Verso/services/clsi/app/js/QuartoRunner.js

import Path from 'node:path'
import { promisify } from 'node:util'
import logger from '@overleaf/logger'
import CommandRunner from './CommandRunner.js'
import fs from 'node:fs'

// Maps currently-running Quarto jobs: compileName → PID (or docker container id)
const ProcessTable = {}

function runQuarto(compileName, options, callback) {
  const { directory, mainFile, image, environment, compileGroup } = options
  const timeout = options.timeout || 60000

  logger.debug(
    { directory, timeout, mainFile, compileGroup },
    'starting quarto compile'
  )

  // For the standalone-HTML export we must render a deck whose frontmatter
  // carries embed-resources (it cannot be set from the CLI: Quarto only honours
  // embed-resources when it is nested under the format, and a document's own
  // format block fully overrides project/CLI metadata). So write a temporary
  // copy of the root .qmd with the options injected and render that instead.
  let renderTarget = mainFile
  if (options.exportMode === 'html-standalone') {
    renderTarget = _writeStandaloneVariant(directory, mainFile)
  }

  // Where cached per-project venvs live (shared across projects, keyed by the
  // requirements.txt hash). Must be on a persistent volume in production.
  const venvBaseDir =
    process.env.PYTHON_VENVS_DIR || '/var/lib/overleaf/data/python-venvs'
  const command = _buildQuartoCommand(
    renderTarget,
    options.exportMode,
    Boolean(options.allowPythonInstall),
    venvBaseDir
  )

  ProcessTable[compileName] = CommandRunner.run(
    compileName,
    command,
    directory,
    image,
    timeout,
    environment || {},
    compileGroup,
    null,
    function (error, output) {
      delete ProcessTable[compileName]

      // Propagate real process-level errors (killed, timed out) but NOT
      // ordinary non-zero exit codes from Quarto itself.  A Quarto compile
      // failure (exit code 1) is not a server error — the absence of
      // output.pdf is sufficient for CompileController to return 'failure'.
      if (error && (error.terminated || error.timedout)) {
        return callback(error)
      }

      // On exit-code-1 errors LocalCommandRunner attaches stdout to the
      // error object; merge it so _writeLogOutput can persist it.
      const combined = output || (error ? { stdout: error.stdout || '' } : null)
      _writeLogOutput(compileName, directory, combined, () =>
        _appendMissingResourceWarnings(directory, () =>
          callback(null, combined)
        )
      )
    }
  )
}

function _buildQuartoCommand(
  renderTarget,
  exportMode,
  allowPythonInstall,
  venvBaseDir
) {
  // Run through a POSIX shell so stderr is merged into stdout (2>&1).
  // LocalCommandRunner replaces $COMPILE_DIR before the shell sees it.
  //
  // We do NOT pass --to or --output: let the YAML frontmatter decide the
  // output format (typst → output.pdf, revealjs → output.html, etc.).
  //
  // For a normal preview compile we do NOT embed resources. A self-contained
  // single-file HTML breaks reveal.js plugins that load/store resources at
  // runtime (e.g. chalkboard, multiplex) and is slow to transfer. Instead
  // Quarto emits the HTML plus a sibling "<basename>_files/" asset directory;
  // the HTML references it with relative paths. Both the html and the asset
  // dir are served from the same .../output/ path, so the relative links
  // resolve. For the 'html-standalone' export, runQuarto instead renders a
  // temporary copy of the deck (renderTarget) whose frontmatter enables
  // embed-resources, producing a single portable file.
  //
  // After render we rename the produced top-level file to output.pdf or
  // output.html. The asset directory keeps its "<basename>_files" name; the
  // renamed output.html still points at it via the unchanged relative refs.
  //
  // The extension merge (cp -rn, no-clobber so user extensions win) and the
  // trailing semicolon (so a missing /opt/quarto-extensions doesn't abort)
  // are kept. mv uses relative paths because LocalCommandRunner.replace()
  // only substitutes the FIRST $COMPILE_DIR and the shell CWD is the dir.
  const inputPath = `$COMPILE_DIR/${renderTarget}`
  const baseName = renderTarget.replace(/\.[^/.]+$/, '') // strip extension

