From 295676cd2bccb06c3d1b56ff749c37371739f069 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <pamstutz@veritasgenetics.com>
Date: Thu, 19 Apr 2018 15:47:23 -0400
Subject: [PATCH] 13076: R SDK online docs include both README and method docs.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
---
 doc/Rakefile                        | 52 +++++++++++++++++++++++++++--
 doc/_config.yml                     |  3 +-
 doc/sdk/R/index.html.textile.liquid | 15 ---------
 sdk/R/createDoc.R                   |  7 ++--
 4 files changed, 56 insertions(+), 21 deletions(-)
 delete mode 100644 doc/sdk/R/index.html.textile.liquid

diff --git a/doc/Rakefile b/doc/Rakefile
index 4870eb19e2..4ba2f1af8d 100644
--- a/doc/Rakefile
+++ b/doc/Rakefile
@@ -28,11 +28,59 @@ end
 file "sdk/R/arvados/index.html" do |t|
   `which R`
   if $? == 0
+    tgt = Dir.pwd
+    Dir.mkdir("sdk/R/arvados")
+    docfiles = []
     Dir.chdir("../sdk/R/") do
-      STDERR.puts `Rscript createDoc.R README.Rmd index.html 2>&1`
+      STDERR.puts `Rscript createDoc.R README.Rmd #{tgt}/sdk/R/README.md 2>&1`
+      Dir.entries("man").each do |rd|
+        if rd[-3..-1] == ".Rd"
+          htmlfile = "#{rd[0..-4]}.html"
+          `R CMD Rdconv -t html man/#{rd} > #{tgt}/sdk/R/arvados/#{htmlfile}`
+          docfiles << htmlfile
+        end
+      end
     end
     raise if $? != 0
-    cp_r("../sdk/R/README.html", "sdk/R/")
+
+    File.open("sdk/R/README.md", "r") do |rd|
+    File.open("sdk/R/index.html.md", "w") do |fn|
+      fn.write(<<-EOF
+---
+layout: default
+navsection: sdk
+navmenu: R
+title: "R SDK Overview"
+...
+
+#{rd.read.gsub("```", "\n~~~\n").gsub(/^[ ]+/, "")}
+EOF
+              )
+      end
+    end
+
+    File.open("sdk/R/arvados/index.html.textile.liquid", "w") do |fn|
+      fn.write(<<-EOF
+---
+layout: default
+navsection: sdk
+navmenu: R
+title: "R Reference"
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+EOF
+              )
+
+      docfiles.sort.each do |d|
+        fn.write("* \"#{d[0..-6]}\":#{d}\n")
+      end
+
+    end
   else
     puts "Warning: R not found, R documentation will not be generated".colorize(:light_red)
   end
diff --git a/doc/_config.yml b/doc/_config.yml
index 011be51062..a1885987ff 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -105,7 +105,8 @@ navbar:
       - sdk/go/index.html.textile.liquid
       - sdk/go/example.html.textile.liquid
     - R:
-      - sdk/R/index.html.textile.liquid
+      - sdk/R/index.html.md
+      - sdk/R/arvados/index.html.textile.liquid
     - Perl:
       - sdk/perl/index.html.textile.liquid
       - sdk/perl/example.html.textile.liquid
diff --git a/doc/sdk/R/index.html.textile.liquid b/doc/sdk/R/index.html.textile.liquid
deleted file mode 100644
index 1d7803a48a..0000000000
--- a/doc/sdk/R/index.html.textile.liquid
+++ /dev/null
@@ -1,15 +0,0 @@
----
-layout: default
-navsection: sdk
-navmenu: R
-title: "R Reference"
-
-no_nav_left: true
-...
-{% comment %}
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-{% endcomment %}
-
-notextile. <iframe src="README.html" style="width:100%; height:100%; border:none" />
diff --git a/sdk/R/createDoc.R b/sdk/R/createDoc.R
index 8d4c5ba042..73e088ecb6 100644
--- a/sdk/R/createDoc.R
+++ b/sdk/R/createDoc.R
@@ -12,8 +12,9 @@ inputFile <- args[[1]] # .Rmd file
 outputFile <- args[[2]] # .html file
 
 # Create and fill temp .md file from existing .Rmd file
-tempMdFile <- tempfile("tempREADME", fileext = "md")
-knitr::knit(inputFile, tempMdFile) 
+#tempMdFile <- tempfile("tempREADME", fileext = "md")
+knitr::knit(inputFile, outputFile)
+#knitr::knit(inputFile, tempMdFile)
 
 # Generate HTML from temporary .md file
-markdown::markdownToHTML(tempMdFile, outputFile) 
+#markdown::markdownToHTML(tempMdFile, outputFile)
-- 
2.30.2