Merge branch 'master' into bg-support-other-runtimes

port coffee changes to js

services/clsi/.dockerignore

@@ -5,5 +5,6 @@ gitrev
 .npm
 .nvmrc
 nodemon.json
-app.js
-**/js/*
+cache/
+compiles/
+db/

services/clsi/.eslintrc

@@ -0,0 +1,64 @@
+// this file was auto-generated, do not edit it directly.
+// instead run bin/update_build_scripts from
+// https://github.com/sharelatex/sharelatex-dev-environment
+{
+  "extends": [
+    "standard",
+    "prettier",
+    "prettier/standard"
+  ],
+  "parserOptions": {
+    "ecmaVersion": 2017
+  },
+  "plugins": [
+    "mocha",
+    "chai-expect",
+    "chai-friendly"
+  ],
+  "env": {
+    "node": true,
+    "mocha": true
+  },
+  "rules": {
+    // Swap the no-unused-expressions rule with a more chai-friendly one
+    "no-unused-expressions": 0,
+    "chai-friendly/no-unused-expressions": "error"
+  },
+  "overrides": [
+    {
+      // Test specific rules
+      "files": ["test/**/*.js"],
+      "globals": {
+        "expect": true
+      },
+      "rules": {
+        // mocha-specific rules
+        "mocha/handle-done-callback": "error",
+        "mocha/no-exclusive-tests": "error",
+        "mocha/no-global-tests": "error",
+        "mocha/no-identical-title": "error",
+        "mocha/no-nested-tests": "error",
+        "mocha/no-pending-tests": "error",
+        "mocha/no-skipped-tests": "error",
+        "mocha/no-mocha-arrows": "error",
+
+        // chai-specific rules
+        "chai-expect/missing-assertion": "error",
+        "chai-expect/terminating-properties": "error",
+
+        // prefer-arrow-callback applies to all callbacks, not just ones in mocha tests.
+        // we don't enforce this at the top-level - just in tests to manage `this` scope
+        // based on mocha's context mechanism
+        "mocha/prefer-arrow-callback": "error"
+      }
+    },
+    {
+      // Backend specific rules
+      "files": ["app/**/*.js", "app.js", "index.js"],
+      "rules": {
+        // don't allow console.log in backend code
+        "no-console": "error"
+      }
+    }
+  ]
+}

services/clsi/.gitignore

@@ -1,13 +1,7 @@
 **.swp
 node_modules
-app/js
-test/unit/js
-test/smoke/js
-test/acceptance/js
 test/acceptance/fixtures/tmp
 compiles
-app.js
-**/*.map
 .DS_Store
 *~
 cache

services/clsi/.nvmrc

@@ -1 +1 @@
-10.15.0
+10.19.0

services/clsi/.prettierrc

@@ -0,0 +1,7 @@
+# This file was auto-generated, do not edit it directly.
+# Instead run bin/update_build_scripts from
+# https://github.com/sharelatex/sharelatex-dev-environment
+{
+  "semi": false,
+  "singleQuote": true
+}

services/clsi/.travis.yml

@@ -1,15 +0,0 @@
-language: node_js
-
-before_install:
-    - npm install -g grunt-cli
-
-install:
-    - npm install
-    - grunt install
-
-script:
-    - grunt test:unit
-
-services:
-    - redis-server
-    - mongodb

services/clsi/Dockerfile

@@ -1,6 +1,16 @@
-FROM gcr.io/overleaf-ops/node:10.19.0 as app
+# This file was auto-generated, do not edit it directly.
+# Instead run bin/update_build_scripts from
+# https://github.com/sharelatex/sharelatex-dev-environment
+
+FROM node:10.19.0 as base
 
 WORKDIR /app
+COPY install_deps.sh /app
+RUN chmod 0755 ./install_deps.sh && ./install_deps.sh
+ENTRYPOINT ["/bin/sh", "entrypoint.sh"]
+COPY entrypoint.sh /app
+
+FROM base as app
 
 #wildcard as some files may not be in all repos
 COPY package*.json npm-shrink*.json /app/
@@ -10,14 +20,11 @@ RUN npm install --quiet
 COPY . /app
 
 
-RUN npm run compile:all
 
-FROM gcr.io/overleaf-ops/node:10.19.0
+FROM base
 
 COPY --from=app /app /app
-
-WORKDIR /app
-RUN chmod 0755 ./install_deps.sh && ./install_deps.sh
-ENTRYPOINT ["/bin/sh", "entrypoint.sh"]
+RUN mkdir -p cache compiles db \
+&&  chown node:node cache compiles db
 
 CMD ["node", "--expose-gc", "app.js"]

services/clsi/Jenkinsfile

@@ -16,6 +16,7 @@ pipeline {
   }
 
   stages {
+
     stage('Install') {
       steps {
         withCredentials([usernamePassword(credentialsId: 'GITHUB_INTEGRATION', usernameVariable: 'GH_AUTH_USERNAME', passwordVariable: 'GH_AUTH_PASSWORD')]) {
@@ -36,6 +37,13 @@ pipeline {
       }
     }
 
+    stage('Linting') {
+      steps {
+        sh 'DOCKER_COMPOSE_FLAGS="-f docker-compose.ci.yml" make format'
+        sh 'DOCKER_COMPOSE_FLAGS="-f docker-compose.ci.yml" make lint'
+      }
+    }
+
     stage('Unit Tests') {
       steps {
         sh 'DOCKER_COMPOSE_FLAGS="-f docker-compose.ci.yml" make test_unit'

services/clsi/Makefile

@@ -1,11 +1,12 @@
 # This file was auto-generated, do not edit it directly.
 # Instead run bin/update_build_scripts from
 # https://github.com/sharelatex/sharelatex-dev-environment
-# Version: 1.1.24
 
 BUILD_NUMBER ?= local
 BRANCH_NAME ?= $(shell git rev-parse --abbrev-ref HEAD)
 PROJECT_NAME = clsi
+BUILD_DIR_NAME = $(shell pwd | xargs basename | tr -cd '[a-zA-Z0-9_.\-]')
+
 DOCKER_COMPOSE_FLAGS ?= -f docker-compose.yml
 DOCKER_COMPOSE := BUILD_NUMBER=$(BUILD_NUMBER) \
 	BRANCH_NAME=$(BRANCH_NAME) \
@@ -13,29 +14,64 @@ DOCKER_COMPOSE := BUILD_NUMBER=$(BUILD_NUMBER) \
 	MOCHA_GREP=${MOCHA_GREP} \
 	docker-compose ${DOCKER_COMPOSE_FLAGS}
 
+DOCKER_COMPOSE_TEST_ACCEPTANCE = \
+	COMPOSE_PROJECT_NAME=test_acceptance_$(BUILD_DIR_NAME) $(DOCKER_COMPOSE)
+
+DOCKER_COMPOSE_TEST_UNIT = \
+	COMPOSE_PROJECT_NAME=test_unit_$(BUILD_DIR_NAME) $(DOCKER_COMPOSE)
+
 clean:
 	docker rmi ci/$(PROJECT_NAME):$(BRANCH_NAME)-$(BUILD_NUMBER)
 	docker rmi gcr.io/overleaf-ops/$(PROJECT_NAME):$(BRANCH_NAME)-$(BUILD_NUMBER)
-	rm -f app.js
-	rm -rf app/js
-	rm -rf test/unit/js
-	rm -rf test/acceptance/js
 
-test: test_unit test_acceptance
+format:
+	$(DOCKER_COMPOSE) run --rm test_unit npm run format
+
+format_fix:
+	$(DOCKER_COMPOSE) run --rm test_unit npm run format:fix
+
+lint:
+	$(DOCKER_COMPOSE) run --rm test_unit npm run lint
+
+test: format lint test_unit test_acceptance
 
 test_unit:
-	@[ ! -d test/unit ] && echo "clsi has no unit tests" || $(DOCKER_COMPOSE) run --rm test_unit
+ifneq (,$(wildcard test/unit))
+	$(DOCKER_COMPOSE_TEST_UNIT) run --rm test_unit
+	$(MAKE) test_unit_clean
+endif
 
-test_acceptance: test_clean test_acceptance_pre_run test_acceptance_run
+test_clean: test_unit_clean
+test_unit_clean:
+ifneq (,$(wildcard test/unit))
+	$(DOCKER_COMPOSE_TEST_UNIT) down -v -t 0
+endif
+
+test_acceptance: test_acceptance_clean test_acceptance_pre_run test_acceptance_run
+	$(MAKE) test_acceptance_clean
+
+test_acceptance_debug: test_acceptance_clean test_acceptance_pre_run test_acceptance_run_debug
+	$(MAKE) test_acceptance_clean
 
 test_acceptance_run:
-	@[ ! -d test/acceptance ] && echo "clsi has no acceptance tests" || $(DOCKER_COMPOSE) run --rm test_acceptance
+ifneq (,$(wildcard test/acceptance))
+	$(DOCKER_COMPOSE_TEST_ACCEPTANCE) run --rm test_acceptance
+endif
+
+test_acceptance_run_debug:
+ifneq (,$(wildcard test/acceptance))
+	$(DOCKER_COMPOSE_TEST_ACCEPTANCE) run -p 127.0.0.9:19999:19999 --rm test_acceptance npm run test:acceptance -- --inspect=0.0.0.0:19999 --inspect-brk
+endif
 
-test_clean:
-	$(DOCKER_COMPOSE) down -v -t 0
+test_clean: test_acceptance_clean
+test_acceptance_clean:
+	$(DOCKER_COMPOSE_TEST_ACCEPTANCE) down -v -t 0
 
 test_acceptance_pre_run:
-	@[ ! -f test/acceptance/js/scripts/pre-run ] && echo "clsi has no pre acceptance tests task" || $(DOCKER_COMPOSE) run --rm test_acceptance test/acceptance/js/scripts/pre-run
+ifneq (,$(wildcard test/acceptance/js/scripts/pre-run))
+	$(DOCKER_COMPOSE_TEST_ACCEPTANCE) run --rm test_acceptance test/acceptance/js/scripts/pre-run
+endif
+
 build:
 	docker build --pull --tag ci/$(PROJECT_NAME):$(BRANCH_NAME)-$(BUILD_NUMBER) \
 		--tag gcr.io/overleaf-ops/$(PROJECT_NAME):$(BRANCH_NAME)-$(BUILD_NUMBER) \
@@ -48,4 +84,5 @@ publish:
 
 	docker push $(DOCKER_REPO)/$(PROJECT_NAME):$(BRANCH_NAME)-$(BUILD_NUMBER)
 
+
 .PHONY: clean test test_unit test_acceptance test_clean build publish

services/clsi/app.coffee

@@ -1,244 +0,0 @@
-Metrics = require "metrics-sharelatex"
-Metrics.initialize("clsi")
-
-CompileController = require "./app/js/CompileController"
-Settings = require "settings-sharelatex"
-logger = require "logger-sharelatex"
-logger.initialize("clsi")
-if Settings.sentry?.dsn?
-	logger.initializeErrorReporting(Settings.sentry.dsn)
-
-smokeTest = require "smoke-test-sharelatex"
-ContentTypeMapper = require "./app/js/ContentTypeMapper"
-Errors = require './app/js/Errors'
-
-Path = require "path"
-fs = require "fs"
-
-
-Metrics.open_sockets.monitor(logger)
-Metrics.memory.monitor(logger)
-
-ProjectPersistenceManager = require "./app/js/ProjectPersistenceManager"
-OutputCacheManager = require "./app/js/OutputCacheManager"
-
-require("./app/js/db").sync()
-
-express = require "express"
-bodyParser = require "body-parser"
-app = express()
-
-Metrics.injectMetricsRoute(app)
-app.use Metrics.http.monitor(logger)
-
-# Compile requests can take longer than the default two
-# minutes (including file download time), so bump up the 
-# timeout a bit.
-TIMEOUT = 10 * 60 * 1000
-app.use (req, res, next) ->
-	req.setTimeout TIMEOUT
-	res.setTimeout TIMEOUT
-	res.removeHeader("X-Powered-By")
-	next()
-
-app.param 'project_id', (req, res, next, project_id) ->
-	if project_id?.match /^[a-zA-Z0-9_-]+$/
-		next()
-	else
-		next new Error("invalid project id")
-
-app.param 'user_id', (req, res, next, user_id) ->
-	if user_id?.match /^[0-9a-f]{24}$/
-		next()
-	else
-		next new Error("invalid user id")
-
-app.param 'build_id', (req, res, next, build_id) ->
-	if build_id?.match OutputCacheManager.BUILD_REGEX
-		next()
-	else
-		next new Error("invalid build id #{build_id}")
-
-
-app.post   "/project/:project_id/compile", bodyParser.json(limit: Settings.compileSizeLimit), CompileController.compile
-app.post   "/project/:project_id/compile/stop", CompileController.stopCompile
-app.delete "/project/:project_id", CompileController.clearCache
-
-app.get  "/project/:project_id/sync/code", CompileController.syncFromCode
-app.get  "/project/:project_id/sync/pdf", CompileController.syncFromPdf
-app.get  "/project/:project_id/wordcount", CompileController.wordcount
-app.get  "/project/:project_id/status", CompileController.status
-
-# Per-user containers
-app.post   "/project/:project_id/user/:user_id/compile", bodyParser.json(limit: Settings.compileSizeLimit), CompileController.compile
-app.post   "/project/:project_id/user/:user_id/compile/stop", CompileController.stopCompile
-app.delete "/project/:project_id/user/:user_id", CompileController.clearCache
-
-app.get  "/project/:project_id/user/:user_id/sync/code", CompileController.syncFromCode
-app.get  "/project/:project_id/user/:user_id/sync/pdf", CompileController.syncFromPdf
-app.get  "/project/:project_id/user/:user_id/wordcount", CompileController.wordcount
-
-ForbidSymlinks = require "./app/js/StaticServerForbidSymlinks"
-
-# create a static server which does not allow access to any symlinks
-# avoids possible mismatch of root directory between middleware check
-# and serving the files
-staticServer = ForbidSymlinks express.static, Settings.path.compilesDir, setHeaders: (res, path, stat) ->
-	if Path.basename(path) == "output.pdf"
-		# Calculate an etag in the same way as nginx
-		# https://github.com/tj/send/issues/65
-		etag = (path, stat) ->
-			'"' + Math.ceil(+stat.mtime / 1000).toString(16) +
-			'-' + Number(stat.size).toString(16) + '"'
-		res.set("Etag", etag(path, stat))
-	res.set("Content-Type", ContentTypeMapper.map(path))
-
-app.get "/project/:project_id/user/:user_id/build/:build_id/output/*", (req, res, next) ->
-	# for specific build get the path from the OutputCacheManager (e.g. .clsi/buildId)
-	req.url = "/#{req.params.project_id}-#{req.params.user_id}/" + OutputCacheManager.path(req.params.build_id, "/#{req.params[0]}")
-	staticServer(req, res, next)
-
-app.get "/project/:project_id/build/:build_id/output/*", (req, res, next) ->
-	# for specific build get the path from the OutputCacheManager (e.g. .clsi/buildId)
-	req.url = "/#{req.params.project_id}/" + OutputCacheManager.path(req.params.build_id, "/#{req.params[0]}")
-	staticServer(req, res, next)
-
-app.get "/project/:project_id/user/:user_id/output/*", (req, res, next) ->
-	# for specific user get the path to the top level file
-	req.url = "/#{req.params.project_id}-#{req.params.user_id}/#{req.params[0]}"
-	staticServer(req, res, next)
-
-app.get "/project/:project_id/output/*", (req, res, next) ->
-	if req.query?.build? && req.query.build.match(OutputCacheManager.BUILD_REGEX)
-		# for specific build get the path from the OutputCacheManager (e.g. .clsi/buildId)
-		req.url = "/#{req.params.project_id}/" + OutputCacheManager.path(req.query.build, "/#{req.params[0]}")
-	else
-		req.url = "/#{req.params.project_id}/#{req.params[0]}"
-	staticServer(req, res, next)
-
-app.get "/oops", (req, res, next) ->
-	logger.error {err: "hello"}, "test error"
-	res.send "error\n"
-
-
-app.get "/status", (req, res, next) ->
-	res.send "CLSI is alive\n"
-
-resCacher =
-	contentType:(@setContentType)->
-	send:(@code, @body)->
-
-	#default the server to be down
-	code:500
-	body:{}
-	setContentType:"application/json"
-
-if Settings.smokeTest
-	do runSmokeTest = ->
-		logger.log("running smoke tests")
-		smokeTest.run(require.resolve(__dirname + "/test/smoke/js/SmokeTests.js"))({}, resCacher)
-		setTimeout(runSmokeTest, 30 * 1000)
-
-app.get "/health_check", (req, res)->
-	res.contentType(resCacher?.setContentType)
-	res.status(resCacher?.code).send(resCacher?.body)
-
-app.get "/smoke_test_force", (req, res)->
-	smokeTest.run(require.resolve(__dirname + "/test/smoke/js/SmokeTests.js"))(req, res)
-
-profiler = require "v8-profiler-node8"
-app.get "/profile", (req, res) ->
-	time = parseInt(req.query.time || "1000")
-	profiler.startProfiling("test")
-	setTimeout () ->
-		profile = profiler.stopProfiling("test")
-		res.json(profile)
-	, time
-
-app.get "/heapdump", (req, res)->
-	require('heapdump').writeSnapshot '/tmp/' + Date.now() + '.clsi.heapsnapshot', (err, filename)->
-		res.send filename
-
-app.use (error, req, res, next) ->
-	if error instanceof Errors.NotFoundError
-		logger.warn {err: error, url: req.url}, "not found error"
-		return res.sendStatus(404)
-	else
-		logger.error {err: error, url: req.url}, "server error"
-		res.sendStatus(error?.statusCode || 500)
-
-net = require "net"
-os = require "os"
-
-STATE = "up"
-
-
-loadTcpServer = net.createServer (socket) ->
-	socket.on "error", (err)->
-		if err.code == "ECONNRESET"
-			# this always comes up, we don't know why
-			return
-		logger.err err:err, "error with socket on load check"
-		socket.destroy()
-	
-	if STATE == "up" and Settings.internal.load_balancer_agent.report_load
-		currentLoad = os.loadavg()[0]
-
-		# staging clis's have 1 cpu core only
-		if os.cpus().length == 1
-			availableWorkingCpus = 1
-		else
-			availableWorkingCpus = os.cpus().length - 1
-
-		freeLoad = availableWorkingCpus - currentLoad
-		freeLoadPercentage = Math.round((freeLoad / availableWorkingCpus) * 100)
-		if freeLoadPercentage <= 0
-			freeLoadPercentage = 1 # when its 0 the server is set to drain and will move projects to different servers
-		socket.write("up, #{freeLoadPercentage}%\n", "ASCII")
-		socket.end()
-	else
-		socket.write("#{STATE}\n", "ASCII")
-		socket.end()
-
-loadHttpServer = express()
-
-loadHttpServer.post "/state/up", (req, res, next) ->
-	STATE = "up"
-	logger.info "getting message to set server to down"
-	res.sendStatus 204
-
-loadHttpServer.post "/state/down", (req, res, next) ->
-	STATE = "down"
-	logger.info "getting message to set server to down"
-	res.sendStatus 204
-
-loadHttpServer.post "/state/maint", (req, res, next) ->
-	STATE = "maint"
-	logger.info "getting message to set server to maint"
-	res.sendStatus 204
-	
-
-port = (Settings.internal?.clsi?.port or 3013)
-host = (Settings.internal?.clsi?.host or "localhost")
-
-load_tcp_port = Settings.internal.load_balancer_agent.load_port
-load_http_port = Settings.internal.load_balancer_agent.local_port
-
-if !module.parent # Called directly
-	app.listen port, host, (error) ->
-		logger.info "CLSI starting up, listening on #{host}:#{port}"
-
-	loadTcpServer.listen load_tcp_port, host, (error) ->
-		throw error if error?
-		logger.info "Load tcp agent listening on load port #{load_tcp_port}"
-
-	loadHttpServer.listen load_http_port, host, (error) ->
-		throw error if error?
-		logger.info "Load http agent listening on load port #{load_http_port}"
-
-module.exports = app
-
-setInterval () ->
-	ProjectPersistenceManager.clearExpiredProjects()
-, tenMinutes = 10 * 60 * 1000
-

services/clsi/app.js

@@ -0,0 +1,371 @@
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let tenMinutes
+const Metrics = require('metrics-sharelatex')
+Metrics.initialize('clsi')
+
+const CompileController = require('./app/js/CompileController')
+const Settings = require('settings-sharelatex')
+const logger = require('logger-sharelatex')
+logger.initialize('clsi')
+if ((Settings.sentry != null ? Settings.sentry.dsn : undefined) != null) {
+  logger.initializeErrorReporting(Settings.sentry.dsn)
+}
+
+const smokeTest = require('smoke-test-sharelatex')
+const ContentTypeMapper = require('./app/js/ContentTypeMapper')
+const Errors = require('./app/js/Errors')
+
+const Path = require('path')
+
+Metrics.open_sockets.monitor(logger)
+Metrics.memory.monitor(logger)
+
+const ProjectPersistenceManager = require('./app/js/ProjectPersistenceManager')
+const OutputCacheManager = require('./app/js/OutputCacheManager')
+
+require('./app/js/db').sync()
+
+const express = require('express')
+const bodyParser = require('body-parser')
+const app = express()
+
+Metrics.injectMetricsRoute(app)
+app.use(Metrics.http.monitor(logger))
+
+// Compile requests can take longer than the default two
+// minutes (including file download time), so bump up the
+// timeout a bit.
+const TIMEOUT = 10 * 60 * 1000
+app.use(function(req, res, next) {
+  req.setTimeout(TIMEOUT)
+  res.setTimeout(TIMEOUT)
+  res.removeHeader('X-Powered-By')
+  return next()
+})
+
+app.param('project_id', function(req, res, next, project_id) {
+  if (project_id != null ? project_id.match(/^[a-zA-Z0-9_-]+$/) : undefined) {
+    return next()
+  } else {
+    return next(new Error('invalid project id'))
+  }
+})
+
+app.param('user_id', function(req, res, next, user_id) {
+  if (user_id != null ? user_id.match(/^[0-9a-f]{24}$/) : undefined) {
+    return next()
+  } else {
+    return next(new Error('invalid user id'))
+  }
+})
+
+app.param('build_id', function(req, res, next, build_id) {
+  if (
+    build_id != null
+      ? build_id.match(OutputCacheManager.BUILD_REGEX)
+      : undefined
+  ) {
+    return next()
+  } else {
+    return next(new Error(`invalid build id ${build_id}`))
+  }
+})
+
+app.post(
+  '/project/:project_id/compile',
+  bodyParser.json({ limit: Settings.compileSizeLimit }),
+  CompileController.compile
+)
+app.post('/project/:project_id/compile/stop', CompileController.stopCompile)
+app.delete('/project/:project_id', CompileController.clearCache)
+
+app.get('/project/:project_id/sync/code', CompileController.syncFromCode)
+app.get('/project/:project_id/sync/pdf', CompileController.syncFromPdf)
+app.get('/project/:project_id/wordcount', CompileController.wordcount)
+app.get('/project/:project_id/status', CompileController.status)
+
+// Per-user containers
+app.post(
+  '/project/:project_id/user/:user_id/compile',
+  bodyParser.json({ limit: Settings.compileSizeLimit }),
+  CompileController.compile
+)
+app.post(
+  '/project/:project_id/user/:user_id/compile/stop',
+  CompileController.stopCompile
+)
+app.delete('/project/:project_id/user/:user_id', CompileController.clearCache)
+
+app.get(
+  '/project/:project_id/user/:user_id/sync/code',
+  CompileController.syncFromCode
+)
+app.get(
+  '/project/:project_id/user/:user_id/sync/pdf',
+  CompileController.syncFromPdf
+)
+app.get(
+  '/project/:project_id/user/:user_id/wordcount',
+  CompileController.wordcount
+)
+
+const ForbidSymlinks = require('./app/js/StaticServerForbidSymlinks')
+
+// create a static server which does not allow access to any symlinks
+// avoids possible mismatch of root directory between middleware check
+// and serving the files
+const staticServer = ForbidSymlinks(express.static, Settings.path.compilesDir, {
+  setHeaders(res, path, stat) {
+    if (Path.basename(path) === 'output.pdf') {
+      // Calculate an etag in the same way as nginx
+      // https://github.com/tj/send/issues/65
+      const etag = (path, stat) =>
+        `"${Math.ceil(+stat.mtime / 1000).toString(16)}` +
+        '-' +
+        Number(stat.size).toString(16) +
+        '"'
+      res.set('Etag', etag(path, stat))
+    }
+    return res.set('Content-Type', ContentTypeMapper.map(path))
+  }
+})
+
+app.get('/project/:project_id/user/:user_id/build/:build_id/output/*', function(
+  req,
+  res,
+  next
+) {
+  // for specific build get the path from the OutputCacheManager (e.g. .clsi/buildId)
+  req.url =
+    `/${req.params.project_id}-${req.params.user_id}/` +
+    OutputCacheManager.path(req.params.build_id, `/${req.params[0]}`)
+  return staticServer(req, res, next)
+})
+
+app.get('/project/:project_id/build/:build_id/output/*', function(
+  req,
+  res,
+  next
+) {
+  // for specific build get the path from the OutputCacheManager (e.g. .clsi/buildId)
+  req.url =
+    `/${req.params.project_id}/` +
+    OutputCacheManager.path(req.params.build_id, `/${req.params[0]}`)
+  return staticServer(req, res, next)
+})
+
+app.get('/project/:project_id/user/:user_id/output/*', function(
+  req,
+  res,
+  next
+) {
+  // for specific user get the path to the top level file
+  req.url = `/${req.params.project_id}-${req.params.user_id}/${req.params[0]}`
+  return staticServer(req, res, next)
+})
+
+app.get('/project/:project_id/output/*', function(req, res, next) {
+  if (
+    (req.query != null ? req.query.build : undefined) != null &&
+    req.query.build.match(OutputCacheManager.BUILD_REGEX)
+  ) {
+    // for specific build get the path from the OutputCacheManager (e.g. .clsi/buildId)
+    req.url =
+      `/${req.params.project_id}/` +
+      OutputCacheManager.path(req.query.build, `/${req.params[0]}`)
+  } else {
+    req.url = `/${req.params.project_id}/${req.params[0]}`
+  }
+  return staticServer(req, res, next)
+})
+
+app.get('/oops', function(req, res, next) {
+  logger.error({ err: 'hello' }, 'test error')
+  return res.send('error\n')
+})
+
+app.get('/status', (req, res, next) => res.send('CLSI is alive\n'))
+
+const resCacher = {
+  contentType(setContentType) {
+    this.setContentType = setContentType
+  },
+  send(code, body) {
+    this.code = code
+    this.body = body
+  },
+
+  // default the server to be down
+  code: 500,
+  body: {},
+  setContentType: 'application/json'
+}
+
+let shutdownTime
+if (Settings.processLifespanLimitMs) {
+  Settings.processLifespanLimitMs +=
+    Settings.processLifespanLimitMs * (Math.random() / 10)
+  shutdownTime = Date.now() + Settings.processLifespanLimitMs
+  logger.info('Lifespan limited to ', shutdownTime)
+}
+
+const checkIfProcessIsTooOld = function(cont) {
+  if (shutdownTime && shutdownTime < Date.now()) {
+    logger.log('shutting down, process is too old')
+    resCacher.send = function() {}
+    resCacher.code = 500
+    resCacher.body = { processToOld: true }
+  } else {
+    cont()
+  }
+}
+
+if (Settings.smokeTest) {
+  const runSmokeTest = function() {
+    checkIfProcessIsTooOld(function() {
+      logger.log('running smoke tests')
+      smokeTest.run(
+        require.resolve(__dirname + '/test/smoke/js/SmokeTests.js')
+      )({}, resCacher)
+      return setTimeout(runSmokeTest, 30 * 1000)
+    })
+  }
+  runSmokeTest()
+}
+
+app.get('/health_check', function(req, res) {
+  res.contentType(resCacher.setContentType)
+  return res.status(resCacher.code).send(resCacher.body)
+})
+
+app.get('/smoke_test_force', (req, res) =>
+  smokeTest.run(require.resolve(__dirname + '/test/smoke/js/SmokeTests.js'))(
+    req,
+    res
+  )
+)
+
+app.use(function(error, req, res, next) {
+  if (error instanceof Errors.NotFoundError) {
+    logger.warn({ err: error, url: req.url }, 'not found error')
+    return res.sendStatus(404)
+  } else {
+    logger.error({ err: error, url: req.url }, 'server error')
+    return res.sendStatus((error != null ? error.statusCode : undefined) || 500)
+  }
+})
+
+const net = require('net')
+const os = require('os')
+
+let STATE = 'up'
+
+const loadTcpServer = net.createServer(function(socket) {
+  socket.on('error', function(err) {
+    if (err.code === 'ECONNRESET') {
+      // this always comes up, we don't know why
+      return
+    }
+    logger.err({ err }, 'error with socket on load check')
+    return socket.destroy()
+  })
+
+  if (STATE === 'up' && Settings.internal.load_balancer_agent.report_load) {
+    let availableWorkingCpus
+    const currentLoad = os.loadavg()[0]
+
+    // staging clis's have 1 cpu core only
+    if (os.cpus().length === 1) {
+      availableWorkingCpus = 1
+    } else {
+      availableWorkingCpus = os.cpus().length - 1
+    }
+
+    const freeLoad = availableWorkingCpus - currentLoad
+    let freeLoadPercentage = Math.round((freeLoad / availableWorkingCpus) * 100)
+    if (freeLoadPercentage <= 0) {
+      freeLoadPercentage = 1 // when its 0 the server is set to drain and will move projects to different servers
+    }
+    socket.write(`up, ${freeLoadPercentage}%\n`, 'ASCII')
+    return socket.end()
+  } else {
+    socket.write(`${STATE}\n`, 'ASCII')
+    return socket.end()
+  }
+})
+
+const loadHttpServer = express()
+
+loadHttpServer.post('/state/up', function(req, res, next) {
+  STATE = 'up'
+  logger.info('getting message to set server to down')
+  return res.sendStatus(204)
+})
+
+loadHttpServer.post('/state/down', function(req, res, next) {
+  STATE = 'down'
+  logger.info('getting message to set server to down')
+  return res.sendStatus(204)
+})
+
+loadHttpServer.post('/state/maint', function(req, res, next) {
+  STATE = 'maint'
+  logger.info('getting message to set server to maint')
+  return res.sendStatus(204)
+})
+
+const port =
+  __guard__(
+    Settings.internal != null ? Settings.internal.clsi : undefined,
+    x => x.port
+  ) || 3013
+const host =
+  __guard__(
+    Settings.internal != null ? Settings.internal.clsi : undefined,
+    x1 => x1.host
+  ) || 'localhost'
+
+const load_tcp_port = Settings.internal.load_balancer_agent.load_port
+const load_http_port = Settings.internal.load_balancer_agent.local_port
+
+if (!module.parent) {
+  // Called directly
+  app.listen(port, host, error =>
+    logger.info(`CLSI starting up, listening on ${host}:${port}`)
+  )
+
+  loadTcpServer.listen(load_tcp_port, host, function(error) {
+    if (error != null) {
+      throw error
+    }
+    return logger.info(`Load tcp agent listening on load port ${load_tcp_port}`)
+  })
+
+  loadHttpServer.listen(load_http_port, host, function(error) {
+    if (error != null) {
+      throw error
+    }
+    return logger.info(
+      `Load http agent listening on load port ${load_http_port}`
+    )
+  })
+}
+
+module.exports = app
+
+setInterval(
+  () => ProjectPersistenceManager.clearExpiredProjects(),
+  (tenMinutes = 10 * 60 * 1000)
+)
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/app/coffee/CommandRunner.coffee

