genome-mcp

Instructions

Implementation Reference

• src/genome_mcp/core/tools.py:254-351 (handler)

  The primary handler function for the 'get_data' tool. Decorated with @mcp.tool() for automatic registration in FastMCP. Handles query parsing, validation, execution via QueryExecutor, error handling, and result formatting.
  async def get_data( query: str | list[str], query_type: str = "auto", data_type: str = "gene", format: str = "simple", species: str = "human", max_results: int = 20, ) -> ToolResult: """ 智能数据获取接口 - 统一处理所有查询类型 自动识别查询类型： - "TP53" → 基因信息查询 - "P04637" → 蛋白质详细信息查询 - "cancer" → 基因搜索 - "protein kinase" → 蛋白质功能搜索 - "chr17:7565097-7590856" → 区域搜索 - "TP53, BRCA1" → 批量基因信息 - "breast cancer genes" → 智能搜索 - "TP53 homologs" → 同源基因查询 - "evolutionary conservation" → 进化分析查询 Args: query: 查询内容（可以是基因ID、蛋白质ID、搜索词、区域、ID列表、进化相关查询） query_type: 查询类型（auto/info/search/region/protein/gene_protein/ortholog/evolution） data_type: 数据类型（gene/protein/gene_protein/ortholog/evolution） format: 返回格式（simple/detailed/raw） species: 物种（默认：human，支持9606/human/mouse/rat等） max_results: 最大结果数（默认：20） Returns: 查询结果字典，包含基因和/或蛋白质信息 Examples: # 基因信息查询 get_data("TP53") get_data("TP53", format="detailed") # 批量查询 get_data(["TP53", "BRCA1", "BRCA2"]) # 区域搜索 get_data("chr17:7565097-7590856") # 蛋白质查询 get_data("P04637", data_type="protein") # 基因-蛋白质整合查询 get_data("TP53", data_type="gene_protein") # 蛋白质功能搜索 get_data("tumor suppressor", data_type="protein") """ try: # 验证通用参数 validated_max_results, validated_species, validated_query_type = ( validate_common_params( max_results=max_results, species=species, query_type=query_type ) ) # 根据data_type参数调整查询类型 if data_type == "protein" and validated_query_type == "auto": validated_query_type = "protein" elif data_type == "gene_protein" and validated_query_type == "auto": validated_query_type = "gene_protein" elif data_type == "ortholog" and validated_query_type == "auto": validated_query_type = "ortholog" elif data_type == "evolution" and validated_query_type == "auto": validated_query_type = "evolution" elif data_type == "gene" and validated_query_type == "auto": validated_query_type = "auto" # 保持原有的自动识别 # 解析查询意图 parsed = QueryParser.parse(query, validated_query_type) # 使用验证后的物种信息 if "organism" not in parsed.params: parsed.params["organism"] = validated_species # 执行查询 result = await _query_executor.execute( parsed, max_results=validated_max_results ) # 格式化结果 if format == "simple": return _format_simple_result(result) elif format == "detailed": return result else: return result except ValidationError as e: return format_simple_error(e, query=query, operation="get_data") except Exception as e: return format_simple_error(e, query=query, operation="get_data")
• src/genome_mcp/main.py:34-41 (registration)

  Top-level registration of all tools by calling create_mcp_tools(mcp), which defines and registers the get_data tool among others.
  from .core.tools import create_mcp_resources, create_mcp_tools # 创建MCP实例 mcp = FastMCP("Genome MCP", version="0.2.5") # 注册所有资源和工具 create_mcp_resources(mcp) create_mcp_tools(mcp)
• src/genome_mcp/core/tools.py:255-286 (schema)

  Function signature providing input schema via type hints (query: str|list[str], query_type: str='auto', etc.) and return type ToolResult, used by FastMCP for tool schema.
  query: str | list[str], query_type: str = "auto", data_type: str = "gene", format: str = "simple", species: str = "human", max_results: int = 20, ) -> ToolResult: """ 智能数据获取接口 - 统一处理所有查询类型 自动识别查询类型： - "TP53" → 基因信息查询 - "P04637" → 蛋白质详细信息查询 - "cancer" → 基因搜索 - "protein kinase" → 蛋白质功能搜索 - "chr17:7565097-7590856" → 区域搜索 - "TP53, BRCA1" → 批量基因信息 - "breast cancer genes" → 智能搜索 - "TP53 homologs" → 同源基因查询 - "evolutionary conservation" → 进化分析查询 Args: query: 查询内容（可以是基因ID、蛋白质ID、搜索词、区域、ID列表、进化相关查询） query_type: 查询类型（auto/info/search/region/protein/gene_protein/ortholog/evolution） data_type: 数据类型（gene/protein/gene_protein/ortholog/evolution） format: 返回格式（simple/detailed/raw） species: 物种（默认：human，支持9606/human/mouse/rat等） max_results: 最大结果数（默认：20） Returns: 查询结果字典，包含基因和/或蛋白质信息