[R] Serialize data.frame to database

[Rainer Schuermann]

Maybe a simple

dbWriteTable( db, "frames", iris )

does what you want?



On Monday 15 July 2013 23:43:18 Simon Zehnder wrote:
> Dear R-Users,
> 
> I need a very fast and reliable database solution so I try to serialize a data.frame (to binary data) and to store this data to an SQLite database. 
> 
> This is what I tried to do:
> 
> library(RSQLite)
> con <- dbDriver("SQLite")
> db <- dbConnect(con, "test")
> dbSendQuery(db, 'CREATE TABLE frames("simID" INT, "data" BLOB)')
> data.bin <- serialize(iris, NULL, ascii = FALSE)
> dbSendQuery(db, paste("INSERT INTO frames VALUES(1, X'", data.bin, "')", sep = ""))
> data.bin2 <- dbGetQuery(db, "SELECT DATA FROM frames WHERE simID = 1")
> data.bin2
>   data
> 1   58
> 
> So, only the first entry of data.bin is saved to the database. I tried to first convert the binary data to raw data:
> data.raw <- rawToChar(data.bin)
> Error in rawToChar(data.bin) :
>   embedded nul in string: 'X\n\0\0\0\002\0\003\0\001\0\002\003\0\0\0\003\023\0\0\0\005\0\0\0\016\0\0\0\x96@\024ffffff@\023\x99\x99\x99\x99\x99\x9a@\022\xcc\xcc\xcc\xcc\xcc\xcd@\022ffffff@\024\0\0\0\0\0\0@\025\x99\x99\x99\x99\x99\x9a@\022ffffff@\024\0\0\0\0\0\0@\021\x99\x99\x99\x99\x99\x9a@\023\x99\x99\x99\x99\x99\x9a@\025\x99\x99\x99\x99\x99\x9a@\023333333@\023333333@\021333333@\027333333@\026\xcc\xcc\xcc\xcc\xcc\xcd@\025\x99\x99\x99\x99\x99\x9a@\024ffffff@\026\xcc\xcc\xcc\xcc\xcc\xcd@\024ffffff@\025\x99\x99\x99\x99\x99\x9a@\024ffffff@\022ffffff@\024ffffff@\023333333@\024\0\0\0\0\0\0@\024\0\0\0\0\0\0@\024\xcc\xcc\xcc\xcc\xcc\xcd@\024\xcc\xcc\xcc\xcc\xcc\xcd@\022\xcc\xcc\xcc\xcc\xcc\xcd@\023333333@\025\x99\x99\x99\x99\x99\x9a@\024\xcc\xcc\xcc\xcc\xcc\xcd@\026\0\0\0\0\0\0@\023\x99\x99\x99\x99\x99\x9a@\024\0\0\0\0\0\0@\026\0\0\0\0\0\0@\023\x99\x99\x99\x99\x99\x9a@\021\x99\x99\x99\x99\x99\x9a@\024ffffff@\024\0\0\0\0\0\0@\022\0\0\0\0\0\0@\021\x99\x99\x99\x99\x99\x9a@\024\0\0\0\0\!
>  0\0
> 
> I don't know what this error should tell me. Then I tried to use the ASCII format
> 
> data.ascii <- serialize(iris, NULL, ascii = TRUE)
> data.raw <- rawToChar(data.ascii)
> dbSendQuery(db, "DELETE FROM frames")
> dbSendQuery(db, paste("INSERT INTO frames VALUES(1, X'", data.raw, "')", sep = ""))
> Error in sqliteExecStatement(conn, statement, ...) :
>   RS-DBI driver: (error in statement: unrecognized token: "X'A
> 
> This also does not work. It seems the driver does not deal that nicely with the regular INSERT query for BLOB objects in SQLite. Then I used a simpler way:
> 
> dbSendQuery(db, "DELETE FROM frames")
> dbSendQuery(db, "DROP TABLE frames")
> dbSendQuery(db, 'CREATE TABLE frames("simID" INT, "data" TEXT DEFAULT NULL)')
> dbSendQuery(db, paste("INSERT INTO frames VALUES(1, '", data.raw, "')", sep = ""))
> data.bin2 <- dbGetQuery(db, "SELECT data FROM frames WHERE simID = 1")
> 
> Nice, that worked. Now I want to unserialize the data:
> 
> unserialize(data.bin2)
> Error in unserialize(data.bin2) : 'connection' must be a connection
> 
> unserialize(data.bin2[1, 'data'])
> Error in unserialize(data.bin2[1, "data"]) :
>   character vectors are no longer accepted by unserialize()
> 
> I feel a little stuck here, but I am very sure, that converting data.frames to binary data and storing them to a database is not that unusual. So I hope somebody has already done this and could give me the missing piece.
> 
> 
> Best
> 
> Simon
> 
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