@@ -1,11 +0,0 @@
-Settings = require "settings-sharelatex"
-logger = require "logger-sharelatex"
-
-if Settings.clsi?.dockerRunner == true
-	commandRunnerPath = "./DockerRunner"
-else 
-	commandRunnerPath = "./LocalCommandRunner"
-logger.info commandRunnerPath:commandRunnerPath, "selecting command runner for clsi"
-CommandRunner = require(commandRunnerPath)
-
-module.exports = CommandRunner

services/clsi/app/coffee/CompileController.coffee

@@ -1,119 +0,0 @@
-RequestParser = require "./RequestParser"
-CompileManager = require "./CompileManager"
-Settings = require "settings-sharelatex"
-Metrics = require "./Metrics"
-ProjectPersistenceManager = require "./ProjectPersistenceManager"
-logger = require "logger-sharelatex"
-Errors = require "./Errors"
-
-module.exports = CompileController =
-	compile: (req, res, next = (error) ->) ->
-		timer = new Metrics.Timer("compile-request")
-		RequestParser.parse req.body, (error, request) ->
-			return next(error) if error?
-			request.project_id = req.params.project_id
-			request.user_id = req.params.user_id if req.params.user_id?
-			ProjectPersistenceManager.markProjectAsJustAccessed request.project_id, (error) ->
-				return next(error) if error?
-				CompileManager.doCompileWithLock request, (error, outputFiles = []) ->
-					if error instanceof Errors.AlreadyCompilingError
-						code = 423 # Http 423 Locked
-						status = "compile-in-progress"
-					else if error instanceof Errors.FilesOutOfSyncError
-						code = 409 # Http 409 Conflict
-						status = "retry"
-					else if error?.terminated
-						status = "terminated"
-					else if error?.validate
-						status = "validation-#{error.validate}"
-					else if error?.timedout
-						status = "timedout"
-						logger.log err: error, project_id: request.project_id, "timeout running compile"
-					else if error?
-						status = "error"
-						code = 500
-						logger.warn err: error, project_id: request.project_id, "error running compile"
-					else
-						status = "failure"
-						for file in outputFiles
-							if file.path?.match(/output\.pdf$/)
-								status = "success"
-
-						if status == "failure"
-							logger.warn project_id: request.project_id, outputFiles:outputFiles, "project failed to compile successfully, no output.pdf generated"
-
-						# log an error if any core files are found
-						for file in outputFiles
-							if file.path is "core"
-								logger.error project_id:request.project_id, req:req, outputFiles:outputFiles, "core file found in output"
-
-					if error?
-						outputFiles = error.outputFiles || []
-
-					timer.done()
-					res.status(code or 200).send {
-						compile:
-							status: status
-							error:  error?.message or error
-							outputFiles: outputFiles.map (file) ->
-								url:
-									"#{Settings.apis.clsi.url}/project/#{request.project_id}" +
-									(if request.user_id? then "/user/#{request.user_id}" else "") +
-									(if file.build? then "/build/#{file.build}" else "") +
-									"/output/#{file.path}"
-								path: file.path
-								type: file.type
-								build: file.build
-					}
-
-	stopCompile: (req, res, next) ->
-		{project_id, user_id} = req.params
-		CompileManager.stopCompile project_id, user_id, (error) ->
-			return next(error) if error?
-			res.sendStatus(204)
-
-	clearCache: (req, res, next = (error) ->) ->
-		ProjectPersistenceManager.clearProject req.params.project_id, req.params.user_id, (error) ->
-			return next(error) if error?
-			res.sendStatus(204) # No content
-
-	syncFromCode: (req, res, next = (error) ->) ->
-		file   = req.query.file
-		line   = parseInt(req.query.line, 10)
-		column = parseInt(req.query.column, 10)
-		project_id = req.params.project_id
-		user_id = req.params.user_id
-		CompileManager.syncFromCode project_id, user_id, file, line, column, (error, pdfPositions) ->
-			return next(error) if error?
-			res.json {
-				pdf: pdfPositions
-			}
-
-	syncFromPdf: (req, res, next = (error) ->) ->
-		page   = parseInt(req.query.page, 10)
-		h      = parseFloat(req.query.h)
-		v      = parseFloat(req.query.v)
-		project_id = req.params.project_id
-		user_id = req.params.user_id
-		CompileManager.syncFromPdf project_id, user_id, page, h, v, (error, codePositions) ->
-			return next(error) if error?
-			res.json {
-				code: codePositions
-			}
-
-	wordcount: (req, res, next = (error) ->) ->
-		file   = req.query.file || "main.tex"
-		project_id = req.params.project_id
-		user_id = req.params.user_id
-		image = req.query.image
-		logger.log {image, file, project_id}, "word count request"
-
-		CompileManager.wordcount project_id, user_id, file, image, (error, result) ->
-			return next(error) if error?
-			res.json {
-				texcount: result
-			}
-
-	status: (req, res, next = (error)-> )->
-		res.send("OK")
-

services/clsi/app/coffee/CompileManager.coffee

@@ -1,345 +0,0 @@
-ResourceWriter = require "./ResourceWriter"
-LatexRunner = require "./LatexRunner"
-OutputFileFinder = require "./OutputFileFinder"
-OutputCacheManager = require "./OutputCacheManager"
-Settings = require("settings-sharelatex")
-Path = require "path"
-logger = require "logger-sharelatex"
-Metrics = require "./Metrics"
-child_process = require "child_process"
-DraftModeManager = require "./DraftModeManager"
-TikzManager = require "./TikzManager"
-LockManager = require "./LockManager"
-fs = require("fs")
-fse = require "fs-extra"
-os = require("os")
-async = require "async"
-Errors = require './Errors'
-CommandRunner = require "./CommandRunner"
-
-getCompileName = (project_id, user_id) ->
-	if user_id? then "#{project_id}-#{user_id}" else project_id
-
-getCompileDir = (project_id, user_id) ->
-	Path.join(Settings.path.compilesDir, getCompileName(project_id, user_id))
-
-module.exports = CompileManager =
-
-	doCompileWithLock: (request, callback = (error, outputFiles) ->) ->
-		compileDir = getCompileDir(request.project_id, request.user_id)
-		lockFile = Path.join(compileDir, ".project-lock")
-		# use a .project-lock file in the compile directory to prevent
-		# simultaneous compiles
-		fse.ensureDir compileDir, (error) ->
-			return callback(error) if error?
-			LockManager.runWithLock lockFile, (releaseLock) ->
-				CompileManager.doCompile(request, releaseLock)
-			, callback
-
-	doCompile: (request, callback = (error, outputFiles) ->) ->
-		compileDir = getCompileDir(request.project_id, request.user_id)
-		timer = new Metrics.Timer("write-to-disk")
-		logger.log project_id: request.project_id, user_id: request.user_id, "syncing resources to disk"
-		ResourceWriter.syncResourcesToDisk request, compileDir, (error, resourceList) ->
-			# NOTE: resourceList is insecure, it should only be used to exclude files from the output list
-			if error? and error instanceof Errors.FilesOutOfSyncError
-				logger.warn project_id: request.project_id, user_id: request.user_id, "files out of sync, please retry"
-				return callback(error)
-			else if error?
-				logger.err err:error, project_id: request.project_id, user_id: request.user_id, "error writing resources to disk"
-				return callback(error)
-			logger.log project_id: request.project_id, user_id: request.user_id, time_taken: Date.now() - timer.start, "written files to disk"
-			timer.done()
-
-			injectDraftModeIfRequired = (callback) ->
-				if request.draft
-					DraftModeManager.injectDraftMode Path.join(compileDir, request.rootResourcePath), callback
-				else
-					callback()
-
-			createTikzFileIfRequired = (callback) ->
-				TikzManager.checkMainFile compileDir, request.rootResourcePath, resourceList, (error, needsMainFile) ->
-					return callback(error) if error?
-					if needsMainFile
-						TikzManager.injectOutputFile compileDir, request.rootResourcePath, callback
-					else
-						callback()
-
-			# set up environment variables for chktex
-			env = {}
-			# only run chktex on LaTeX files (not knitr .Rtex files or any others)
-			isLaTeXFile = request.rootResourcePath?.match(/\.tex$/i)
-			if request.check? and isLaTeXFile
-				env['CHKTEX_OPTIONS'] = '-nall -e9 -e10 -w15 -w16'
-				env['CHKTEX_ULIMIT_OPTIONS'] = '-t 5 -v 64000'
-				if request.check is 'error'
-					env['CHKTEX_EXIT_ON_ERROR'] =  1
-				if request.check is 'validate'
-					env['CHKTEX_VALIDATE'] =  1
-
-			# apply a series of file modifications/creations for draft mode and tikz
-			async.series [injectDraftModeIfRequired, createTikzFileIfRequired], (error) ->
-				return callback(error) if error?
-				timer = new Metrics.Timer("run-compile")
-				# find the image tag to log it as a metric, e.g. 2015.1 (convert . to - for graphite)
-				tag = request.imageName?.match(/:(.*)/)?[1]?.replace(/\./g,'-') or "default"
-				tag = "other" if not request.project_id.match(/^[0-9a-f]{24}$/) # exclude smoke test
-				Metrics.inc("compiles")
-				Metrics.inc("compiles-with-image.#{tag}")
-				compileName = getCompileName(request.project_id, request.user_id)
-				LatexRunner.runLatex compileName, {
-					directory: compileDir
-					mainFile:  request.rootResourcePath
-					compiler:  request.compiler
-					timeout:   request.timeout
-					image:     request.imageName
-					flags:     request.flags
-					environment: env
-				}, (error, output, stats, timings) ->
-					# request was for validation only
-					if request.check is "validate"
-						result = if error?.code then "fail" else "pass"
-						error = new Error("validation")
-						error.validate = result
-					# request was for compile, and failed on validation
-					if request.check is "error" and error?.message is 'exited'
-						error = new Error("compilation")
-						error.validate = "fail"
-					# compile was killed by user, was a validation, or a compile which failed validation
-					if error?.terminated or error?.validate or error?.timedout
-						OutputFileFinder.findOutputFiles resourceList, compileDir, (err, outputFiles) ->
-							return callback(err) if err?
-							error.outputFiles = outputFiles  # return output files so user can check logs
-							callback(error)
-						return
-					# compile completed normally
-					return callback(error) if error?
-					Metrics.inc("compiles-succeeded")
-					for metric_key, metric_value of stats or {}
-						Metrics.count(metric_key, metric_value)
-					for metric_key, metric_value of timings or {}
-						Metrics.timing(metric_key, metric_value)
-					loadavg = os.loadavg?()
-					Metrics.gauge("load-avg", loadavg[0]) if loadavg?
-					ts = timer.done()
-					logger.log {project_id: request.project_id, user_id: request.user_id, time_taken: ts, stats:stats, timings:timings, loadavg:loadavg}, "done compile"
-					if stats?["latex-runs"] > 0
-						Metrics.timing("run-compile-per-pass", ts / stats["latex-runs"])
-					if stats?["latex-runs"] > 0 and timings?["cpu-time"] > 0
-						Metrics.timing("run-compile-cpu-time-per-pass", timings["cpu-time"] / stats["latex-runs"])
-
-					OutputFileFinder.findOutputFiles resourceList, compileDir, (error, outputFiles) ->
-						return callback(error) if error?
-						OutputCacheManager.saveOutputFiles outputFiles, compileDir,  (error, newOutputFiles) ->
-							callback null, newOutputFiles
-
-	stopCompile: (project_id, user_id, callback = (error) ->) ->
-		compileName = getCompileName(project_id, user_id)
-		LatexRunner.killLatex compileName, callback
-
-	clearProject: (project_id, user_id, _callback = (error) ->) ->
-		callback = (error) ->
-			_callback(error)
-			_callback = () ->
-
-		compileDir = getCompileDir(project_id, user_id)
-
-		CompileManager._checkDirectory compileDir, (err, exists) ->
-			return callback(err) if err?
-			return callback() if not exists # skip removal if no directory present
-
-			proc = child_process.spawn "rm", ["-r", compileDir]
-
-			proc.on "error", callback
-
-			stderr = ""
-			proc.stderr.on "data", (chunk) -> stderr += chunk.toString()
-
-			proc.on "close", (code) ->
-				if code == 0
-					return callback(null)
-				else
-					return callback(new Error("rm -r #{compileDir} failed: #{stderr}"))
-
-	_findAllDirs: (callback = (error, allDirs) ->) ->
-		root = Settings.path.compilesDir
-		fs.readdir root, (err, files) ->
-			return callback(err) if err?
-			allDirs = (Path.join(root, file) for file in files)
-			callback(null, allDirs)
-
-	clearExpiredProjects: (max_cache_age_ms, callback = (error) ->) ->
-		now = Date.now()
-		# action for each directory
-		expireIfNeeded = (checkDir, cb) ->
-			fs.stat checkDir, (err, stats) ->
-				return cb() if err?  # ignore errors checking directory
-				age = now - stats.mtime
-				hasExpired = (age > max_cache_age_ms)
-				if hasExpired then fse.remove(checkDir, cb) else cb()
-		# iterate over all project directories
-		CompileManager._findAllDirs (error, allDirs) ->
-			return callback() if error?
-			async.eachSeries allDirs, expireIfNeeded,	callback
-
-	_checkDirectory: (compileDir, callback = (error, exists) ->) ->
-		fs.lstat compileDir, (err, stats) ->
-			if err?.code is 'ENOENT'
-				return callback(null, false) #  directory does not exist
-			else if err?
-				logger.err {dir: compileDir, err:err}, "error on stat of project directory for removal"
-				return callback(err)
-			else if not stats?.isDirectory()
-				logger.err {dir: compileDir, stats:stats}, "bad project directory for removal"
-				return callback new Error("project directory is not directory")
-			else
-				callback(null, true) # directory exists
-
-	syncFromCode: (project_id, user_id, file_name, line, column, callback = (error, pdfPositions) ->) ->
-		# If LaTeX was run in a virtual environment, the file path that synctex expects
-		# might not match the file path on the host. The .synctex.gz file however, will be accessed
-		# wherever it is on the host.
-		compileName = getCompileName(project_id, user_id)
-		base_dir = Settings.path.synctexBaseDir(compileName)
-		file_path = base_dir + "/" + file_name
-		compileDir = getCompileDir(project_id, user_id)
-		synctex_path =  "#{base_dir}/output.pdf"
-		command = ["code", synctex_path, file_path, line, column]
-		fse.ensureDir compileDir, (error) ->
-			if error?
-				logger.err {error, project_id, user_id, file_name}, "error ensuring dir for sync from code"
-				return callback(error)
-			CompileManager._runSynctex project_id, user_id, command, (error, stdout) ->
-				return callback(error) if error?
-				logger.log project_id: project_id, user_id:user_id, file_name: file_name, line: line, column: column, command:command, stdout: stdout, "synctex code output"
-				callback null, CompileManager._parseSynctexFromCodeOutput(stdout)
-
-	syncFromPdf: (project_id, user_id, page, h, v, callback = (error, filePositions) ->) ->
-		compileName = getCompileName(project_id, user_id)
-		compileDir = getCompileDir(project_id, user_id)
-		base_dir = Settings.path.synctexBaseDir(compileName)
-		synctex_path =  "#{base_dir}/output.pdf"
-		command = ["pdf", synctex_path, page, h, v]
-		fse.ensureDir compileDir, (error) ->
-			if error?
-				logger.err {error, project_id, user_id, file_name}, "error ensuring dir for sync to code"
-				return callback(error)
-			CompileManager._runSynctex  project_id, user_id, command, (error, stdout) ->
-				return callback(error) if error?
-				logger.log project_id: project_id, user_id:user_id, page: page, h: h, v:v, stdout: stdout, "synctex pdf output"
-				callback null, CompileManager._parseSynctexFromPdfOutput(stdout, base_dir)
-
-	_checkFileExists: (path, callback = (error) ->) ->
-		synctexDir = Path.dirname(path)
-		synctexFile = Path.join(synctexDir, "output.synctex.gz")
-		fs.stat synctexDir, (error, stats) ->
-			if error?.code is 'ENOENT'
-				return callback(new Errors.NotFoundError("called synctex with no output directory"))
-			return callback(error) if error?
-			fs.stat synctexFile, (error, stats) ->
-				if error?.code is 'ENOENT'
-					return callback(new Errors.NotFoundError("called synctex with no output file"))
-				return callback(error) if error?
-				return callback(new Error("not a file")) if not stats?.isFile()
-				callback()
-
-	_runSynctex: (project_id, user_id, command, callback = (error, stdout) ->) ->
-		seconds = 1000
-
-		command.unshift("/opt/synctex")
-
-		directory = getCompileDir(project_id, user_id)
-		timeout = 60 * 1000 # increased to allow for large projects
-		compileName = getCompileName(project_id, user_id)
-		CommandRunner.run compileName, command, directory, Settings.clsi?.docker.image, timeout, {}, (error, output) ->
-			if error?
-				logger.err err:error, command:command, project_id:project_id, user_id:user_id, "error running synctex"
-				return callback(error)
-			callback(null, output.stdout)
-
-	_parseSynctexFromCodeOutput: (output) ->
-		results = []
-		for line in output.split("\n")
-			[node, page, h, v, width, height] = line.split("\t")
-			if node == "NODE"
-				results.push {
-					page:   parseInt(page, 10)
-					h:      parseFloat(h)
-					v:      parseFloat(v)
-					height: parseFloat(height)
-					width:  parseFloat(width)
-				}
-		return results
-
-	_parseSynctexFromPdfOutput: (output, base_dir) ->
-		results = []
-		for line in output.split("\n")
-			[node, file_path, line, column] = line.split("\t")
-			if node == "NODE"
-				file = file_path.slice(base_dir.length + 1)
-				results.push {
-					file: file
-					line: parseInt(line, 10)
-					column: parseInt(column, 10)
-				}
-		return results
-
-
-	wordcount: (project_id, user_id, file_name, image, callback = (error, pdfPositions) ->) ->
-		logger.log project_id:project_id, user_id:user_id, file_name:file_name, image:image, "running wordcount"
-		file_path = "$COMPILE_DIR/" + file_name
-		command = [ "texcount", '-nocol', '-inc', file_path, "-out=" + file_path + ".wc"]
-		compileDir = getCompileDir(project_id, user_id)
-		timeout = 60 * 1000
-		compileName = getCompileName(project_id, user_id)
-		fse.ensureDir compileDir, (error) ->
-			if error?
-				logger.err {error, project_id, user_id, file_name}, "error ensuring dir for sync from code"
-				return callback(error)
-			CommandRunner.run compileName, command, compileDir, image, timeout, {}, (error) ->
-				return callback(error) if error?
-				fs.readFile compileDir + "/" + file_name + ".wc", "utf-8", (err, stdout) ->
-					if err?
-						#call it node_err so sentry doesn't use random path error as unique id so it can't be ignored
-						logger.err node_err:err, command:command, compileDir:compileDir, project_id:project_id, user_id:user_id, "error reading word count output"
-						return callback(err)
-					results = CompileManager._parseWordcountFromOutput(stdout)
-					logger.log project_id:project_id, user_id:user_id, wordcount: results, "word count results"
-					callback null, results
-
-	_parseWordcountFromOutput: (output) ->
-		results = {
-			encode: ""
-			textWords: 0
-			headWords: 0
-			outside: 0
-			headers: 0
-			elements: 0
-			mathInline: 0
-			mathDisplay: 0
-			errors: 0
-			messages: ""
-		}
-		for line in output.split("\n")
-			[data, info] = line.split(":")
-			if data.indexOf("Encoding") > -1
-				results['encode'] = info.trim()
-			if data.indexOf("in text") > -1
-				results['textWords'] = parseInt(info, 10)
-			if data.indexOf("in head") > -1
-				results['headWords'] = parseInt(info, 10)
-			if data.indexOf("outside") > -1
-				results['outside'] = parseInt(info, 10)
-			if data.indexOf("of head") > -1
-				results['headers'] = parseInt(info, 10)
-			if data.indexOf("Number of floats/tables/figures") > -1
-				results['elements'] = parseInt(info, 10)
-			if data.indexOf("Number of math inlines") > -1
-				results['mathInline'] = parseInt(info, 10)
-			if data.indexOf("Number of math displayed") > -1
-				results['mathDisplay'] = parseInt(info, 10)
-			if data is "(errors"  # errors reported as (errors:123)
-				results['errors'] = parseInt(info, 10)
-			if line.indexOf("!!! ") > -1  # errors logged as !!! message !!!
-				results['messages'] += line + "\n"
-		return results

services/clsi/app/coffee/ContentTypeMapper.coffee

@@ -1,24 +0,0 @@
-Path = require 'path'
-
-# here we coerce html, css and js to text/plain,
-# otherwise choose correct mime type based on file extension,
-# falling back to octet-stream
-module.exports = ContentTypeMapper =
-	map: (path) ->
-		switch Path.extname(path)
-			when '.txt', '.html', '.js', '.css', '.svg'
-				return 'text/plain'
-			when '.csv'
-				return 'text/csv'
-			when '.pdf'
-				return 'application/pdf'
-			when '.png'
-				return 'image/png'
-			when '.jpg', '.jpeg'
-				return 'image/jpeg'
-			when '.tiff'
-				return 'image/tiff'
-			when '.gif'
-				return 'image/gif'
-			else
-				return 'application/octet-stream'

services/clsi/app/coffee/DbQueue.coffee

@@ -1,13 +0,0 @@
-async = require "async"
-Settings = require "settings-sharelatex"
-logger = require("logger-sharelatex")
-queue = async.queue((task, cb)->
-		task(cb)
-	, Settings.parallelSqlQueryLimit)
-
-queue.drain = ()->
-	logger.debug('all items have been processed')
-
-module.exports = 
-	queue: queue
-

services/clsi/app/coffee/DockerLockManager.coffee

@@ -1,56 +0,0 @@
-logger = require "logger-sharelatex"
-
-LockState = {} # locks for docker container operations, by container name
-
-module.exports = LockManager =
-
-	MAX_LOCK_HOLD_TIME: 15000  # how long we can keep a lock
-	MAX_LOCK_WAIT_TIME: 10000  # how long we wait for a lock
-	LOCK_TEST_INTERVAL: 1000   # retry time
-
-	tryLock: (key, callback = (err, gotLock) ->) ->
-		existingLock = LockState[key]
-		if existingLock? # the lock is already taken, check how old it is
-			lockAge = Date.now() - existingLock.created
-			if lockAge < LockManager.MAX_LOCK_HOLD_TIME
-				return callback(null, false) # we didn't get the lock, bail out
-			else
-				logger.error {key: key, lock: existingLock, age:lockAge}, "taking old lock by force"
-		# take the lock
-		LockState[key] = lockValue = {created: Date.now()}
-		callback(null, true, lockValue)
-
-	getLock: (key, callback = (error, lockValue) ->) ->
-		startTime = Date.now()
-		do attempt = () ->
-			LockManager.tryLock key, (error, gotLock, lockValue) ->
-				return callback(error) if error?
-				if gotLock
-					callback(null, lockValue)
-				else if Date.now() - startTime > LockManager.MAX_LOCK_WAIT_TIME
-					e = new Error("Lock timeout")
-					e.key = key
-					return callback(e)
-				else
-					setTimeout attempt, LockManager.LOCK_TEST_INTERVAL
-
-	releaseLock: (key, lockValue, callback = (error) ->) ->
-		existingLock = LockState[key]
-		if existingLock is lockValue # lockValue is an object, so we can test by reference
-			delete LockState[key] # our lock, so we can free it
-			callback()
-		else if existingLock? # lock exists but doesn't match ours
-			logger.error {key:key, lock: existingLock}, "tried to release lock taken by force"
-			callback()
-		else
-			logger.error {key:key, lock: existingLock}, "tried to release lock that has gone"
-			callback()
-
-	runWithLock: (key, runner = ( (releaseLock = (error) ->) -> ), callback = ( (error) -> )) ->
-		LockManager.getLock key, (error, lockValue) ->
-			return callback(error) if error?
-			runner (error1, args...) ->
-				LockManager.releaseLock key, lockValue, (error2) ->
-					error = error1 or error2
-					return callback(error) if error?
-					callback(null, args...)

services/clsi/app/coffee/DockerRunner.coffee

@@ -1,360 +0,0 @@
-Settings = require "settings-sharelatex"
-logger = require "logger-sharelatex"
-Docker = require("dockerode")
-dockerode = new Docker()
-crypto = require "crypto"
-async = require "async"
-LockManager = require "./DockerLockManager"
-fs = require "fs"
-Path = require 'path'
-_ = require "underscore"
-
-logger.info "using docker runner"
-
-usingSiblingContainers = () ->
-	Settings?.path?.sandboxedCompilesHostDir?
-
-module.exports = DockerRunner =
-	ERR_NOT_DIRECTORY: new Error("not a directory")
-	ERR_TERMINATED: new Error("terminated")
-	ERR_EXITED: new Error("exited")
-	ERR_TIMED_OUT: new Error("container timed out")
-
-	run: (project_id, command, directory, image, timeout, environment, callback = (error, output) ->) ->
-
-		if usingSiblingContainers()
-			_newPath = Settings.path.sandboxedCompilesHostDir
-			logger.log {path: _newPath}, "altering bind path for sibling containers"
-			# Server Pro, example:
-			#   '/var/lib/sharelatex/data/compiles/<project-id>'
-			#   ... becomes ...
-			#   '/opt/sharelatex_data/data/compiles/<project-id>'
-			directory = Path.join(Settings.path.sandboxedCompilesHostDir, Path.basename(directory))
-
-		volumes = {}
-		volumes[directory] = "/compile"
-
-		command = (arg.toString().replace?('$COMPILE_DIR', "/compile") for arg in command)
-		if !image?
-			image = Settings.clsi.docker.image
-
-		if Settings.texliveImageNameOveride?
-			img = image.split("/")
-			image = "#{Settings.texliveImageNameOveride}/#{img[2]}"
-
-		options      = DockerRunner._getContainerOptions(command, image, volumes, timeout, environment)
-		fingerprint  = DockerRunner._fingerprintContainer(options)
-		options.name = name = "project-#{project_id}-#{fingerprint}"
-
-		# logOptions = _.clone(options)
-		# logOptions?.HostConfig?.SecurityOpt = "secomp used, removed in logging"
-		logger.log project_id: project_id, "running docker container"
-		DockerRunner._runAndWaitForContainer options, volumes, timeout, (error, output) ->
-			if error?.message?.match("HTTP code is 500")
-				logger.log err: error, project_id: project_id, "error running container so destroying and retrying"
-				DockerRunner.destroyContainer name, null, true, (error) ->
-					return callback(error) if error?
-					DockerRunner._runAndWaitForContainer options, volumes, timeout, callback
-			else
-				callback(error, output)
-
-		return name # pass back the container name to allow it to be killed
-
-	kill: (container_id, callback = (error) ->) ->
-		logger.log container_id: container_id, "sending kill signal to container"
-		container = dockerode.getContainer(container_id)
-		container.kill (error) ->
-			if error? and error?.message?.match?(/Cannot kill container .* is not running/)
-				logger.warn err: error, container_id: container_id, "container not running, continuing"
-				error = null
-			if error?
-				logger.error err: error, container_id: container_id, "error killing container"
-				return callback(error)
-			else
-				callback()
-
-	_runAndWaitForContainer: (options, volumes, timeout, _callback = (error, output) ->) ->
-		callback = (args...) ->
-			_callback(args...)
-			# Only call the callback once
-			_callback = () ->
-
-		name = options.name
-
-		streamEnded = false
-		containerReturned = false
-		output = {}
-
-		callbackIfFinished = () ->
-			if streamEnded and containerReturned
-				callback(null, output)
-
-		attachStreamHandler = (error, _output) ->
-			return callback(error) if error?
-			output = _output
-			streamEnded = true
-			callbackIfFinished()
-
-		DockerRunner.startContainer options, volumes, attachStreamHandler, (error, containerId) ->
-			return callback(error) if error?
-			
-			DockerRunner.waitForContainer name, timeout, (error, exitCode) ->
-				return callback(error) if error?
-				if exitCode is 137  # exit status from kill -9
-					err = DockerRunner.ERR_TERMINATED
-					err.terminated = true
-					return callback(err)
-				if exitCode is 1 # exit status from chktex
-					err = DockerRunner.ERR_EXITED
-					err.code = exitCode
-					return callback(err)
-				containerReturned = true
-				options?.HostConfig?.SecurityOpt = null #small log line
-				logger.log err:err, exitCode:exitCode, options:options, "docker container has exited"
-				callbackIfFinished()
-
-	_getContainerOptions: (command, image, volumes, timeout, environment) ->
-		timeoutInSeconds = timeout / 1000
-
-		dockerVolumes = {}
-		for hostVol, dockerVol of volumes
-			dockerVolumes[dockerVol] = {}
-
-			if volumes[hostVol].slice(-3).indexOf(":r") == -1
-				volumes[hostVol] = "#{dockerVol}:rw"
-
-		# merge settings and environment parameter
-		env = {}
-		for src in [Settings.clsi.docker.env, environment or {}]
-			env[key] = value for key, value of src
-		# set the path based on the image year
-		if m = image.match /:([0-9]+)\.[0-9]+/
-			year = m[1]
-		else
-			year = "2014"
-		env['PATH'] = "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/texlive/#{year}/bin/x86_64-linux/"
-		options =
-			"Cmd"             : command,
-			"Image"           : image
-			"Volumes"         : dockerVolumes
-			"WorkingDir"      : "/compile"
-			"NetworkDisabled" : true
-			"Memory"          : 1024 * 1024 * 1024 * 1024 # 1 Gb
-			"User"            : Settings.clsi.docker.user
-			"Env"             : ("#{key}=#{value}" for key, value of env)	# convert the environment hash to an array
-			"HostConfig"      :
-				"Binds": ("#{hostVol}:#{dockerVol}" for hostVol, dockerVol of volumes)
-				"LogConfig": {"Type": "none", "Config": {}}
-				"Ulimits": [{'Name': 'cpu', 'Soft': timeoutInSeconds+5, 'Hard': timeoutInSeconds+10}]
-				"CapDrop": "ALL"
-				"SecurityOpt": ["no-new-privileges"]
-
-		if Settings.path?.synctexBinHostPath?
-			options["HostConfig"]["Binds"].push("#{Settings.path.synctexBinHostPath}:/opt/synctex:ro")
-
-		if Settings.clsi.docker.runtime?
-			options["HostConfig"]["Runtime"] = Settings.clsi.docker.runtime
-
-		if Settings.clsi.docker.seccomp_profile?
-			options.HostConfig.SecurityOpt.push "seccomp=#{Settings.clsi.docker.seccomp_profile}"
-
-		return options
-
-	_fingerprintContainer: (containerOptions) ->
-		# Yay, Hashing!
-		json = JSON.stringify(containerOptions)
-		return crypto.createHash("md5").update(json).digest("hex")
-
-	startContainer: (options, volumes, attachStreamHandler, callback) ->
-		LockManager.runWithLock options.name, (releaseLock) ->
-			# Check that volumes exist before starting the container.
-			# When a container is started with volume pointing to a
-			# non-existent directory then docker creates the directory but
-			# with root ownership.
-			DockerRunner._checkVolumes options, volumes, (err) ->
-				return releaseLock(err) if err?
-				DockerRunner._startContainer options, volumes, attachStreamHandler, releaseLock
-		, callback
-
-	# Check that volumes exist and are directories
-	_checkVolumes: (options, volumes, callback = (error, containerName) ->) ->
-		if usingSiblingContainers()
-			# Server Pro, with sibling-containers active, skip checks
-			return callback(null)
-
-		checkVolume = (path, cb) ->
-			fs.stat path, (err, stats) ->
-				return cb(err) if err?
-				return cb(DockerRunner.ERR_NOT_DIRECTORY) if not stats?.isDirectory()
-				cb()
-		jobs = []
-		for vol of volumes
-			do (vol) ->
-				jobs.push (cb) -> checkVolume(vol, cb)
-		async.series jobs, callback
-
-	_startContainer: (options, volumes, attachStreamHandler, callback = ((error, output) ->)) ->
-		callback = _.once(callback)
-		name = options.name
-
-		logger.log {container_name: name}, "starting container"
-		container = dockerode.getContainer(name)
-
-		createAndStartContainer = ->
-			dockerode.createContainer options, (error, container) ->
-				return callback(error) if error?
-				startExistingContainer()
-
-		startExistingContainer = ->
-			DockerRunner.attachToContainer options.name, attachStreamHandler, (error)->
-				return callback(error) if error?
-				container.start (error) ->
-					if error? and error?.statusCode != 304 #already running
-						return callback(error)
-					else
-						callback()
-
-		container.inspect (error, stats)->
-			if error?.statusCode == 404
-				createAndStartContainer()
-			else if error?
-				logger.err {container_name: name, error:error}, "unable to inspect container to start"
-				return callback(error)
-			else
-				startExistingContainer()
-
-
-	attachToContainer: (containerId, attachStreamHandler, attachStartCallback) ->
-		container = dockerode.getContainer(containerId)
-		container.attach {stdout: 1, stderr: 1, stream: 1}, (error, stream) ->
-			if error?
-				logger.error err: error, container_id: containerId, "error attaching to container"
-				return attachStartCallback(error)
-			else
-				attachStartCallback()
-
-
-			logger.log container_id: containerId, "attached to container"
-
-			MAX_OUTPUT = 1024 * 1024 # limit output to 1MB
-			createStringOutputStream = (name) ->
-				return {
-					data: ""
-					overflowed: false
-					write: (data) ->
-						return if @overflowed
-						if @data.length < MAX_OUTPUT
-							@data += data
-						else
-							logger.error container_id: containerId, length: @data.length, maxLen: MAX_OUTPUT, "#{name} exceeds max size"
-							@data += "(...truncated at #{MAX_OUTPUT} chars...)"
-							@overflowed = true
-							# kill container if too much output
-							# docker.containers.kill(containerId, () ->)
-				}
-
-			stdout = createStringOutputStream "stdout"
-			stderr = createStringOutputStream "stderr"
-
-			container.modem.demuxStream(stream, stdout, stderr)
-
-			stream.on "error", (err) ->
-				logger.error err: err, container_id: containerId, "error reading from container stream"
-
-			stream.on "end", () ->
-				attachStreamHandler null, {stdout: stdout.data, stderr: stderr.data}
-
-	waitForContainer: (containerId, timeout, _callback = (error, exitCode) ->) ->
-		callback = (args...) ->
-			_callback(args...)
-			# Only call the callback once
-			_callback = () ->
-
-		container = dockerode.getContainer(containerId)
-
-		timedOut = false
-		timeoutId = setTimeout () ->
-			timedOut = true
-			logger.log container_id: containerId, "timeout reached, killing container"
-			container.kill(() ->)
-		, timeout
-
-		logger.log container_id: containerId, "waiting for docker container"
-		container.wait (error, res) ->
-			if error?
-				clearTimeout timeoutId
-				logger.error err: error, container_id: containerId, "error waiting for container"
-				return callback(error)
-			if timedOut
-				logger.log containerId: containerId, "docker container timed out"
-				error = DockerRunner.ERR_TIMED_OUT
-				error.timedout = true
-				callback error
-			else
-				clearTimeout timeoutId
-				logger.log container_id: containerId, exitCode: res.StatusCode, "docker container returned"
-				callback null, res.StatusCode
-
-	destroyContainer: (containerName, containerId, shouldForce, callback = (error) ->) ->
-		# We want the containerName for the lock and, ideally, the
-		# containerId to delete.  There is a bug in the docker.io module
-		# where if you delete by name and there is an error, it throws an
-		# async exception, but if you delete by id it just does a normal
-		# error callback. We fall back to deleting by name if no id is
-		# supplied.
-		LockManager.runWithLock containerName, (releaseLock) ->
-			DockerRunner._destroyContainer containerId or containerName, shouldForce, releaseLock
-		, callback
-
-	_destroyContainer: (containerId, shouldForce, callback = (error) ->) ->
-		logger.log container_id: containerId, "destroying docker container"
-		container = dockerode.getContainer(containerId)
-		container.remove {force: shouldForce == true}, (error) ->
-			if error? and error?.statusCode == 404
-				logger.warn err: error, container_id: containerId, "container not found, continuing"
-				error = null
-			if error?
-				logger.error err: error, container_id: containerId, "error destroying container"
-			else
-				logger.log container_id: containerId, "destroyed container"
-			callback(error)
-
-	# handle expiry of docker containers
-
-	MAX_CONTAINER_AGE: Settings.clsi.docker.maxContainerAge or oneHour = 60 * 60 * 1000
-
-	examineOldContainer: (container, callback = (error, name, id, ttl)->) ->
-		name = container.Name or container.Names?[0]
-		created = container.Created * 1000 # creation time is returned in seconds
-		now = Date.now()
-		age = now - created
-		maxAge = DockerRunner.MAX_CONTAINER_AGE
-		ttl = maxAge - age
-		logger.log {containerName: name, created: created, now: now, age: age, maxAge: maxAge, ttl: ttl}, "checking whether to destroy container"
-		callback(null, name, container.Id, ttl)
-
-	destroyOldContainers: (callback = (error) ->) ->
-		dockerode.listContainers all: true, (error, containers) ->
-			return callback(error) if error?
-			jobs = []
-			for container in containers or []
-				do (container) ->
-					DockerRunner.examineOldContainer container, (err, name, id, ttl) ->
-						if name.slice(0, 9) == '/project-' && ttl <= 0
-							jobs.push	(cb) ->
-								DockerRunner.destroyContainer name, id, false, () -> cb()
-								# Ignore errors because some containers get stuck but
-								# will be destroyed next time
-			async.series jobs, callback
-
-	startContainerMonitor: () ->
-		logger.log {maxAge: DockerRunner.MAX_CONTAINER_AGE}, "starting container expiry"
-		# randomise the start time
-		randomDelay = Math.floor(Math.random() * 5 * 60 * 1000)
-		setTimeout () ->
-			setInterval () ->
-				DockerRunner.destroyOldContainers()
-			, oneHour = 60 * 60 * 1000
-		, randomDelay
-
-DockerRunner.startContainerMonitor()