  let tail =
    `(mv ${baseName}.pdf output.pdf 2>/dev/null || ` +
    `mv ${baseName}.html output.html 2>/dev/null)`

  if (exportMode === 'pdf-slides') {
    // After producing output.html, print it to output-slides.pdf with decktape
    // (headless Chromium via Puppeteer). The CLSI runtime user has no writable
    // HOME, so Chromium's crashpad can't create its database and the browser
    // dies on launch ("chrome_crashpad_handler: --database is required").
    // Point HOME / XDG dirs / the Chromium user-data-dir at a fresh writable
    // temp dir to give it somewhere to write.
    //   --no-sandbox: Chromium can't sandbox as a non-root container user
    //   --disable-dev-shm-usage: a tiny container /dev/shm crashes Chromium
    //   --disable-gpu: there is no GPU in the container
    tail +=
      ` && CHROME_HOME="$(mktemp -d)" && ` +
      `HOME="$CHROME_HOME" XDG_CONFIG_HOME="$CHROME_HOME" ` +
      `XDG_CACHE_HOME="$CHROME_HOME" decktape ` +
      `--chrome-arg=--no-sandbox ` +
      `--chrome-arg=--disable-dev-shm-usage ` +
      `--chrome-arg=--disable-gpu ` +
      `--chrome-arg=--user-data-dir="$CHROME_HOME/data" ` +
      `"$(pwd)/output.html" output-slides.pdf 2>&1`
  }

  // For the standalone export, remove the temporary render copy afterwards so
  // it can't be mistaken for a project file or picked up by a later preview
  // compile. Runs regardless of render success (";").
  const cleanup =
    exportMode === 'html-standalone'
      ? `; rm -rf ${baseName}.qmd ${baseName}_files`
      : ''

  const venvPrep = allowPythonInstall ? _pythonVenvPrep(venvBaseDir) : ''

  const cmd =
    `mkdir -p _extensions && ` +
    `cp -rn /opt/quarto-extensions/_extensions/. _extensions/ 2>/dev/null; ` +
    venvPrep +
    `quarto render ${inputPath} 2>&1 && ` +
    tail +
    cleanup
  return ['/bin/sh', '-c', cmd]
}

// Shell snippet (run before `quarto render`, in the compile dir) that installs
// a project's requirements.txt into a venv cached by the file's sha256 and
// points Quarto at it via QUARTO_PYTHON. Notes:
//   - The venv is shared across projects/compiles (keyed by content hash), so
//     identical dependency sets are built once.
//   - --system-site-packages keeps the bundled scientific stack + ipykernel
//     visible, so only the *extra* packages are installed.
//   - A per-hash flock serialises concurrent compiles building the same venv.
//   - Everything is merged to stdout so pip output/errors land in output.log;
//     on failure QUARTO_PYTHON is left unset and the render falls back to the
//     base interpreter (the missing-package error then surfaces normally).
//   - Only $-shell vars / $(...) are used (no ${...}) to avoid clashing with
//     JS template interpolation; only ${venvBaseDir} is substituted by JS.
function _pythonVenvPrep(venvBaseDir) {
  return (
    `if [ -f requirements.txt ]; then ` +
    `VBASE="${venvBaseDir}"; ` +
    `RHASH=$(sha256sum requirements.txt 2>/dev/null | cut -d" " -f1); ` +
    `if [ -n "$RHASH" ]; then ` +
    `VDIR="$VBASE/$RHASH"; mkdir -p "$VBASE" 2>/dev/null; ` +
    `( flock 9 || exit 0; ` +
    `if [ ! -f "$VDIR/.verso-ready" ]; then ` +
    `echo "Installing Python packages from requirements.txt..."; rm -rf "$VDIR"; ` +
    `python3 -m venv --system-site-packages "$VDIR" ` +
    `&& "$VDIR/bin/pip" install --no-input --disable-pip-version-check -r requirements.txt ` +
    // Register a python3 kernelspec INSIDE the venv (argv -> the venv's python)
    // so Quarto runs the kernel in the venv, not the base /usr/bin/python3 from
    // the global kernelspec. ipykernel is visible via --system-site-packages.
    `&& "$VDIR/bin/python3" -m ipykernel install --sys-prefix --name python3 --display-name "Python 3" ` +
    `&& touch "$VDIR/.verso-ready" ` +
    `|| echo "ERROR: Failed to install Python packages from requirements.txt"; ` +
    `fi ` +
    `) 9>"$VBASE/.$RHASH.lock" 2>&1; ` +
    `if [ -f "$VDIR/.verso-ready" ]; then export QUARTO_PYTHON="$VDIR/bin/python3"; fi; ` +
    `fi; ` +
    `fi; `
  )
}

