Implement using @naupaka 's suggestions

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

diff --git a/bin/generate_md_episodes.R b/bin/generate_md_episodes.R
index 91bf512656132d5f22f63dd562d665ab21855798..6c27d9c9245fc5b6d1c5aaa82af2ea4073e59b80 100644 (file)
--- a/bin/generate_md_episodes.R
+++ b/bin/generate_md_episodes.R
@@ -1,15 +1,52 @@
-if (require("knitr")) {
-    if (packageVersion("knitr") < '1.9.19') {
+generate_md_episodes <- function() {
+
+    library("methods")
+    
+    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") && packageVersion("checkpoint") >=  '0.4.0') {
+        required_pkgs <-
+             checkpoint:::scanForPackages(project = "_episodes_rmd",
+                                          verbose=FALSE, use.knitr = TRUE)$pkgs
+    } else {
+        stop("The checkpoint package (>= 0.4.0) is required to build the lessons.")
     }
-} else stop("knitr 1.9.20 or above is needed to build the lessons.")
 
-if (!require("stringr"))
-    stop("The package stringr is required for generating the lessons.")
+    missing_pkgs <- required_pkgs[!(required_pkgs %in% rownames(installed.packages()))]
 
-src_rmd <- list.files(pattern = "??-*.Rmd$", path = "_episodes_rmd", full.names = TRUE)
-dest_md <- file.path("_episodes", gsub("Rmd$", "md", basename(src_rmd)))
+    if (length(missing_pkgs)) {
+        message("Installing missing required packages: ",
+                paste(missing_pkgs, collapse=", "))
+        install.packages(missing_pkgs)
+    }
 
-for (i in seq_along(src_rmd)) {
-    knitr::knit(src_rmd[i], output = dest_md[i])
+    ## find all the Rmd files, and generate 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)
+    
+    # Read the generated md files and add comments advising not to edit them
+    vapply(dest_md, 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))
+    },
+    character(1))
 }
+
+generate_md_episodes()