services/clsi/app/coffee/DraftModeManager.coffee

@@ -1,24 +0,0 @@
-fs = require "fs"
-logger = require "logger-sharelatex"
-
-module.exports = DraftModeManager =
-	injectDraftMode: (filename, callback = (error) ->) ->
-		fs.readFile filename, "utf8", (error, content) ->
-			return callback(error) if error?
-			# avoid adding draft mode more than once
-			if content?.indexOf("\\documentclass\[draft") >= 0
-				return callback()
-			modified_content = DraftModeManager._injectDraftOption content
-			logger.log {
-				content: content.slice(0,1024), # \documentclass is normally v near the top
-				modified_content: modified_content.slice(0,1024),
-				filename
-			}, "injected draft class"
-			fs.writeFile filename, modified_content, callback
-	
-	_injectDraftOption: (content) ->
-		content
-			# With existing options (must be first, otherwise both are applied)
-			.replace(/\\documentclass\[/g, "\\documentclass[draft,")
-			# Without existing options
-			.replace(/\\documentclass\{/g, "\\documentclass[draft]{")

services/clsi/app/coffee/Errors.coffee

@@ -1,25 +0,0 @@
-NotFoundError = (message) ->
-	error = new Error(message)
-	error.name = "NotFoundError"
-	error.__proto__ = NotFoundError.prototype
-	return error
-NotFoundError.prototype.__proto__ = Error.prototype
-
-FilesOutOfSyncError = (message) ->
-	error = new Error(message)
-	error.name = "FilesOutOfSyncError"
-	error.__proto__ = FilesOutOfSyncError.prototype
-	return error
-FilesOutOfSyncError.prototype.__proto__ = Error.prototype
-
-AlreadyCompilingError = (message) ->
-	error = new Error(message)
-	error.name = "AlreadyCompilingError"
-	error.__proto__ = AlreadyCompilingError.prototype
-	return error
-AlreadyCompilingError.prototype.__proto__ = Error.prototype
-
-module.exports = Errors =
-	NotFoundError: NotFoundError
-	FilesOutOfSyncError: FilesOutOfSyncError
-	AlreadyCompilingError: AlreadyCompilingError

services/clsi/app/coffee/LatexRunner.coffee

@@ -1,95 +0,0 @@
-Path = require "path"
-Settings = require "settings-sharelatex"
-logger = require "logger-sharelatex"
-Metrics = require "./Metrics"
-CommandRunner = require "./CommandRunner"
-
-ProcessTable = {}  # table of currently running jobs (pids or docker container names)
-
-module.exports = LatexRunner =
-	runLatex: (project_id, options, callback = (error) ->) ->
-		{directory, mainFile, compiler, timeout, image, environment, flags} = options
-		compiler ||= "pdflatex"
-		timeout  ||= 60000 # milliseconds
-
-		logger.log directory: directory, compiler: compiler, timeout: timeout, mainFile: mainFile, environment: environment, flags:flags, "starting compile"
-
-		# We want to run latexmk on the tex file which we will automatically
-		# generate from the Rtex/Rmd/md file.
-		mainFile = mainFile.replace(/\.(Rtex|md|Rmd)$/, ".tex")
-
-		if compiler == "pdflatex"
-			command = LatexRunner._pdflatexCommand mainFile, flags
-		else if compiler == "latex"
-			command = LatexRunner._latexCommand mainFile, flags
-		else if compiler == "xelatex"
-			command = LatexRunner._xelatexCommand mainFile, flags
-		else if compiler == "lualatex"
-			command = LatexRunner._lualatexCommand mainFile, flags
-		else
-			return callback new Error("unknown compiler: #{compiler}")
-
-		if Settings.clsi?.strace
-			command = ["strace", "-o", "strace", "-ff"].concat(command)
-
-		id = "#{project_id}" # record running project under this id
-
-		ProcessTable[id] = CommandRunner.run project_id, command, directory, image, timeout, environment, (error, output) ->
-			delete ProcessTable[id]
-			return callback(error) if error?
-			runs = output?.stderr?.match(/^Run number \d+ of .*latex/mg)?.length or 0
-			failed = if output?.stdout?.match(/^Latexmk: Errors/m)? then 1 else 0
-			# counters from latexmk output
-			stats = {}
-			stats["latexmk-errors"] = failed
-			stats["latex-runs"] = runs
-			stats["latex-runs-with-errors"] = if failed then runs else 0
-			stats["latex-runs-#{runs}"] = 1
-			stats["latex-runs-with-errors-#{runs}"] = if failed then 1 else 0
-			# timing information from /usr/bin/time
-			timings = {}
-			stderr = output?.stderr
-			timings["cpu-percent"] = stderr?.match(/Percent of CPU this job got: (\d+)/m)?[1] or 0
-			timings["cpu-time"] = stderr?.match(/User time.*: (\d+.\d+)/m)?[1] or 0
-			timings["sys-time"] = stderr?.match(/System time.*: (\d+.\d+)/m)?[1] or 0
-			callback error, output, stats, timings
-
-	killLatex: (project_id, callback = (error) ->) ->
-		id = "#{project_id}"
-		logger.log {id:id}, "killing running compile"
-		if not ProcessTable[id]?
-			logger.warn {id}, "no such project to kill"
-			return callback(null)
-		else
-			CommandRunner.kill ProcessTable[id], callback
-
-	_latexmkBaseCommand: (flags) ->
-		args = ["latexmk", "-cd", "-f", "-jobname=output", "-auxdir=$COMPILE_DIR", "-outdir=$COMPILE_DIR", "-synctex=1","-interaction=batchmode"]
-		if flags
-			args = args.concat(flags)
-		(Settings?.clsi?.latexmkCommandPrefix || []).concat(args)
-
-	_pdflatexCommand: (mainFile, flags) ->
-		LatexRunner._latexmkBaseCommand(flags).concat [
-			"-pdf",
-			Path.join("$COMPILE_DIR", mainFile)
-		]
-
-	_latexCommand: (mainFile, flags) ->
-		LatexRunner._latexmkBaseCommand(flags).concat [
-			"-pdfdvi",
-			Path.join("$COMPILE_DIR", mainFile)
-		]
-
-	_xelatexCommand: (mainFile, flags) ->
-		LatexRunner._latexmkBaseCommand(flags).concat [
-			"-xelatex",
-			Path.join("$COMPILE_DIR", mainFile)
-		]
-
-	_lualatexCommand: (mainFile, flags) ->
-		LatexRunner._latexmkBaseCommand(flags).concat [
-			"-lualatex",
-			Path.join("$COMPILE_DIR", mainFile)
-		]
-

services/clsi/app/coffee/LocalCommandRunner.coffee

@@ -1,48 +0,0 @@
-spawn = require("child_process").spawn
-logger = require "logger-sharelatex"
-
-logger.info "using standard command runner"
-
-module.exports = CommandRunner =
-	run: (project_id, command, directory, image, timeout, environment, callback = (error) ->) ->
-		command = (arg.toString().replace('$COMPILE_DIR', directory) for arg in command)
-		logger.log project_id: project_id, command: command, directory: directory, "running command"
-		logger.warn "timeouts and sandboxing are not enabled with CommandRunner"
-
-		# merge environment settings
-		env = {}
-		env[key] = value for key, value of process.env
-		env[key] = value for key, value of environment
-
-		# run command as detached process so it has its own process group (which can be killed if needed)
-		proc = spawn command[0], command.slice(1), cwd: directory, env: env
-
-		stdout = ""
-		proc.stdout.on "data", (data)->
-			stdout += data
-
-		proc.on "error", (err)->
-			logger.err err:err, project_id:project_id, command: command, directory: directory, "error running command"
-			callback(err)
-
-		proc.on "close", (code, signal) ->
-			logger.info code:code, signal:signal, project_id:project_id, "command exited"
-			if signal is 'SIGTERM' # signal from kill method below
-				err = new Error("terminated")
-				err.terminated = true
-				return callback(err)
-			else if code is 1 # exit status from chktex
-				err = new Error("exited")
-				err.code = code
-				return callback(err)
-			else
-				callback(null, {"stdout": stdout})
-
-		return proc.pid # return process id to allow job to be killed if necessary
-
-	kill: (pid, callback = (error) ->) ->
-		try
-			process.kill -pid # kill all processes in group
-		catch err
-			return callback(err)
-		callback()

services/clsi/app/coffee/LockManager.coffee

@@ -1,31 +0,0 @@
-Settings = require('settings-sharelatex')
-logger = require "logger-sharelatex"
-Lockfile = require('lockfile') # from https://github.com/npm/lockfile
-Errors = require "./Errors"
-fs = require("fs")
-Path = require("path")
-module.exports = LockManager =
-	LOCK_TEST_INTERVAL: 1000 # 50ms between each test of the lock
-	MAX_LOCK_WAIT_TIME: 15000 # 10s maximum time to spend trying to get the lock
-	LOCK_STALE: 5*60*1000 # 5 mins time until lock auto expires
-
-	runWithLock: (path, runner = ((releaseLock = (error) ->) ->), callback = ((error) ->)) ->
-		lockOpts =
-			wait: @MAX_LOCK_WAIT_TIME
-			pollPeriod: @LOCK_TEST_INTERVAL
-			stale: @LOCK_STALE
-		Lockfile.lock path, lockOpts, (error) ->
-			if error?.code is 'EEXIST'
-				return callback new Errors.AlreadyCompilingError("compile in progress")
-			else if error?
-				fs.lstat path, (statLockErr, statLock)->
-					fs.lstat Path.dirname(path), (statDirErr, statDir)->
-						fs.readdir Path.dirname(path), (readdirErr, readdirDir)->
-							logger.err error:error, path:path, statLock:statLock, statLockErr:statLockErr, statDir:statDir, statDirErr: statDirErr, readdirErr:readdirErr, readdirDir:readdirDir, "unable to get lock"
-							return callback(error)
-			else
-				runner (error1, args...) ->
-					Lockfile.unlock path, (error2) ->
-						error = error1 or error2
-						return callback(error) if error?
-						callback(null, args...)

services/clsi/app/coffee/Metrics.coffee

@@ -1,2 +0,0 @@
-module.exports = require "metrics-sharelatex"
-

services/clsi/app/coffee/OutputCacheManager.coffee

@@ -1,199 +0,0 @@
-async = require "async"
-fs = require "fs"
-fse = require "fs-extra"
-Path = require "path"
-logger = require "logger-sharelatex"
-_ = require "underscore"
-Settings = require "settings-sharelatex"
-crypto = require "crypto"
-
-OutputFileOptimiser = require "./OutputFileOptimiser"
-
-module.exports = OutputCacheManager =
-	CACHE_SUBDIR: '.cache/clsi'
-	ARCHIVE_SUBDIR: '.archive/clsi'
-	# build id is HEXDATE-HEXRANDOM from Date.now()and RandomBytes
-	# for backwards compatibility, make the randombytes part optional
-	BUILD_REGEX: /^[0-9a-f]+(-[0-9a-f]+)?$/
-	CACHE_LIMIT: 2  # maximum number of cache directories
-	CACHE_AGE: 60*60*1000 # up to one hour old
-
-	path: (buildId, file) ->
-		# used by static server, given build id return '.cache/clsi/buildId'
-		if buildId.match OutputCacheManager.BUILD_REGEX
-			return Path.join(OutputCacheManager.CACHE_SUBDIR, buildId, file)
-		else
-			# for invalid build id, return top level
-			return file
-
-	generateBuildId: (callback = (error, buildId) ->) ->
-		# generate a secure build id from Date.now() and 8 random bytes in hex
-		crypto.randomBytes 8, (err, buf) ->
-			return callback(err) if err?
-			random = buf.toString('hex')
-			date = Date.now().toString(16)
-			callback err, "#{date}-#{random}"
-
-	saveOutputFiles: (outputFiles, compileDir, callback = (error) ->) ->
-		OutputCacheManager.generateBuildId (err, buildId) ->
-			return callback(err) if err?
-			OutputCacheManager.saveOutputFilesInBuildDir outputFiles, compileDir, buildId, callback
-
-	saveOutputFilesInBuildDir: (outputFiles, compileDir, buildId, callback = (error) ->) ->
-		# make a compileDir/CACHE_SUBDIR/build_id directory and
-		# copy all the output files into it
-		cacheRoot = Path.join(compileDir, OutputCacheManager.CACHE_SUBDIR)
-		# Put the files into a new cache subdirectory
-		cacheDir = Path.join(compileDir, OutputCacheManager.CACHE_SUBDIR, buildId)
-		# Is it a per-user compile? check if compile directory is PROJECTID-USERID
-		perUser = Path.basename(compileDir).match(/^[0-9a-f]{24}-[0-9a-f]{24}$/)
-
-		# Archive logs in background
-		if Settings.clsi?.archive_logs or Settings.clsi?.strace
-			OutputCacheManager.archiveLogs outputFiles, compileDir, buildId, (err) ->
-				if err?
-					logger.warn err:err, "erroring archiving log files"
-
-		# make the new cache directory
-		fse.ensureDir cacheDir, (err) ->
-			if err?
-				logger.error err: err, directory: cacheDir, "error creating cache directory"
-				callback(err, outputFiles)
-			else
-				# copy all the output files into the new cache directory
-				results = []
-				async.mapSeries outputFiles, (file, cb) ->
-					# don't send dot files as output, express doesn't serve them
-					if OutputCacheManager._fileIsHidden(file.path)
-						logger.debug compileDir: compileDir, path: file.path, "ignoring dotfile in output"
-						return cb()
-					# copy other files into cache directory if valid
-					newFile = _.clone(file)
-					[src, dst] = [Path.join(compileDir, file.path), Path.join(cacheDir, file.path)]
-					OutputCacheManager._checkFileIsSafe src, (err, isSafe) ->
-						return cb(err) if err?
-						if !isSafe
-							return cb()
-						OutputCacheManager._checkIfShouldCopy src, (err, shouldCopy) ->
-							return cb(err) if err?
-							if !shouldCopy
-								return cb()
-							OutputCacheManager._copyFile src, dst, (err) ->
-								return cb(err) if err?
-								newFile.build = buildId  # attach a build id if we cached the file
-								results.push newFile
-								cb()
-				, (err) ->
-					if err?
-						# pass back the original files if we encountered *any* error
-						callback(err, outputFiles)
-						# clean up the directory we just created
-						fse.remove cacheDir, (err) ->
-							if err?
-								logger.error err: err, dir: cacheDir, "error removing cache dir after failure"
-					else
-						# pass back the list of new files in the cache
-						callback(err, results)
-						# let file expiry run in the background, expire all previous files if per-user
-						OutputCacheManager.expireOutputFiles cacheRoot, {keep: buildId, limit: if perUser then 1 else null}
-
-	archiveLogs: (outputFiles, compileDir, buildId, callback = (error) ->) ->
-		archiveDir = Path.join(compileDir, OutputCacheManager.ARCHIVE_SUBDIR, buildId)
-		logger.log {dir: archiveDir}, "archiving log files for project"
-		fse.ensureDir archiveDir, (err) ->
-			return callback(err) if err?
-			async.mapSeries outputFiles, (file, cb) ->
-				[src, dst] = [Path.join(compileDir, file.path), Path.join(archiveDir, file.path)]
-				OutputCacheManager._checkFileIsSafe src, (err, isSafe) ->
-					return cb(err) if err?
-					return cb() if !isSafe
-					OutputCacheManager._checkIfShouldArchive src, (err, shouldArchive) ->
-						return cb(err) if err?
-						return cb() if !shouldArchive
-						OutputCacheManager._copyFile src, dst, cb
-			, callback
-
-	expireOutputFiles: (cacheRoot, options, callback = (error) ->) ->
-		# look in compileDir for build dirs and delete if > N or age of mod time > T
-		fs.readdir cacheRoot, (err, results) ->
-			if err?
-				return callback(null) if err.code == 'ENOENT'	# cache directory is empty
-				logger.error err: err, project_id: cacheRoot, "error clearing cache"
-				return callback(err)
-
-			dirs =  results.sort().reverse()
-			currentTime = Date.now()
-
-			isExpired = (dir, index) ->
-				return false if options?.keep == dir
-				# remove any directories over the requested (non-null) limit
-				return true if options?.limit? and index > options.limit
-				# remove any directories over the hard limit
-				return true if index > OutputCacheManager.CACHE_LIMIT
-				# we can get the build time from the first part of the directory name DDDD-RRRR
-				# DDDD is date and RRRR is random bytes
-				dirTime = parseInt(dir.split('-')?[0], 16)
-				age = currentTime - dirTime
-				return age > OutputCacheManager.CACHE_AGE
-
-			toRemove = _.filter(dirs, isExpired)
-
-			removeDir = (dir, cb) ->
-				fse.remove Path.join(cacheRoot, dir), (err, result) ->
-					logger.log cache: cacheRoot, dir: dir, "removed expired cache dir"
-					if err?
-						logger.error err: err, dir: dir, "cache remove error"
-					cb(err, result)
-
-			async.eachSeries toRemove, (dir, cb) ->
-				removeDir dir, cb
-			, callback
-
-	_fileIsHidden: (path) ->
-		return path?.match(/^\.|\/\./)?
-
-	_checkFileIsSafe: (src, callback = (error, isSafe) ->) ->
-		# check if we have a valid file to copy into the cache
-		fs.stat src, (err, stats) ->
-			if err?.code is 'ENOENT'
-				logger.warn err: err, file: src, "file has disappeared before copying to build cache"
-				callback(err, false)
-			else if err?
-				# some other problem reading the file
-				logger.error err: err, file: src, "stat error for file in cache"
-				callback(err, false)
-			else if not stats.isFile()
-				# other filetype - reject it
-				logger.warn src: src, stat: stats, "nonfile output - refusing to copy to cache"
-				callback(null, false)
-			else
-				# it's a plain file, ok to copy
-				callback(null, true)
-
-	_copyFile: (src, dst, callback) ->
-		# copy output file into the cache
-		fse.copy src, dst, (err) ->
-			if err?.code is 'ENOENT'
-				logger.warn err: err, file: src, "file has disappeared when copying to build cache"
-				callback(err, false)
-			else if err?
-				logger.error err: err, src: src, dst: dst, "copy error for file in cache"
-				callback(err)
-			else
-				if Settings.clsi?.optimiseInDocker
-					# don't run any optimisations on the pdf when they are done
-					# in the docker container
-					callback()
-				else
-					# call the optimiser for the file too
-					OutputFileOptimiser.optimiseFile src, dst, callback
-
-	_checkIfShouldCopy: (src, callback = (err, shouldCopy) ->) ->
-		return callback(null, !Path.basename(src).match(/^strace/))
-
-	_checkIfShouldArchive: (src, callback = (err, shouldCopy) ->) ->
-		if Path.basename(src).match(/^strace/)
-			return callback(null, true)
-		if Settings.clsi?.archive_logs and Path.basename(src) in ["output.log", "output.blg"]
-			return callback(null, true)
-		return callback(null, false)

services/clsi/app/coffee/OutputFileFinder.coffee

@@ -1,50 +0,0 @@
-async = require "async"
-fs = require "fs"
-Path = require "path"
-spawn = require("child_process").spawn
-logger = require "logger-sharelatex"
-
-module.exports = OutputFileFinder =
-	findOutputFiles: (resources, directory, callback = (error, outputFiles, allFiles) ->) ->
-		incomingResources = {}
-		for resource in resources
-			incomingResources[resource.path] = true
-			
-		OutputFileFinder._getAllFiles directory, (error, allFiles = []) ->
-			if error?
-				logger.err err:error, "error finding all output files"
-				return callback(error)
-			outputFiles = []
-			for file in allFiles
-				if !incomingResources[file]
-					outputFiles.push {
-						path: file
-						type: file.match(/\.([^\.]+)$/)?[1]
-					}
-			callback null, outputFiles, allFiles
-
-	_getAllFiles: (directory, _callback = (error, fileList) ->) ->
-		callback = (error, fileList) ->
-			_callback(error, fileList)
-			_callback = () ->
-
-		# don't include clsi-specific files/directories in the output list
-		EXCLUDE_DIRS = ["-name", ".cache", "-o", "-name", ".archive","-o", "-name", ".project-*"]
-		args = [directory, "(", EXCLUDE_DIRS..., ")", "-prune", "-o", "-type", "f", "-print"]
-		logger.log args: args, "running find command"
-
-		proc = spawn("find", args)
-		stdout = ""
-		proc.stdout.on "data", (chunk) ->
-			stdout += chunk.toString()	
-		proc.on "error", callback	
-		proc.on "close", (code) ->
-			if code != 0
-				logger.warn {directory, code}, "find returned error, directory likely doesn't exist"
-				return callback null, []
-			fileList = stdout.trim().split("\n")
-			fileList = fileList.map (file) ->
-				# Strip leading directory
-				path = Path.relative(directory, file)
-			return callback null, fileList
-

services/clsi/app/coffee/OutputFileOptimiser.coffee

@@ -1,55 +0,0 @@
-fs = require "fs"
-Path = require "path"
-spawn = require("child_process").spawn
-logger = require "logger-sharelatex"
-Metrics = require "./Metrics"
-_ = require "underscore"
-
-module.exports = OutputFileOptimiser =
-
-	optimiseFile: (src, dst, callback = (error) ->) ->
-		# check output file (src) and see if we can optimise it, storing
-		# the result in the build directory (dst)
-		if src.match(/\/output\.pdf$/)
-			OutputFileOptimiser.checkIfPDFIsOptimised src, (err, isOptimised) ->
-				return callback(null) if err? or isOptimised
-				OutputFileOptimiser.optimisePDF src, dst, callback
-		else
-			callback (null)
-
-	checkIfPDFIsOptimised: (file, callback) ->
-		SIZE = 16*1024 # check the header of the pdf
-		result = new Buffer(SIZE)
-		result.fill(0) # prevent leakage of uninitialised buffer
-		fs.open file, "r", (err, fd) ->
-			return callback(err) if err?
-			fs.read fd, result, 0, SIZE, 0, (errRead, bytesRead, buffer) ->
-				fs.close fd, (errClose) ->
-					return callback(errRead) if errRead?
-					return callback(errClose) if errReadClose?
-					isOptimised = buffer.toString('ascii').indexOf("/Linearized 1") >= 0
-					callback(null, isOptimised)
-
-	optimisePDF: (src, dst, callback = (error) ->) ->
-		tmpOutput = dst + '.opt'
-		args = ["--linearize", src, tmpOutput]
-		logger.log args: args, "running qpdf command"
-
-		timer = new Metrics.Timer("qpdf")
-		proc = spawn("qpdf", args)
-		stdout = ""
-		proc.stdout.on "data", (chunk) ->
-			stdout += chunk.toString()
-		callback = _.once(callback) # avoid double call back for error and close event
-		proc.on "error", (err) ->
-			logger.warn {err, args}, "qpdf failed"
-			callback(null) # ignore the error
-		proc.on "close", (code) ->
-			timer.done()
-			if code != 0
-				logger.warn {code, args}, "qpdf returned error"
-				return callback(null) # ignore the error
-			fs.rename tmpOutput, dst, (err) ->
-				if err?
-					logger.warn {tmpOutput, dst}, "failed to rename output of qpdf command"
-				callback(null) # ignore the error

services/clsi/app/coffee/ProjectPersistenceManager.coffee

@@ -1,84 +0,0 @@
-UrlCache = require "./UrlCache"
-CompileManager = require "./CompileManager"
-db = require "./db"
-dbQueue = require "./DbQueue"
-async = require "async"
-logger = require "logger-sharelatex"
-oneDay = 24 * 60 * 60 * 1000
-Settings = require "settings-sharelatex"
-
-module.exports = ProjectPersistenceManager =
-
-	EXPIRY_TIMEOUT: Settings.project_cache_length_ms || oneDay * 2.5
-
-	markProjectAsJustAccessed: (project_id, callback = (error) ->) ->
-		job = (cb)->
-			db.Project.findOrCreate(where: {project_id: project_id})
-				.spread(
-					(project, created) ->
-						project.updateAttributes(lastAccessed: new Date())
-							.then(() -> cb())
-							.error cb
-				)
-				.error cb
-		dbQueue.queue.push(job, callback)
-
-
-	clearExpiredProjects: (callback = (error) ->) ->
-		ProjectPersistenceManager._findExpiredProjectIds (error, project_ids) ->
-			return callback(error) if error?
-			logger.log project_ids: project_ids, "clearing expired projects"
-			jobs = for project_id in (project_ids or [])
-				do (project_id) ->
-					(callback) ->
-						ProjectPersistenceManager.clearProjectFromCache project_id, (err) ->
-							if err?
-								logger.error err: err, project_id: project_id, "error clearing project"
-							callback()
-			async.series jobs, (error) ->
-				return callback(error) if error?
-				CompileManager.clearExpiredProjects ProjectPersistenceManager.EXPIRY_TIMEOUT, (error) ->
-					callback() # ignore any errors from deleting directories
-
-	clearProject: (project_id, user_id, callback = (error) ->) ->
-		logger.log project_id: project_id, user_id:user_id, "clearing project for user"
-		CompileManager.clearProject project_id, user_id, (error) ->
-			return callback(error) if error?
-			ProjectPersistenceManager.clearProjectFromCache project_id, (error) ->
-				return callback(error) if error?
-				callback()
-
-	clearProjectFromCache: (project_id, callback = (error) ->) ->
-		logger.log project_id: project_id, "clearing project from cache"
-		UrlCache.clearProject project_id, (error) ->
-			if error?
-				logger.err error:error, project_id: project_id, "error clearing project from cache"
-				return callback(error) 
-			ProjectPersistenceManager._clearProjectFromDatabase project_id, (error) ->
-				if error?
-					logger.err error:error, project_id:project_id, "error clearing project from database"
-				callback(error)
-
-	_clearProjectFromDatabase: (project_id, callback = (error) ->) ->
-		logger.log project_id:project_id, "clearing project from database"
-		job = (cb)->
-			db.Project.destroy(where: {project_id: project_id})
-				.then(() -> cb())
-				.error cb
-		dbQueue.queue.push(job, callback)
-
-
-	_findExpiredProjectIds: (callback = (error, project_ids) ->) ->
-		job = (cb)->
-			keepProjectsFrom = new Date(Date.now() - ProjectPersistenceManager.EXPIRY_TIMEOUT)
-			q = {}
-			q[db.op.lt] = keepProjectsFrom
-			db.Project.findAll(where:{lastAccessed:q})
-				.then((projects) ->
-					cb null, projects.map((project) -> project.project_id)
-				).error cb
-
-		dbQueue.queue.push(job, callback)
-
-
-logger.log {EXPIRY_TIMEOUT: ProjectPersistenceManager.EXPIRY_TIMEOUT}, "project assets kept timeout"

