R/utils.R

In PacificBiosciences/pbcommandr: R Package for generating reports using SMRT-Link

#' Convert a resolved condition JSON into a CSV for resubmission using the web portal.
#'
#' This is utility function to convert resolved json files back into
#' data that can be input into the web tool for resubmission.  Useful for restarting users jobs.
#'
#' condId,host,jobId
#' A_30662,smrtlink-beta,030662
#' B_30733,smrtlink-beta,030733
#' C_31988,smrtlink-beta,031988
#' D_32051,smrtlink-beta,032051
#' E_31989,smrtlink-beta,031989
#' F_32052,smrtlink-beta,032052
#' G_32175,smrtlink-beta,032175
#' H_32288,smrtlink-beta,032288
#' I_32332,smrtlink-beta,032332
#' J_32504,smrtlink-beta,032504
#' K_32539,smrtlink-beta,032539
#' L_32425,smrtlink-beta,032425
#' Example:  printConditionCSV("/pbi/dept/secondary/siv/smrtlink/smrtlink-internal/services_ui/smrtlink_services_ui-internal-0.9.0-185199/reseq-conditions/reseq-conditions-495705c0-5d80-4716-9713-c79023855773.json")
#' @export
printConditionCSV <- function(fname) {
  d = jsonlite::fromJSON(fname)
  conds = d[[2]]
  returnLine <- function(x) {
    aln = as.character(x["alignmentset"])
    cond = x["condId"]
    sp = strsplit(aln, "/")[[1]]
    id = sp[12]
    server = sp[7]
    paste(cond, server, id, sep = ",")
  }
  res = apply(conds, 1, returnLine)
  message(paste(c("condId,host,jobId", res), collapse = "\n"))
}