R/link_data_file.R

In NiklasTR/dcp_helper: Create metadata and job files for distributed cell profiler

#' Fill a JSON template with a specific metadata path and metadata groupings
#'
#' @param name
#'
#' @return
#' @export
#' @import jsonlite
#' @import parallel
#'
#' @examples
link_data_file <- function(metadata_split_path, json_template, json_path, path_base,
                           path_to_metadata = 'dcp_helper/metadata/'){
  json_new <- json_template #propably not needed

  json_new$data_file <- metadata_split_path %>% #str_sub(21, -1) #10, -1
    str_extract(pattern = paste0(path_to_metadata, "0000\\d+__\\d+-\\d\\d-\\d+T\\d+_\\d+_\\d+-Measurement_\\d/.*"))

  json_new$output <- paste0("flatfield/",
                            str_extract(pattern = "0000\\d+__\\d+-\\d\\d-\\d+T\\d+_\\d+_\\d+-Measurement_\\d", string = metadata_split_path))

  # I create the path for the grouping data that was previously generated using a python script. #TODO - incorporate the python script's function into R
  grouping_path <-  metadata_split_path %>% str_sub(.,1, -5) %>% paste0(., "batch.txt")
  # I import the grouping text after trimming the last comma
  grouping <- readLines(grouping_path) %>% paste(. , collapse = " ") %>% str_sub(., 1, -3) %>% paste("[", ., "]") %>% fromJSON()

  # Now I insert the grouping into the JSON
  json_new$groups <- grouping

  # Finally I write my results
  name_metadata <- metadata_split_path %>% str_split(pattern = "/") %>% unlist() %>% tail(1) %>% str_sub(1, -5)
  name_json <- json_path %>% str_split(pattern = "/") %>% unlist() %>% tail(1) %>% str_sub(1, -15)

  write_json(json_new, pretty = TRUE, path = paste0(path_base, name_json, "_", name_metadata, ".json"), auto_unbox = TRUE)
  print(paste0("created ", paste0(path_base, name_json, "_", name_metadata, ".json")))

}