services/clsi/app/coffee/RequestParser.coffee

@@ -1,128 +0,0 @@
-settings = require("settings-sharelatex")
-
-module.exports = RequestParser =
-	VALID_COMPILERS: ["pdflatex", "latex", "xelatex", "lualatex"]
-	MAX_TIMEOUT: 600
-
-	parse: (body, callback = (error, data) ->) ->
-		response = {}
-
-		if !body.compile?
-			return callback "top level object should have a compile attribute"
-
-		compile = body.compile
-		compile.options ||= {}
-
-		try
-			response.compiler = @_parseAttribute "compiler",
-				compile.options.compiler,
-				validValues: @VALID_COMPILERS
-				default: "pdflatex"
-				type: "string"
-			response.timeout = @_parseAttribute "timeout",
-				compile.options.timeout
-				default: RequestParser.MAX_TIMEOUT
-				type: "number"
-			response.imageName = @_parseAttribute "imageName",
-				compile.options.imageName,
-				type: "string"
-			response.draft = @_parseAttribute "draft",
-				compile.options.draft,
-				default: false,
-				type: "boolean"
-			response.check = @_parseAttribute "check",
-				compile.options.check,
-				type: "string"
-			response.flags = @_parseAttribute "flags",
-				compile.options.flags,
-				default: [],
-				type: "object"
-
-			# The syncType specifies whether the request contains all
-			# resources (full) or only those resources to be updated
-			# in-place (incremental).
-			response.syncType = @_parseAttribute "syncType",
-				compile.options.syncType,
-				validValues: ["full", "incremental"]
-				type: "string"
-
-			# The syncState is an identifier passed in with the request
-			# which has the property that it changes when any resource is
-			# added, deleted, moved or renamed.
-			#
-			# on syncType full the syncState identifier is passed in and
-			# stored
-			#
-			# on syncType incremental the syncState identifier must match
-			# the stored value
-			response.syncState = @_parseAttribute "syncState",
-				compile.options.syncState,
-				type: "string"
-
-			if response.timeout > RequestParser.MAX_TIMEOUT
-				response.timeout = RequestParser.MAX_TIMEOUT
-			response.timeout = response.timeout * 1000 # milliseconds
-
-			response.resources = (@_parseResource(resource) for resource in (compile.resources or []))
-
-			rootResourcePath = @_parseAttribute "rootResourcePath",
-				compile.rootResourcePath
-				default: "main.tex"
-				type: "string"
-			originalRootResourcePath = rootResourcePath
-			sanitizedRootResourcePath = RequestParser._sanitizePath(rootResourcePath)
-			response.rootResourcePath = RequestParser._checkPath(sanitizedRootResourcePath)
-
-			for resource in response.resources
-				if resource.path == originalRootResourcePath
-					resource.path = sanitizedRootResourcePath
-		catch error
-			return callback error
-
-		callback null, response
-
-	_parseResource: (resource) ->
-		if !resource.path? or typeof resource.path != "string"
-			throw "all resources should have a path attribute"
-
-		if resource.modified?
-			modified = new Date(resource.modified)
-			if isNaN(modified.getTime())
-				throw "resource modified date could not be understood: #{resource.modified}"
-
-		if !resource.url? and !resource.content?
-			throw "all resources should have either a url or content attribute"
-		if resource.content? and typeof resource.content != "string"
-			throw "content attribute should be a string"
-		if resource.url? and typeof resource.url != "string"
-			throw "url attribute should be a string"
-
-		return {
-			path: resource.path
-			modified: modified
-			url: resource.url
-			content: resource.content
-		}
-
-	_parseAttribute: (name, attribute, options) ->
-		if attribute?
-			if options.validValues?
-				if options.validValues.indexOf(attribute) == -1
-					throw "#{name} attribute should be one of: #{options.validValues.join(", ")}"
-			if options.type?
-				if typeof attribute != options.type
-					throw "#{name} attribute should be a #{options.type}"
-		else
-			return options.default if options.default?
-		return attribute
-
-	_sanitizePath: (path) ->
-		# See http://php.net/manual/en/function.escapeshellcmd.php
-		path.replace(/[\#\&\;\`\|\*\?\~\<\>\^\(\)\[\]\{\}\$\\\x0A\xFF\x00]/g, "")
-
-	_checkPath: (path) ->
-		# check that the request does not use a relative path
-		for dir in path.split('/')
-			if dir == '..'
-				throw "relative path in root resource"
-		return path

services/clsi/app/coffee/ResourceStateManager.coffee

@@ -1,72 +0,0 @@
-Path = require "path"
-fs = require "fs"
-logger = require "logger-sharelatex"
-settings = require("settings-sharelatex")
-Errors = require "./Errors"
-SafeReader = require "./SafeReader"
-
-module.exports = ResourceStateManager =
-
-	# The sync state is an identifier which must match for an
-	# incremental update to be allowed.
-	#
-	# The initial value is passed in and stored on a full
-	# compile, along with the list of resources..
-	#
-	# Subsequent incremental compiles must come with the same value - if
-	# not they will be rejected with a 409 Conflict response. The
-	# previous list of resources is returned.
-	#
-	# An incremental compile can only update existing files with new
-	# content.  The sync state identifier must change if any docs or
-	# files are moved, added, deleted or renamed.
-
-	SYNC_STATE_FILE: ".project-sync-state"
-	SYNC_STATE_MAX_SIZE: 128*1024
-
-	saveProjectState: (state, resources, basePath, callback = (error) ->) ->
-		stateFile = Path.join(basePath, @SYNC_STATE_FILE)
-		if not state? # remove the file if no state passed in
-			logger.log state:state, basePath:basePath, "clearing sync state"
-			fs.unlink stateFile, (err) ->
-				if err? and err.code isnt 'ENOENT'
-					return callback(err)
-				else
-					return callback()
-		else
-			logger.log state:state, basePath:basePath, "writing sync state"
-			resourceList = (resource.path for resource in resources)
-			fs.writeFile stateFile, [resourceList..., "stateHash:#{state}"].join("\n"), callback
-
-	checkProjectStateMatches: (state, basePath, callback = (error, resources) ->) ->
-		stateFile = Path.join(basePath, @SYNC_STATE_FILE)
-		size = @SYNC_STATE_MAX_SIZE
-		SafeReader.readFile stateFile, size, 'utf8', (err, result, bytesRead) ->
-			return callback(err) if err?
-			if bytesRead is size
-				logger.error file:stateFile, size:size, bytesRead:bytesRead, "project state file truncated"
-			[resourceList..., oldState] = result?.toString()?.split("\n") or []
-			newState = "stateHash:#{state}"
-			logger.log state:state, oldState: oldState, basePath:basePath, stateMatches: (newState is oldState), "checking sync state"
-			if newState isnt oldState
-				return callback new Errors.FilesOutOfSyncError("invalid state for incremental update")
-			else
-				resources = ({path: path} for path in resourceList)
-				callback(null, resources)
-
-	checkResourceFiles: (resources, allFiles, basePath, callback = (error) ->) ->
-		# check the paths are all relative to current directory
-		for file in resources or []
-			for dir in file?.path?.split('/')
-				if dir == '..'
-					return callback new Error("relative path in resource file list")
-		# check if any of the input files are not present in list of files
-		seenFile = {}
-		for file in allFiles
-			seenFile[file] = true
-		missingFiles = (resource.path for resource in resources when not seenFile[resource.path])
-		if missingFiles?.length > 0
-			logger.err missingFiles:missingFiles, basePath:basePath, allFiles:allFiles, resources:resources, "missing input files for project"
-			return callback new Errors.FilesOutOfSyncError("resource files missing in incremental update")
-		else
-			callback()

services/clsi/app/coffee/ResourceWriter.coffee

@@ -1,142 +0,0 @@
-UrlCache = require "./UrlCache"
-Path = require "path"
-fs = require "fs"
-async = require "async"
-mkdirp = require "mkdirp"
-OutputFileFinder = require "./OutputFileFinder"
-ResourceStateManager = require "./ResourceStateManager"
-Metrics = require "./Metrics"
-logger = require "logger-sharelatex"
-settings = require("settings-sharelatex")
-
-parallelFileDownloads = settings.parallelFileDownloads or 1
-
-module.exports = ResourceWriter =
-
-	syncResourcesToDisk: (request, basePath, callback = (error, resourceList) ->) ->
-		if request.syncType is "incremental"
-			logger.log project_id: request.project_id, user_id: request.user_id, "incremental sync"
-			ResourceStateManager.checkProjectStateMatches request.syncState, basePath, (error, resourceList) ->
-				return callback(error) if error?
-				ResourceWriter._removeExtraneousFiles resourceList, basePath, (error, outputFiles, allFiles) ->
-					return callback(error) if error?
-					ResourceStateManager.checkResourceFiles resourceList, allFiles, basePath, (error) ->
-						return callback(error) if error?
-						ResourceWriter.saveIncrementalResourcesToDisk request.project_id, request.resources, basePath, (error) ->
-							return callback(error) if error?
-							callback(null, resourceList)
-		else
-			logger.log project_id: request.project_id, user_id: request.user_id, "full sync"
-			@saveAllResourcesToDisk request.project_id, request.resources, basePath, (error) ->
-				return callback(error) if error?
-				ResourceStateManager.saveProjectState request.syncState, request.resources, basePath, (error) ->
-					return callback(error) if error?
-					callback(null, request.resources)
-
-	saveIncrementalResourcesToDisk: (project_id, resources, basePath, callback = (error) ->) ->
-		@_createDirectory basePath, (error) =>
-			return callback(error) if error?
-			jobs = for resource in resources
-				do (resource) =>
-					(callback) => @_writeResourceToDisk(project_id, resource, basePath, callback)
-			async.parallelLimit jobs, parallelFileDownloads, callback
-
-	saveAllResourcesToDisk: (project_id, resources, basePath, callback = (error) ->) ->
-		@_createDirectory basePath, (error) =>
-			return callback(error) if error?
-			@_removeExtraneousFiles resources, basePath, (error) =>
-				return callback(error) if error?
-				jobs = for resource in resources
-					do (resource) =>
-						(callback) => @_writeResourceToDisk(project_id, resource, basePath, callback)
-				async.parallelLimit jobs, parallelFileDownloads, callback
-
-	_createDirectory: (basePath, callback = (error) ->) ->
-		fs.mkdir basePath, (err) ->
-			if err?
-				if err.code is 'EEXIST'
-					return callback()
-				else
-					logger.log {err: err, dir:basePath}, "error creating directory"
-					return callback(err)
-			else
-				return callback()
-
-	_removeExtraneousFiles: (resources, basePath, _callback = (error, outputFiles, allFiles) ->) ->
-		timer = new Metrics.Timer("unlink-output-files")
-		callback = (error, result...) ->
-			timer.done()
-			_callback(error, result...)
-
-		OutputFileFinder.findOutputFiles resources, basePath, (error, outputFiles, allFiles) ->
-			return callback(error) if error?
-
-			jobs = []
-			for file in outputFiles or []
-				do (file) ->
-					path = file.path
-					should_delete = true
-					if path.match(/^output\./) or path.match(/\.aux$/) or path.match(/^cache\//) # knitr cache
-						should_delete = false
-					if path.match(/^output-.*/) # Tikz cached figures (default case)
-						should_delete = false
-					if path.match(/\.(pdf|dpth|md5)$/) # Tikz cached figures (by extension)
-						should_delete = false
-					if path.match(/\.(pygtex|pygstyle)$/) or path.match(/(^|\/)_minted-[^\/]+\//) # minted files/directory
-						should_delete = false
-					if path.match(/\.md\.tex$/) or path.match(/(^|\/)_markdown_[^\/]+\//) # markdown files/directory
-						should_delete = false
-					if path.match(/-eps-converted-to\.pdf$/) # Epstopdf generated files
-						should_delete = false 
-					if path == "output.pdf" or path == "output.dvi" or path == "output.log" or path == "output.xdv"
-						should_delete = true
-					if path == "output.tex" # created by TikzManager if present in output files
-						should_delete = true
-					if should_delete
-						jobs.push (callback) -> ResourceWriter._deleteFileIfNotDirectory Path.join(basePath, path), callback
-
-			async.series jobs, (error) ->
-				return callback(error) if error?
-				callback(null, outputFiles, allFiles)
-
-	_deleteFileIfNotDirectory: (path, callback = (error) ->) ->
-		fs.stat path, (error, stat) ->
-			if error? and error.code is 'ENOENT'
-				return callback()
-			else if error?
-				logger.err {err: error, path: path}, "error stating file in deleteFileIfNotDirectory"
-				return callback(error)
-			else if stat.isFile()
-				fs.unlink path, (error) ->
-					if error?
-						logger.err {err: error, path: path}, "error removing file in deleteFileIfNotDirectory"
-						callback(error)
-					else
-						callback()
-			else
-				callback()
-
-	_writeResourceToDisk: (project_id, resource, basePath, callback = (error) ->) ->
-		ResourceWriter.checkPath basePath, resource.path, (error, path) ->
-			return callback(error) if error?
-			mkdirp Path.dirname(path), (error) ->
-				return callback(error) if error?
-				# TODO: Don't overwrite file if it hasn't been modified
-				if resource.url?
-					UrlCache.downloadUrlToFile project_id, resource.url, path, resource.modified, (err)->
-						if err?
-							logger.err err:err, project_id:project_id, path:path, resource_url:resource.url, modified:resource.modified, "error downloading file for resources"
-						callback() #try and continue compiling even if http resource can not be downloaded at this time
-				else
-					process = require("process")
-					fs.writeFile path, resource.content, callback
-					try 
-						result = fs.lstatSync(path)
-					catch e
-
-	checkPath: (basePath, resourcePath, callback) ->
-		path = Path.normalize(Path.join(basePath, resourcePath))
-		if (path.slice(0, basePath.length + 1) != basePath + "/")
-			return callback new Error("resource path is outside root directory")
-		else
-			return callback(null, path)

services/clsi/app/coffee/SafeReader.coffee

@@ -1,25 +0,0 @@
-fs = require "fs"
-logger = require "logger-sharelatex"
-
-module.exports = SafeReader =
-
-	# safely read up to size bytes from a file and return result as a
-	# string
-
-	readFile: (file, size, encoding, callback = (error, result) ->) ->
-		fs.open file, 'r', (err, fd) ->
-			return callback() if err? and err.code is 'ENOENT'
-			return callback(err) if err?
-
-			# safely return always closing the file
-			callbackWithClose = (err, result...) ->
-				fs.close fd, (err1) ->
-					return callback(err) if err?
-					return callback(err1) if err1?
-					callback(null, result...)
-
-			buff = new Buffer(size, 0) # fill with zeros
-			fs.read fd, buff, 0, buff.length, 0, (err, bytesRead, buffer) ->
-				return callbackWithClose(err) if err?
-				result = buffer.toString(encoding, 0, bytesRead)
-				callbackWithClose(null, result, bytesRead)

services/clsi/app/coffee/StaticServerForbidSymlinks.coffee

@@ -1,41 +0,0 @@
-Path = require("path")
-fs = require("fs")
-Settings = require("settings-sharelatex")
-logger = require("logger-sharelatex")
-url = require "url"
-
-module.exports = ForbidSymlinks = (staticFn, root, options) ->
-	expressStatic = staticFn root, options
-	basePath = Path.resolve(root)
-	return (req, res, next) ->
-		path = url.parse(req.url)?.pathname
-		# check that the path is of the form /project_id_or_name/path/to/file.log
-		if result = path.match(/^\/?([a-zA-Z0-9_-]+)\/(.*)/)
-			project_id = result[1]
-			file = result[2]
-		else
-			logger.warn path: path, "unrecognized file request"
-			return res.sendStatus(404)
-		# check that the file does not use a relative path
-		for dir in file.split('/')
-			if dir == '..'
-				logger.warn path: path, "attempt to use a relative path"
-				return res.sendStatus(404)
-		# check that the requested path is normalized
-		requestedFsPath = "#{basePath}/#{project_id}/#{file}"
-		if requestedFsPath != Path.normalize(requestedFsPath)
-				logger.error path: requestedFsPath, "requestedFsPath is not normalized"
-				return res.sendStatus(404)
-		# check that the requested path is not a symlink
-		fs.realpath requestedFsPath, (err, realFsPath)->
-			if err?
-				if err.code == 'ENOENT'
-					return res.sendStatus(404)
-				else
-					logger.error err:err, requestedFsPath:requestedFsPath, realFsPath:realFsPath, path: req.params[0], project_id: req.params.project_id, "error checking file access"
-					return res.sendStatus(500)
-			else if requestedFsPath != realFsPath
-				logger.warn requestedFsPath:requestedFsPath, realFsPath:realFsPath, path: req.params[0], project_id: req.params.project_id, "trying to access a different file (symlink), aborting"
-				return res.sendStatus(404)
-			else
-				expressStatic(req, res, next)

services/clsi/app/coffee/TikzManager.coffee

@@ -1,37 +0,0 @@
-fs = require "fs"
-Path = require "path"
-ResourceWriter = require "./ResourceWriter"
-SafeReader = require "./SafeReader"
-logger = require "logger-sharelatex"
-
-# for \tikzexternalize or pstool to work the main file needs to match the
-# jobname.  Since we set the -jobname to output, we have to create a
-# copy of the main file as 'output.tex'.
-
-module.exports = TikzManager =
-
-	checkMainFile: (compileDir, mainFile, resources, callback = (error, needsMainFile) ->) ->
-		# if there's already an output.tex file, we don't want to touch it
-		for resource in resources
-			if resource.path is "output.tex"
-				logger.log compileDir: compileDir, mainFile: mainFile, "output.tex already in resources"
-				return callback(null, false)
-		# if there's no output.tex, see if we are using tikz/pgf or pstool in the main file
-		ResourceWriter.checkPath compileDir, mainFile, (error, path) ->
-			return callback(error) if error?
-			SafeReader.readFile path, 65536, "utf8", (error, content) ->
-				return callback(error) if error?
-				usesTikzExternalize = content?.indexOf("\\tikzexternalize") >= 0
-				usesPsTool = content?.indexOf("{pstool}") >= 0
-				logger.log compileDir: compileDir, mainFile: mainFile, usesTikzExternalize:usesTikzExternalize, usesPsTool: usesPsTool, "checked for packages needing main file as output.tex"
-				needsMainFile = (usesTikzExternalize || usesPsTool)
-				callback null, needsMainFile
-
-	injectOutputFile: (compileDir, mainFile, callback = (error) ->) ->
-		ResourceWriter.checkPath compileDir, mainFile, (error, path) ->
-			return callback(error) if error?
-			fs.readFile path, "utf8", (error, content) ->
-				return callback(error) if error?
-				logger.log compileDir: compileDir, mainFile: mainFile, "copied file to output.tex as project uses packages which require it"
-				# use wx flag to ensure that output file does not already exist
-				fs.writeFile Path.join(compileDir, "output.tex"), content, {flag:'wx'}, callback

services/clsi/app/coffee/UrlCache.coffee

@@ -1,134 +0,0 @@
-db = require("./db")
-dbQueue = require "./DbQueue"
-UrlFetcher = require("./UrlFetcher")
-Settings = require("settings-sharelatex")
-crypto = require("crypto")
-fs = require("fs")
-logger = require "logger-sharelatex"
-async = require "async"
-
-module.exports = UrlCache =
-	downloadUrlToFile: (project_id, url, destPath, lastModified, callback = (error) ->) ->
-		UrlCache._ensureUrlIsInCache project_id, url, lastModified, (error, pathToCachedUrl) =>
-			return callback(error) if error?
-			UrlCache._copyFile pathToCachedUrl, destPath, (error) ->
-				if error?
-					UrlCache._clearUrlDetails project_id, url, () ->
-						callback(error)
-				else
-					callback(error)
-
-	clearProject: (project_id, callback = (error) ->) ->
-		UrlCache._findAllUrlsInProject project_id, (error, urls) ->
-			logger.log project_id: project_id, url_count: urls.length, "clearing project URLs"
-			return callback(error) if error?
-			jobs = for url in (urls or [])
-				do (url) ->
-					(callback) ->
-						UrlCache._clearUrlFromCache project_id, url, (error) ->
-							if error?
-								logger.error err: error, project_id: project_id, url: url, "error clearing project URL"
-							callback()
-			async.series jobs, callback
-
-	_ensureUrlIsInCache: (project_id, url, lastModified, callback = (error, pathOnDisk) ->) ->
-		if lastModified?
-			# MYSQL only stores dates to an accuracy of a second but the incoming lastModified might have milliseconds.
-			# So round down to seconds
-			lastModified = new Date(Math.floor(lastModified.getTime() / 1000) * 1000)
-		UrlCache._doesUrlNeedDownloading project_id, url, lastModified, (error, needsDownloading) =>
-			return callback(error) if error?
-			if needsDownloading
-				logger.log url: url, lastModified: lastModified, "downloading URL"
-				UrlFetcher.pipeUrlToFile url, UrlCache._cacheFilePathForUrl(project_id, url), (error) =>
-					return callback(error) if error?
-					UrlCache._updateOrCreateUrlDetails project_id, url, lastModified, (error) =>
-						return callback(error) if error?
-						callback null, UrlCache._cacheFilePathForUrl(project_id, url)
-			else
-				logger.log url: url, lastModified: lastModified, "URL is up to date in cache"
-				callback null, UrlCache._cacheFilePathForUrl(project_id, url)
-	
-	_doesUrlNeedDownloading: (project_id, url, lastModified, callback = (error, needsDownloading) ->) ->
-		if !lastModified?
-			return callback null, true
-		UrlCache._findUrlDetails project_id, url, (error, urlDetails) ->
-			return callback(error) if error?
-			if !urlDetails? or !urlDetails.lastModified? or urlDetails.lastModified.getTime() < lastModified.getTime()
-				return callback null, true
-			else
-				return callback null, false
-
-	_cacheFileNameForUrl: (project_id, url) ->
-		project_id + ":" + crypto.createHash("md5").update(url).digest("hex")
-
-	_cacheFilePathForUrl: (project_id, url) ->
-		"#{Settings.path.clsiCacheDir}/#{UrlCache._cacheFileNameForUrl(project_id, url)}"
-
-	_copyFile: (from, to, _callback = (error) ->) ->
-		callbackOnce = (error) ->
-			if error?
-				logger.error err: error, from:from, to:to, "error copying file from cache"
-			_callback(error)
-			_callback = () ->
-		writeStream = fs.createWriteStream(to)
-		readStream = fs.createReadStream(from)
-		writeStream.on "error", callbackOnce
-		readStream.on "error", callbackOnce
-		writeStream.on "close", callbackOnce
-		writeStream.on "open", () ->
-			readStream.pipe(writeStream)
-
-	_clearUrlFromCache: (project_id, url, callback = (error) ->) ->
-		UrlCache._clearUrlDetails project_id, url, (error) ->
-			return callback(error) if error?
-			UrlCache._deleteUrlCacheFromDisk project_id, url, (error) ->
-				return callback(error) if error?
-				callback null
-
-	_deleteUrlCacheFromDisk: (project_id, url, callback = (error) ->) ->
-		fs.unlink UrlCache._cacheFilePathForUrl(project_id, url), (error) ->
-			if error? and error.code != 'ENOENT' # no error if the file isn't present
-				return callback(error)
-			else
-				return callback()
-
-	_findUrlDetails: (project_id, url, callback = (error, urlDetails) ->) ->
-		job = (cb)->
-			db.UrlCache.find(where: { url: url, project_id: project_id })
-				.then((urlDetails) -> cb null, urlDetails)
-				.error cb
-		dbQueue.queue.push job, callback
-
-	_updateOrCreateUrlDetails: (project_id, url, lastModified, callback = (error) ->) ->
-		job = (cb)->
-			db.UrlCache.findOrCreate(where: {url: url, project_id: project_id})
-				.spread(
-					(urlDetails, created) ->
-						urlDetails.updateAttributes(lastModified: lastModified)
-							.then(() -> cb())
-							.error(cb)
-				)
-				.error cb
-		dbQueue.queue.push(job, callback)
-
-	_clearUrlDetails: (project_id, url, callback = (error) ->) ->
-		job = (cb)->
-			db.UrlCache.destroy(where: {url: url, project_id: project_id})
-				.then(() -> cb null)
-				.error cb
-		dbQueue.queue.push(job, callback)
-
-
-	_findAllUrlsInProject: (project_id, callback = (error, urls) ->) ->
-		job = (cb)->
-			db.UrlCache.findAll(where: { project_id: project_id })
-				.then(
-					(urlEntries) ->
-						cb null, urlEntries.map((entry) -> entry.url)
-				)
-				.error cb
-		dbQueue.queue.push(job, callback)
-
-		
-		

services/clsi/app/coffee/UrlFetcher.coffee

@@ -1,70 +0,0 @@
-request = require("request").defaults(jar: false)
-fs = require("fs")
-logger = require "logger-sharelatex"
-settings = require("settings-sharelatex")
-URL = require('url');
-
-oneMinute = 60 * 1000
-
-module.exports = UrlFetcher =
-	pipeUrlToFile: (url, filePath, _callback = (error) ->) ->
-		callbackOnce = (error) ->
-			clearTimeout timeoutHandler if timeoutHandler?
-			_callback(error)
-			_callback = () ->
-
-		if settings.filestoreDomainOveride?
-			p = URL.parse(url).path
-			url = "#{settings.filestoreDomainOveride}#{p}"
-		timeoutHandler = setTimeout () ->
-			timeoutHandler = null
-			logger.error url:url, filePath: filePath, "Timed out downloading file to cache"
-			callbackOnce(new Error("Timed out downloading file to cache #{url}"))
-			# FIXME: maybe need to close fileStream here
-		, 3 * oneMinute
-
-		logger.log url:url, filePath: filePath, "started downloading url to cache"
-		urlStream = request.get({url: url, timeout: oneMinute})
-		urlStream.pause() # stop data flowing until we are ready
-
-		# attach handlers before setting up pipes
-		urlStream.on "error", (error) ->
-			logger.error err: error, url:url, filePath: filePath, "error downloading url"
-			callbackOnce(error or new Error("Something went wrong downloading the URL #{url}"))
-
-		urlStream.on "end", () ->
-			logger.log url:url, filePath: filePath, "finished downloading file into cache"
-
-		urlStream.on "response", (res) ->
-			if res.statusCode >= 200 and res.statusCode < 300
-				fileStream = fs.createWriteStream(filePath)
-
-				# attach handlers before setting up pipes
-				fileStream.on 'error', (error) ->
-					logger.error err: error, url:url, filePath: filePath, "error writing file into cache"
-					fs.unlink filePath, (err) ->
-						if err?
-							logger.err err: err, filePath: filePath, "error deleting file from cache"
-						callbackOnce(error)
-
-				fileStream.on 'finish', () ->
-					logger.log url:url, filePath: filePath, "finished writing file into cache"
-					callbackOnce()
-
-				fileStream.on 'pipe', () ->
-					logger.log url:url, filePath: filePath, "piping into filestream"
-
-				urlStream.pipe(fileStream)
-				urlStream.resume() # now we are ready to handle the data
-			else
-				logger.error statusCode: res.statusCode, url:url, filePath: filePath, "unexpected status code downloading url to cache"
-				# https://nodejs.org/api/http.html#http_class_http_clientrequest
-				# If you add a 'response' event handler, then you must consume
-				# the data from the response object, either by calling
-				# response.read() whenever there is a 'readable' event, or by
-				# adding a 'data' handler, or by calling the .resume()
-				# method. Until the data is consumed, the 'end' event will not
-				# fire. Also, until the data is read it will consume memory
-				# that can eventually lead to a 'process out of memory' error.
-				urlStream.resume() # discard the data
-				callbackOnce(new Error("URL returned non-success status code: #{res.statusCode} #{url}"))

services/clsi/app/coffee/db.coffee

@@ -1,55 +0,0 @@
-Sequelize = require("sequelize")
-Settings = require("settings-sharelatex")
-_ = require("underscore")
-logger = require "logger-sharelatex"
-
-options = _.extend {logging:false}, Settings.mysql.clsi
-
-logger.log dbPath:Settings.mysql.clsi.storage, "connecting to db"
-
-sequelize = new Sequelize(
-	Settings.mysql.clsi.database,
-	Settings.mysql.clsi.username,
-	Settings.mysql.clsi.password,
-	options
-)
-
-if Settings.mysql.clsi.dialect == "sqlite"
-	logger.log "running PRAGMA journal_mode=WAL;"
-	sequelize.query("PRAGMA journal_mode=WAL;")
-	sequelize.query("PRAGMA synchronous=OFF;")
-	sequelize.query("PRAGMA read_uncommitted = true;")
-
-module.exports =
-	UrlCache: sequelize.define("UrlCache", {
-		url: Sequelize.STRING
-		project_id: Sequelize.STRING
-		lastModified: Sequelize.DATE
-	}, {
-		indexes: [
-			{fields: ['url', 'project_id']},
-			{fields: ['project_id']}
-		]
-	})
-
-	Project: sequelize.define("Project", {
-		project_id: {type: Sequelize.STRING, primaryKey: true}
-		lastAccessed: Sequelize.DATE
-	}, {
-		indexes: [
-			{fields: ['lastAccessed']}
-		]
-	})
-
-	op: Sequelize.Op
-	
-	sync: () -> 
-		logger.log dbPath:Settings.mysql.clsi.storage, "syncing db schema"
-		sequelize.sync()
-			.then(-> 
-				logger.log "db sync complete"
-			).catch((err)->
-				console.log err, "error syncing"
-			)
-
-	

services/clsi/app/js/CommandRunner.js

@@ -0,0 +1,20 @@
+// TODO: This file was created by bulk-decaffeinate.
+// Sanity-check the conversion and remove this comment.
+/*
+ * decaffeinate suggestions:
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let commandRunnerPath
+const Settings = require('settings-sharelatex')
+const logger = require('logger-sharelatex')
+
+if ((Settings.clsi != null ? Settings.clsi.dockerRunner : undefined) === true) {
+  commandRunnerPath = './DockerRunner'
+} else {
+  commandRunnerPath = './LocalCommandRunner'
+}
+logger.info({ commandRunnerPath }, 'selecting command runner for clsi')
+const CommandRunner = require(commandRunnerPath)
+
+module.exports = CommandRunner

