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rrjdbcr-dbi

dbGetQuery and dbReadTable failing to return a really large table DBI


I have a really large table (8M rows) that I need to import in R on which I will be doing some processing. Problem is when I try to bring it in R using the DBI package I get an error

My code is below

options(java.parameters = "-Xmx8048m") 
psql.jdbc.driver <- "../postgresql-42.2.1.jar"
jdbc.url <- "jdbc:postgresql://server_url:port"
pgsql <- JDBC("org.postgresql.Driver", psql.jdbc.driver, "`")
con <- dbConnect(pgsql, jdbc.url, user="", password= '')
tbl <- dbGetQuery(con, "SELECT * FROM my_table;")

And the error I get is

Error in .verify.JDBC.result(r, "Unable to retrieve JDBC result set for ",  : 
Unable to retrieve JDBC result set for SELECT * FROM my_table; (Ran out of memory retrieving query results.) 

I can understand its because the result set is too big but I am not sure how to retrieve it by batches instead of all of it together. I have tried using dBSendQuery, dbReadTable and dbGetQuery all of them give the same error.

Any help would be appreciated!


Solution

  • I got it to work by using the RPostgreSQL package instead of the default RJDBC and DBI package. It was able to do a sendQuery and then used fetch recursively to get the data in chunks of 10,000.

    main_tbl <- dbFetch(postgres_query, n=-1) #didnt work so tried in chunks 
    df<- data.frame()
    while (!dbHasCompleted(postgres_query)) {
      chunk <- dbFetch(postgres_query, 10000)
      print(nrow(chunk))
      df = rbind(df, chunk)
    }