ Returns array of items")
    count = len(result['data'])
    first = result['data'][0] if result['data'] else {}

---

Common Patterns

Error Handling Checklist

✅ Always set timeout (30s recommended)
✅ Catch specific exceptions (Timeout, ConnectionError, HTTPError)
✅ Return error dicts, never raise in run()
✅ Include helpful context in error messages
✅ Handle JSON parsing errors
✅ Validate required parameters

Parameter Design Best Practices

Mutually Exclusive Parameters (CRITICAL)

When creating tools that accept EITHER parameterA OR parameterB, both parameters MUST be nullable.

❌ WRONG - Will cause validation errors:

{
  "parameter": {
    "type": "object",
    "properties": {
      "id": {
        "type": "integer",
        "description": "Numeric ID"
      },
      "name": {
        "type": "string",
        "description": "Name string (alternative to id)"
      }
    }
  }
}

Problem: When user provides only name, validation fails because id is None and not of type integer.

✅ CORRECT - Make mutually exclusive parameters nullable:

{
  "parameter": {
    "type": "object",
    "properties": {
      "id": {
        "type": ["integer", "null"],
        "description": "Numeric ID"
      },
      "name": {
        "type": ["string", "null"],
        "description": "Name string (alternative to id)"
      }
    }
  }
}

Common patterns requiring nullable parameters:

• id OR name (get by ID or by name)
• acronym OR name (search by symbol or full name)
• gene_id OR gene_symbol
• neuron_id OR neuron_name
• Optional filter parameters (filter_field, filter_value)

Optional Parameters

All optional parameters should be nullable:

{
  "filter_field": {
    "type": ["string", "null"],
    "description": "Optional filter field"
  },
  "limit": {
    "type": ["integer", "null"],
    "description": "Optional result limit",
    "default": 10
  }
}

Parameter Naming Consistency

Use consistent, descriptive parameter names:

• ✅ gene_id, gene_symbol, tax_id - Clear and specific
• ❌ id, query, q - Too generic, causes confusion

Check API documentation for parameter names:

• Match official API parameter names when possible
• Use snake_case for Python/JSON consistency
• Document the mapping if API uses different names

Test Examples

Use REAL IDs in test_examples, never placeholders:

{
  "test_examples": [
    {
      "gene_id": "7157"  // ✅ Real TP53 gene ID
    },
    {
      "gene_symbol": "BRCA1",  // ✅ Real gene symbol
      "taxon": "9606"  // ✅ Real human tax ID
    }
  ]
}

❌ AVOID:

{
  "test_examples": [
    {
      "gene_id": "TEST123"  // ❌ Fake ID
    },
    {
      "gene_id": "example_id"  // ❌ Placeholder
    }
  ]
}

Return Schema and Data Structure

Document whether data is object, array, or string:

{
  "name": "MyAPI_get_item",
  "description": "Get single item by ID. Returns object with item details.",
  "return_schema": {
    "oneOf": [
      {
        "type": "object",
        "properties": {
          "data": {
            "type": "object",  // ← Specify: single object
            "properties": {
              "id": {"type": "string"},
              "name": {"type": "string"}
            }
          }
        }
      }
    ]
  }
}

{
  "name": "MyAPI_search",
  "description": "Search items. Returns array of matching items.",
  "return_schema": {
    "oneOf": [
      {
        "type": "object",
        "properties": {
          "data": {
            "type": "array",  // ← Specify: array of results
            "items": {
              "type": "object",
              "properties": {
                "id": {"type": "string"}
              }
            }
          }
        }
      }
    ]
  }
}

Dependency Management

Check package size FIRST:

curl -s https://pypi.org/pypi/PACKAGE/json | python3 -c "
import json, sys
data = json.load(sys.stdin)
print(f'Dependencies: {len(data[\"info\"][\"requires_dist\"] or [])}')
"

Classification:

• Core (<100MB, universal use) → [project.dependencies]
• Optional (>100MB or niche) → [project.optional-dependencies]

In code:

try:
    import optional_package
except ImportError:
    return {
        "status": "error",
        "error": "Install with: pip install optional_package"
    }

