R/get.sraDate.R

In palmid: RdRP Analysis Suite

#' get.sraDate
#'
#' Retrieve the "Load_Date" for a set of SRA 'run_id'
#'
#' @param run_ids character, SRA 'run_id'
#' @param con     pq-connection, use SerratusConnect()
#' @param ordinal boolean, return 'run_ids' ordered vector [F]
#' @param as.df   boolean, return run_id, date data.frame [F]
#' @return POSIXct, date object vector
#' @keywords palmid Serratus timeline
#' @examples
#' \donttest{
#' con <- SerratusConnect()
#' palm.date   <- get.sraDate("SRR9968562", con)
#' }
#' @import RPostgreSQL
#' @import dplyr ggplot2
#' @export
# Retrieve date from input of sra run_ids
get.sraDate <- function(run_ids, con, ordinal = FALSE, as.df = FALSE) {
  # Bind Local Variables
  run <- load_date <- NULL

  # get contigs containing palm_ids
  sra.date <- tbl(con, "srarun") %>%
    filter(run %in% run_ids) %>%
    select(run, load_date) %>%
    as.data.frame()
    colnames(sra.date) <- c("run_id", "date")

  #sra.date <- parse_datetime( sradate$load_data)
  #sra.date <- format( sradate, format = "%y-%m")

  if (ordinal){
    # Left join on palm_ids to make a unique vector
    ord.date <- data.frame( run_id = run_ids )
    ord.date <- merge(ord.date, sra.date, all.x = T)
    ord.date <- ord.date[ match(run_ids, ord.date$run_id), ]

    return(ord.date$date)

  } else if (as.df){
    colnames(sra.date) <- c("run_id","date")
  } else {
    sra.date <- data.frame( date = sra.date[,2])
  }

  return(sra.date)
}