archive/tests/test_fix_validation.R

# 测试修复后的KEGG/GO分析代码
library(AnnotationDbi)

# 测试清理基因符号函数
test_clean_gene_symbols <- function() {
  cat("=== 测试清理基因符号函数 ===\n")

  # 测试数据
  test_genes <- c(
    "TP53", "tp53", "TP53 ", "TP-53", "TP53.1", "TP53-ps",
    "Trp53", "trp53", "Trp53 ", "Trp-53", "Trp53.2", "Trp53-rs",
    "ENSG00000141510", "ENSMUSG00000059552", "12345", "gene1"
  )

  cat("原始基因符号:\n")
  print(test_genes)

  # 测试人类基因清理
  cat("\n--- 人类基因清理结果 ---\n")
  human_cleaned <- sapply(test_genes, function(gene) {
    # 模拟clean_gene_symbols函数逻辑
    cleaned <- trimws(gene)
    cleaned <- gsub("[\t\n\r]", "", cleaned)
    cleaned <- gsub("\\.[0-9]+$", "", cleaned)
    cleaned <- gsub("-ps$", "", cleaned, ignore.case = TRUE)
    cleaned <- gsub("-rs$", "", cleaned, ignore.case = TRUE)
    cleaned <- gsub("-as$", "", cleaned, ignore.case = TRUE)
    cleaned <- toupper(cleaned)
    cleaned <- gsub("[^[:alnum:]]", "", cleaned)
    return(cleaned)
  })
  print(human_cleaned)

  # 测试小鼠基因清理
  cat("\n--- 小鼠基因清理结果 ---\n")
  mouse_cleaned <- sapply(test_genes, function(gene) {
    # 模拟clean_gene_symbols函数逻辑
    cleaned <- trimws(gene)
    cleaned <- gsub("[\t\n\r]", "", cleaned)
    cleaned <- gsub("\\.[0-9]+$", "", cleaned)
    cleaned <- gsub("-ps$", "", cleaned, ignore.case = TRUE)
    cleaned <- gsub("-rs$", "", cleaned, ignore.case = TRUE)
    cleaned <- gsub("-as$", "", cleaned, ignore.case = TRUE)

    # 小鼠基因：首字母大写，其余小写
    if (grepl("^[A-Za-z]", cleaned)) {
      cleaned <- paste0(toupper(substr(cleaned, 1, 1)), tolower(substr(cleaned, 2, nchar(cleaned))))
    }

    cleaned <- gsub("[^[:alnum:]]", "", cleaned)
    return(cleaned)
  })
  print(mouse_cleaned)
}

# 测试智能转换函数逻辑
test_smart_conversion_logic <- function() {
  cat("\n=== 测试智能转换函数逻辑 ===\n")

  # 模拟smart_gene_conversion函数的逻辑
  simulate_smart_conversion <- function(gene_ids, keytypes_to_try = c("SYMBOL", "ALIAS", "ENSEMBL", "ENTREZID")) {
    cat("输入基因ID:", paste(gene_ids, collapse=", "), "\n")

    for (keytype in keytypes_to_try) {
      cat("\n尝试keytype:", keytype, "\n")

      # 模拟数据库查询
      if (keytype == "SYMBOL") {
        # 假设数据库中存在的SYMBOL
        valid_symbols <- c("TP53", "BRCA1", "EGFR", "MYC", "ACTB", "GAPDH")
        matched <- gene_ids[gene_ids %in% valid_symbols]
        if (length(matched) > 0) {
          cat("  匹配到", length(matched), "个基因:", paste(matched, collapse=", "), "\n")
          return(list(
            converted = matched,
            keytype_used = keytype,
            matched_count = length(matched),
            success_count = length(matched)
          ))
        }
      } else if (keytype == "ENSEMBL") {
        # 假设数据库中存在的ENSEMBL ID
        valid_ensembl <- c("ENSG00000141510", "ENSG00000012048", "ENSG00000146648")
        matched <- gene_ids[gene_ids %in% valid_ensembl]
        if (length(matched) > 0) {
          cat("  匹配到", length(matched), "个ENSEMBL ID:", paste(matched, collapse=", "), "\n")
          return(list(
            converted = matched,
            keytype_used = keytype,
            matched_count = length(matched),
            success_count = length(matched)
          ))
        }
      }
    }

    cat("\n所有keytype尝试都失败了\n")
    return(NULL)
  }

  # 测试不同ID类型的基因
  test_cases <- list(
    c("TP53", "BRCA1", "NOT_A_GENE"),
    c("ENSG00000141510", "ENSG00000012048", "INVALID_ID"),
    c("TP53", "ENSG00000141510", "12345")
  )

  for (i in seq_along(test_cases)) {
    cat("\n--- 测试用例", i, "---\n")
    result <- simulate_smart_conversion(test_cases[[i]])
    if (!is.null(result)) {
      cat("转换成功! 使用的keytype:", result$keytype_used, "\n")
      cat("成功转换的基因:", paste(result$converted, collapse=", "), "\n")
    }
  }
}

# 测试错误处理
test_error_handling <- function() {
  cat("\n=== 测试错误处理逻辑 ===\n")

  # 模拟mapIds可能出现的错误
  simulate_mapIds_error <- function(keys, keytype) {
    if (keytype == "SYMBOL" && any(!keys %in% c("TP53", "BRCA1", "EGFR"))) {
      stop("None of the keys entered are valid keys for 'SYMBOL'")
    }
    return(keys)
  }

  # 测试错误情况
  test_keys <- c("TP53", "INVALID_GENE", "BRCA1")

  cat("测试基因:", paste(test_keys, collapse=", "), "\n")

  tryCatch({
    result <- simulate_mapIds_error(test_keys, "SYMBOL")
    cat("mapIds成功:", paste(result, collapse=", "), "\n")
  }, error = function(e) {
    cat("mapIds错误:", e$message, "\n")
    cat("这是预期的错误，我们的修复应该能处理这种情况\n")
  })
}

# 运行所有测试
cat("开始验证修复后的代码...\n")
test_clean_gene_symbols()
test_smart_conversion_logic()
test_error_handling()

cat("\n=== 修复总结 ===\n")
cat("1. 改进了基因符号清理函数：\n")
cat("   - 去除版本号（.1, .2等）\n")
cat("   - 去除假基因后缀（-ps, -rs, -as）\n")
cat("   - 标准化大小写（人类：大写，小鼠：首字母大写）\n")
cat("   - 去除特殊字符\n")
cat("\n2. 添加了智能基因符号转换函数：\n")
cat("   - 自动尝试不同的keytype（SYMBOL, ALIAS, ENSEMBL, ENTREZID）\n")
cat("   - 先验证基因ID是否在当前keytype中有效\n")
cat("   - 提供详细的转换统计信息\n")
cat("\n3. 改进了错误处理：\n")
cat("   - 当直接使用SYMBOL keytype失败时，会尝试其他keytype\n")
cat("   - 提供更详细的错误信息和用户反馈\n")
cat("\n这些修复应该能彻底解决'None of the keys entered are valid keys for SYMBOL'错误。\n")