services/clsi/app/js/CompileController.js

@@ -0,0 +1,238 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let CompileController
+const RequestParser = require('./RequestParser')
+const CompileManager = require('./CompileManager')
+const Settings = require('settings-sharelatex')
+const Metrics = require('./Metrics')
+const ProjectPersistenceManager = require('./ProjectPersistenceManager')
+const logger = require('logger-sharelatex')
+const Errors = require('./Errors')
+
+module.exports = CompileController = {
+  compile(req, res, next) {
+    if (next == null) {
+      next = function(error) {}
+    }
+    const timer = new Metrics.Timer('compile-request')
+    return RequestParser.parse(req.body, function(error, request) {
+      if (error != null) {
+        return next(error)
+      }
+      request.project_id = req.params.project_id
+      if (req.params.user_id != null) {
+        request.user_id = req.params.user_id
+      }
+      return ProjectPersistenceManager.markProjectAsJustAccessed(
+        request.project_id,
+        function(error) {
+          if (error != null) {
+            return next(error)
+          }
+          return CompileManager.doCompileWithLock(request, function(
+            error,
+            outputFiles
+          ) {
+            let code, status
+            if (outputFiles == null) {
+              outputFiles = []
+            }
+            if (error instanceof Errors.AlreadyCompilingError) {
+              code = 423 // Http 423 Locked
+              status = 'compile-in-progress'
+            } else if (error instanceof Errors.FilesOutOfSyncError) {
+              code = 409 // Http 409 Conflict
+              status = 'retry'
+            } else if (error != null ? error.terminated : undefined) {
+              status = 'terminated'
+            } else if (error != null ? error.validate : undefined) {
+              status = `validation-${error.validate}`
+            } else if (error != null ? error.timedout : undefined) {
+              status = 'timedout'
+              logger.log(
+                { err: error, project_id: request.project_id },
+                'timeout running compile'
+              )
+            } else if (error != null) {
+              status = 'error'
+              code = 500
+              logger.warn(
+                { err: error, project_id: request.project_id },
+                'error running compile'
+              )
+            } else {
+              let file
+              status = 'failure'
+              for (file of Array.from(outputFiles)) {
+                if (
+                  file.path != null
+                    ? file.path.match(/output\.pdf$/)
+                    : undefined
+                ) {
+                  status = 'success'
+                }
+              }
+
+              if (status === 'failure') {
+                logger.warn(
+                  { project_id: request.project_id, outputFiles },
+                  'project failed to compile successfully, no output.pdf generated'
+                )
+              }
+
+              // log an error if any core files are found
+              for (file of Array.from(outputFiles)) {
+                if (file.path === 'core') {
+                  logger.error(
+                    { project_id: request.project_id, req, outputFiles },
+                    'core file found in output'
+                  )
+                }
+              }
+            }
+
+            if (error != null) {
+              outputFiles = error.outputFiles || []
+            }
+
+            timer.done()
+            return res.status(code || 200).send({
+              compile: {
+                status,
+                error: (error != null ? error.message : undefined) || error,
+                outputFiles: outputFiles.map(file => ({
+                  url:
+                    `${Settings.apis.clsi.url}/project/${request.project_id}` +
+                    (request.user_id != null
+                      ? `/user/${request.user_id}`
+                      : '') +
+                    (file.build != null ? `/build/${file.build}` : '') +
+                    `/output/${file.path}`,
+                  path: file.path,
+                  type: file.type,
+                  build: file.build
+                }))
+              }
+            })
+          })
+        }
+      )
+    })
+  },
+
+  stopCompile(req, res, next) {
+    const { project_id, user_id } = req.params
+    return CompileManager.stopCompile(project_id, user_id, function(error) {
+      if (error != null) {
+        return next(error)
+      }
+      return res.sendStatus(204)
+    })
+  },
+
+  clearCache(req, res, next) {
+    if (next == null) {
+      next = function(error) {}
+    }
+    return ProjectPersistenceManager.clearProject(
+      req.params.project_id,
+      req.params.user_id,
+      function(error) {
+        if (error != null) {
+          return next(error)
+        }
+        return res.sendStatus(204)
+      }
+    )
+  }, // No content
+
+  syncFromCode(req, res, next) {
+    if (next == null) {
+      next = function(error) {}
+    }
+    const { file } = req.query
+    const line = parseInt(req.query.line, 10)
+    const column = parseInt(req.query.column, 10)
+    const { project_id } = req.params
+    const { user_id } = req.params
+    return CompileManager.syncFromCode(
+      project_id,
+      user_id,
+      file,
+      line,
+      column,
+      function(error, pdfPositions) {
+        if (error != null) {
+          return next(error)
+        }
+        return res.json({
+          pdf: pdfPositions
+        })
+      }
+    )
+  },
+
+  syncFromPdf(req, res, next) {
+    if (next == null) {
+      next = function(error) {}
+    }
+    const page = parseInt(req.query.page, 10)
+    const h = parseFloat(req.query.h)
+    const v = parseFloat(req.query.v)
+    const { project_id } = req.params
+    const { user_id } = req.params
+    return CompileManager.syncFromPdf(project_id, user_id, page, h, v, function(
+      error,
+      codePositions
+    ) {
+      if (error != null) {
+        return next(error)
+      }
+      return res.json({
+        code: codePositions
+      })
+    })
+  },
+
+  wordcount(req, res, next) {
+    if (next == null) {
+      next = function(error) {}
+    }
+    const file = req.query.file || 'main.tex'
+    const { project_id } = req.params
+    const { user_id } = req.params
+    const { image } = req.query
+    logger.log({ image, file, project_id }, 'word count request')
+
+    return CompileManager.wordcount(project_id, user_id, file, image, function(
+      error,
+      result
+    ) {
+      if (error != null) {
+        return next(error)
+      }
+      return res.json({
+        texcount: result
+      })
+    })
+  },
+
+  status(req, res, next) {
+    if (next == null) {
+      next = function(error) {}
+    }
+    return res.send('OK')
+  }
+}

services/clsi/app/js/CompileManager.js

@@ -0,0 +1,705 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-return-assign,
+    no-undef,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let CompileManager
+const ResourceWriter = require('./ResourceWriter')
+const LatexRunner = require('./LatexRunner')
+const OutputFileFinder = require('./OutputFileFinder')
+const OutputCacheManager = require('./OutputCacheManager')
+const Settings = require('settings-sharelatex')
+const Path = require('path')
+const logger = require('logger-sharelatex')
+const Metrics = require('./Metrics')
+const child_process = require('child_process')
+const DraftModeManager = require('./DraftModeManager')
+const TikzManager = require('./TikzManager')
+const LockManager = require('./LockManager')
+const fs = require('fs')
+const fse = require('fs-extra')
+const os = require('os')
+const async = require('async')
+const Errors = require('./Errors')
+const CommandRunner = require('./CommandRunner')
+
+const getCompileName = function(project_id, user_id) {
+  if (user_id != null) {
+    return `${project_id}-${user_id}`
+  } else {
+    return project_id
+  }
+}
+
+const getCompileDir = (project_id, user_id) =>
+  Path.join(Settings.path.compilesDir, getCompileName(project_id, user_id))
+
+module.exports = CompileManager = {
+  doCompileWithLock(request, callback) {
+    if (callback == null) {
+      callback = function(error, outputFiles) {}
+    }
+    const compileDir = getCompileDir(request.project_id, request.user_id)
+    const lockFile = Path.join(compileDir, '.project-lock')
+    // use a .project-lock file in the compile directory to prevent
+    // simultaneous compiles
+    return fse.ensureDir(compileDir, function(error) {
+      if (error != null) {
+        return callback(error)
+      }
+      return LockManager.runWithLock(
+        lockFile,
+        releaseLock => CompileManager.doCompile(request, releaseLock),
+        callback
+      )
+    })
+  },
+
+  doCompile(request, callback) {
+    if (callback == null) {
+      callback = function(error, outputFiles) {}
+    }
+    const compileDir = getCompileDir(request.project_id, request.user_id)
+    let timer = new Metrics.Timer('write-to-disk')
+    logger.log(
+      { project_id: request.project_id, user_id: request.user_id },
+      'syncing resources to disk'
+    )
+    return ResourceWriter.syncResourcesToDisk(request, compileDir, function(
+      error,
+      resourceList
+    ) {
+      // NOTE: resourceList is insecure, it should only be used to exclude files from the output list
+      if (error != null && error instanceof Errors.FilesOutOfSyncError) {
+        logger.warn(
+          { project_id: request.project_id, user_id: request.user_id },
+          'files out of sync, please retry'
+        )
+        return callback(error)
+      } else if (error != null) {
+        logger.err(
+          {
+            err: error,
+            project_id: request.project_id,
+            user_id: request.user_id
+          },
+          'error writing resources to disk'
+        )
+        return callback(error)
+      }
+      logger.log(
+        {
+          project_id: request.project_id,
+          user_id: request.user_id,
+          time_taken: Date.now() - timer.start
+        },
+        'written files to disk'
+      )
+      timer.done()
+
+      const injectDraftModeIfRequired = function(callback) {
+        if (request.draft) {
+          return DraftModeManager.injectDraftMode(
+            Path.join(compileDir, request.rootResourcePath),
+            callback
+          )
+        } else {
+          return callback()
+        }
+      }
+
+      const createTikzFileIfRequired = callback =>
+        TikzManager.checkMainFile(
+          compileDir,
+          request.rootResourcePath,
+          resourceList,
+          function(error, needsMainFile) {
+            if (error != null) {
+              return callback(error)
+            }
+            if (needsMainFile) {
+              return TikzManager.injectOutputFile(
+                compileDir,
+                request.rootResourcePath,
+                callback
+              )
+            } else {
+              return callback()
+            }
+          }
+        )
+      // set up environment variables for chktex
+      const env = {}
+      // only run chktex on LaTeX files (not knitr .Rtex files or any others)
+      const isLaTeXFile =
+        request.rootResourcePath != null
+          ? request.rootResourcePath.match(/\.tex$/i)
+          : undefined
+      if (request.check != null && isLaTeXFile) {
+        env.CHKTEX_OPTIONS = '-nall -e9 -e10 -w15 -w16'
+        env.CHKTEX_ULIMIT_OPTIONS = '-t 5 -v 64000'
+        if (request.check === 'error') {
+          env.CHKTEX_EXIT_ON_ERROR = 1
+        }
+        if (request.check === 'validate') {
+          env.CHKTEX_VALIDATE = 1
+        }
+      }
+
+      // apply a series of file modifications/creations for draft mode and tikz
+      return async.series(
+        [injectDraftModeIfRequired, createTikzFileIfRequired],
+        function(error) {
+          if (error != null) {
+            return callback(error)
+          }
+          timer = new Metrics.Timer('run-compile')
+          // find the image tag to log it as a metric, e.g. 2015.1 (convert . to - for graphite)
+          let tag =
+            __guard__(
+              __guard__(
+                request.imageName != null
+                  ? request.imageName.match(/:(.*)/)
+                  : undefined,
+                x1 => x1[1]
+              ),
+              x => x.replace(/\./g, '-')
+            ) || 'default'
+          if (!request.project_id.match(/^[0-9a-f]{24}$/)) {
+            tag = 'other'
+          } // exclude smoke test
+          Metrics.inc('compiles')
+          Metrics.inc(`compiles-with-image.${tag}`)
+          const compileName = getCompileName(
+            request.project_id,
+            request.user_id
+          )
+          return LatexRunner.runLatex(
+            compileName,
+            {
+              directory: compileDir,
+              mainFile: request.rootResourcePath,
+              compiler: request.compiler,
+              timeout: request.timeout,
+              image: request.imageName,
+              flags: request.flags,
+              environment: env
+            },
+            function(error, output, stats, timings) {
+              // request was for validation only
+              let metric_key, metric_value
+              if (request.check === 'validate') {
+                const result = (error != null
+                ? error.code
+                : undefined)
+                  ? 'fail'
+                  : 'pass'
+                error = new Error('validation')
+                error.validate = result
+              }
+              // request was for compile, and failed on validation
+              if (
+                request.check === 'error' &&
+                (error != null ? error.message : undefined) === 'exited'
+              ) {
+                error = new Error('compilation')
+                error.validate = 'fail'
+              }
+              // compile was killed by user, was a validation, or a compile which failed validation
+              if (
+                (error != null ? error.terminated : undefined) ||
+                (error != null ? error.validate : undefined) ||
+                (error != null ? error.timedout : undefined)
+              ) {
+                OutputFileFinder.findOutputFiles(
+                  resourceList,
+                  compileDir,
+                  function(err, outputFiles) {
+                    if (err != null) {
+                      return callback(err)
+                    }
+                    error.outputFiles = outputFiles // return output files so user can check logs
+                    return callback(error)
+                  }
+                )
+                return
+              }
+              // compile completed normally
+              if (error != null) {
+                return callback(error)
+              }
+              Metrics.inc('compiles-succeeded')
+              const object = stats || {}
+              for (metric_key in object) {
+                metric_value = object[metric_key]
+                Metrics.count(metric_key, metric_value)
+              }
+              const object1 = timings || {}
+              for (metric_key in object1) {
+                metric_value = object1[metric_key]
+                Metrics.timing(metric_key, metric_value)
+              }
+              const loadavg =
+                typeof os.loadavg === 'function' ? os.loadavg() : undefined
+              if (loadavg != null) {
+                Metrics.gauge('load-avg', loadavg[0])
+              }
+              const ts = timer.done()
+              logger.log(
+                {
+                  project_id: request.project_id,
+                  user_id: request.user_id,
+                  time_taken: ts,
+                  stats,
+                  timings,
+                  loadavg
+                },
+                'done compile'
+              )
+              if ((stats != null ? stats['latex-runs'] : undefined) > 0) {
+                Metrics.timing('run-compile-per-pass', ts / stats['latex-runs'])
+              }
+              if (
+                (stats != null ? stats['latex-runs'] : undefined) > 0 &&
+                (timings != null ? timings['cpu-time'] : undefined) > 0
+              ) {
+                Metrics.timing(
+                  'run-compile-cpu-time-per-pass',
+                  timings['cpu-time'] / stats['latex-runs']
+                )
+              }
+
+              return OutputFileFinder.findOutputFiles(
+                resourceList,
+                compileDir,
+                function(error, outputFiles) {
+                  if (error != null) {
+                    return callback(error)
+                  }
+                  return OutputCacheManager.saveOutputFiles(
+                    outputFiles,
+                    compileDir,
+                    (error, newOutputFiles) => callback(null, newOutputFiles)
+                  )
+                }
+              )
+            }
+          )
+        }
+      )
+    })
+  },
+
+  stopCompile(project_id, user_id, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const compileName = getCompileName(project_id, user_id)
+    return LatexRunner.killLatex(compileName, callback)
+  },
+
+  clearProject(project_id, user_id, _callback) {
+    if (_callback == null) {
+      _callback = function(error) {}
+    }
+    const callback = function(error) {
+      _callback(error)
+      return (_callback = function() {})
+    }
+
+    const compileDir = getCompileDir(project_id, user_id)
+
+    return CompileManager._checkDirectory(compileDir, function(err, exists) {
+      if (err != null) {
+        return callback(err)
+      }
+      if (!exists) {
+        return callback()
+      } // skip removal if no directory present
+
+      const proc = child_process.spawn('rm', ['-r', compileDir])
+
+      proc.on('error', callback)
+
+      let stderr = ''
+      proc.stderr.on('data', chunk => (stderr += chunk.toString()))
+
+      return proc.on('close', function(code) {
+        if (code === 0) {
+          return callback(null)
+        } else {
+          return callback(new Error(`rm -r ${compileDir} failed: ${stderr}`))
+        }
+      })
+    })
+  },
+
+  _findAllDirs(callback) {
+    if (callback == null) {
+      callback = function(error, allDirs) {}
+    }
+    const root = Settings.path.compilesDir
+    return fs.readdir(root, function(err, files) {
+      if (err != null) {
+        return callback(err)
+      }
+      const allDirs = Array.from(files).map(file => Path.join(root, file))
+      return callback(null, allDirs)
+    })
+  },
+
+  clearExpiredProjects(max_cache_age_ms, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const now = Date.now()
+    // action for each directory
+    const expireIfNeeded = (checkDir, cb) =>
+      fs.stat(checkDir, function(err, stats) {
+        if (err != null) {
+          return cb()
+        } // ignore errors checking directory
+        const age = now - stats.mtime
+        const hasExpired = age > max_cache_age_ms
+        if (hasExpired) {
+          return fse.remove(checkDir, cb)
+        } else {
+          return cb()
+        }
+      })
+    // iterate over all project directories
+    return CompileManager._findAllDirs(function(error, allDirs) {
+      if (error != null) {
+        return callback()
+      }
+      return async.eachSeries(allDirs, expireIfNeeded, callback)
+    })
+  },
+
+  _checkDirectory(compileDir, callback) {
+    if (callback == null) {
+      callback = function(error, exists) {}
+    }
+    return fs.lstat(compileDir, function(err, stats) {
+      if ((err != null ? err.code : undefined) === 'ENOENT') {
+        return callback(null, false) //  directory does not exist
+      } else if (err != null) {
+        logger.err(
+          { dir: compileDir, err },
+          'error on stat of project directory for removal'
+        )
+        return callback(err)
+      } else if (!(stats != null ? stats.isDirectory() : undefined)) {
+        logger.err(
+          { dir: compileDir, stats },
+          'bad project directory for removal'
+        )
+        return callback(new Error('project directory is not directory'))
+      } else {
+        return callback(null, true)
+      }
+    })
+  }, // directory exists
+
+  syncFromCode(project_id, user_id, file_name, line, column, callback) {
+    // If LaTeX was run in a virtual environment, the file path that synctex expects
+    // might not match the file path on the host. The .synctex.gz file however, will be accessed
+    // wherever it is on the host.
+    if (callback == null) {
+      callback = function(error, pdfPositions) {}
+    }
+    const compileName = getCompileName(project_id, user_id)
+    const base_dir = Settings.path.synctexBaseDir(compileName)
+    const file_path = base_dir + '/' + file_name
+    const compileDir = getCompileDir(project_id, user_id)
+    const synctex_path = `${base_dir}/output.pdf`
+    const command = ['code', synctex_path, file_path, line, column]
+    return fse.ensureDir(compileDir, function(error) {
+      if (error != null) {
+        logger.err(
+          { error, project_id, user_id, file_name },
+          'error ensuring dir for sync from code'
+        )
+        return callback(error)
+      }
+      return CompileManager._runSynctex(project_id, user_id, command, function(
+        error,
+        stdout
+      ) {
+        if (error != null) {
+          return callback(error)
+        }
+        logger.log(
+          { project_id, user_id, file_name, line, column, command, stdout },
+          'synctex code output'
+        )
+        return callback(
+          null,
+          CompileManager._parseSynctexFromCodeOutput(stdout)
+        )
+      })
+    })
+  },
+
+  syncFromPdf(project_id, user_id, page, h, v, callback) {
+    if (callback == null) {
+      callback = function(error, filePositions) {}
+    }
+    const compileName = getCompileName(project_id, user_id)
+    const compileDir = getCompileDir(project_id, user_id)
+    const base_dir = Settings.path.synctexBaseDir(compileName)
+    const synctex_path = `${base_dir}/output.pdf`
+    const command = ['pdf', synctex_path, page, h, v]
+    return fse.ensureDir(compileDir, function(error) {
+      if (error != null) {
+        logger.err(
+          { error, project_id, user_id, file_name },
+          'error ensuring dir for sync to code'
+        )
+        return callback(error)
+      }
+      return CompileManager._runSynctex(project_id, user_id, command, function(
+        error,
+        stdout
+      ) {
+        if (error != null) {
+          return callback(error)
+        }
+        logger.log(
+          { project_id, user_id, page, h, v, stdout },
+          'synctex pdf output'
+        )
+        return callback(
+          null,
+          CompileManager._parseSynctexFromPdfOutput(stdout, base_dir)
+        )
+      })
+    })
+  },
+
+  _checkFileExists(path, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const synctexDir = Path.dirname(path)
+    const synctexFile = Path.join(synctexDir, 'output.synctex.gz')
+    return fs.stat(synctexDir, function(error, stats) {
+      if ((error != null ? error.code : undefined) === 'ENOENT') {
+        return callback(
+          new Errors.NotFoundError('called synctex with no output directory')
+        )
+      }
+      if (error != null) {
+        return callback(error)
+      }
+      return fs.stat(synctexFile, function(error, stats) {
+        if ((error != null ? error.code : undefined) === 'ENOENT') {
+          return callback(
+            new Errors.NotFoundError('called synctex with no output file')
+          )
+        }
+        if (error != null) {
+          return callback(error)
+        }
+        if (!(stats != null ? stats.isFile() : undefined)) {
+          return callback(new Error('not a file'))
+        }
+        return callback()
+      })
+    })
+  },
+
+  _runSynctex(project_id, user_id, command, callback) {
+    if (callback == null) {
+      callback = function(error, stdout) {}
+    }
+    const seconds = 1000
+
+    command.unshift('/opt/synctex')
+
+    const directory = getCompileDir(project_id, user_id)
+    const timeout = 60 * 1000 // increased to allow for large projects
+    const compileName = getCompileName(project_id, user_id)
+    return CommandRunner.run(
+      compileName,
+      command,
+      directory,
+      Settings.clsi != null ? Settings.clsi.docker.image : undefined,
+      timeout,
+      {},
+      function(error, output) {
+        if (error != null) {
+          logger.err(
+            { err: error, command, project_id, user_id },
+            'error running synctex'
+          )
+          return callback(error)
+        }
+        return callback(null, output.stdout)
+      }
+    )
+  },
+
+  _parseSynctexFromCodeOutput(output) {
+    const results = []
+    for (const line of Array.from(output.split('\n'))) {
+      const [node, page, h, v, width, height] = Array.from(line.split('\t'))
+      if (node === 'NODE') {
+        results.push({
+          page: parseInt(page, 10),
+          h: parseFloat(h),
+          v: parseFloat(v),
+          height: parseFloat(height),
+          width: parseFloat(width)
+        })
+      }
+    }
+    return results
+  },
+
+  _parseSynctexFromPdfOutput(output, base_dir) {
+    const results = []
+    for (let line of Array.from(output.split('\n'))) {
+      let column, file_path, node
+      ;[node, file_path, line, column] = Array.from(line.split('\t'))
+      if (node === 'NODE') {
+        const file = file_path.slice(base_dir.length + 1)
+        results.push({
+          file,
+          line: parseInt(line, 10),
+          column: parseInt(column, 10)
+        })
+      }
+    }
+    return results
+  },
+
+  wordcount(project_id, user_id, file_name, image, callback) {
+    if (callback == null) {
+      callback = function(error, pdfPositions) {}
+    }
+    logger.log({ project_id, user_id, file_name, image }, 'running wordcount')
+    const file_path = `$COMPILE_DIR/${file_name}`
+    const command = [
+      'texcount',
+      '-nocol',
+      '-inc',
+      file_path,
+      `-out=${file_path}.wc`
+    ]
+    const compileDir = getCompileDir(project_id, user_id)
+    const timeout = 60 * 1000
+    const compileName = getCompileName(project_id, user_id)
+    return fse.ensureDir(compileDir, function(error) {
+      if (error != null) {
+        logger.err(
+          { error, project_id, user_id, file_name },
+          'error ensuring dir for sync from code'
+        )
+        return callback(error)
+      }
+      return CommandRunner.run(
+        compileName,
+        command,
+        compileDir,
+        image,
+        timeout,
+        {},
+        function(error) {
+          if (error != null) {
+            return callback(error)
+          }
+          return fs.readFile(
+            compileDir + '/' + file_name + '.wc',
+            'utf-8',
+            function(err, stdout) {
+              if (err != null) {
+                // call it node_err so sentry doesn't use random path error as unique id so it can't be ignored
+                logger.err(
+                  { node_err: err, command, compileDir, project_id, user_id },
+                  'error reading word count output'
+                )
+                return callback(err)
+              }
+              const results = CompileManager._parseWordcountFromOutput(stdout)
+              logger.log(
+                { project_id, user_id, wordcount: results },
+                'word count results'
+              )
+              return callback(null, results)
+            }
+          )
+        }
+      )
+    })
+  },
+
+  _parseWordcountFromOutput(output) {
+    const results = {
+      encode: '',
+      textWords: 0,
+      headWords: 0,
+      outside: 0,
+      headers: 0,
+      elements: 0,
+      mathInline: 0,
+      mathDisplay: 0,
+      errors: 0,
+      messages: ''
+    }
+    for (const line of Array.from(output.split('\n'))) {
+      const [data, info] = Array.from(line.split(':'))
+      if (data.indexOf('Encoding') > -1) {
+        results.encode = info.trim()
+      }
+      if (data.indexOf('in text') > -1) {
+        results.textWords = parseInt(info, 10)
+      }
+      if (data.indexOf('in head') > -1) {
+        results.headWords = parseInt(info, 10)
+      }
+      if (data.indexOf('outside') > -1) {
+        results.outside = parseInt(info, 10)
+      }
+      if (data.indexOf('of head') > -1) {
+        results.headers = parseInt(info, 10)
+      }
+      if (data.indexOf('Number of floats/tables/figures') > -1) {
+        results.elements = parseInt(info, 10)
+      }
+      if (data.indexOf('Number of math inlines') > -1) {
+        results.mathInline = parseInt(info, 10)
+      }
+      if (data.indexOf('Number of math displayed') > -1) {
+        results.mathDisplay = parseInt(info, 10)
+      }
+      if (data === '(errors') {
+        // errors reported as (errors:123)
+        results.errors = parseInt(info, 10)
+      }
+      if (line.indexOf('!!! ') > -1) {
+        // errors logged as !!! message !!!
+        results.messages += line + '\n'
+      }
+    }
+    return results
+  }
+}
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/app/js/ContentTypeMapper.js

@@ -0,0 +1,38 @@
+/* eslint-disable
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+let ContentTypeMapper
+const Path = require('path')
+
+// here we coerce html, css and js to text/plain,
+// otherwise choose correct mime type based on file extension,
+// falling back to octet-stream
+module.exports = ContentTypeMapper = {
+  map(path) {
+    switch (Path.extname(path)) {
+      case '.txt':
+      case '.html':
+      case '.js':
+      case '.css':
+      case '.svg':
+        return 'text/plain'
+      case '.csv':
+        return 'text/csv'
+      case '.pdf':
+        return 'application/pdf'
+      case '.png':
+        return 'image/png'
+      case '.jpg':
+      case '.jpeg':
+        return 'image/jpeg'
+      case '.tiff':
+        return 'image/tiff'
+      case '.gif':
+        return 'image/gif'
+      default:
+        return 'application/octet-stream'
+    }
+  }
+}

services/clsi/app/js/DbQueue.js

@@ -0,0 +1,18 @@
+// TODO: This file was created by bulk-decaffeinate.
+// Sanity-check the conversion and remove this comment.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const async = require('async')
+const Settings = require('settings-sharelatex')
+const logger = require('logger-sharelatex')
+const queue = async.queue(
+  (task, cb) => task(cb),
+  Settings.parallelSqlQueryLimit
+)
+
+queue.drain = () => logger.debug('all items have been processed')
+
+module.exports = { queue }

services/clsi/app/js/DockerLockManager.js

@@ -0,0 +1,113 @@
+/* eslint-disable
+    handle-callback-err,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let LockManager
+const logger = require('logger-sharelatex')
+
+const LockState = {} // locks for docker container operations, by container name
+
+module.exports = LockManager = {
+  MAX_LOCK_HOLD_TIME: 15000, // how long we can keep a lock
+  MAX_LOCK_WAIT_TIME: 10000, // how long we wait for a lock
+  LOCK_TEST_INTERVAL: 1000, // retry time
+
+  tryLock(key, callback) {
+    let lockValue
+    if (callback == null) {
+      callback = function(err, gotLock) {}
+    }
+    const existingLock = LockState[key]
+    if (existingLock != null) {
+      // the lock is already taken, check how old it is
+      const lockAge = Date.now() - existingLock.created
+      if (lockAge < LockManager.MAX_LOCK_HOLD_TIME) {
+        return callback(null, false) // we didn't get the lock, bail out
+      } else {
+        logger.error(
+          { key, lock: existingLock, age: lockAge },
+          'taking old lock by force'
+        )
+      }
+    }
+    // take the lock
+    LockState[key] = lockValue = { created: Date.now() }
+    return callback(null, true, lockValue)
+  },
+
+  getLock(key, callback) {
+    let attempt
+    if (callback == null) {
+      callback = function(error, lockValue) {}
+    }
+    const startTime = Date.now()
+    return (attempt = () =>
+      LockManager.tryLock(key, function(error, gotLock, lockValue) {
+        if (error != null) {
+          return callback(error)
+        }
+        if (gotLock) {
+          return callback(null, lockValue)
+        } else if (Date.now() - startTime > LockManager.MAX_LOCK_WAIT_TIME) {
+          const e = new Error('Lock timeout')
+          e.key = key
+          return callback(e)
+        } else {
+          return setTimeout(attempt, LockManager.LOCK_TEST_INTERVAL)
+        }
+      }))()
+  },
+
+  releaseLock(key, lockValue, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const existingLock = LockState[key]
+    if (existingLock === lockValue) {
+      // lockValue is an object, so we can test by reference
+      delete LockState[key] // our lock, so we can free it
+      return callback()
+    } else if (existingLock != null) {
+      // lock exists but doesn't match ours
+      logger.error(
+        { key, lock: existingLock },
+        'tried to release lock taken by force'
+      )
+      return callback()
+    } else {
+      logger.error(
+        { key, lock: existingLock },
+        'tried to release lock that has gone'
+      )
+      return callback()
+    }
+  },
+
+  runWithLock(key, runner, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return LockManager.getLock(key, function(error, lockValue) {
+      if (error != null) {
+        return callback(error)
+      }
+      return runner((error1, ...args) =>
+        LockManager.releaseLock(key, lockValue, function(error2) {
+          error = error1 || error2
+          if (error != null) {
+            return callback(error)
+          }
+          return callback(null, ...Array.from(args))
+        })
+      )
+    })
+  }
+}

