SQLite事务失败

Question

我正在使用R和一些外部软件执行数千次计算。 为了跟踪这一点，我在SQLite3数据库的R中构建了一个管道。 为了完成任务，我将其设置为允许计算集群上的多个节点运行R脚本。 当然，我们需要保持原子化，所以我正在积极开始交易。

为了避免崩溃的脚本试图让数据库锁的时候，我已经试图开始一个事务，如果失败，等待，然后将下面的代码重试：

dbBeginTransaction <- function(dbconn, state='DEFERRED', timeout=5, retries=10) { 
    state <- toupper(state) 
    if (!state %in% c('DEFERRED','IMMEDIATE','EXCLUSIVE')) stop('Attempt at illegal transaction.') 
    res <- NULL 
    exit <- FALSE 
    for (i in 1:retries) { 
    try(
     res <- dbSendQuery(dbconn, paste('BEGIN',state,'TRANSACTION;')) 
     , silent=TRUE 
    ) 
    # res is null if above query fails. 
    err <- dbGetException(dbconn) 
    if (err$errorNum == 0) { ## OK 
     #return(TRUE) 
     exit <- TRUE 
     break 
    } else if (err$errorNum == 5) { ## Database locked. 
     if (i == retries+1) { 
     cat('Database still locked after',i,'attempts.\n',file=stderr()) 
     #return(FALSE) 
     exit <- FALSE 
     break 
     } else { 
     Sys.sleep(timeout) 
     } 
    } else { 
     ## errorNum == 1 ## Already within transaction. 
     cat(err$errorMsg, '\n', file = stderr()) 
     #return(FALSE) 
     exit <- FALSE 
     break 
    } 
    } 
    invisible(exit) 
} 


    ## Usage: 
    insert_results <- function(results) { 
    ## Some preparing of results 
    if (dbBeginTransaction(conn, 'EXCLUSIVE') == FALSE) return(FALSE) 
    dbSendPreparedQuery(conn, 'INSERT INTO results (...) VALUES (...);', results) 
    dbCommit(conn) 
    } 

    ## After a computation: 
    results <- magic() 
    if (!insert_results(results)) stop('Could not save results') 

当调试，它的工作原理应该如此。但每一个现在，然后我得到这个奇怪的错误，并且脚本崩溃：

Error in sqliteSendQuery(conn, statement, bind.data) : 
    rsqlite_query_send: could not execute: database is locked 
Calls: dbSendPreparedQuery ... dbSendPreparedQuery -> .local -> sqliteSendQuery -> .Call 
Execution halted 

我无法捉摸发生了什么，我还没有重现错误。 错误很明显，但我会认为我的例程阻止了它。

有关为什么会发生这种情况的任何想法？

我在linux下运行R，由所见：

> sessionInfo() 
R version 3.1.2 (2014-10-31) 
Platform: x86_64-unknown-linux-gnu (64-bit) 

locale: 
[1] LC_CTYPE=en_US  LC_NUMERIC=C   LC_TIME=en_US 
[4] LC_COLLATE=en_US  LC_MONETARY=en_US LC_MESSAGES=en_US 
[7] LC_PAPER=en_US  LC_NAME=C   LC_ADDRESS=C 
[10] LC_TELEPHONE=C  LC_MEASUREMENT=en_US LC_IDENTIFICATION=C 

attached base packages: 
[1] stats  graphics grDevices utils  datasets methods base 

other attached packages: 
[1] RSQLite_1.0.0 DBI_0.3.1 

Answer 1

今天今天在办公室遇到了这个问题。这是我的同事的建议：可以通过确保每次执行数据库连接并对dbCommit（con）进行某种数据库更改来解决此问题。新的代码应该是这样的：

dbBeginTransaction <- function(dbconn, state='DEFERRED', timeout=5, retries=10) { 
    state <- toupper(state) 
    if (!state %in% c('DEFERRED','IMMEDIATE','EXCLUSIVE')) stop('Attempt at illegal transaction.') 
    res <- NULL 
    exit <- FALSE 
    for (i in 1:retries) { 
    try(
     dbBegin(dbconn) 
     res <- dbSendQuery(dbconn, paste('BEGIN',state,'TRANSACTION;')) 
     , silent=TRUE 
    ) 
    # res is null if above query fails. 
    err <- dbGetException(dbconn) 
    if (err$errorNum == 0) { ## OK 
     #return(TRUE) 
     exit <- TRUE 
     break 
    } else if (err$errorNum == 5) { ## Database locked. 
     if (i == retries+1) { 
     cat('Database still locked after',i,'attempts.\n',file=stderr()) 
     #return(FALSE) 
     exit <- FALSE 
     break 
     } else { 
     Sys.sleep(timeout) 
     } 
    } else { 
     ## errorNum == 1 ## Already within transaction. 
     cat(err$errorMsg, '\n', file = stderr()) 
     #return(FALSE) 
     exit <- FALSE 
     break 
    } 
    } 
    invisible(exit) 
} 


    ## Usage: 
    insert_results <- function(results) { 
    ## Some preparing of results 
    if (dbBeginTransaction(conn, 'EXCLUSIVE') == FALSE) return(FALSE) 
    dbSendPreparedQuery(conn, 'INSERT INTO results (...) VALUES (...);', results) 
    dbCommit(conn) 
    } 

    ## After a computation: 
    results <- magic() 
    if (!insert_results(results)) stop('Could not save results') 

我解决了只是你的开始的任何交易与数据库

dbBeginTransaction <- function(dbconn, state='DEFERRED', timeout=5, retries=10) { 
    state <- toupper(state) 
    if (!state %in% c('DEFERRED','IMMEDIATE','EXCLUSIVE')) stop('Attempt at illegal transaction.') 
    res <- NULL 
    exit <- FALSE 
    for (i in 1:retries) { 
    try(
     res <- dbSendQuery(dbconn, paste('BEGIN',state,'TRANSACTION;')) 
     , silent=TRUE 
     dbCommit(dbconn) 
    ) 
    # res is null if above query fails. 
    err <- dbGetException(dbconn) 
    if (err$errorNum == 0) { ## OK 
     #return(TRUE) 
     exit <- TRUE 
     break 
    } else if (err$errorNum == 5) { ## Database locked. 
     if (i == retries+1) { 
     cat('Database still locked after',i,'attempts.\n',file=stderr()) 
     #return(FALSE) 
     exit <- FALSE 
     break 
     } else { 
     Sys.sleep(timeout) 
     } 
    } else { 
     ## errorNum == 1 ## Already within transaction. 
     cat(err$errorMsg, '\n', file = stderr()) 
     #return(FALSE) 
     exit <- FALSE 
     break 
    } 
    } 
    invisible(exit) 
} 


    ## Usage: 
    insert_results <- function(results) { 
    ## Some preparing of results 
    if (dbBeginTransaction(conn, 'EXCLUSIVE') == FALSE) return(FALSE) 
    dbSendPreparedQuery(conn, 'INSERT INTO results (...) VALUES (...);', results) 
    dbCommit(conn) 
    } 

    ## After a computation: 
    results <- magic() 
    if (!insert_results(results)) stop('Could not save results')