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[rnaseq-cwl-training.git] / bin / generate_md_episodes.R

diff --git a/bin/generate_md_episodes.R b/bin/generate_md_episodes.R
index 6d8a2d784339382bb2c8c85bfd34b25efb4b5faa..7fb4c5a53312c9546c1a8b18d111c1b1a6cce8e2 100644 (file)
--- a/bin/generate_md_episodes.R
+++ b/bin/generate_md_episodes.R
@@ -1,36 +1,44 @@
 generate_md_episodes <- function() {
 
-    if (require("knitr") && packageVersion("knitr") < '1.9.19')
-        stop("knitr must be version 1.9.20 or higher")
-
-    if (!require("stringr"))
-        stop("The package stringr is required for generating the lessons.")
-
-    if (require("checkpoint")) {
-        required_pkgs <-
-            checkpoint:::projectScanPackages(project = "_episodes_rmd",
-                                             verbose=FALSE, use.knitr = TRUE)$pkgs
-    } else {
-        stop("The checkpoint package is required to build the lessons.")
-    }
-
-    missing_pkgs <- required_pkgs[!(required_pkgs %in% rownames(installed.packages()))]
-
-    if (length(missing_pkgs)) {
-        message("Installing missing required packages: ",
-                paste(missing_pkgs, collapse=", "))
-        install.packages(missing_pkgs)
-    }
-
-    ## find all the Rmd files, and generates the paths for their respective outputs
-    src_rmd <- list.files(pattern = "??-*.Rmd$", path = "_episodes_rmd", full.names = TRUE)
-    dest_md <- file.path("_episodes", gsub("Rmd$", "md", basename(src_rmd)))
-
-    ## knit the Rmd into markdown
-    mapply(function(x, y) {
-        knitr::knit(x, output = y)
-    }, src_rmd, dest_md)
-
+  # avoid ansi color characters from being printed in the output
+  op <- options()
+  on.exit(options(op), add = TRUE)
+  options(crayon.enabled = FALSE)
+  ## get the Rmd file to process from the command line, and generate the path
+  ## for their respective outputs
+  args  <- commandArgs(trailingOnly = TRUE)
+  if (!identical(length(args), 2L)) {
+    stop("input and output file must be passed to the script")
+  }
+
+  src_rmd <- args[1]
+  dest_md <- args[2]
+
+  ## knit the Rmd into markdown
+  knitr::knit(src_rmd, output = dest_md)
+
+  # Read the generated md files and add comments advising not to edit them
+  add_no_edit_comment <- function(y) {
+    con <- file(y)
+    mdfile <- readLines(con)
+    if (mdfile[1] != "---")
+      stop("Input file does not have a valid header")
+    mdfile <- append(
+      mdfile,
+      "# Please do not edit this file directly; it is auto generated.",
+      after = 1
+    )
+    mdfile <- append(
+      mdfile,
+      paste("# Instead, please edit", basename(y), "in _episodes_rmd/"),
+      after = 2
+    )
+    writeLines(mdfile, con)
+    close(con)
+    return(paste("Warning added to YAML header of", y))
+  }
+
+  vapply(dest_md, add_no_edit_comment, character(1))
 }
 
 generate_md_episodes()