services/clsi/app/js/DockerRunner.js

@@ -0,0 +1,695 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-return-assign,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS205: Consider reworking code to avoid use of IIFEs
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let DockerRunner, oneHour
+const Settings = require('settings-sharelatex')
+const logger = require('logger-sharelatex')
+const Docker = require('dockerode')
+const dockerode = new Docker()
+const crypto = require('crypto')
+const async = require('async')
+const LockManager = require('./DockerLockManager')
+const fs = require('fs')
+const Path = require('path')
+const _ = require('underscore')
+
+logger.info('using docker runner')
+
+const usingSiblingContainers = () =>
+  __guard__(
+    Settings != null ? Settings.path : undefined,
+    x => x.sandboxedCompilesHostDir
+  ) != null
+
+let containerMonitorTimeout
+let containerMonitorInterval
+
+module.exports = DockerRunner = {
+  ERR_NOT_DIRECTORY: new Error('not a directory'),
+  ERR_TERMINATED: new Error('terminated'),
+  ERR_EXITED: new Error('exited'),
+  ERR_TIMED_OUT: new Error('container timed out'),
+
+  run(project_id, command, directory, image, timeout, environment, callback) {
+    let name
+    if (callback == null) {
+      callback = function(error, output) {}
+    }
+    if (usingSiblingContainers()) {
+      const _newPath = Settings.path.sandboxedCompilesHostDir
+      logger.log(
+        { path: _newPath },
+        'altering bind path for sibling containers'
+      )
+      // Server Pro, example:
+      //   '/var/lib/sharelatex/data/compiles/<project-id>'
+      //   ... becomes ...
+      //   '/opt/sharelatex_data/data/compiles/<project-id>'
+      directory = Path.join(
+        Settings.path.sandboxedCompilesHostDir,
+        Path.basename(directory)
+      )
+    }
+
+    const volumes = {}
+    volumes[directory] = '/compile'
+
+    command = Array.from(command).map(arg =>
+      __guardMethod__(arg.toString(), 'replace', o =>
+        o.replace('$COMPILE_DIR', '/compile')
+      )
+    )
+    if (image == null) {
+      ;({ image } = Settings.clsi.docker)
+    }
+
+    if (Settings.texliveImageNameOveride != null) {
+      const img = image.split('/')
+      image = `${Settings.texliveImageNameOveride}/${img[2]}`
+    }
+
+    const options = DockerRunner._getContainerOptions(
+      command,
+      image,
+      volumes,
+      timeout,
+      environment
+    )
+    const fingerprint = DockerRunner._fingerprintContainer(options)
+    options.name = name = `project-${project_id}-${fingerprint}`
+
+    // logOptions = _.clone(options)
+    // logOptions?.HostConfig?.SecurityOpt = "secomp used, removed in logging"
+    logger.log({ project_id }, 'running docker container')
+    DockerRunner._runAndWaitForContainer(options, volumes, timeout, function(
+      error,
+      output
+    ) {
+      if (error && error.statusCode === 500) {
+        logger.log(
+          { err: error, project_id },
+          'error running container so destroying and retrying'
+        )
+        return DockerRunner.destroyContainer(name, null, true, function(error) {
+          if (error != null) {
+            return callback(error)
+          }
+          return DockerRunner._runAndWaitForContainer(
+            options,
+            volumes,
+            timeout,
+            callback
+          )
+        })
+      } else {
+        return callback(error, output)
+      }
+    })
+
+    return name
+  }, // pass back the container name to allow it to be killed
+
+  kill(container_id, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    logger.log({ container_id }, 'sending kill signal to container')
+    const container = dockerode.getContainer(container_id)
+    return container.kill(function(error) {
+      if (
+        error != null &&
+        __guardMethod__(error != null ? error.message : undefined, 'match', o =>
+          o.match(/Cannot kill container .* is not running/)
+        )
+      ) {
+        logger.warn(
+          { err: error, container_id },
+          'container not running, continuing'
+        )
+        error = null
+      }
+      if (error != null) {
+        logger.error({ err: error, container_id }, 'error killing container')
+        return callback(error)
+      } else {
+        return callback()
+      }
+    })
+  },
+
+  _runAndWaitForContainer(options, volumes, timeout, _callback) {
+    if (_callback == null) {
+      _callback = function(error, output) {}
+    }
+    const callback = function(...args) {
+      _callback(...Array.from(args || []))
+      // Only call the callback once
+      return (_callback = function() {})
+    }
+
+    const { name } = options
+
+    let streamEnded = false
+    let containerReturned = false
+    let output = {}
+
+    const callbackIfFinished = function() {
+      if (streamEnded && containerReturned) {
+        return callback(null, output)
+      }
+    }
+
+    const attachStreamHandler = function(error, _output) {
+      if (error != null) {
+        return callback(error)
+      }
+      output = _output
+      streamEnded = true
+      return callbackIfFinished()
+    }
+
+    return DockerRunner.startContainer(
+      options,
+      volumes,
+      attachStreamHandler,
+      function(error, containerId) {
+        if (error != null) {
+          return callback(error)
+        }
+
+        return DockerRunner.waitForContainer(name, timeout, function(
+          error,
+          exitCode
+        ) {
+          let err
+          if (error != null) {
+            return callback(error)
+          }
+          if (exitCode === 137) {
+            // exit status from kill -9
+            err = DockerRunner.ERR_TERMINATED
+            err.terminated = true
+            return callback(err)
+          }
+          if (exitCode === 1) {
+            // exit status from chktex
+            err = DockerRunner.ERR_EXITED
+            err.code = exitCode
+            return callback(err)
+          }
+          containerReturned = true
+          __guard__(
+            options != null ? options.HostConfig : undefined,
+            x => (x.SecurityOpt = null)
+          ) // small log line
+          logger.log({ err, exitCode, options }, 'docker container has exited')
+          return callbackIfFinished()
+        })
+      }
+    )
+  },
+
+  _getContainerOptions(command, image, volumes, timeout, environment) {
+    let m, year
+    let key, value, hostVol, dockerVol
+    const timeoutInSeconds = timeout / 1000
+
+    const dockerVolumes = {}
+    for (hostVol in volumes) {
+      dockerVol = volumes[hostVol]
+      dockerVolumes[dockerVol] = {}
+
+      if (volumes[hostVol].slice(-3).indexOf(':r') === -1) {
+        volumes[hostVol] = `${dockerVol}:rw`
+      }
+    }
+
+    // merge settings and environment parameter
+    const env = {}
+    for (const src of [Settings.clsi.docker.env, environment || {}]) {
+      for (key in src) {
+        value = src[key]
+        env[key] = value
+      }
+    }
+    // set the path based on the image year
+    if ((m = image.match(/:([0-9]+)\.[0-9]+/))) {
+      year = m[1]
+    } else {
+      year = '2014'
+    }
+    env.PATH = `/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/texlive/${year}/bin/x86_64-linux/`
+    const options = {
+      Cmd: command,
+      Image: image,
+      Volumes: dockerVolumes,
+      WorkingDir: '/compile',
+      NetworkDisabled: true,
+      Memory: 1024 * 1024 * 1024 * 1024, // 1 Gb
+      User: Settings.clsi.docker.user,
+      Env: (() => {
+        const result = []
+        for (key in env) {
+          value = env[key]
+          result.push(`${key}=${value}`)
+        }
+        return result
+      })(), // convert the environment hash to an array
+      HostConfig: {
+        Binds: (() => {
+          const result1 = []
+          for (hostVol in volumes) {
+            dockerVol = volumes[hostVol]
+            result1.push(`${hostVol}:${dockerVol}`)
+          }
+          return result1
+        })(),
+        LogConfig: { Type: 'none', Config: {} },
+        Ulimits: [
+          {
+            Name: 'cpu',
+            Soft: timeoutInSeconds + 5,
+            Hard: timeoutInSeconds + 10
+          }
+        ],
+        CapDrop: 'ALL',
+        SecurityOpt: ['no-new-privileges']
+      }
+    }
+
+    if (
+      (Settings.path != null ? Settings.path.synctexBinHostPath : undefined) !=
+      null
+    ) {
+      options.HostConfig.Binds.push(
+        `${Settings.path.synctexBinHostPath}:/opt/synctex:ro`
+      )
+    }
+
+    if (Settings.clsi.docker.seccomp_profile != null) {
+      options.HostConfig.SecurityOpt.push(
+        `seccomp=${Settings.clsi.docker.seccomp_profile}`
+      )
+    }
+
+    if (Settings.clsi.docker.runtime) {
+      options.HostConfig.Runtime = Settings.clsi.docker.runtime
+    }
+
+    return options
+  },
+
+  _fingerprintContainer(containerOptions) {
+    // Yay, Hashing!
+    const json = JSON.stringify(containerOptions)
+    return crypto
+      .createHash('md5')
+      .update(json)
+      .digest('hex')
+  },
+
+  startContainer(options, volumes, attachStreamHandler, callback) {
+    return LockManager.runWithLock(
+      options.name,
+      releaseLock =>
+        // Check that volumes exist before starting the container.
+        // When a container is started with volume pointing to a
+        // non-existent directory then docker creates the directory but
+        // with root ownership.
+        DockerRunner._checkVolumes(options, volumes, function(err) {
+          if (err != null) {
+            return releaseLock(err)
+          }
+          return DockerRunner._startContainer(
+            options,
+            volumes,
+            attachStreamHandler,
+            releaseLock
+          )
+        }),
+
+      callback
+    )
+  },
+
+  // Check that volumes exist and are directories
+  _checkVolumes(options, volumes, callback) {
+    if (callback == null) {
+      callback = function(error, containerName) {}
+    }
+    if (usingSiblingContainers()) {
+      // Server Pro, with sibling-containers active, skip checks
+      return callback(null)
+    }
+
+    const checkVolume = (path, cb) =>
+      fs.stat(path, function(err, stats) {
+        if (err != null) {
+          return cb(err)
+        }
+        if (!(stats != null ? stats.isDirectory() : undefined)) {
+          return cb(DockerRunner.ERR_NOT_DIRECTORY)
+        }
+        return cb()
+      })
+    const jobs = []
+    for (const vol in volumes) {
+      ;(vol => jobs.push(cb => checkVolume(vol, cb)))(vol)
+    }
+    return async.series(jobs, callback)
+  },
+
+  _startContainer(options, volumes, attachStreamHandler, callback) {
+    if (callback == null) {
+      callback = function(error, output) {}
+    }
+    callback = _.once(callback)
+    const { name } = options
+
+    logger.log({ container_name: name }, 'starting container')
+    const container = dockerode.getContainer(name)
+
+    const createAndStartContainer = () =>
+      dockerode.createContainer(options, function(error, container) {
+        if (error != null) {
+          return callback(error)
+        }
+        return startExistingContainer()
+      })
+    var startExistingContainer = () =>
+      DockerRunner.attachToContainer(
+        options.name,
+        attachStreamHandler,
+        function(error) {
+          if (error != null) {
+            return callback(error)
+          }
+          return container.start(function(error) {
+            if (
+              error != null &&
+              (error != null ? error.statusCode : undefined) !== 304
+            ) {
+              // already running
+              return callback(error)
+            } else {
+              return callback()
+            }
+          })
+        }
+      )
+    return container.inspect(function(error, stats) {
+      if ((error != null ? error.statusCode : undefined) === 404) {
+        return createAndStartContainer()
+      } else if (error != null) {
+        logger.err(
+          { container_name: name, error },
+          'unable to inspect container to start'
+        )
+        return callback(error)
+      } else {
+        return startExistingContainer()
+      }
+    })
+  },
+
+  attachToContainer(containerId, attachStreamHandler, attachStartCallback) {
+    const container = dockerode.getContainer(containerId)
+    return container.attach({ stdout: 1, stderr: 1, stream: 1 }, function(
+      error,
+      stream
+    ) {
+      if (error != null) {
+        logger.error(
+          { err: error, container_id: containerId },
+          'error attaching to container'
+        )
+        return attachStartCallback(error)
+      } else {
+        attachStartCallback()
+      }
+
+      logger.log({ container_id: containerId }, 'attached to container')
+
+      const MAX_OUTPUT = 1024 * 1024 // limit output to 1MB
+      const createStringOutputStream = function(name) {
+        return {
+          data: '',
+          overflowed: false,
+          write(data) {
+            if (this.overflowed) {
+              return
+            }
+            if (this.data.length < MAX_OUTPUT) {
+              return (this.data += data)
+            } else {
+              logger.error(
+                {
+                  container_id: containerId,
+                  length: this.data.length,
+                  maxLen: MAX_OUTPUT
+                },
+                `${name} exceeds max size`
+              )
+              this.data += `(...truncated at ${MAX_OUTPUT} chars...)`
+              return (this.overflowed = true)
+            }
+          }
+          // kill container if too much output
+          // docker.containers.kill(containerId, () ->)
+        }
+      }
+
+      const stdout = createStringOutputStream('stdout')
+      const stderr = createStringOutputStream('stderr')
+
+      container.modem.demuxStream(stream, stdout, stderr)
+
+      stream.on('error', err =>
+        logger.error(
+          { err, container_id: containerId },
+          'error reading from container stream'
+        )
+      )
+
+      return stream.on('end', () =>
+        attachStreamHandler(null, { stdout: stdout.data, stderr: stderr.data })
+      )
+    })
+  },
+
+  waitForContainer(containerId, timeout, _callback) {
+    if (_callback == null) {
+      _callback = function(error, exitCode) {}
+    }
+    const callback = function(...args) {
+      _callback(...Array.from(args || []))
+      // Only call the callback once
+      return (_callback = function() {})
+    }
+
+    const container = dockerode.getContainer(containerId)
+
+    let timedOut = false
+    const timeoutId = setTimeout(function() {
+      timedOut = true
+      logger.log(
+        { container_id: containerId },
+        'timeout reached, killing container'
+      )
+      return container.kill(function() {})
+    }, timeout)
+
+    logger.log({ container_id: containerId }, 'waiting for docker container')
+    return container.wait(function(error, res) {
+      if (error != null) {
+        clearTimeout(timeoutId)
+        logger.error(
+          { err: error, container_id: containerId },
+          'error waiting for container'
+        )
+        return callback(error)
+      }
+      if (timedOut) {
+        logger.log({ containerId }, 'docker container timed out')
+        error = DockerRunner.ERR_TIMED_OUT
+        error.timedout = true
+        return callback(error)
+      } else {
+        clearTimeout(timeoutId)
+        logger.log(
+          { container_id: containerId, exitCode: res.StatusCode },
+          'docker container returned'
+        )
+        return callback(null, res.StatusCode)
+      }
+    })
+  },
+
+  destroyContainer(containerName, containerId, shouldForce, callback) {
+    // We want the containerName for the lock and, ideally, the
+    // containerId to delete.  There is a bug in the docker.io module
+    // where if you delete by name and there is an error, it throws an
+    // async exception, but if you delete by id it just does a normal
+    // error callback. We fall back to deleting by name if no id is
+    // supplied.
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return LockManager.runWithLock(
+      containerName,
+      releaseLock =>
+        DockerRunner._destroyContainer(
+          containerId || containerName,
+          shouldForce,
+          releaseLock
+        ),
+      callback
+    )
+  },
+
+  _destroyContainer(containerId, shouldForce, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    logger.log({ container_id: containerId }, 'destroying docker container')
+    const container = dockerode.getContainer(containerId)
+    return container.remove({ force: shouldForce === true }, function(error) {
+      if (
+        error != null &&
+        (error != null ? error.statusCode : undefined) === 404
+      ) {
+        logger.warn(
+          { err: error, container_id: containerId },
+          'container not found, continuing'
+        )
+        error = null
+      }
+      if (error != null) {
+        logger.error(
+          { err: error, container_id: containerId },
+          'error destroying container'
+        )
+      } else {
+        logger.log({ container_id: containerId }, 'destroyed container')
+      }
+      return callback(error)
+    })
+  },
+
+  // handle expiry of docker containers
+
+  MAX_CONTAINER_AGE:
+    Settings.clsi.docker.maxContainerAge || (oneHour = 60 * 60 * 1000),
+
+  examineOldContainer(container, callback) {
+    if (callback == null) {
+      callback = function(error, name, id, ttl) {}
+    }
+    const name =
+      container.Name ||
+      (container.Names != null ? container.Names[0] : undefined)
+    const created = container.Created * 1000 // creation time is returned in seconds
+    const now = Date.now()
+    const age = now - created
+    const maxAge = DockerRunner.MAX_CONTAINER_AGE
+    const ttl = maxAge - age
+    logger.log(
+      { containerName: name, created, now, age, maxAge, ttl },
+      'checking whether to destroy container'
+    )
+    return callback(null, name, container.Id, ttl)
+  },
+
+  destroyOldContainers(callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return dockerode.listContainers({ all: true }, function(error, containers) {
+      if (error != null) {
+        return callback(error)
+      }
+      const jobs = []
+      for (const container of Array.from(containers || [])) {
+        ;(container =>
+          DockerRunner.examineOldContainer(container, function(
+            err,
+            name,
+            id,
+            ttl
+          ) {
+            if (name.slice(0, 9) === '/project-' && ttl <= 0) {
+              return jobs.push(cb =>
+                DockerRunner.destroyContainer(name, id, false, () => cb())
+              )
+            }
+          }))(container)
+      }
+      // Ignore errors because some containers get stuck but
+      // will be destroyed next time
+      return async.series(jobs, callback)
+    })
+  },
+
+  startContainerMonitor() {
+    logger.log(
+      { maxAge: DockerRunner.MAX_CONTAINER_AGE },
+      'starting container expiry'
+    )
+
+    // guarantee only one monitor is running
+    DockerRunner.stopContainerMonitor()
+
+    // randomise the start time
+    const randomDelay = Math.floor(Math.random() * 5 * 60 * 1000)
+    containerMonitorTimeout = setTimeout(() => {
+      containerMonitorInterval = setInterval(
+        () => DockerRunner.destroyOldContainers(),
+        (oneHour = 60 * 60 * 1000)
+      )
+    }, randomDelay)
+  },
+
+  stopContainerMonitor() {
+    if (containerMonitorTimeout) {
+      clearTimeout(containerMonitorTimeout)
+      containerMonitorTimeout = undefined
+    }
+    if (containerMonitorInterval) {
+      clearInterval(containerMonitorTimeout)
+      containerMonitorTimeout = undefined
+    }
+  }
+}
+
+DockerRunner.startContainerMonitor()
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}
+function __guardMethod__(obj, methodName, transform) {
+  if (
+    typeof obj !== 'undefined' &&
+    obj !== null &&
+    typeof obj[methodName] === 'function'
+  ) {
+    return transform(obj, methodName)
+  } else {
+    return undefined
+  }
+}

services/clsi/app/js/DraftModeManager.js

@@ -0,0 +1,57 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-useless-escape,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let DraftModeManager
+const fs = require('fs')
+const logger = require('logger-sharelatex')
+
+module.exports = DraftModeManager = {
+  injectDraftMode(filename, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return fs.readFile(filename, 'utf8', function(error, content) {
+      if (error != null) {
+        return callback(error)
+      }
+      // avoid adding draft mode more than once
+      if (
+        (content != null
+          ? content.indexOf('\\documentclass[draft')
+          : undefined) >= 0
+      ) {
+        return callback()
+      }
+      const modified_content = DraftModeManager._injectDraftOption(content)
+      logger.log(
+        {
+          content: content.slice(0, 1024), // \documentclass is normally v near the top
+          modified_content: modified_content.slice(0, 1024),
+          filename
+        },
+        'injected draft class'
+      )
+      return fs.writeFile(filename, modified_content, callback)
+    })
+  },
+
+  _injectDraftOption(content) {
+    return (
+      content
+        // With existing options (must be first, otherwise both are applied)
+        .replace(/\\documentclass\[/g, '\\documentclass[draft,')
+        // Without existing options
+        .replace(/\\documentclass\{/g, '\\documentclass[draft]{')
+    )
+  }
+}

services/clsi/app/js/Errors.js

@@ -0,0 +1,36 @@
+/* eslint-disable
+    no-proto,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+let Errors
+var NotFoundError = function(message) {
+  const error = new Error(message)
+  error.name = 'NotFoundError'
+  error.__proto__ = NotFoundError.prototype
+  return error
+}
+NotFoundError.prototype.__proto__ = Error.prototype
+
+var FilesOutOfSyncError = function(message) {
+  const error = new Error(message)
+  error.name = 'FilesOutOfSyncError'
+  error.__proto__ = FilesOutOfSyncError.prototype
+  return error
+}
+FilesOutOfSyncError.prototype.__proto__ = Error.prototype
+
+var AlreadyCompilingError = function(message) {
+  const error = new Error(message)
+  error.name = 'AlreadyCompilingError'
+  error.__proto__ = AlreadyCompilingError.prototype
+  return error
+}
+AlreadyCompilingError.prototype.__proto__ = Error.prototype
+
+module.exports = Errors = {
+  NotFoundError,
+  FilesOutOfSyncError,
+  AlreadyCompilingError
+}

services/clsi/app/js/LatexRunner.js

@@ -0,0 +1,204 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-return-assign,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let LatexRunner
+const Path = require('path')
+const Settings = require('settings-sharelatex')
+const logger = require('logger-sharelatex')
+const Metrics = require('./Metrics')
+const CommandRunner = require('./CommandRunner')
+
+const ProcessTable = {} // table of currently running jobs (pids or docker container names)
+
+module.exports = LatexRunner = {
+  runLatex(project_id, options, callback) {
+    let command
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    let {
+      directory,
+      mainFile,
+      compiler,
+      timeout,
+      image,
+      environment,
+      flags
+    } = options
+    if (!compiler) {
+      compiler = 'pdflatex'
+    }
+    if (!timeout) {
+      timeout = 60000
+    } // milliseconds
+
+    logger.log(
+      { directory, compiler, timeout, mainFile, environment, flags },
+      'starting compile'
+    )
+
+    // We want to run latexmk on the tex file which we will automatically
+    // generate from the Rtex/Rmd/md file.
+    mainFile = mainFile.replace(/\.(Rtex|md|Rmd)$/, '.tex')
+
+    if (compiler === 'pdflatex') {
+      command = LatexRunner._pdflatexCommand(mainFile, flags)
+    } else if (compiler === 'latex') {
+      command = LatexRunner._latexCommand(mainFile, flags)
+    } else if (compiler === 'xelatex') {
+      command = LatexRunner._xelatexCommand(mainFile, flags)
+    } else if (compiler === 'lualatex') {
+      command = LatexRunner._lualatexCommand(mainFile, flags)
+    } else {
+      return callback(new Error(`unknown compiler: ${compiler}`))
+    }
+
+    if (Settings.clsi != null ? Settings.clsi.strace : undefined) {
+      command = ['strace', '-o', 'strace', '-ff'].concat(command)
+    }
+
+    const id = `${project_id}` // record running project under this id
+
+    return (ProcessTable[id] = CommandRunner.run(
+      project_id,
+      command,
+      directory,
+      image,
+      timeout,
+      environment,
+      function(error, output) {
+        delete ProcessTable[id]
+        if (error != null) {
+          return callback(error)
+        }
+        const runs =
+          __guard__(
+            __guard__(output != null ? output.stderr : undefined, x1 =>
+              x1.match(/^Run number \d+ of .*latex/gm)
+            ),
+            x => x.length
+          ) || 0
+        const failed =
+          __guard__(output != null ? output.stdout : undefined, x2 =>
+            x2.match(/^Latexmk: Errors/m)
+          ) != null
+            ? 1
+            : 0
+        // counters from latexmk output
+        const stats = {}
+        stats['latexmk-errors'] = failed
+        stats['latex-runs'] = runs
+        stats['latex-runs-with-errors'] = failed ? runs : 0
+        stats[`latex-runs-${runs}`] = 1
+        stats[`latex-runs-with-errors-${runs}`] = failed ? 1 : 0
+        // timing information from /usr/bin/time
+        const timings = {}
+        const stderr = output != null ? output.stderr : undefined
+        timings['cpu-percent'] =
+          __guard__(
+            stderr != null
+              ? stderr.match(/Percent of CPU this job got: (\d+)/m)
+              : undefined,
+            x3 => x3[1]
+          ) || 0
+        timings['cpu-time'] =
+          __guard__(
+            stderr != null
+              ? stderr.match(/User time.*: (\d+.\d+)/m)
+              : undefined,
+            x4 => x4[1]
+          ) || 0
+        timings['sys-time'] =
+          __guard__(
+            stderr != null
+              ? stderr.match(/System time.*: (\d+.\d+)/m)
+              : undefined,
+            x5 => x5[1]
+          ) || 0
+        return callback(error, output, stats, timings)
+      }
+    ))
+  },
+
+  killLatex(project_id, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const id = `${project_id}`
+    logger.log({ id }, 'killing running compile')
+    if (ProcessTable[id] == null) {
+      logger.warn({ id }, 'no such project to kill')
+      return callback(null)
+    } else {
+      return CommandRunner.kill(ProcessTable[id], callback)
+    }
+  },
+
+  _latexmkBaseCommand(flags) {
+    let args = [
+      'latexmk',
+      '-cd',
+      '-f',
+      '-jobname=output',
+      '-auxdir=$COMPILE_DIR',
+      '-outdir=$COMPILE_DIR',
+      '-synctex=1',
+      '-interaction=batchmode'
+    ]
+    if (flags) {
+      args = args.concat(flags)
+    }
+    return (
+      __guard__(
+        Settings != null ? Settings.clsi : undefined,
+        x => x.latexmkCommandPrefix
+      ) || []
+    ).concat(args)
+  },
+
+  _pdflatexCommand(mainFile, flags) {
+    return LatexRunner._latexmkBaseCommand(flags).concat([
+      '-pdf',
+      Path.join('$COMPILE_DIR', mainFile)
+    ])
+  },
+
+  _latexCommand(mainFile, flags) {
+    return LatexRunner._latexmkBaseCommand(flags).concat([
+      '-pdfdvi',
+      Path.join('$COMPILE_DIR', mainFile)
+    ])
+  },
+
+  _xelatexCommand(mainFile, flags) {
+    return LatexRunner._latexmkBaseCommand(flags).concat([
+      '-xelatex',
+      Path.join('$COMPILE_DIR', mainFile)
+    ])
+  },
+
+  _lualatexCommand(mainFile, flags) {
+    return LatexRunner._latexmkBaseCommand(flags).concat([
+      '-lualatex',
+      Path.join('$COMPILE_DIR', mainFile)
+    ])
+  }
+}
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/app/js/LocalCommandRunner.js

@@ -0,0 +1,91 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-return-assign,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let CommandRunner
+const { spawn } = require('child_process')
+const logger = require('logger-sharelatex')
+
+logger.info('using standard command runner')
+
+module.exports = CommandRunner = {
+  run(project_id, command, directory, image, timeout, environment, callback) {
+    let key, value
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    command = Array.from(command).map(arg =>
+      arg.toString().replace('$COMPILE_DIR', directory)
+    )
+    logger.log({ project_id, command, directory }, 'running command')
+    logger.warn('timeouts and sandboxing are not enabled with CommandRunner')
+
+    // merge environment settings
+    const env = {}
+    for (key in process.env) {
+      value = process.env[key]
+      env[key] = value
+    }
+    for (key in environment) {
+      value = environment[key]
+      env[key] = value
+    }
+
+    // run command as detached process so it has its own process group (which can be killed if needed)
+    const proc = spawn(command[0], command.slice(1), { cwd: directory, env })
+
+    let stdout = ''
+    proc.stdout.on('data', data => (stdout += data))
+
+    proc.on('error', function(err) {
+      logger.err(
+        { err, project_id, command, directory },
+        'error running command'
+      )
+      return callback(err)
+    })
+
+    proc.on('close', function(code, signal) {
+      let err
+      logger.info({ code, signal, project_id }, 'command exited')
+      if (signal === 'SIGTERM') {
+        // signal from kill method below
+        err = new Error('terminated')
+        err.terminated = true
+        return callback(err)
+      } else if (code === 1) {
+        // exit status from chktex
+        err = new Error('exited')
+        err.code = code
+        return callback(err)
+      } else {
+        return callback(null, { stdout: stdout })
+      }
+    })
+
+    return proc.pid
+  }, // return process id to allow job to be killed if necessary
+
+  kill(pid, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    try {
+      process.kill(-pid) // kill all processes in group
+    } catch (err) {
+      return callback(err)
+    }
+    return callback()
+  }
+}

services/clsi/app/js/LockManager.js

@@ -0,0 +1,72 @@
+/* eslint-disable
+    handle-callback-err,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let LockManager
+const Settings = require('settings-sharelatex')
+const logger = require('logger-sharelatex')
+const Lockfile = require('lockfile') // from https://github.com/npm/lockfile
+const Errors = require('./Errors')
+const fs = require('fs')
+const Path = require('path')
+module.exports = LockManager = {
+  LOCK_TEST_INTERVAL: 1000, // 50ms between each test of the lock
+  MAX_LOCK_WAIT_TIME: 15000, // 10s maximum time to spend trying to get the lock
+  LOCK_STALE: 5 * 60 * 1000, // 5 mins time until lock auto expires
+
+  runWithLock(path, runner, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const lockOpts = {
+      wait: this.MAX_LOCK_WAIT_TIME,
+      pollPeriod: this.LOCK_TEST_INTERVAL,
+      stale: this.LOCK_STALE
+    }
+    return Lockfile.lock(path, lockOpts, function(error) {
+      if ((error != null ? error.code : undefined) === 'EEXIST') {
+        return callback(new Errors.AlreadyCompilingError('compile in progress'))
+      } else if (error != null) {
+        return fs.lstat(path, (statLockErr, statLock) =>
+          fs.lstat(Path.dirname(path), (statDirErr, statDir) =>
+            fs.readdir(Path.dirname(path), function(readdirErr, readdirDir) {
+              logger.err(
+                {
+                  error,
+                  path,
+                  statLock,
+                  statLockErr,
+                  statDir,
+                  statDirErr,
+                  readdirErr,
+                  readdirDir
+                },
+                'unable to get lock'
+              )
+              return callback(error)
+            })
+          )
+        )
+      } else {
+        return runner((error1, ...args) =>
+          Lockfile.unlock(path, function(error2) {
+            error = error1 || error2
+            if (error != null) {
+              return callback(error)
+            }
+            return callback(null, ...Array.from(args))
+          })
+        )
+      }
+    })
+  }
+}

services/clsi/app/js/Metrics.js

@@ -0,0 +1,3 @@
+// TODO: This file was created by bulk-decaffeinate.
+// Sanity-check the conversion and remove this comment.
+module.exports = require('metrics-sharelatex')

services/clsi/app/js/OutputCacheManager.js

@@ -0,0 +1,399 @@
+/* eslint-disable
+    handle-callback-err,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS104: Avoid inline assignments
+ * DS204: Change includes calls to have a more natural evaluation order
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let OutputCacheManager
+const async = require('async')
+const fs = require('fs')
+const fse = require('fs-extra')
+const Path = require('path')
+const logger = require('logger-sharelatex')
+const _ = require('underscore')
+const Settings = require('settings-sharelatex')
+const crypto = require('crypto')
+
+const OutputFileOptimiser = require('./OutputFileOptimiser')
+
+module.exports = OutputCacheManager = {
+  CACHE_SUBDIR: '.cache/clsi',
+  ARCHIVE_SUBDIR: '.archive/clsi',
+  // build id is HEXDATE-HEXRANDOM from Date.now()and RandomBytes
+  // for backwards compatibility, make the randombytes part optional
+  BUILD_REGEX: /^[0-9a-f]+(-[0-9a-f]+)?$/,
+  CACHE_LIMIT: 2, // maximum number of cache directories
+  CACHE_AGE: 60 * 60 * 1000, // up to one hour old
+
+  path(buildId, file) {
+    // used by static server, given build id return '.cache/clsi/buildId'
+    if (buildId.match(OutputCacheManager.BUILD_REGEX)) {
+      return Path.join(OutputCacheManager.CACHE_SUBDIR, buildId, file)
+    } else {
+      // for invalid build id, return top level
+      return file
+    }
+  },
+
+  generateBuildId(callback) {
+    // generate a secure build id from Date.now() and 8 random bytes in hex
+    if (callback == null) {
+      callback = function(error, buildId) {}
+    }
+    return crypto.randomBytes(8, function(err, buf) {
+      if (err != null) {
+        return callback(err)
+      }
+      const random = buf.toString('hex')
+      const date = Date.now().toString(16)
+      return callback(err, `${date}-${random}`)
+    })
+  },
+
+  saveOutputFiles(outputFiles, compileDir, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return OutputCacheManager.generateBuildId(function(err, buildId) {
+      if (err != null) {
+        return callback(err)
+      }
+      return OutputCacheManager.saveOutputFilesInBuildDir(
+        outputFiles,
+        compileDir,
+        buildId,
+        callback
+      )
+    })
+  },
+
+  saveOutputFilesInBuildDir(outputFiles, compileDir, buildId, callback) {
+    // make a compileDir/CACHE_SUBDIR/build_id directory and
+    // copy all the output files into it
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const cacheRoot = Path.join(compileDir, OutputCacheManager.CACHE_SUBDIR)
+    // Put the files into a new cache subdirectory
+    const cacheDir = Path.join(
+      compileDir,
+      OutputCacheManager.CACHE_SUBDIR,
+      buildId
+    )
+    // Is it a per-user compile? check if compile directory is PROJECTID-USERID
+    const perUser = Path.basename(compileDir).match(
+      /^[0-9a-f]{24}-[0-9a-f]{24}$/
+    )
+
+    // Archive logs in background
+    if (
+      (Settings.clsi != null ? Settings.clsi.archive_logs : undefined) ||
+      (Settings.clsi != null ? Settings.clsi.strace : undefined)
+    ) {
+      OutputCacheManager.archiveLogs(outputFiles, compileDir, buildId, function(
+        err
+      ) {
+        if (err != null) {
+          return logger.warn({ err }, 'erroring archiving log files')
+        }
+      })
+    }
+
+    // make the new cache directory
+    return fse.ensureDir(cacheDir, function(err) {
+      if (err != null) {
+        logger.error(
+          { err, directory: cacheDir },
+          'error creating cache directory'
+        )
+        return callback(err, outputFiles)
+      } else {
+        // copy all the output files into the new cache directory
+        const results = []
+        return async.mapSeries(
+          outputFiles,
+          function(file, cb) {
+            // don't send dot files as output, express doesn't serve them
+            if (OutputCacheManager._fileIsHidden(file.path)) {
+              logger.debug(
+                { compileDir, path: file.path },
+                'ignoring dotfile in output'
+              )
+              return cb()
+            }
+            // copy other files into cache directory if valid
+            const newFile = _.clone(file)
+            const [src, dst] = Array.from([
+              Path.join(compileDir, file.path),
+              Path.join(cacheDir, file.path)
+            ])
+            return OutputCacheManager._checkFileIsSafe(src, function(
+              err,
+              isSafe
+            ) {
+              if (err != null) {
+                return cb(err)
+              }
+              if (!isSafe) {
+                return cb()
+              }
+              return OutputCacheManager._checkIfShouldCopy(src, function(
+                err,
+                shouldCopy
+              ) {
+                if (err != null) {
+                  return cb(err)
+                }
+                if (!shouldCopy) {
+                  return cb()
+                }
+                return OutputCacheManager._copyFile(src, dst, function(err) {
+                  if (err != null) {
+                    return cb(err)
+                  }
+                  newFile.build = buildId // attach a build id if we cached the file
+                  results.push(newFile)
+                  return cb()
+                })
+              })
+            })
+          },
+          function(err) {
+            if (err != null) {
+              // pass back the original files if we encountered *any* error
+              callback(err, outputFiles)
+              // clean up the directory we just created
+              return fse.remove(cacheDir, function(err) {
+                if (err != null) {
+                  return logger.error(
+                    { err, dir: cacheDir },
+                    'error removing cache dir after failure'
+                  )
+                }
+              })
+            } else {
+              // pass back the list of new files in the cache
+              callback(err, results)
+              // let file expiry run in the background, expire all previous files if per-user
+              return OutputCacheManager.expireOutputFiles(cacheRoot, {
+                keep: buildId,
+                limit: perUser ? 1 : null
+              })
+            }
+          }
+        )
+      }
+    })
+  },
+
+  archiveLogs(outputFiles, compileDir, buildId, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const archiveDir = Path.join(
+      compileDir,
+      OutputCacheManager.ARCHIVE_SUBDIR,
+      buildId
+    )
+    logger.log({ dir: archiveDir }, 'archiving log files for project')
+    return fse.ensureDir(archiveDir, function(err) {
+      if (err != null) {
+        return callback(err)
+      }
+      return async.mapSeries(
+        outputFiles,
+        function(file, cb) {
+          const [src, dst] = Array.from([
+            Path.join(compileDir, file.path),
+            Path.join(archiveDir, file.path)
+          ])
+          return OutputCacheManager._checkFileIsSafe(src, function(
+            err,
+            isSafe
+          ) {
+            if (err != null) {
+              return cb(err)
+            }
+            if (!isSafe) {
+              return cb()
+            }
+            return OutputCacheManager._checkIfShouldArchive(src, function(
+              err,
+              shouldArchive
+            ) {
+              if (err != null) {
+                return cb(err)
+              }
+              if (!shouldArchive) {
+                return cb()
+              }
+              return OutputCacheManager._copyFile(src, dst, cb)
+            })
+          })
+        },
+        callback
+      )
+    })
+  },
+
+  expireOutputFiles(cacheRoot, options, callback) {
+    // look in compileDir for build dirs and delete if > N or age of mod time > T
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return fs.readdir(cacheRoot, function(err, results) {
+      if (err != null) {
+        if (err.code === 'ENOENT') {
+          return callback(null)
+        } // cache directory is empty
+        logger.error({ err, project_id: cacheRoot }, 'error clearing cache')
+        return callback(err)
+      }
+
+      const dirs = results.sort().reverse()
+      const currentTime = Date.now()
+
+      const isExpired = function(dir, index) {
+        if ((options != null ? options.keep : undefined) === dir) {
+          return false
+        }
+        // remove any directories over the requested (non-null) limit
+        if (
+          (options != null ? options.limit : undefined) != null &&
+          index > options.limit
+        ) {
+          return true
+        }
+        // remove any directories over the hard limit
+        if (index > OutputCacheManager.CACHE_LIMIT) {
+          return true
+        }
+        // we can get the build time from the first part of the directory name DDDD-RRRR
+        // DDDD is date and RRRR is random bytes
+        const dirTime = parseInt(
+          __guard__(dir.split('-'), x => x[0]),
+          16
+        )
+        const age = currentTime - dirTime
+        return age > OutputCacheManager.CACHE_AGE
+      }
+
+      const toRemove = _.filter(dirs, isExpired)
+
+      const removeDir = (dir, cb) =>
+        fse.remove(Path.join(cacheRoot, dir), function(err, result) {
+          logger.log({ cache: cacheRoot, dir }, 'removed expired cache dir')
+          if (err != null) {
+            logger.error({ err, dir }, 'cache remove error')
+          }
+          return cb(err, result)
+        })
+      return async.eachSeries(
+        toRemove,
+        (dir, cb) => removeDir(dir, cb),
+        callback
+      )
+    })
+  },
+
+  _fileIsHidden(path) {
+    return (path != null ? path.match(/^\.|\/\./) : undefined) != null
+  },
+
+  _checkFileIsSafe(src, callback) {
+    // check if we have a valid file to copy into the cache
+    if (callback == null) {
+      callback = function(error, isSafe) {}
+    }
+    return fs.stat(src, function(err, stats) {
+      if ((err != null ? err.code : undefined) === 'ENOENT') {
+        logger.warn(
+          { err, file: src },
+          'file has disappeared before copying to build cache'
+        )
+        return callback(err, false)
+      } else if (err != null) {
+        // some other problem reading the file
+        logger.error({ err, file: src }, 'stat error for file in cache')
+        return callback(err, false)
+      } else if (!stats.isFile()) {
+        // other filetype - reject it
+        logger.warn(
+          { src, stat: stats },
+          'nonfile output - refusing to copy to cache'
+        )
+        return callback(null, false)
+      } else {
+        // it's a plain file, ok to copy
+        return callback(null, true)
+      }
+    })
+  },
+
+  _copyFile(src, dst, callback) {
+    // copy output file into the cache
+    return fse.copy(src, dst, function(err) {
+      if ((err != null ? err.code : undefined) === 'ENOENT') {
+        logger.warn(
+          { err, file: src },
+          'file has disappeared when copying to build cache'
+        )
+        return callback(err, false)
+      } else if (err != null) {
+        logger.error({ err, src, dst }, 'copy error for file in cache')
+        return callback(err)
+      } else {
+        if (
+          Settings.clsi != null ? Settings.clsi.optimiseInDocker : undefined
+        ) {
+          // don't run any optimisations on the pdf when they are done
+          // in the docker container
+          return callback()
+        } else {
+          // call the optimiser for the file too
+          return OutputFileOptimiser.optimiseFile(src, dst, callback)
+        }
+      }
+    })
+  },
+
+  _checkIfShouldCopy(src, callback) {
+    if (callback == null) {
+      callback = function(err, shouldCopy) {}
+    }
+    return callback(null, !Path.basename(src).match(/^strace/))
+  },
+
+  _checkIfShouldArchive(src, callback) {
+    let needle
+    if (callback == null) {
+      callback = function(err, shouldCopy) {}
+    }
+    if (Path.basename(src).match(/^strace/)) {
+      return callback(null, true)
+    }
+    if (
+      (Settings.clsi != null ? Settings.clsi.archive_logs : undefined) &&
+      ((needle = Path.basename(src)),
+      ['output.log', 'output.blg'].includes(needle))
+    ) {
+      return callback(null, true)
+    }
+    return callback(null, false)
+  }
+}
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/app/js/OutputFileFinder.js

