mirror of
https://github.com/mims-harvard/ToolUniverse.git
synced 2026-09-19 07:31:47 +08:00
Shanghua Gao
9f7070ed7b
### **Visualization Suite** - 2D/3D molecular visualization with interactive HTML output - Protein structure rendering with multiple visualization styles - Scientific plotting with Plotly, Matplotlib, and NetworkX ### **Coding API** - Type-safe function calling: `from tooluniverse.tools import ToolName` - Dynamic tool access: `tu.tools.ToolName()` - Built-in caching and error handling ### **Health Check System** - New `tooluniverse-doctor` CLI tool - Automatic dependency validation and bulk fix commands ### **Expanded Tool Ecosystem** - 50+ new scientific tools - Clinical guidelines (NICE, WHO, Europe PMC)
146 lines
5.0 KiB
Python
146 lines
5.0 KiB
Python
#!/usr/bin/env python3
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"""
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ToolUniverse Coding API Examples
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Demonstrates various methods for calling tools using the coding API
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"""
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from tooluniverse import ToolUniverse
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from pathlib import Path
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# =============================================================================
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# Method 1: Dynamic Function-Style Calling
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# =============================================================================
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# Description: Call tools like regular Python functions through tu.tools
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# Syntax: tu.tools.ToolName(parameter=value)
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tu = ToolUniverse()
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tu.load_tools()
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# Basic function-style calling
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result1 = tu.tools.UniProt_get_entry_by_accession(accession="P05067")
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# Error handling for non-existent tools
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try:
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tu.tools.NonExistentTool(some_param="test")
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except AttributeError as e:
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# Handle non-existent tool error
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pass
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# Caching functionality
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result2 = tu.tools.UniProt_get_entry_by_accession(
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accession="P05067",
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use_cache=True
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)
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# Lifecycle management
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tu.tools.refresh()
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tu.tools.eager_load(["UniProt_get_entry_by_accession"])
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# =============================================================================
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# Method 2: Generated Tools Calling
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# =============================================================================
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# Description: Use pre-generated tools for type-safe tool calling
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# Syntax: from tooluniverse.tools import ToolName
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# Note: Tools are auto-generated: python scripts/build_tools.py
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# Import generated tools
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from tooluniverse.tools import UniProt_get_entry_by_accession
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from tooluniverse.exceptions import ToolValidationError
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# Call tool function directly
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result3 = UniProt_get_entry_by_accession(accession="P05067")
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# Structured error handling
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try:
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result4 = UniProt_get_entry_by_accession(accession="invalid")
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except ToolValidationError as e:
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# Handle structured validation errors
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# e.next_steps contains suggested actions
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# e.retriable indicates if retry is possible
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pass
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# =============================================================================
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# Method 3: Traditional JSON-Based Calling
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# =============================================================================
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# Description: Use original JSON-based calling method
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# Syntax: tu.run_one_function({'name': 'ToolName', 'arguments': {...}})
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# Basic JSON calling
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result5 = tu.run_one_function({
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"name": "UniProt_get_entry_by_accession",
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"arguments": {"accession": "P05067"}
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})
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# Error scenarios with JSON calling
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error_scenarios = [
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{
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"name": "Non-existent tool",
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"call": lambda: tu.tools.NonExistentTool(param="test")
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},
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{
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"name": "Invalid parameters",
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"call": lambda: tu.run_one_function({
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"name": "UniProt_get_entry_by_accession",
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"arguments": {"invalid_param": "test"}
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})
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},
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{
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"name": "Missing required parameter",
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"call": lambda: tu.run_one_function({
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"name": "UniProt_get_entry_by_accession",
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"arguments": {}
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})
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}
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]
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# Test error scenarios
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for scenario in error_scenarios:
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try:
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result = scenario["call"]()
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# Check for dual-format error response
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if isinstance(result, dict) and "error" in result:
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# Handle error response format
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error_details = result.get("error_details", {})
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# error_details contains: type, retriable, next_steps
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pass
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except Exception as e:
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# Handle exception-based errors
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pass
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# =============================================================================
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# Method 4: Multiple Individual Calls
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# =============================================================================
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# Description: Execute multiple tools individually (alternative to batch calling)
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# Syntax: Multiple tu.run_one_function() calls
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result6a = tu.run_one_function({
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"name": "UniProt_get_entry_by_accession",
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"arguments": {"accession": "P05067"}
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})
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result6b = tu.run_one_function({
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"name": "UniProt_get_entry_by_accession",
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"arguments": {"accession": "P12345"}
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})
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# =============================================================================
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# Method 5: Tool Discovery and Dynamic Selection
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# =============================================================================
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# Description: Discover and call tools dynamically
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# Syntax: getattr(tu.tools, 'ToolName')(parameters)
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tool_name = "UniProt_get_entry_by_accession"
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if hasattr(tu.tools, tool_name):
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tool_func = getattr(tu.tools, tool_name)
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result7 = tool_func(accession="P05067")
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# =============================================================================
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# Summary of Methods
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# =============================================================================
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# All methods return the same type of result objects.
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# Choose the method that best fits your use case:
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# - Dynamic calling: Most intuitive for single tool calls
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# - Generated SDK: Type-safe with IDE support
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# - JSON-based: Useful for dynamic tool selection
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# - Batch calling: Efficient for multiple tool calls
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# - Dynamic selection: Good for programmatic tool discovery |