bin/boilerplate/README.md: fix typo

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

diff --git a/bin/generate_md_episodes.R b/bin/generate_md_episodes.R
index 4ea9835037a81c7e9c657681b12c46cfa30b235f..7f37a7b1cfd519be08f6f828745e52598102fe2e 100644 (file)
--- a/bin/generate_md_episodes.R
+++ b/bin/generate_md_episodes.R
@@ -1,38 +1,59 @@
 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)$pkgs
-    } else {
-        stop("The checkpoint package (>= 0.4.0) is required to build the lessons.")
-    }
-
-    missing_pkgs <- required_pkgs[!(required_pkgs %in% rownames(installed.packages()))]
-
-    if (length(missing_pkgs)) {
-        message("Installing missing required packages: ",
-                paste(missing_pkgs, collapse=", "))
-        install.packages(missing_pkgs)
-    }
-
-    ## find all the Rmd files, and generate the paths for their respective outputs
-    src_rmd <- list.files(pattern = "??-*.Rmd$", 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)
-
+  library("methods")
+  
+  if (!require("remotes", quietly = TRUE)) {
+    install.packages("remotes", repos = c(CRAN = "https://cloud.r-project.org/"))
+  }
+
+  if (!require("requirements", quietly = TRUE)) {
+    remotes::install_github("hadley/requirements")
+  }
+
+  required_pkgs <- unique(c(
+    ## Packages for episodes
+    requirements:::req_dir("_episodes_rmd"),
+    ## Pacakges for tools
+    requirements:::req_dir("bin")
+  ))
+
+  missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
+
+  if (length(missing_pkgs)) {
+    message("Installing missing required packages: ",
+            paste(missing_pkgs, collapse=", "))
+    install.packages(missing_pkgs)
+  }
+
+  if (require("knitr") && packageVersion("knitr") < '1.9.19')
+    stop("knitr must be version 1.9.20 or higher")
+
+  ## 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
+    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()