// Write a temporary copy of the root .qmd with embed-resources enabled in its
// frontmatter, returning the temp filename to render. On any problem (no
// frontmatter, not a nested revealjs deck, read/write error) it falls back to
// the original mainFile — the export then just isn't self-contained, which is
// no worse than before. The temp file lives in the same directory so relative
// resources (images, _extensions) still resolve.
function _writeStandaloneVariant(directory, mainFile) {
  try {
    const content = fs.readFileSync(Path.join(directory, mainFile), 'utf8')
    const transformed = _injectRevealjsStandaloneOptions(content)
    if (!transformed) return mainFile
    const base = mainFile.replace(/\.[^/.]+$/, '')
    const tempName = `${base}.verso-standalone.qmd`
    fs.writeFileSync(Path.join(directory, tempName), transformed)
    return tempName
  } catch (err) {
    logger.warn({ err, directory, mainFile }, 'could not prepare standalone qmd')
    return mainFile
  }
}

// Inject the self-contained options into the `revealjs:` block of a deck's
// YAML frontmatter. embed-resources/self-contained-math inline all CSS/JS/
// images/MathJax into one portable file; chalkboard must be off (it is
// incompatible with embed-resources and would error the render). Keys already
// present in the block are overwritten in place (so we never create duplicate
// YAML keys, e.g. an existing `chalkboard: true`); missing keys are inserted.
// Returns the new document text, or null if it isn't a nested-revealjs deck we
// can safely edit.
function _injectRevealjsStandaloneOptions(content) {
  const fmMatch = content.match(/^(---\r?\n)([\s\S]*?)(\r?\n---\r?\n?)/)
  if (!fmMatch) return null
  const [, open, body, close] = fmMatch
  const lines = body.split('\n')

  const revealIdx = lines.findIndex(l => /^\s*revealjs:\s*$/.test(l))
  if (revealIdx === -1) return null // not a `format:\n  revealjs:` deck

  const revealIndent = lines[revealIdx].match(/^(\s*)/)[1]

  // Determine the block's child indent (from the first more-indented line) and
  // where the block ends (the first later line indented at/under revealjs:).
  let childIndent = revealIndent + '  '
  let blockEnd = lines.length
  let seenChild = false
  for (let i = revealIdx + 1; i < lines.length; i++) {
    if (lines[i].trim() === '') continue
    const indent = lines[i].match(/^(\s*)/)[1]
    if (indent.length <= revealIndent.length) {
      blockEnd = i
      break
    }
    if (!seenChild) {
      childIndent = indent
      seenChild = true
    }
  }

  const desired = {
    'embed-resources': 'true',
    'self-contained-math': 'true',
    chalkboard: 'false',
  }

  const present = new Set()
  for (let i = revealIdx + 1; i < blockEnd; i++) {
    const km = lines[i].match(/^\s*([A-Za-z0-9_-]+):/)
    if (km && Object.prototype.hasOwnProperty.call(desired, km[1])) {
      lines[i] = `${childIndent}${km[1]}: ${desired[km[1]]}`
      present.add(km[1])
    }
  }

