[R] Serialize data.frame to database

[Simon Zehnder]

Hi Rainer,

dbWriteTable is a nice function but in my case I need something that can actually save a dataframe in one row of a table. That is why I want to serialize my data.frame. 


Best

Simon


On Jul 16, 2013, at 3:05 PM, Rainer Schuermann <rainer.schuermann at gmx.net> wrote:

> 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
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> - - - - -
> 
> Der NSA keine Chance: e-mail verschluesseln!
> http://www.gpg4win.org/
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.