Pagination Pattern

def _list_items(self, arguments):
    params = {}
    if "page" in arguments:
        params["page"] = arguments["page"]
    if "limit" in arguments:
        params["limit"] = arguments["limit"]
    
    response = requests.get(url, params=params, timeout=30)
    data = response.json()
    
    return {
        "status": "success",
        "data": data.get("items", []),
        "page": data.get("page", 0),
        "total_pages": data.get("total_pages", 1),
        "total_items": data.get("total", 0)
    }

---

Troubleshooting

Tool Doesn't Load (90% of Issues)

Symptoms: Tool count doesn't increase, no error, AttributeError when calling

Cause: Missing Step 2 of registration (default_config.py)

Solution:

# Edit src/tooluniverse/default_config.py
TOOLS_CONFIGS = {
    # ... existing ...
    "your_category": os.path.join(current_dir, "data", "your_category_tools.json"),
}

Verify:

grep "your_category" src/tooluniverse/default_config.py
ls src/tooluniverse/tools/YourCategory_*.py
python3 -c "from tooluniverse import ToolUniverse; tu = ToolUniverse(); tu.load_tools(); print(hasattr(tu.tools, 'YourCategory_op1'))"

Tests Fail with Real APIs

Mock vs Real Testing:

• Mocks test code structure
• Real calls test API integration
• Both needed for confidence

What Real Testing Catches:

• Response structure differences
• Parameter name mismatches
• Unexpected pagination
• Timeout issues
• Data type surprises

---

Reference

Complete Workflow

1. Create Python class with @register_tool
2. Create JSON config with realistic test_examples and return_schema
3. Add to default_config.py ← CRITICAL
4. Generate wrappers: tu.load_tools()
5. Test Level 1 (direct class)
6. Test Level 2 (ToolUniverse interface)
7. Test Level 3 (real API calls)
8. Run python scripts/test_new_tools.py your_tool -v ← MANDATORY
9. Run python scripts/check_tool_name_lengths.py --test-shortening
10. Create examples file
11. Verify all 3 registration steps
12. Document in verification report

For the full development checklist and maintenance phases, see references/implementation-guide.md

Quick Commands

# Validate JSON
python3 -m json.tool src/tooluniverse/data/your_tools.json

# Check Python syntax
python3 -m py_compile src/tooluniverse/your_tool.py

# Verify registration
grep "your_category" src/tooluniverse/default_config.py

# Generate wrappers
PYTHONPATH=src python3 -m tooluniverse.generate_tools --force

# List wrappers
ls src/tooluniverse/tools/YourCategory_*.py

# Run unit tests
pytest tests/unit/test_your_tool.py -v

# MANDATORY: Run test_new_tools.py validation
python scripts/test_new_tools.py your_tool -v

# Count tools
python3 << 'EOF'
from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()
print(f"Total: {len([t for t in dir(tu.tools) if 'YourCategory' in t])} tools")
EOF

Critical Reminders

⚠️ ALWAYS add to default_config.py (Step 2)
⚠️ NEVER raise exceptions in run()
⚠️ ALWAYS use real test_examples
⚠️ ALWAYS test both levels
⚠️ RUN python scripts/test_new_tools.py your_tool -v before submitting
⚠️ KEEP tool names ≤55 characters
⚠️ RETURN standard response format
⚠️ SET timeout on all HTTP requests
⚠️ VERIFY all 3 registration steps
⚠️ USE optional_api_keys for rate-limited APIs that work without keys
⚠️ NEVER add api_key parameter for optional keys - use env vars only

Success Criteria

✅ All 3 registration steps verified
✅ Level 1 tests passing (direct class)
✅ Level 2 tests passing (ToolUniverse interface)
✅ Real API calls working (Level 3)
✅ test_new_tools.py passes with 0 failures ← MANDATORY
✅ Tool names ≤55 characters
✅ test_examples use real IDs
✅ Standard response format used
✅ Helpful error messages
✅ Examples file created
✅ No raised exceptions in run()

When all criteria met → Production Ready 🎉