@@ -0,0 +1,115 @@
+/* eslint-disable
+    handle-callback-err,
+    no-return-assign,
+    no-unused-vars,
+    no-useless-escape,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let OutputFileFinder
+const async = require('async')
+const fs = require('fs')
+const Path = require('path')
+const { spawn } = require('child_process')
+const logger = require('logger-sharelatex')
+
+module.exports = OutputFileFinder = {
+  findOutputFiles(resources, directory, callback) {
+    if (callback == null) {
+      callback = function(error, outputFiles, allFiles) {}
+    }
+    const incomingResources = {}
+    for (const resource of Array.from(resources)) {
+      incomingResources[resource.path] = true
+    }
+
+    return OutputFileFinder._getAllFiles(directory, function(error, allFiles) {
+      if (allFiles == null) {
+        allFiles = []
+      }
+      if (error != null) {
+        logger.err({ err: error }, 'error finding all output files')
+        return callback(error)
+      }
+      const outputFiles = []
+      for (const file of Array.from(allFiles)) {
+        if (!incomingResources[file]) {
+          outputFiles.push({
+            path: file,
+            type: __guard__(file.match(/\.([^\.]+)$/), x => x[1])
+          })
+        }
+      }
+      return callback(null, outputFiles, allFiles)
+    })
+  },
+
+  _getAllFiles(directory, _callback) {
+    if (_callback == null) {
+      _callback = function(error, fileList) {}
+    }
+    const callback = function(error, fileList) {
+      _callback(error, fileList)
+      return (_callback = function() {})
+    }
+
+    // don't include clsi-specific files/directories in the output list
+    const EXCLUDE_DIRS = [
+      '-name',
+      '.cache',
+      '-o',
+      '-name',
+      '.archive',
+      '-o',
+      '-name',
+      '.project-*'
+    ]
+    const args = [
+      directory,
+      '(',
+      ...Array.from(EXCLUDE_DIRS),
+      ')',
+      '-prune',
+      '-o',
+      '-type',
+      'f',
+      '-print'
+    ]
+    logger.log({ args }, 'running find command')
+
+    const proc = spawn('find', args)
+    let stdout = ''
+    proc.stdout.on('data', chunk => (stdout += chunk.toString()))
+    proc.on('error', callback)
+    return proc.on('close', function(code) {
+      if (code !== 0) {
+        logger.warn(
+          { directory, code },
+          "find returned error, directory likely doesn't exist"
+        )
+        return callback(null, [])
+      }
+      let fileList = stdout.trim().split('\n')
+      fileList = fileList.map(function(file) {
+        // Strip leading directory
+        let path
+        return (path = Path.relative(directory, file))
+      })
+      return callback(null, fileList)
+    })
+  }
+}
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/app/js/OutputFileOptimiser.js

@@ -0,0 +1,104 @@
+/* eslint-disable
+    handle-callback-err,
+    no-return-assign,
+    no-undef,
+    no-unused-vars,
+    node/no-deprecated-api,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let OutputFileOptimiser
+const fs = require('fs')
+const Path = require('path')
+const { spawn } = require('child_process')
+const logger = require('logger-sharelatex')
+const Metrics = require('./Metrics')
+const _ = require('underscore')
+
+module.exports = OutputFileOptimiser = {
+  optimiseFile(src, dst, callback) {
+    // check output file (src) and see if we can optimise it, storing
+    // the result in the build directory (dst)
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    if (src.match(/\/output\.pdf$/)) {
+      return OutputFileOptimiser.checkIfPDFIsOptimised(src, function(
+        err,
+        isOptimised
+      ) {
+        if (err != null || isOptimised) {
+          return callback(null)
+        }
+        return OutputFileOptimiser.optimisePDF(src, dst, callback)
+      })
+    } else {
+      return callback(null)
+    }
+  },
+
+  checkIfPDFIsOptimised(file, callback) {
+    const SIZE = 16 * 1024 // check the header of the pdf
+    const result = new Buffer(SIZE)
+    result.fill(0) // prevent leakage of uninitialised buffer
+    return fs.open(file, 'r', function(err, fd) {
+      if (err != null) {
+        return callback(err)
+      }
+      return fs.read(fd, result, 0, SIZE, 0, (errRead, bytesRead, buffer) =>
+        fs.close(fd, function(errClose) {
+          if (errRead != null) {
+            return callback(errRead)
+          }
+          if (typeof errReadClose !== 'undefined' && errReadClose !== null) {
+            return callback(errClose)
+          }
+          const isOptimised =
+            buffer.toString('ascii').indexOf('/Linearized 1') >= 0
+          return callback(null, isOptimised)
+        })
+      )
+    })
+  },
+
+  optimisePDF(src, dst, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const tmpOutput = dst + '.opt'
+    const args = ['--linearize', src, tmpOutput]
+    logger.log({ args }, 'running qpdf command')
+
+    const timer = new Metrics.Timer('qpdf')
+    const proc = spawn('qpdf', args)
+    let stdout = ''
+    proc.stdout.on('data', chunk => (stdout += chunk.toString()))
+    callback = _.once(callback) // avoid double call back for error and close event
+    proc.on('error', function(err) {
+      logger.warn({ err, args }, 'qpdf failed')
+      return callback(null)
+    }) // ignore the error
+    return proc.on('close', function(code) {
+      timer.done()
+      if (code !== 0) {
+        logger.warn({ code, args }, 'qpdf returned error')
+        return callback(null) // ignore the error
+      }
+      return fs.rename(tmpOutput, dst, function(err) {
+        if (err != null) {
+          logger.warn(
+            { tmpOutput, dst },
+            'failed to rename output of qpdf command'
+          )
+        }
+        return callback(null)
+      })
+    })
+  } // ignore the error
+}

services/clsi/app/js/ProjectPersistenceManager.js

@@ -0,0 +1,163 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let ProjectPersistenceManager
+const UrlCache = require('./UrlCache')
+const CompileManager = require('./CompileManager')
+const db = require('./db')
+const dbQueue = require('./DbQueue')
+const async = require('async')
+const logger = require('logger-sharelatex')
+const oneDay = 24 * 60 * 60 * 1000
+const Settings = require('settings-sharelatex')
+
+module.exports = ProjectPersistenceManager = {
+  EXPIRY_TIMEOUT: Settings.project_cache_length_ms || oneDay * 2.5,
+
+  markProjectAsJustAccessed(project_id, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const job = cb =>
+      db.Project.findOrCreate({ where: { project_id } })
+        .spread((project, created) =>
+          project
+            .update({ lastAccessed: new Date() })
+            .then(() => cb())
+            .error(cb)
+        )
+        .error(cb)
+    return dbQueue.queue.push(job, callback)
+  },
+
+  clearExpiredProjects(callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return ProjectPersistenceManager._findExpiredProjectIds(function(
+      error,
+      project_ids
+    ) {
+      if (error != null) {
+        return callback(error)
+      }
+      logger.log({ project_ids }, 'clearing expired projects')
+      const jobs = Array.from(project_ids || []).map(project_id =>
+        (project_id => callback =>
+          ProjectPersistenceManager.clearProjectFromCache(project_id, function(
+            err
+          ) {
+            if (err != null) {
+              logger.error({ err, project_id }, 'error clearing project')
+            }
+            return callback()
+          }))(project_id)
+      )
+      return async.series(jobs, function(error) {
+        if (error != null) {
+          return callback(error)
+        }
+        return CompileManager.clearExpiredProjects(
+          ProjectPersistenceManager.EXPIRY_TIMEOUT,
+          error => callback()
+        )
+      })
+    })
+  }, // ignore any errors from deleting directories
+
+  clearProject(project_id, user_id, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    logger.log({ project_id, user_id }, 'clearing project for user')
+    return CompileManager.clearProject(project_id, user_id, function(error) {
+      if (error != null) {
+        return callback(error)
+      }
+      return ProjectPersistenceManager.clearProjectFromCache(
+        project_id,
+        function(error) {
+          if (error != null) {
+            return callback(error)
+          }
+          return callback()
+        }
+      )
+    })
+  },
+
+  clearProjectFromCache(project_id, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    logger.log({ project_id }, 'clearing project from cache')
+    return UrlCache.clearProject(project_id, function(error) {
+      if (error != null) {
+        logger.err({ error, project_id }, 'error clearing project from cache')
+        return callback(error)
+      }
+      return ProjectPersistenceManager._clearProjectFromDatabase(
+        project_id,
+        function(error) {
+          if (error != null) {
+            logger.err(
+              { error, project_id },
+              'error clearing project from database'
+            )
+          }
+          return callback(error)
+        }
+      )
+    })
+  },
+
+  _clearProjectFromDatabase(project_id, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    logger.log({ project_id }, 'clearing project from database')
+    const job = cb =>
+      db.Project.destroy({ where: { project_id } })
+        .then(() => cb())
+        .error(cb)
+    return dbQueue.queue.push(job, callback)
+  },
+
+  _findExpiredProjectIds(callback) {
+    if (callback == null) {
+      callback = function(error, project_ids) {}
+    }
+    const job = function(cb) {
+      const keepProjectsFrom = new Date(
+        Date.now() - ProjectPersistenceManager.EXPIRY_TIMEOUT
+      )
+      const q = {}
+      q[db.op.lt] = keepProjectsFrom
+      return db.Project.findAll({ where: { lastAccessed: q } })
+        .then(projects =>
+          cb(
+            null,
+            projects.map(project => project.project_id)
+          )
+        )
+        .error(cb)
+    }
+
+    return dbQueue.queue.push(job, callback)
+  }
+}
+
+logger.log(
+  { EXPIRY_TIMEOUT: ProjectPersistenceManager.EXPIRY_TIMEOUT },
+  'project assets kept timeout'
+)

services/clsi/app/js/RequestParser.js

@@ -0,0 +1,217 @@
+/* eslint-disable
+    handle-callback-err,
+    no-control-regex,
+    no-throw-literal,
+    no-unused-vars,
+    no-useless-escape,
+    standard/no-callback-literal,
+    valid-typeof,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS205: Consider reworking code to avoid use of IIFEs
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let RequestParser
+const settings = require('settings-sharelatex')
+
+module.exports = RequestParser = {
+  VALID_COMPILERS: ['pdflatex', 'latex', 'xelatex', 'lualatex'],
+  MAX_TIMEOUT: 600,
+
+  parse(body, callback) {
+    let resource
+    if (callback == null) {
+      callback = function(error, data) {}
+    }
+    const response = {}
+
+    if (body.compile == null) {
+      return callback('top level object should have a compile attribute')
+    }
+
+    const { compile } = body
+    if (!compile.options) {
+      compile.options = {}
+    }
+
+    try {
+      response.compiler = this._parseAttribute(
+        'compiler',
+        compile.options.compiler,
+        {
+          validValues: this.VALID_COMPILERS,
+          default: 'pdflatex',
+          type: 'string'
+        }
+      )
+      response.timeout = this._parseAttribute(
+        'timeout',
+        compile.options.timeout,
+        {
+          default: RequestParser.MAX_TIMEOUT,
+          type: 'number'
+        }
+      )
+      response.imageName = this._parseAttribute(
+        'imageName',
+        compile.options.imageName,
+        { type: 'string' }
+      )
+      response.draft = this._parseAttribute('draft', compile.options.draft, {
+        default: false,
+        type: 'boolean'
+      })
+      response.check = this._parseAttribute('check', compile.options.check, {
+        type: 'string'
+      })
+      response.flags = this._parseAttribute('flags', compile.options.flags, {
+        default: [],
+        type: 'object'
+      })
+
+      // The syncType specifies whether the request contains all
+      // resources (full) or only those resources to be updated
+      // in-place (incremental).
+      response.syncType = this._parseAttribute(
+        'syncType',
+        compile.options.syncType,
+        {
+          validValues: ['full', 'incremental'],
+          type: 'string'
+        }
+      )
+
+      // The syncState is an identifier passed in with the request
+      // which has the property that it changes when any resource is
+      // added, deleted, moved or renamed.
+      //
+      // on syncType full the syncState identifier is passed in and
+      // stored
+      //
+      // on syncType incremental the syncState identifier must match
+      // the stored value
+      response.syncState = this._parseAttribute(
+        'syncState',
+        compile.options.syncState,
+        { type: 'string' }
+      )
+
+      if (response.timeout > RequestParser.MAX_TIMEOUT) {
+        response.timeout = RequestParser.MAX_TIMEOUT
+      }
+      response.timeout = response.timeout * 1000 // milliseconds
+
+      response.resources = (() => {
+        const result = []
+        for (resource of Array.from(compile.resources || [])) {
+          result.push(this._parseResource(resource))
+        }
+        return result
+      })()
+
+      const rootResourcePath = this._parseAttribute(
+        'rootResourcePath',
+        compile.rootResourcePath,
+        {
+          default: 'main.tex',
+          type: 'string'
+        }
+      )
+      const originalRootResourcePath = rootResourcePath
+      const sanitizedRootResourcePath = RequestParser._sanitizePath(
+        rootResourcePath
+      )
+      response.rootResourcePath = RequestParser._checkPath(
+        sanitizedRootResourcePath
+      )
+
+      for (resource of Array.from(response.resources)) {
+        if (resource.path === originalRootResourcePath) {
+          resource.path = sanitizedRootResourcePath
+        }
+      }
+    } catch (error1) {
+      const error = error1
+      return callback(error)
+    }
+
+    return callback(null, response)
+  },
+
+  _parseResource(resource) {
+    let modified
+    if (resource.path == null || typeof resource.path !== 'string') {
+      throw 'all resources should have a path attribute'
+    }
+
+    if (resource.modified != null) {
+      modified = new Date(resource.modified)
+      if (isNaN(modified.getTime())) {
+        throw `resource modified date could not be understood: ${resource.modified}`
+      }
+    }
+
+    if (resource.url == null && resource.content == null) {
+      throw 'all resources should have either a url or content attribute'
+    }
+    if (resource.content != null && typeof resource.content !== 'string') {
+      throw 'content attribute should be a string'
+    }
+    if (resource.url != null && typeof resource.url !== 'string') {
+      throw 'url attribute should be a string'
+    }
+
+    return {
+      path: resource.path,
+      modified,
+      url: resource.url,
+      content: resource.content
+    }
+  },
+
+  _parseAttribute(name, attribute, options) {
+    if (attribute != null) {
+      if (options.validValues != null) {
+        if (options.validValues.indexOf(attribute) === -1) {
+          throw `${name} attribute should be one of: ${options.validValues.join(
+            ', '
+          )}`
+        }
+      }
+      if (options.type != null) {
+        if (typeof attribute !== options.type) {
+          throw `${name} attribute should be a ${options.type}`
+        }
+      }
+    } else {
+      if (options.default != null) {
+        return options.default
+      }
+    }
+    return attribute
+  },
+
+  _sanitizePath(path) {
+    // See http://php.net/manual/en/function.escapeshellcmd.php
+    return path.replace(
+      /[\#\&\;\`\|\*\?\~\<\>\^\(\)\[\]\{\}\$\\\x0A\xFF\x00]/g,
+      ''
+    )
+  },
+
+  _checkPath(path) {
+    // check that the request does not use a relative path
+    for (const dir of Array.from(path.split('/'))) {
+      if (dir === '..') {
+        throw 'relative path in root resource'
+      }
+    }
+    return path
+  }
+}

services/clsi/app/js/ResourceStateManager.js

@@ -0,0 +1,154 @@
+/* eslint-disable
+    handle-callback-err,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS201: Simplify complex destructure assignments
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let ResourceStateManager
+const Path = require('path')
+const fs = require('fs')
+const logger = require('logger-sharelatex')
+const settings = require('settings-sharelatex')
+const Errors = require('./Errors')
+const SafeReader = require('./SafeReader')
+
+module.exports = ResourceStateManager = {
+  // The sync state is an identifier which must match for an
+  // incremental update to be allowed.
+  //
+  // The initial value is passed in and stored on a full
+  // compile, along with the list of resources..
+  //
+  // Subsequent incremental compiles must come with the same value - if
+  // not they will be rejected with a 409 Conflict response. The
+  // previous list of resources is returned.
+  //
+  // An incremental compile can only update existing files with new
+  // content.  The sync state identifier must change if any docs or
+  // files are moved, added, deleted or renamed.
+
+  SYNC_STATE_FILE: '.project-sync-state',
+  SYNC_STATE_MAX_SIZE: 128 * 1024,
+
+  saveProjectState(state, resources, basePath, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const stateFile = Path.join(basePath, this.SYNC_STATE_FILE)
+    if (state == null) {
+      // remove the file if no state passed in
+      logger.log({ state, basePath }, 'clearing sync state')
+      return fs.unlink(stateFile, function(err) {
+        if (err != null && err.code !== 'ENOENT') {
+          return callback(err)
+        } else {
+          return callback()
+        }
+      })
+    } else {
+      logger.log({ state, basePath }, 'writing sync state')
+      const resourceList = Array.from(resources).map(resource => resource.path)
+      return fs.writeFile(
+        stateFile,
+        [...Array.from(resourceList), `stateHash:${state}`].join('\n'),
+        callback
+      )
+    }
+  },
+
+  checkProjectStateMatches(state, basePath, callback) {
+    if (callback == null) {
+      callback = function(error, resources) {}
+    }
+    const stateFile = Path.join(basePath, this.SYNC_STATE_FILE)
+    const size = this.SYNC_STATE_MAX_SIZE
+    return SafeReader.readFile(stateFile, size, 'utf8', function(
+      err,
+      result,
+      bytesRead
+    ) {
+      if (err != null) {
+        return callback(err)
+      }
+      if (bytesRead === size) {
+        logger.error(
+          { file: stateFile, size, bytesRead },
+          'project state file truncated'
+        )
+      }
+      const array =
+        __guard__(result != null ? result.toString() : undefined, x =>
+          x.split('\n')
+        ) || []
+      const adjustedLength = Math.max(array.length, 1)
+      const resourceList = array.slice(0, adjustedLength - 1)
+      const oldState = array[adjustedLength - 1]
+      const newState = `stateHash:${state}`
+      logger.log(
+        { state, oldState, basePath, stateMatches: newState === oldState },
+        'checking sync state'
+      )
+      if (newState !== oldState) {
+        return callback(
+          new Errors.FilesOutOfSyncError('invalid state for incremental update')
+        )
+      } else {
+        const resources = Array.from(resourceList).map(path => ({ path }))
+        return callback(null, resources)
+      }
+    })
+  },
+
+  checkResourceFiles(resources, allFiles, basePath, callback) {
+    // check the paths are all relative to current directory
+    let file
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    for (file of Array.from(resources || [])) {
+      for (const dir of Array.from(
+        __guard__(file != null ? file.path : undefined, x => x.split('/'))
+      )) {
+        if (dir === '..') {
+          return callback(new Error('relative path in resource file list'))
+        }
+      }
+    }
+    // check if any of the input files are not present in list of files
+    const seenFile = {}
+    for (file of Array.from(allFiles)) {
+      seenFile[file] = true
+    }
+    const missingFiles = Array.from(resources)
+      .filter(resource => !seenFile[resource.path])
+      .map(resource => resource.path)
+    if ((missingFiles != null ? missingFiles.length : undefined) > 0) {
+      logger.err(
+        { missingFiles, basePath, allFiles, resources },
+        'missing input files for project'
+      )
+      return callback(
+        new Errors.FilesOutOfSyncError(
+          'resource files missing in incremental update'
+        )
+      )
+    } else {
+      return callback()
+    }
+  }
+}
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/app/js/ResourceWriter.js

@@ -0,0 +1,352 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-return-assign,
+    no-unused-vars,
+    no-useless-escape,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let ResourceWriter
+const UrlCache = require('./UrlCache')
+const Path = require('path')
+const fs = require('fs')
+const async = require('async')
+const OutputFileFinder = require('./OutputFileFinder')
+const ResourceStateManager = require('./ResourceStateManager')
+const Metrics = require('./Metrics')
+const logger = require('logger-sharelatex')
+const settings = require('settings-sharelatex')
+
+const parallelFileDownloads = settings.parallelFileDownloads || 1
+
+module.exports = ResourceWriter = {
+  syncResourcesToDisk(request, basePath, callback) {
+    if (callback == null) {
+      callback = function(error, resourceList) {}
+    }
+    if (request.syncType === 'incremental') {
+      logger.log(
+        { project_id: request.project_id, user_id: request.user_id },
+        'incremental sync'
+      )
+      return ResourceStateManager.checkProjectStateMatches(
+        request.syncState,
+        basePath,
+        function(error, resourceList) {
+          if (error != null) {
+            return callback(error)
+          }
+          return ResourceWriter._removeExtraneousFiles(
+            resourceList,
+            basePath,
+            function(error, outputFiles, allFiles) {
+              if (error != null) {
+                return callback(error)
+              }
+              return ResourceStateManager.checkResourceFiles(
+                resourceList,
+                allFiles,
+                basePath,
+                function(error) {
+                  if (error != null) {
+                    return callback(error)
+                  }
+                  return ResourceWriter.saveIncrementalResourcesToDisk(
+                    request.project_id,
+                    request.resources,
+                    basePath,
+                    function(error) {
+                      if (error != null) {
+                        return callback(error)
+                      }
+                      return callback(null, resourceList)
+                    }
+                  )
+                }
+              )
+            }
+          )
+        }
+      )
+    } else {
+      logger.log(
+        { project_id: request.project_id, user_id: request.user_id },
+        'full sync'
+      )
+      return this.saveAllResourcesToDisk(
+        request.project_id,
+        request.resources,
+        basePath,
+        function(error) {
+          if (error != null) {
+            return callback(error)
+          }
+          return ResourceStateManager.saveProjectState(
+            request.syncState,
+            request.resources,
+            basePath,
+            function(error) {
+              if (error != null) {
+                return callback(error)
+              }
+              return callback(null, request.resources)
+            }
+          )
+        }
+      )
+    }
+  },
+
+  saveIncrementalResourcesToDisk(project_id, resources, basePath, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return this._createDirectory(basePath, error => {
+      if (error != null) {
+        return callback(error)
+      }
+      const jobs = Array.from(resources).map(resource =>
+        (resource => {
+          return callback =>
+            this._writeResourceToDisk(project_id, resource, basePath, callback)
+        })(resource)
+      )
+      return async.parallelLimit(jobs, parallelFileDownloads, callback)
+    })
+  },
+
+  saveAllResourcesToDisk(project_id, resources, basePath, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return this._createDirectory(basePath, error => {
+      if (error != null) {
+        return callback(error)
+      }
+      return this._removeExtraneousFiles(resources, basePath, error => {
+        if (error != null) {
+          return callback(error)
+        }
+        const jobs = Array.from(resources).map(resource =>
+          (resource => {
+            return callback =>
+              this._writeResourceToDisk(
+                project_id,
+                resource,
+                basePath,
+                callback
+              )
+          })(resource)
+        )
+        return async.parallelLimit(jobs, parallelFileDownloads, callback)
+      })
+    })
+  },
+
+  _createDirectory(basePath, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return fs.mkdir(basePath, function(err) {
+      if (err != null) {
+        if (err.code === 'EEXIST') {
+          return callback()
+        } else {
+          logger.log({ err, dir: basePath }, 'error creating directory')
+          return callback(err)
+        }
+      } else {
+        return callback()
+      }
+    })
+  },
+
+  _removeExtraneousFiles(resources, basePath, _callback) {
+    if (_callback == null) {
+      _callback = function(error, outputFiles, allFiles) {}
+    }
+    const timer = new Metrics.Timer('unlink-output-files')
+    const callback = function(error, ...result) {
+      timer.done()
+      return _callback(error, ...Array.from(result))
+    }
+
+    return OutputFileFinder.findOutputFiles(resources, basePath, function(
+      error,
+      outputFiles,
+      allFiles
+    ) {
+      if (error != null) {
+        return callback(error)
+      }
+
+      const jobs = []
+      for (const file of Array.from(outputFiles || [])) {
+        ;(function(file) {
+          const { path } = file
+          let should_delete = true
+          if (
+            path.match(/^output\./) ||
+            path.match(/\.aux$/) ||
+            path.match(/^cache\//)
+          ) {
+            // knitr cache
+            should_delete = false
+          }
+          if (path.match(/^output-.*/)) {
+            // Tikz cached figures (default case)
+            should_delete = false
+          }
+          if (path.match(/\.(pdf|dpth|md5)$/)) {
+            // Tikz cached figures (by extension)
+            should_delete = false
+          }
+          if (
+            path.match(/\.(pygtex|pygstyle)$/) ||
+            path.match(/(^|\/)_minted-[^\/]+\//)
+          ) {
+            // minted files/directory
+            should_delete = false
+          }
+          if (
+            path.match(/\.md\.tex$/) ||
+            path.match(/(^|\/)_markdown_[^\/]+\//)
+          ) {
+            // markdown files/directory
+            should_delete = false
+          }
+          if (path.match(/-eps-converted-to\.pdf$/)) {
+            // Epstopdf generated files
+            should_delete = false
+          }
+          if (
+            path === 'output.pdf' ||
+            path === 'output.dvi' ||
+            path === 'output.log' ||
+            path === 'output.xdv'
+          ) {
+            should_delete = true
+          }
+          if (path === 'output.tex') {
+            // created by TikzManager if present in output files
+            should_delete = true
+          }
+          if (should_delete) {
+            return jobs.push(callback =>
+              ResourceWriter._deleteFileIfNotDirectory(
+                Path.join(basePath, path),
+                callback
+              )
+            )
+          }
+        })(file)
+      }
+
+      return async.series(jobs, function(error) {
+        if (error != null) {
+          return callback(error)
+        }
+        return callback(null, outputFiles, allFiles)
+      })
+    })
+  },
+
+  _deleteFileIfNotDirectory(path, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return fs.stat(path, function(error, stat) {
+      if (error != null && error.code === 'ENOENT') {
+        return callback()
+      } else if (error != null) {
+        logger.err(
+          { err: error, path },
+          'error stating file in deleteFileIfNotDirectory'
+        )
+        return callback(error)
+      } else if (stat.isFile()) {
+        return fs.unlink(path, function(error) {
+          if (error != null) {
+            logger.err(
+              { err: error, path },
+              'error removing file in deleteFileIfNotDirectory'
+            )
+            return callback(error)
+          } else {
+            return callback()
+          }
+        })
+      } else {
+        return callback()
+      }
+    })
+  },
+
+  _writeResourceToDisk(project_id, resource, basePath, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return ResourceWriter.checkPath(basePath, resource.path, function(
+      error,
+      path
+    ) {
+      if (error != null) {
+        return callback(error)
+      }
+      return fs.mkdir(Path.dirname(path), { recursive: true }, function(error) {
+        if (error != null) {
+          return callback(error)
+        }
+        // TODO: Don't overwrite file if it hasn't been modified
+        if (resource.url != null) {
+          return UrlCache.downloadUrlToFile(
+            project_id,
+            resource.url,
+            path,
+            resource.modified,
+            function(err) {
+              if (err != null) {
+                logger.err(
+                  {
+                    err,
+                    project_id,
+                    path,
+                    resource_url: resource.url,
+                    modified: resource.modified
+                  },
+                  'error downloading file for resources'
+                )
+                Metrics.inc('download-failed')
+              }
+              return callback()
+            }
+          ) // try and continue compiling even if http resource can not be downloaded at this time
+        } else {
+          const process = require('process')
+          fs.writeFile(path, resource.content, callback)
+          try {
+            let result
+            return (result = fs.lstatSync(path))
+          } catch (e) {}
+        }
+      })
+    })
+  },
+
+  checkPath(basePath, resourcePath, callback) {
+    const path = Path.normalize(Path.join(basePath, resourcePath))
+    if (path.slice(0, basePath.length + 1) !== basePath + '/') {
+      return callback(new Error('resource path is outside root directory'))
+    } else {
+      return callback(null, path)
+    }
+  }
+}

services/clsi/app/js/SafeReader.js

@@ -0,0 +1,60 @@
+/* eslint-disable
+    handle-callback-err,
+    no-unused-vars,
+    node/no-deprecated-api,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let SafeReader
+const fs = require('fs')
+const logger = require('logger-sharelatex')
+
+module.exports = SafeReader = {
+  // safely read up to size bytes from a file and return result as a
+  // string
+
+  readFile(file, size, encoding, callback) {
+    if (callback == null) {
+      callback = function(error, result) {}
+    }
+    return fs.open(file, 'r', function(err, fd) {
+      if (err != null && err.code === 'ENOENT') {
+        return callback()
+      }
+      if (err != null) {
+        return callback(err)
+      }
+
+      // safely return always closing the file
+      const callbackWithClose = (err, ...result) =>
+        fs.close(fd, function(err1) {
+          if (err != null) {
+            return callback(err)
+          }
+          if (err1 != null) {
+            return callback(err1)
+          }
+          return callback(null, ...Array.from(result))
+        })
+      const buff = new Buffer(size, 0) // fill with zeros
+      return fs.read(fd, buff, 0, buff.length, 0, function(
+        err,
+        bytesRead,
+        buffer
+      ) {
+        if (err != null) {
+          return callbackWithClose(err)
+        }
+        const result = buffer.toString(encoding, 0, bytesRead)
+        return callbackWithClose(null, result, bytesRead)
+      })
+    })
+  }
+}

services/clsi/app/js/StaticServerForbidSymlinks.js

@@ -0,0 +1,94 @@
+/* eslint-disable
+    camelcase,
+    no-cond-assign,
+    no-unused-vars,
+    node/no-deprecated-api,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let ForbidSymlinks
+const Path = require('path')
+const fs = require('fs')
+const Settings = require('settings-sharelatex')
+const logger = require('logger-sharelatex')
+const url = require('url')
+
+module.exports = ForbidSymlinks = function(staticFn, root, options) {
+  const expressStatic = staticFn(root, options)
+  const basePath = Path.resolve(root)
+  return function(req, res, next) {
+    let file, project_id, result
+    const path = __guard__(url.parse(req.url), x => x.pathname)
+    // check that the path is of the form /project_id_or_name/path/to/file.log
+    if ((result = path.match(/^\/?([a-zA-Z0-9_-]+)\/(.*)/))) {
+      project_id = result[1]
+      file = result[2]
+    } else {
+      logger.warn({ path }, 'unrecognized file request')
+      return res.sendStatus(404)
+    }
+    // check that the file does not use a relative path
+    for (const dir of Array.from(file.split('/'))) {
+      if (dir === '..') {
+        logger.warn({ path }, 'attempt to use a relative path')
+        return res.sendStatus(404)
+      }
+    }
+    // check that the requested path is normalized
+    const requestedFsPath = `${basePath}/${project_id}/${file}`
+    if (requestedFsPath !== Path.normalize(requestedFsPath)) {
+      logger.error(
+        { path: requestedFsPath },
+        'requestedFsPath is not normalized'
+      )
+      return res.sendStatus(404)
+    }
+    // check that the requested path is not a symlink
+    return fs.realpath(requestedFsPath, function(err, realFsPath) {
+      if (err != null) {
+        if (err.code === 'ENOENT') {
+          return res.sendStatus(404)
+        } else {
+          logger.error(
+            {
+              err,
+              requestedFsPath,
+              realFsPath,
+              path: req.params[0],
+              project_id: req.params.project_id
+            },
+            'error checking file access'
+          )
+          return res.sendStatus(500)
+        }
+      } else if (requestedFsPath !== realFsPath) {
+        logger.warn(
+          {
+            requestedFsPath,
+            realFsPath,
+            path: req.params[0],
+            project_id: req.params.project_id
+          },
+          'trying to access a different file (symlink), aborting'
+        )
+        return res.sendStatus(404)
+      } else {
+        return expressStatic(req, res, next)
+      }
+    })
+  }
+}
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/app/js/TikzManager.js

