From a4d66ce004c40e4468822f01fc39a6b8087a792a Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Thu, 7 Nov 2024 12:45:16 +0100
Subject: [PATCH] Add QUARTO_KNITR_RSCRIPT_ARGS environment variable

to pass some flags to Rscript run by Quarto for knitr engine. This can
be useful in specific situation like e.g `--max-connections=258` available in R 4.4, or `--vanilla`

Args should be passed a comma separated list of flags.

This is for expert use and there is not check done on the argument being support by RScript or not.
---
 src/execute/rmd.ts                         |  8 ++++++
 tests/docs/knitr/rscript-args.qmd          | 12 +++++++++
 tests/smoke/knitr/rscript-args.test.ts     | 31 ++++++++++++++++++++++
 tests/smoke/render/render-required.test.ts | 11 +++-----
 tests/utils.ts                             | 16 ++++++++++-
 5 files changed, 69 insertions(+), 9 deletions(-)
 create mode 100644 tests/docs/knitr/rscript-args.qmd
 create mode 100644 tests/smoke/knitr/rscript-args.test.ts

diff --git a/src/execute/rmd.ts b/src/execute/rmd.ts
index 3e44f8e7387..97b747a5b0d 100644
--- a/src/execute/rmd.ts
+++ b/src/execute/rmd.ts
@@ -272,11 +272,19 @@ async function callR<T>(
     wd: cwd,
   });
 
+  // QUARTO_KNITR_RSCRIPT_ARGS allows to pass additional arguments to Rscript as comma separated values
+  // e.g. QUARTO_KNITR_RSCRIPT_ARGS="--vanilla,--no-init-file,--max-connections=258"
+  const rscriptArgs = Deno.env.get("QUARTO_KNITR_RSCRIPT_ARGS") || "";
+  const rscriptArgsArray = rscriptArgs.split(",").filter((a) =>
+    a.trim() !== ""
+  );
+
   try {
     const result = await execProcess(
       {
         cmd: [
           await rBinaryPath("Rscript"),
+          ...rscriptArgsArray,
           resourcePath("rmd/rmd.R"),
         ],
         cwd,
diff --git a/tests/docs/knitr/rscript-args.qmd b/tests/docs/knitr/rscript-args.qmd
new file mode 100644
index 00000000000..6212240e6d9
--- /dev/null
+++ b/tests/docs/knitr/rscript-args.qmd
@@ -0,0 +1,12 @@
+---
+title: Rscript args passed to quarto
+format: markdown_strict
+---
+
+```{r}
+#| echo: false
+args <- commandArgs(trailingOnly = FALSE)
+# keep only flags
+args <- args[grep("^--", args)]
+args
+```
diff --git a/tests/smoke/knitr/rscript-args.test.ts b/tests/smoke/knitr/rscript-args.test.ts
new file mode 100644
index 00000000000..d92fd2a31ff
--- /dev/null
+++ b/tests/smoke/knitr/rscript-args.test.ts
@@ -0,0 +1,31 @@
+/*
+ * cache.test.ts
+ *
+ * Copyright (C) 2023 Posit Software, PBC
+ */
+import { fileLoader, setEnvVar, restoreEnvVar } from "../../utils.ts";
+import { testRender } from "../render/render.ts";
+import { ensureFileRegexMatches, noErrorsOrWarnings } from "../../verify.ts";
+
+// Default case should not error
+const rscriptArgsDoc = fileLoader()("knitr/rscript-args.qmd", "markdown_strict");
+testRender(rscriptArgsDoc.input, "markdown_strict", true, [
+  noErrorsOrWarnings,
+]);
+
+// Set special flag through env var
+let rscriptArgs: string | undefined;
+testRender(rscriptArgsDoc.input, "markdown_strict", true, [
+  noErrorsOrWarnings,
+  ensureFileRegexMatches(rscriptArgsDoc.output.outputPath, [
+    /"--vanilla"/, /"--max-connection=258"/]
+  ),
+],
+{
+  setup: async () => {
+    rscriptArgs = setEnvVar("QUARTO_KNITR_RSCRIPT_ARGS", "--vanilla,--max-connections=258");
+  },
+  teardown: async () => {
+    restoreEnvVar("QUARTO_KNITR_RSCRIPT_ARGS", rscriptArgs);
+  },
+});
\ No newline at end of file
diff --git a/tests/smoke/render/render-required.test.ts b/tests/smoke/render/render-required.test.ts
index 4cb83d36bb3..ddc371c8bef 100644
--- a/tests/smoke/render/render-required.test.ts
+++ b/tests/smoke/render/render-required.test.ts
@@ -6,7 +6,7 @@
 */
 
 import { testQuartoCmd } from "../../test.ts";
-import { docs } from "../../utils.ts";
+import { docs, setEnvVar, restoreEnvVar } from "../../utils.ts";
 import { printsMessage } from "../../verify.ts";
 
 const input = docs("quarto-required.qmd");
@@ -27,8 +27,7 @@ testQuartoCmd(
   {
     setup: async () => {
       // Save current version of QUARTO_VERSION_REQUIREMENT env var and set it to a value that will not be satisfied
-      oldVersionRequirement = Deno.env.get("QUARTO_VERSION_REQUIREMENT");
-      Deno.env.set("QUARTO_VERSION_REQUIREMENT", "< 0.0.0");
+      oldVersionRequirement = setEnvVar("QUARTO_VERSION_REQUIREMENT", "< 0.0.0");
       // Mock Deno.exit to throw an error instead of exiting
       // Otherwise we would not check the error assertion
       originalDenoExit = Deno.exit;
@@ -38,11 +37,7 @@ testQuartoCmd(
     },
     teardown: async () => {
       // Restore QUARTO_VERSION_REQUIREMENT
-      if (oldVersionRequirement) {
-        Deno.env.set("QUARTO_VERSION_REQUIREMENT", oldVersionRequirement);
-      } else {
-        Deno.env.delete("QUARTO_VERSION_REQUIREMENT");
-      }
+      restoreEnvVar("QUARTO_VERSION_REQUIREMENT", oldVersionRequirement);
       // Restore Deno.exit
       Deno.exit = originalDenoExit;
     },
diff --git a/tests/utils.ts b/tests/utils.ts
index 7155f6195ea..665f9bce2b0 100644
--- a/tests/utils.ts
+++ b/tests/utils.ts
@@ -114,7 +114,7 @@ export function outputForInput(
     if (baseFormat === "revealjs") {
       outputExt = "html";
     }
-    if (["commonmark", "gfm", "markdown"].some((f) => f === baseFormat)) {
+    if (["commonmark", "gfm", "markdown", "markdown_strict"].some((f) => f === baseFormat)) {
       outputExt = "md";
     }
     if (baseFormat === "csljson") {
@@ -190,3 +190,17 @@ export function fileLoader(...path: string[]) {
 export function quartoDevCmd(): string {
   return Deno.build.os === "windows" ? "quarto.cmd" : "quarto";
 }
+
+export function setEnvVar(name: string, value: string): string | undefined {
+  const originalValue = Deno.env.get(name);
+  Deno.env.set(name, value);
+  return originalValue;
+}
+
+export function restoreEnvVar(name: string, originalValue: string | undefined): void {
+  if (originalValue !== undefined) {
+    Deno.env.set(name, originalValue);
+  } else {
+    Deno.env.delete(name);
+  }
+}