Added md5sums utilities functions, for a faster data loading

R/md5sums_utils.R

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+
+#'  How to ensure quick loading of SomaScan data in tidyfr
+#'
+#'  These utility functions are supposed to aid versioning of the data. It should
+#'  be called after the `data-export.R` step, after only 1 technical check.
+#'  Then a user can generate and save md5sums and make the new data version
+#'  available. These functions use the same input parameters as `data_module.R` 
+#'
+#' @param path \code{character}, the path where to find the folder specified in
+#' the `name` parameter (eg: `/home/user/data/`)
+#' @param name \code{character}, the folder containing version folders
+#' @param version \code{character}, the version to look inside the `name` folder
+#'
+#' @return \code{character}, with md5sum hashes, while names are the absolute
+#' paths to the file that md5sum has refers to
+#' @export
+#'
+#' @examples
+#' 
+#' # The first part is to build a new data version, written as a pseudocode
+#' # step 0 - you modified the data somehow, so redo technical checks on files
+#' # step 1 - export a new version of somalogic data with export_tdf(...)
+#'
+#' # The following steps are my proposed additions
+#'
+#' # step 1 - use build_somalogic_data_Rds(...) to generate pre-processed and
+#' #           quickly readable data.
+#' # step 2 - save md5sum hashes in this new version's folder with 
+#' #           also including the 2 data modules generated in step 1 
+#' #          (save_versioned_md5sums(...))
+#' # 
+#' #################################################################
+#' # now let's simulate what a user could do to load the data      #
+#' #################################################################
+#' path <- "/home/gantonello/chris_somascan_proteomics"
+#' name <- "chris_somalogic_full"
+#' version <- "1.0.3.2"
+#' 
+#' new_md5sums <- get_md5sums(path, name, version)
+#' old_md5sums <- readRDS(file.path(path, name, version, paste0("md5sums_v_", version, ".Rds")))
+#' 
+#' if(!identical(new_md5sums, old_md5sums)){
+#' stop(
+#' paste("One or more files not match the expected md5sums hashes:",
+#' print(
+#' data.frame(
+#'   filename = names(new_md5sums)[new_md5sums != old_md5sums],
+#'   new_hash <- new_md5sums[new_md5sums != old_md5sums],
+#'   old_hash <- old_md5sums[new_md5sums != old_md5sums]
+#'   )
+#'   )
+#' }
+#' 
+#' # load soma_data
+#' soma_data <- readRDS(file.path(path, name, version, "data", "soma_data.Rds"))
+#'
+#' # load soma_ann
+#' soma_ann <- readRDS(file.path(path, name, version, "data", "soma_ann.Rds"))
+
+build_somalogic_data_Rds <- function(path, name, version){
+  soma <- data_module(name = name, 
+                      version = version,
+                      path = path)
+
+  #' save somamers experimental data:
+  #' rows: samples; columns: somamers and sample metadata
+  saveRDS(
+    data(soma), 
+    file = file.path(path, name, version, "data", "soma_data.Rds")
+  )
+
+  #' save somamers metadata:
+  #' rows = somamer, columns: somamers annotations and other metatadata
+  saveRDS(
+    labels(soma), 
+    file = file.path(path, name, version, "data", "soma_ann.Rds")
+  )
+}
+
+get_md5sums <- function(path, name, version){
+  full_path <- file.path(path, name, version, "data")
+  textfiles <- list.files(full_path, pattern = "*", full.names = T)
+  md5sums <- sapply(textfiles, md5sum)
+  return(md5sums)
+}
+
+save_versioned_md5sums <- function(path, name, version){
+  md5sums <- get_md5sums(path, name, version)
+  saveRDS(
+    object = md5sums,
+    file = file.path(path, name, version, paste0("md5sums_v_", version, ".Rds"))
+    )
+}
+