#!/usr/bin/env python3
"""
数据验证模块 - 提供输入验证和清理功能
"""
from typing import Any
class ValidationError(Exception):
"""验证错误异常"""
pass
def validate_gene_list(gene_list: list[str]) -> None:
"""
验证基因列表
Args:
gene_list: 基因列表
Raises:
ValidationError: 如果基因列表无效
"""
if not gene_list:
raise ValidationError("基因列表不能为空")
# 注释掉强制要求2个基因的限制，允许单基因分析
# if len(gene_list) == 1:
# raise ValidationError("基因列表需要至少包含2个基因进行富集分析")
for gene in gene_list:
if not gene or not gene.strip():
raise ValidationError("基因ID不能为空")
if not isinstance(gene, str):
raise ValidationError("基因ID必须是字符串")
def validate_organism(organism: str) -> str:
"""
验证生物体代码
Args:
organism: 生物体代码
Returns:
标准化的生物体代码
Raises:
ValidationError: 如果生物体代码无效
"""
if not organism or not organism.strip():
raise ValidationError("生物体代码不能为空")
organism = organism.strip().upper()
# 支持的KEGG生物体代码（简化版）
valid_organisms = {
"HSA": "hsa", # 人类
"MMU": "mmu", # 小鼠
"RNO": "rno", # 大鼠
"DME": "dme", # 果蝇
"CEL": "cel", # 线虫
"SCE": "sce", # 酵母
}
if organism in valid_organisms:
return valid_organisms[organism]
elif organism in valid_organisms.values():
return organism
else:
raise ValidationError(f"不支持的生物体代码: {organism}")
def validate_parameters(params: dict[str, Any]) -> dict[str, Any]:
"""
验证和标准化参数
Args:
params: 参数字典
Returns:
验证后的参数字典
Raises:
ValidationError: 如果参数无效
"""
validated = {}
# 验证基因列表
if "gene_list" not in params:
raise ValidationError("缺少必需参数: gene_list")
gene_list = params["gene_list"]
if isinstance(gene_list, str):
gene_list = [gene.strip() for gene in gene_list.split(",")]
validate_gene_list(gene_list)
validated["gene_list"] = clean_gene_list(gene_list)
# 验证生物体
organism = params.get("organism", "hsa")
validated["organism"] = validate_organism(organism)
# 验证p值阈值
pvalue_threshold = params.get("pvalue_threshold", 0.05)
if not isinstance(pvalue_threshold, int | float) or not (0 < pvalue_threshold <= 1):
raise ValidationError("pvalue_threshold 必须是0到1之间的数值")
validated["pvalue_threshold"] = float(pvalue_threshold)
# 验证最小基因数量
min_gene_count = params.get("min_gene_count", 2)
if not isinstance(min_gene_count, int) or min_gene_count < 1:
raise ValidationError("min_gene_count 必须是大于0的整数")
validated["min_gene_count"] = int(min_gene_count)
return validated
def clean_gene_list(gene_list: list[str]) -> list[str]:
"""
清理基因列表，去除重复和无效项
Args:
gene_list: 原始基因列表
Returns:
清理后的基因列表
"""
cleaned = []
seen = set()
for gene in gene_list:
if isinstance(gene, str):
gene_clean = gene.strip()
if gene_clean and gene_clean not in seen:
# 过滤掉明显无效的基因ID
if (
gene_clean
and not gene_clean.isspace()
and len(gene_clean) >= 2 # 基因ID通常至少2个字符
and gene_clean.replace("_", "")
.replace("-", "")
.isalnum() # 基因ID通常只包含字母、数字、下划线、连字符
and gene_clean.lower()
not in ["invalid", "unknown", "test", "dummy"]
): # 过滤常见的测试词汇
cleaned.append(gene_clean)
seen.add(gene_clean)
return cleaned