  const additions = Object.keys(desired)
    .filter(k => !present.has(k))
    .map(k => `${childIndent}${k}: ${desired[k]}`)
  if (additions.length) lines.splice(revealIdx + 1, 0, ...additions)

  return open + lines.join('\n') + close + content.slice(fmMatch[0].length)
}

function _writeLogOutput(compileName, directory, output, callback) {
  const content = (output && output.stdout) || ''
  if (!content) return callback()
  // Write to output.log so the PDF-preview log panel picks it up
  const logFile = Path.join(directory, 'output.log')
  fs.unlink(logFile, () => {
    fs.writeFile(logFile, content, { flag: 'wx' }, err => {
      if (err) {
        logger.error({ err, compileName, logFile }, 'error writing quarto log')
      }
      callback()
    })
  })
}

// Quarto's HTML/RevealJS output is NOT self-contained (we deliberately dropped
// --embed-resources so reveal plugins like chalkboard work). A side effect is
// that pandoc no longer tries to fetch referenced media, so a missing image or
// video produces no compile-time warning — it just renders broken in the
// browser. To restore that feedback, scan the produced output.html for local
// media references and emit a [WARNING] for any that don't exist on disk. The
// [WARNING] prefix is understood by the Quarto/Typst log parser on the web
// side, so these surface in the Warnings tab like any other.
//
// Only HTML output is scanned: PDF output (Typst) already hard-errors on a
// missing image, so it needs no extra check.
function _appendMissingResourceWarnings(directory, callback) {
  const htmlFile = Path.join(directory, 'output.html')
  fs.readFile(htmlFile, 'utf8', (err, html) => {
    if (err) return callback() // no HTML output (e.g. a PDF compile)

    const missing = _extractLocalMediaRefs(html).filter(ref => {
      try {
        return !fs.existsSync(Path.join(directory, decodeURIComponent(ref)))
      } catch {
        return false
      }
    })
    if (missing.length === 0) return callback()

    const warnings =
      missing
        .map(
          ref =>
            `[WARNING] Missing resource: ${ref} (referenced in the document ` +
            `but not found in the project — it will appear broken)`
        )
        .join('\n') + '\n'
    fs.appendFile(Path.join(directory, 'output.log'), '\n' + warnings, () =>
      callback()
    )
  })
}

// Pull local media references (img/video/audio/iframe src, poster, RevealJS
// data-background-*) out of the rendered HTML. External URLs, data URIs and
// in-page anchors are ignored; Quarto's own generated assets (under
// <basename>_files/) exist on disk, so they never get flagged.
function _extractLocalMediaRefs(html) {
  const refs = new Set()
  const attrRegex =
    /(?:src|poster|data-background-image|data-background-video)\s*=\s*["']([^"']+)["']/gi
  let match
  while ((match = attrRegex.exec(html)) !== null) {
    const url = match[1].trim()
    if (!url) continue
    // Skip absolute URLs, protocol-relative, data/blob URIs and anchors.
    if (/^(?:[a-z]+:|\/\/|\/|#|data:|blob:)/i.test(url)) continue
    const clean = url.split(/[?#]/)[0] // drop query string / fragment
    if (clean) refs.add(clean)
  }
  return [...refs]
}

function isRunning(compileName) {
  return ProcessTable[compileName] != null
}

function killQuarto(compileName, callback) {
  logger.debug({ compileName }, 'killing running quarto compile')
  if (!isRunning(compileName)) {
    logger.warn({ compileName }, 'no such compile to kill')
    return callback(null)
  }
  CommandRunner.kill(ProcessTable[compileName], callback)
}

export default {
  isRunning,
  runQuarto,
  killQuarto,
  promises: {
    runQuarto: promisify(runQuarto),
    killQuarto: promisify(killQuarto),
  },
}