使用 R 池包连接到 PostgreSQL 数据库

Question

我有一个用 R plumber that connects to a PostgreSQL database using RPostgreSQL and pool 构建的 API（尽管如果我使用的是 Shiny 应用程序，这也适用）：

# create the connection pool
pool <- dbPool(
  drv = PostgreSQL(),
  host = Sys.getenv("DB_HOST"),
  port = 5432,
  dbname = "db",
  user = Sys.getenv("DB_USER"),
  password = Sys.getenv("DB_PASSWORD")
)

# start the API
pr <- plumb("plumber.R")

# on stop, close the pool
pr$registerHooks(
  list("exit" = function() { poolClose(pool) })
)

我想每天导入新数据。最简单的方法是创建一个新数据库并将其推广到生产环境：

CREATE DATABASE db_new;
-- create the tables
-- bulk-insert the data
SELECT pg_terminate_backend (pid) FROM pg_stat_activity WHERE datname = 'db';
DROP DATABASE db;
ALTER DATABASE db_new RENAME TO db;

这速度很快，并且可以最大限度地减少停机时间。问题是 pool 然后失去与数据库的连接并且不会自动尝试重新连接：

> tbl(pool, "users")
Error in postgresqlExecStatement(conn, statement, ...) : 
  RS-DBI driver: (could not Retrieve the result : FATAL:  terminating connection due to administrator command
server closed the connection unexpectedly
    This probably means the server terminated abnormally
    before or while processing the request.
)

即使我不是每天都更换数据库，数据库服务器偶尔也会重启，这也会导致我的应用程序崩溃。重新连接似乎不是池、RPostgreSQL 或 DBI 的功能。有谁知道解决这个问题的方法吗？

Answer 1

我最近遇到了类似的问题，因为 MySQL 个连接在超过实例的 wait_timeout 时被关闭。我遇到了 your post on RStudio Community，并受到了您的解决方案的启发。如果您仍在使用它，并且正在寻找一种解决方案，在包装您使用的实际功能时避免额外查询，这里有一个 reprex 展示了我想出的东西，以及一个证明它有效的例子：

library(dplyr, warn.conflicts = FALSE)
library(pool)
library(RMariaDB)

generate_safe_query <- function(pool) {
  function(db_function, ...) {
    tryCatch({
      db_function(pool, ...)
    }, error = function(e) {
      if (grepl("Lost connection to MySQL server during query", e$message)) {
        # Preserve `validationInterval` so that it can be restored
        validation_interval <- pool$validationInterval
        # Trigger destruction of dead connection
        pool$validationInterval <- 0
        refreshed_connection <- poolCheckout(pool)
        poolReturn(refreshed_connection)
        # Restore original `validationInterval`
        pool$validationInterval <- validation_interval
        # Execute the query with the new connection
        db_function(pool, ...)
      } else {
        # Unexpected error
        stop(e)
      }
    })
  }
}

mysql_pool <- dbPool(MariaDB(),
                     host = "127.0.0.1",
                     username = "root",
                     password = "",
                     dbname = "test")

safe_query <- generate_safe_query(mysql_pool)

# Works
safe_query(tbl, "notes")
#> # Source:   table<notes> [?? x 2]
#> # Database: mysql 8.0.15 [root@127.0.0.1:/test]
#>      id note 
#>   <int> <chr>
#> 1     1 NOTE1

# Set the `wait_timeout` to 5 seconds for this session
invisible(safe_query(dbExecute, "SET SESSION wait_timeout = 5"))

# Wait longer than `wait_timeout` to trigger a disconnect
Sys.sleep(6)

# Still works; warning will appear notifying that connection was
# destroyed and replaced with a new one
safe_query(tbl, "notes")
#> Warning: It wasn't possible to activate and/or validate the object. Trying
#> again with a new object.
#> # Source:   table<notes> [?? x 2]
#> # Database: mysql 8.0.15 [root@127.0.0.1:/test]
#>      id note 
#>   <int> <chr>
#> 1     1 NOTE1

safe_query(poolClose)
# Or, equivalently: 
# poolClose(mysql_pool)

^{由 reprex package (v0.3.0)}

于 2019-05-30 创建

generate_safe_query 返回的函数适用于任何数据库查询函数（例如 dbExecute、dbGetQuery 等）。显然，您需要更新它匹配的错误消息以满足您的需要。

我还打开了我自己的 Community topic 选项，我认为应该包含在 dbPool 中，这将减少对此类解决方法的需求。

Answer 2

我正在使用具有以下功能的普通 DBI（无池）以始终为 DBI 调用提供活动连接（例如 DBI::dbExistsTable(rdsConnect(), "mytable")）。

#' Connect returns a database connection.
#' Retrieves the connection parameters from configuration.
#' 
#' FIXME: dbIsValid is not implemented
#' https://github.com/tomoakin/RPostgreSQL/issues/76
#' workaround implemented with isPostgresqlIdCurrent()
#' @return rds allocated connection
rdsConnect <- function() {
  if (!((exists("rds") && (isPostgresqlIdCurrent(rds))))) {
    source('./config.R', local = TRUE)
    print("New PostgreSQL connection")
    rds <<- DBI::dbConnect(RPostgreSQL::PostgreSQL(),
      dbname = rds_params("rds_database"),
      host = rds_params("rds_host"),
      user = rds_params("rds_user"),
      password = rds_params("rds_password")
    )
  } else print("Valid PostgreSQL connection")
  return(rds)
}

使用 R 池包连接到 PostgreSQL 数据库

Reconnect to PostgreSQL database with R's pool package

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