Can't get results from sqlite database with opencpu

I have a relatively simple function to fetch some data from a sqlite database:

library(RSQLite)
db.select <- function(table="mydata", vars, rows=c()) {
  vars <- paste(unlist(vars), collapse=", ")
  q <- paste("SELECT ", vars, " FROM ", table, sep="")

  if (length(rows) > 0) {
    rows <- paste(as.character(rows), collapse=", ")
    q <- paste(q, " WHERE row in (", rows, ")", sep="")
 }

  con <- DBI::dbConnect(RSQLite::SQLite(), "/abs/path/to.db")
  res <- DBI::dbSendQuery(con, q)
  data <- DBI::dbFetch(res)
  DBI::dbClearResult(res)
  DBI::dbDisconnect(con)
  data
}

      

        
        
        
      

    

When I run this code in R (or RStudio), this works great for me:

> db.select(vars = c("gc_content"), rows=c(1:5))
   gc_content
1       44.30
2       41.22
3       48.51
4       60.83
5       45.21

      

        
        
        
      

    

However, I was unable to get data at all using this function via opencpu:

$ curl http://localhost/ocpu/user/bertjan/library/RParcoords/R/db.select/json -H "Content-Type: application/json" -d '{"vars":["gc_content"]}'
RS-DBI driver: (could not connect to dbname:
unable to open database file
)

In call:
sqliteNewConnection(drv, ...)

      

        
        
        
      

    

I double checked that the file exists, checks its permissions, sets read and write permissions for everyone, but no luck at all. Any input would be appreciated.

Edit 1: Tried the changes suggested by @Jeroen in the apparmor setup to no avail. Which helped a bit by adding the following line to the custom file:

/full/path/to/db rw,

      

        
        
        
      

    

However, it only helped me that I got the error:

RS-DBI driver: (error in instruction: database is locked)

In the call: sqliteExecStatement (conn, statement, ...)

Which is strange, since I don't get this error when I execute exactly the same code (with the same database file) in RStudio.

Edit 2: As suggested by Hadley Wickham ( https://twitter.com/hadleywickham/status/526739851974955008 ), I simplified the function using dbGetQuery:

db.select <- function(table="mydata", vars, rows=c()) {
  vars <- paste(unlist(vars), collapse=", ")
  q <- paste("SELECT ", vars, " FROM ", table, sep="")

  if (length(rows) > 0) {
    rows <- paste(as.character(rows), collapse=", ")
    q <- paste(q, " WHERE row in (", rows, ")", sep="")
  }

  con <- DBI::dbConnect(RSQLite::SQLite(), "/home/bertjan/cstr.db")
  data <- DBI::dbGetQuery(con, q)
  DBI::dbDisconnect(con)
  data
}

      

        
        
        
      

    

However, to no avail since I get the same behavior (works in R studio, gives a locked database message when issuing the curl command).

Edit 3: Actually still seems to be an AppArmor problem. I get:

Oct 27 15:50:52 Stef kernel: [899068.612784] type=1400 audit(1414421452.965:232): apparmor="DENIED" operation="file_lock" profile="opencpu-exec" name="/path/to/db" pid=9708 comm="apache2" requested_mask="k" denied_mask="k" fsuid=33 ouid=1000

      

        
        
        
      

    

Solution: Finally found it. In the end it seemed like it was a pure AppArmor problem. I had to change:

/full/path/to/db rw,

      

        
        
        
      

    

to

/full/path/to/db rwk,

      

        
        
        
      

    

(Note k) to enable file locking.