add_intendedfor_bold

#!/usr/bin/env Rscript

library(jsonlite)

#read in command line arguments.
args <- commandArgs(trailingOnly = FALSE)

scriptpath <- dirname(sub("--file=", "", grep("--file=", args, fixed=TRUE, value=TRUE), fixed=TRUE))
argpos <- grep("--args", args, fixed=TRUE)
if (length(argpos) > 0L) {
   args <- args[(argpos+1):length(args)]
} else {
  args <- c()
}

if (length(args) == 0L) { stop("Expect at least one top-level subject directory") }

#needs to be a path to top of subject directory (can also be multiple paths)

fpath <- args
#fpath <- "/gpfs/group/mnh5174/default/Michael/fmriprep_pipeline_test/bids/sub-048"

if (!all(fex <- file.exists(fpath))) { stop("Cannot locate dir: ", fpath[!fex]) }

cur_user <- Sys.info()[["user"]] #to verify paths

make_writable <- function(file, user) {
  ff <- file.info(file)
  mode <- as.numeric(ff[["mode"]])

  if (file.access(file, 2) == -1) {
    if (ff[["uname"]] != user) {
      #add group write permission
      Sys.chmod(file, mode+20)
    } else {
      #add user write permission
      Sys.chmod(file, mode+200)
    }
    return(mode) #for resetting
  } else {
    return(NULL)
  }
}

for (fp in fpath) {  
  bold_files <- list.files(path=file.path(fp, "func"), pattern=".*_bold\\.nii\\.gz", full.names=TRUE)
  fmap_files <- list.files(path=file.path(fp, "fmap"), pattern=".*_epi\\.nii\\.gz", full.names=TRUE)

  bold_rel <- sub(".*/sub-\\d+/(.*)$", "\\1", bold_files, perl=TRUE) #IntendedFor must be relative to subject path, starting with func/
  for (f in fmap_files) {
    jfile <- sub(".nii.gz", ".json", f, fixed=TRUE)
    j <- read_json(path=jfile)
    j$IntendedFor <- bold_rel
    message("In ", jfile, ", adding IntendedFor: ", paste(bold_files, collapse=", "))
    #json file must be writeable; if not, chmod it
    orig_mode <- make_writable(jfile, cur_user)
    write_json(j, path=jfile, pretty=TRUE, auto_unbox=TRUE, digits=NA)
    if (!is.null(orig_mode)) { Sys.chmod(jfile, orig_mode) } #restore original permission
  }
}