R/create_sqlite.R

In khondula/rodm2: Use an ODM2 Database in R

#' Make a new ODM2 sqlite database
#'
#' @param dir Name of existing directory for the sqlite database file to be
#'   created in. Defaults to current directory
#' @param filename Filename for sqlite database file. Defaults to "odm2",
#'   making a file called odm2.sqlite
#' @param connect Whether or not to return the database connection object
#' @return Returns database connecton object if connect = TRUE, otherwise just
#'   creates file.
#'
#' @details This function copies a template sqlite file with the ODM2 schema,
#' \href{http://vocabulary.odm2.org/}{controlled vocabularies}, and units to
#' the specified location.
#' @export
#'
#' @examples
#' db <- create_sqlite(dir = tempdir(), connect = TRUE)
#'

create_sqlite <- function(dir = ".",
                          filename = "odm2.sqlite",
                          connect = FALSE){

  path <- file.path(dir)

  template_file <- system.file("odm2-template.sqlite",
                               package = "rodm2")

  file.copy(template_file, path)
  file.rename(file.path(dir, "odm2-template.sqlite"),
              file.path(dir, filename))

  invisible(template_file)

  if(connect){
    return(DBI::dbConnect(RSQLite::SQLite(),
                          dbname = file.path(dir, filename)))
    }
}

#' Connect to an existing ODM2 sqlite database
#'
#' @param filename Filename for sqlite database file. Defaults to "odm2"
#' @param dir Name of existing directory where database file is stored. Defaults
#'   to current working directory
#'
#' @details This function returns a database connection object to be used in
#'   subsequent inserts and queries.
#' @return A database connection object
#' @export
#'
#' @examples
#' create_sqlite(dir = tempdir())
#' db <- connect_sqlite(filename = "odm2.sqlite")
#'
connect_sqlite <- function(filename = "odm2.sqlite", dir = "."){

  path <- file.path(dir, filename)
  conn_obj <- DBI::dbConnect(RSQLite::SQLite(), path)

  return(conn_obj)
}

#' Disconnect from connect ODM2 sqlite database
#'
#' @param db database connection object
#'
#' @details This function is a simple wrapper around dbDisconnect
#' @return A message about how to reconnect
#' @export
#'
#' @examples
#' db <- create_sqlite(dir = tempdir(), connect = TRUE)
#' disconnect_sqlite(db)
#'
disconnect_sqlite <- function(db = db){
  db_filename <- basename(db@dbname)
  DBI::dbDisconnect(db)

  message(glue::glue("Database connection closed.\nReconnect using connect_sqlite(\"{db_filename}\") or create a new database with create_sqlite()."))
}