@@ -0,0 +1,94 @@
+/* eslint-disable
+    handle-callback-err,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let TikzManager
+const fs = require('fs')
+const Path = require('path')
+const ResourceWriter = require('./ResourceWriter')
+const SafeReader = require('./SafeReader')
+const logger = require('logger-sharelatex')
+
+// for \tikzexternalize or pstool to work the main file needs to match the
+// jobname.  Since we set the -jobname to output, we have to create a
+// copy of the main file as 'output.tex'.
+
+module.exports = TikzManager = {
+  checkMainFile(compileDir, mainFile, resources, callback) {
+    // if there's already an output.tex file, we don't want to touch it
+    if (callback == null) {
+      callback = function(error, needsMainFile) {}
+    }
+    for (const resource of Array.from(resources)) {
+      if (resource.path === 'output.tex') {
+        logger.log({ compileDir, mainFile }, 'output.tex already in resources')
+        return callback(null, false)
+      }
+    }
+    // if there's no output.tex, see if we are using tikz/pgf or pstool in the main file
+    return ResourceWriter.checkPath(compileDir, mainFile, function(
+      error,
+      path
+    ) {
+      if (error != null) {
+        return callback(error)
+      }
+      return SafeReader.readFile(path, 65536, 'utf8', function(error, content) {
+        if (error != null) {
+          return callback(error)
+        }
+        const usesTikzExternalize =
+          (content != null
+            ? content.indexOf('\\tikzexternalize')
+            : undefined) >= 0
+        const usesPsTool =
+          (content != null ? content.indexOf('{pstool}') : undefined) >= 0
+        logger.log(
+          { compileDir, mainFile, usesTikzExternalize, usesPsTool },
+          'checked for packages needing main file as output.tex'
+        )
+        const needsMainFile = usesTikzExternalize || usesPsTool
+        return callback(null, needsMainFile)
+      })
+    })
+  },
+
+  injectOutputFile(compileDir, mainFile, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return ResourceWriter.checkPath(compileDir, mainFile, function(
+      error,
+      path
+    ) {
+      if (error != null) {
+        return callback(error)
+      }
+      return fs.readFile(path, 'utf8', function(error, content) {
+        if (error != null) {
+          return callback(error)
+        }
+        logger.log(
+          { compileDir, mainFile },
+          'copied file to output.tex as project uses packages which require it'
+        )
+        // use wx flag to ensure that output file does not already exist
+        return fs.writeFile(
+          Path.join(compileDir, 'output.tex'),
+          content,
+          { flag: 'wx' },
+          callback
+        )
+      })
+    })
+  }
+}

services/clsi/app/js/UrlCache.js

@@ -0,0 +1,278 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-return-assign,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let UrlCache
+const db = require('./db')
+const dbQueue = require('./DbQueue')
+const UrlFetcher = require('./UrlFetcher')
+const Settings = require('settings-sharelatex')
+const crypto = require('crypto')
+const fs = require('fs')
+const logger = require('logger-sharelatex')
+const async = require('async')
+
+module.exports = UrlCache = {
+  downloadUrlToFile(project_id, url, destPath, lastModified, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return UrlCache._ensureUrlIsInCache(
+      project_id,
+      url,
+      lastModified,
+      (error, pathToCachedUrl) => {
+        if (error != null) {
+          return callback(error)
+        }
+        return UrlCache._copyFile(pathToCachedUrl, destPath, function(error) {
+          if (error != null) {
+            return UrlCache._clearUrlDetails(project_id, url, () =>
+              callback(error)
+            )
+          } else {
+            return callback(error)
+          }
+        })
+      }
+    )
+  },
+
+  clearProject(project_id, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return UrlCache._findAllUrlsInProject(project_id, function(error, urls) {
+      logger.log(
+        { project_id, url_count: urls.length },
+        'clearing project URLs'
+      )
+      if (error != null) {
+        return callback(error)
+      }
+      const jobs = Array.from(urls || []).map(url =>
+        (url => callback =>
+          UrlCache._clearUrlFromCache(project_id, url, function(error) {
+            if (error != null) {
+              logger.error(
+                { err: error, project_id, url },
+                'error clearing project URL'
+              )
+            }
+            return callback()
+          }))(url)
+      )
+      return async.series(jobs, callback)
+    })
+  },
+
+  _ensureUrlIsInCache(project_id, url, lastModified, callback) {
+    if (callback == null) {
+      callback = function(error, pathOnDisk) {}
+    }
+    if (lastModified != null) {
+      // MYSQL only stores dates to an accuracy of a second but the incoming lastModified might have milliseconds.
+      // So round down to seconds
+      lastModified = new Date(Math.floor(lastModified.getTime() / 1000) * 1000)
+    }
+    return UrlCache._doesUrlNeedDownloading(
+      project_id,
+      url,
+      lastModified,
+      (error, needsDownloading) => {
+        if (error != null) {
+          return callback(error)
+        }
+        if (needsDownloading) {
+          logger.log({ url, lastModified }, 'downloading URL')
+          return UrlFetcher.pipeUrlToFile(
+            url,
+            UrlCache._cacheFilePathForUrl(project_id, url),
+            error => {
+              if (error != null) {
+                return callback(error)
+              }
+              return UrlCache._updateOrCreateUrlDetails(
+                project_id,
+                url,
+                lastModified,
+                error => {
+                  if (error != null) {
+                    return callback(error)
+                  }
+                  return callback(
+                    null,
+                    UrlCache._cacheFilePathForUrl(project_id, url)
+                  )
+                }
+              )
+            }
+          )
+        } else {
+          logger.log({ url, lastModified }, 'URL is up to date in cache')
+          return callback(null, UrlCache._cacheFilePathForUrl(project_id, url))
+        }
+      }
+    )
+  },
+
+  _doesUrlNeedDownloading(project_id, url, lastModified, callback) {
+    if (callback == null) {
+      callback = function(error, needsDownloading) {}
+    }
+    if (lastModified == null) {
+      return callback(null, true)
+    }
+    return UrlCache._findUrlDetails(project_id, url, function(
+      error,
+      urlDetails
+    ) {
+      if (error != null) {
+        return callback(error)
+      }
+      if (
+        urlDetails == null ||
+        urlDetails.lastModified == null ||
+        urlDetails.lastModified.getTime() < lastModified.getTime()
+      ) {
+        return callback(null, true)
+      } else {
+        return callback(null, false)
+      }
+    })
+  },
+
+  _cacheFileNameForUrl(project_id, url) {
+    return (
+      project_id +
+      ':' +
+      crypto
+        .createHash('md5')
+        .update(url)
+        .digest('hex')
+    )
+  },
+
+  _cacheFilePathForUrl(project_id, url) {
+    return `${Settings.path.clsiCacheDir}/${UrlCache._cacheFileNameForUrl(
+      project_id,
+      url
+    )}`
+  },
+
+  _copyFile(from, to, _callback) {
+    if (_callback == null) {
+      _callback = function(error) {}
+    }
+    const callbackOnce = function(error) {
+      if (error != null) {
+        logger.error({ err: error, from, to }, 'error copying file from cache')
+      }
+      _callback(error)
+      return (_callback = function() {})
+    }
+    const writeStream = fs.createWriteStream(to)
+    const readStream = fs.createReadStream(from)
+    writeStream.on('error', callbackOnce)
+    readStream.on('error', callbackOnce)
+    writeStream.on('close', callbackOnce)
+    return writeStream.on('open', () => readStream.pipe(writeStream))
+  },
+
+  _clearUrlFromCache(project_id, url, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return UrlCache._clearUrlDetails(project_id, url, function(error) {
+      if (error != null) {
+        return callback(error)
+      }
+      return UrlCache._deleteUrlCacheFromDisk(project_id, url, function(error) {
+        if (error != null) {
+          return callback(error)
+        }
+        return callback(null)
+      })
+    })
+  },
+
+  _deleteUrlCacheFromDisk(project_id, url, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    return fs.unlink(UrlCache._cacheFilePathForUrl(project_id, url), function(
+      error
+    ) {
+      if (error != null && error.code !== 'ENOENT') {
+        // no error if the file isn't present
+        return callback(error)
+      } else {
+        return callback()
+      }
+    })
+  },
+
+  _findUrlDetails(project_id, url, callback) {
+    if (callback == null) {
+      callback = function(error, urlDetails) {}
+    }
+    const job = cb =>
+      db.UrlCache.findOne({ where: { url, project_id } })
+        .then(urlDetails => cb(null, urlDetails))
+        .error(cb)
+    return dbQueue.queue.push(job, callback)
+  },
+
+  _updateOrCreateUrlDetails(project_id, url, lastModified, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const job = cb =>
+      db.UrlCache.findOrCreate({ where: { url, project_id } })
+        .spread((urlDetails, created) =>
+          urlDetails
+            .update({ lastModified })
+            .then(() => cb())
+            .error(cb)
+        )
+        .error(cb)
+    return dbQueue.queue.push(job, callback)
+  },
+
+  _clearUrlDetails(project_id, url, callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    const job = cb =>
+      db.UrlCache.destroy({ where: { url, project_id } })
+        .then(() => cb(null))
+        .error(cb)
+    return dbQueue.queue.push(job, callback)
+  },
+
+  _findAllUrlsInProject(project_id, callback) {
+    if (callback == null) {
+      callback = function(error, urls) {}
+    }
+    const job = cb =>
+      db.UrlCache.findAll({ where: { project_id } })
+        .then(urlEntries =>
+          cb(
+            null,
+            urlEntries.map(entry => entry.url)
+          )
+        )
+        .error(cb)
+    return dbQueue.queue.push(job, callback)
+  }
+}

services/clsi/app/js/UrlFetcher.js

@@ -0,0 +1,120 @@
+/* eslint-disable
+    handle-callback-err,
+    no-return-assign,
+    no-unused-vars,
+    node/no-deprecated-api,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let UrlFetcher
+const request = require('request').defaults({ jar: false })
+const fs = require('fs')
+const logger = require('logger-sharelatex')
+const settings = require('settings-sharelatex')
+const URL = require('url')
+
+const oneMinute = 60 * 1000
+
+module.exports = UrlFetcher = {
+  pipeUrlToFile(url, filePath, _callback) {
+    if (_callback == null) {
+      _callback = function(error) {}
+    }
+    const callbackOnce = function(error) {
+      if (timeoutHandler != null) {
+        clearTimeout(timeoutHandler)
+      }
+      _callback(error)
+      return (_callback = function() {})
+    }
+
+    if (settings.filestoreDomainOveride != null) {
+      const p = URL.parse(url).path
+      url = `${settings.filestoreDomainOveride}${p}`
+    }
+    var timeoutHandler = setTimeout(
+      function() {
+        timeoutHandler = null
+        logger.error({ url, filePath }, 'Timed out downloading file to cache')
+        return callbackOnce(
+          new Error(`Timed out downloading file to cache ${url}`)
+        )
+      },
+      // FIXME: maybe need to close fileStream here
+      3 * oneMinute
+    )
+
+    logger.log({ url, filePath }, 'started downloading url to cache')
+    const urlStream = request.get({ url, timeout: oneMinute })
+    urlStream.pause() // stop data flowing until we are ready
+
+    // attach handlers before setting up pipes
+    urlStream.on('error', function(error) {
+      logger.error({ err: error, url, filePath }, 'error downloading url')
+      return callbackOnce(
+        error || new Error(`Something went wrong downloading the URL ${url}`)
+      )
+    })
+
+    urlStream.on('end', () =>
+      logger.log({ url, filePath }, 'finished downloading file into cache')
+    )
+
+    return urlStream.on('response', function(res) {
+      if (res.statusCode >= 200 && res.statusCode < 300) {
+        const fileStream = fs.createWriteStream(filePath)
+
+        // attach handlers before setting up pipes
+        fileStream.on('error', function(error) {
+          logger.error(
+            { err: error, url, filePath },
+            'error writing file into cache'
+          )
+          return fs.unlink(filePath, function(err) {
+            if (err != null) {
+              logger.err({ err, filePath }, 'error deleting file from cache')
+            }
+            return callbackOnce(error)
+          })
+        })
+
+        fileStream.on('finish', function() {
+          logger.log({ url, filePath }, 'finished writing file into cache')
+          return callbackOnce()
+        })
+
+        fileStream.on('pipe', () =>
+          logger.log({ url, filePath }, 'piping into filestream')
+        )
+
+        urlStream.pipe(fileStream)
+        return urlStream.resume() // now we are ready to handle the data
+      } else {
+        logger.error(
+          { statusCode: res.statusCode, url, filePath },
+          'unexpected status code downloading url to cache'
+        )
+        // https://nodejs.org/api/http.html#http_class_http_clientrequest
+        // If you add a 'response' event handler, then you must consume
+        // the data from the response object, either by calling
+        // response.read() whenever there is a 'readable' event, or by
+        // adding a 'data' handler, or by calling the .resume()
+        // method. Until the data is consumed, the 'end' event will not
+        // fire. Also, until the data is read it will consume memory
+        // that can eventually lead to a 'process out of memory' error.
+        urlStream.resume() // discard the data
+        return callbackOnce(
+          new Error(
+            `URL returned non-success status code: ${res.statusCode} ${url}`
+          )
+        )
+      }
+    })
+  }
+}

services/clsi/app/js/db.js

@@ -0,0 +1,67 @@
+/* eslint-disable
+    no-console,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Sequelize = require('sequelize')
+const Settings = require('settings-sharelatex')
+const _ = require('underscore')
+const logger = require('logger-sharelatex')
+
+const options = _.extend({ logging: false }, Settings.mysql.clsi)
+
+logger.log({ dbPath: Settings.mysql.clsi.storage }, 'connecting to db')
+
+const sequelize = new Sequelize(
+  Settings.mysql.clsi.database,
+  Settings.mysql.clsi.username,
+  Settings.mysql.clsi.password,
+  options
+)
+
+if (Settings.mysql.clsi.dialect === 'sqlite') {
+  logger.log('running PRAGMA journal_mode=WAL;')
+  sequelize.query('PRAGMA journal_mode=WAL;')
+  sequelize.query('PRAGMA synchronous=OFF;')
+  sequelize.query('PRAGMA read_uncommitted = true;')
+}
+
+module.exports = {
+  UrlCache: sequelize.define(
+    'UrlCache',
+    {
+      url: Sequelize.STRING,
+      project_id: Sequelize.STRING,
+      lastModified: Sequelize.DATE
+    },
+    {
+      indexes: [{ fields: ['url', 'project_id'] }, { fields: ['project_id'] }]
+    }
+  ),
+
+  Project: sequelize.define(
+    'Project',
+    {
+      project_id: { type: Sequelize.STRING, primaryKey: true },
+      lastAccessed: Sequelize.DATE
+    },
+    {
+      indexes: [{ fields: ['lastAccessed'] }]
+    }
+  ),
+
+  op: Sequelize.Op,
+
+  sync() {
+    logger.log({ dbPath: Settings.mysql.clsi.storage }, 'syncing db schema')
+    return sequelize
+      .sync()
+      .then(() => logger.log('db sync complete'))
+      .catch(err => console.log(err, 'error syncing'))
+  }
+}

services/clsi/bin/install_texlive_gce.sh

@@ -1,21 +0,0 @@
-#!/bin/sh
-METADATA=http://metadata.google.internal./computeMetadata/v1
-SVC_ACCT=$METADATA/instance/service-accounts/default
-PROJECT_URL=$METADATA/project/project-id
-ACCESS_TOKEN=$(curl -s -H 'Metadata-Flavor: Google' $SVC_ACCT/token | cut -d'"' -f 4)
-if [ -z "$ACCESS_TOKEN" ]; then
-	echo "No acccess token to download texlive-full images from google container, continuing without downloading. This is likely not a google cloud enviroment."
-	exit 0
-fi
-PROJECT=$(curl -s -H 'Metadata-Flavor: Google' $PROJECT_URL)
-if [ -z "$PROJECT" ]; then
-	echo "No project name to download texlive-full images from google container, continuing without downloading. This is likely not a google cloud enviroment."
-	exit 0
-fi
-docker login -u '_token' -p $ACCESS_TOKEN https://gcr.io
-docker pull --all-tags gcr.io/$PROJECT/texlive-full
-cp /app/bin/synctex /app/bin/synctex-mount/synctex
-
-echo "Finished downloading texlive-full images"
-
-

services/clsi/buildscript.txt

@@ -1,10 +1,11 @@
 clsi
---language=coffeescript
---node-version=10.15.0
 --acceptance-creds=None
---dependencies=mongo,redis
+--data-dirs=cache,compiles,db
+--dependencies=
 --docker-repos=gcr.io/overleaf-ops
+--env-add=
 --env-pass-through=TEXLIVE_IMAGE
---build-target=docker
---script-version=1.1.24
+--language=es
+--node-version=10.19.0
 --public-repo=True
+--script-version=2.1.0

services/clsi/config/settings.defaults.coffee

@@ -1,72 +0,0 @@
-Path = require "path"
-
-module.exports =
-	# Options are passed to Sequelize.
-	# See http://sequelizejs.com/documentation#usage-options for details
-	mysql:
-		clsi:
-			database: "clsi"
-			username: "clsi"
-			dialect: "sqlite"
-			storage: process.env["SQLITE_PATH"] or Path.resolve(__dirname + "/../db.sqlite")
-			pool:
-				max: 1
-				min: 1
-			retry:
-				max: 10
-
-	compileSizeLimit:  process.env["COMPILE_SIZE_LIMIT"] or "7mb"
-	
-	path:
-		compilesDir:  Path.resolve(__dirname + "/../compiles")
-		clsiCacheDir: Path.resolve(__dirname + "/../cache")
-		synctexBaseDir: (project_id) -> Path.join(@compilesDir, project_id)
-
-	internal:
-		clsi:
-			port: 3013
-			host: process.env["LISTEN_ADDRESS"] or "localhost"
-			
-		load_balancer_agent:
-			report_load:true
-			load_port: 3048
-			local_port: 3049
-	apis:
-		clsi:
-			url: "http://#{process.env['CLSI_HOST'] or 'localhost'}:3013"
-
-			
-	smokeTest: process.env["SMOKE_TEST"] or false
-	project_cache_length_ms: 1000 * 60 * 60 * 24
-	parallelFileDownloads: process.env["FILESTORE_PARALLEL_FILE_DOWNLOADS"] or 1
-	parallelSqlQueryLimit: process.env["FILESTORE_PARALLEL_SQL_QUERY_LIMIT"] or 1
-	filestoreDomainOveride: process.env["FILESTORE_DOMAIN_OVERRIDE"]
-	texliveImageNameOveride: process.env["TEX_LIVE_IMAGE_NAME_OVERRIDE"]
-	sentry:
-		dsn: process.env['SENTRY_DSN']
-
-
-if process.env["DOCKER_RUNNER"]
-	module.exports.clsi =
-		dockerRunner: process.env["DOCKER_RUNNER"] == "true"
-		docker:
-			runtime: process.env["DOCKER_RUNTIME"]
-			image: process.env["TEXLIVE_IMAGE"] or "quay.io/sharelatex/texlive-full:2017.1"
-			env:
-				HOME: "/tmp"
-			socketPath: "/var/run/docker.sock"
-			user: process.env["TEXLIVE_IMAGE_USER"] or "tex"
-		expireProjectAfterIdleMs: 24 * 60 * 60 * 1000
-		checkProjectsIntervalMs: 10 * 60 * 1000
-
-	try
-		seccomp_profile_path = Path.resolve(__dirname + "/../seccomp/clsi-profile.json")
-		module.exports.clsi.docker.seccomp_profile = JSON.stringify(JSON.parse(require("fs").readFileSync(seccomp_profile_path)))
-	catch error
-		console.log error, "could not load seccom profile from #{seccomp_profile_path}"
-
-	module.exports.path.synctexBaseDir = -> "/compile"	
-	
-	module.exports.path.sandboxedCompilesHostDir = process.env["COMPILES_HOST_DIR"]
-
-	module.exports.path.synctexBinHostPath = process.env["SYNCTEX_BIN_HOST_PATH"]

services/clsi/config/settings.defaults.js

@@ -0,0 +1,102 @@
+const Path = require('path')
+
+module.exports = {
+  // Options are passed to Sequelize.
+  // See http://sequelizejs.com/documentation#usage-options for details
+  mysql: {
+    clsi: {
+      database: 'clsi',
+      username: 'clsi',
+      dialect: 'sqlite',
+      storage:
+        process.env.SQLITE_PATH || Path.resolve(__dirname + '/../db/db.sqlite'),
+      pool: {
+        max: 1,
+        min: 1
+      },
+      retry: {
+        max: 10
+      }
+    }
+  },
+
+  compileSizeLimit: process.env.COMPILE_SIZE_LIMIT || '7mb',
+
+  processLifespanLimitMs:
+    parseInt(process.env.PROCESS_LIFE_SPAN_LIMIT_MS) || 60 * 60 * 24 * 1000 * 2,
+
+  path: {
+    compilesDir: Path.resolve(__dirname + '/../compiles'),
+    clsiCacheDir: Path.resolve(__dirname + '/../cache'),
+    synctexBaseDir(project_id) {
+      return Path.join(this.compilesDir, project_id)
+    }
+  },
+
+  internal: {
+    clsi: {
+      port: 3013,
+      host: process.env.LISTEN_ADDRESS || 'localhost'
+    },
+
+    load_balancer_agent: {
+      report_load: true,
+      load_port: 3048,
+      local_port: 3049
+    }
+  },
+  apis: {
+    clsi: {
+      url: `http://${process.env.CLSI_HOST || 'localhost'}:3013`
+    }
+  },
+
+  smokeTest: process.env.SMOKE_TEST || false,
+  project_cache_length_ms: 1000 * 60 * 60 * 24,
+  parallelFileDownloads: process.env.FILESTORE_PARALLEL_FILE_DOWNLOADS || 1,
+  parallelSqlQueryLimit: process.env.FILESTORE_PARALLEL_SQL_QUERY_LIMIT || 1,
+  filestoreDomainOveride: process.env.FILESTORE_DOMAIN_OVERRIDE,
+  texliveImageNameOveride: process.env.TEX_LIVE_IMAGE_NAME_OVERRIDE,
+  sentry: {
+    dsn: process.env.SENTRY_DSN
+  }
+}
+
+if (process.env.DOCKER_RUNNER) {
+  let seccomp_profile_path
+  module.exports.clsi = {
+    dockerRunner: process.env.DOCKER_RUNNER === 'true',
+    docker: {
+      runtime: process.env.DOCKER_RUNTIME,
+      image:
+        process.env.TEXLIVE_IMAGE || 'quay.io/sharelatex/texlive-full:2017.1',
+      env: {
+        HOME: '/tmp'
+      },
+      socketPath: '/var/run/docker.sock',
+      user: process.env.TEXLIVE_IMAGE_USER || 'tex'
+    },
+    expireProjectAfterIdleMs: 24 * 60 * 60 * 1000,
+    checkProjectsIntervalMs: 10 * 60 * 1000
+  }
+
+  try {
+    seccomp_profile_path = Path.resolve(
+      __dirname + '/../seccomp/clsi-profile.json'
+    )
+    module.exports.clsi.docker.seccomp_profile = JSON.stringify(
+      JSON.parse(require('fs').readFileSync(seccomp_profile_path))
+    )
+  } catch (error) {
+    console.log(
+      error,
+      `could not load seccom profile from ${seccomp_profile_path}`
+    )
+  }
+
+  module.exports.path.synctexBaseDir = () => '/compile'
+
+  module.exports.path.sandboxedCompilesHostDir = process.env.COMPILES_HOST_DIR
+
+  module.exports.path.synctexBinHostPath = process.env.SYNCTEX_BIN_HOST_PATH
+}

services/clsi/db/.gitignore

@@ -0,0 +1,2 @@
+*
+!.gitignore

services/clsi/docker-compose-config.yml

@@ -1,4 +1,4 @@
-version: "2"
+version: "2.3"
 
 services:
   dev:

services/clsi/docker-compose.ci.yml

@@ -1,9 +1,8 @@
 # This file was auto-generated, do not edit it directly.
 # Instead run bin/update_build_scripts from
 # https://github.com/sharelatex/sharelatex-dev-environment
-# Version: 1.1.24
 
-version: "2"
+version: "2.3"
 
 services:
   test_unit:
@@ -27,13 +26,9 @@ services:
       MOCHA_GREP: ${MOCHA_GREP}
       NODE_ENV: test
       TEXLIVE_IMAGE:
-    depends_on:
-      - mongo
-      - redis
     command: npm run test:acceptance:_run
 
 
-
   tar:
     build: .
     image: ci/$PROJECT_NAME:$BRANCH_NAME-$BUILD_NUMBER
@@ -41,9 +36,3 @@ services:
       - ./:/tmp/build/
     command: tar -czf /tmp/build/build.tar.gz --exclude=build.tar.gz --exclude-vcs .
     user: root
-
-  redis:
-    image: redis
-
-  mongo:
-    image: mongo:3.4

services/clsi/docker-compose.yml

@@ -1,13 +1,14 @@
 # This file was auto-generated, do not edit it directly.
 # Instead run bin/update_build_scripts from
 # https://github.com/sharelatex/sharelatex-dev-environment
-# Version: 1.1.24
 
-version: "2"
+version: "2.3"
 
 services:
   test_unit:
-    build: .
+    build:
+      context: .
+      target: base
     volumes:
       - .:/app
     working_dir: /app
@@ -17,7 +18,9 @@ services:
     command: npm run test:unit
 
   test_acceptance:
-    build: .
+    build:
+      context: .
+      target: base
     volumes:
       - .:/app
     working_dir: /app
@@ -32,25 +35,5 @@ services:
       MOCHA_GREP: ${MOCHA_GREP}
       LOG_LEVEL: ERROR
       NODE_ENV: test
-    depends_on:
-      - mongo
-      - redis
     command: npm run test:acceptance
 
-
-
-  tar:
-    build: .
-    image: ci/$PROJECT_NAME:$BRANCH_NAME-$BUILD_NUMBER
-    volumes:
-      - ./:/tmp/build/
-    command: tar -czf /tmp/build/build.tar.gz --exclude=build.tar.gz --exclude-vcs .
-    user: root
-
-  redis:
-    image: redis
-
-  mongo:
-    image: mongo:3.4
-
-

services/clsi/entrypoint.sh

@@ -1,25 +1,18 @@
 #!/bin/sh
 
-echo "Changing permissions of /var/run/docker.sock for sibling containers"
-ls -al /var/run/docker.sock
-docker --version
-cat /etc/passwd
+docker --version >&2
 
+# add the node user to the docker group on the host
 DOCKER_GROUP=$(stat -c '%g' /var/run/docker.sock)
 groupadd --non-unique --gid ${DOCKER_GROUP} dockeronhost
 usermod -aG dockeronhost node
 
-mkdir -p /app/cache
-chown -R node:node /app/cache
+# compatibility: initial volume setup
+chown node:node /app/cache
+chown node:node /app/compiles
+chown node:node /app/db
 
-mkdir -p /app/compiles
-chown -R node:node /app/compiles
+# make synctex available for remount in compiles
+cp /app/bin/synctex /app/bin/synctex-mount/synctex
 
-chown -R node:node /app/bin/synctex
-mkdir -p /app/test/acceptance/fixtures/tmp/
-chown -R node:node /app
-
-chown -R node:node /app/bin
-
-./bin/install_texlive_gce.sh
 exec runuser -u node -- "$@"

services/clsi/nodemon.json

@@ -10,10 +10,9 @@
   },
 
   "watch": [
-    "app/coffee/",
-    "app.coffee",
+    "app/js/",
+    "app.js",
     "config/"
   ],
-  "ext": "coffee"
-
+  "ext": "js"
 }

services/clsi/npm-shrinkwrap.json

@@ -1,3619 +0,0 @@
-{
-  "name": "node-clsi",
-  "version": "0.1.4",
-  "lockfileVersion": 1,
-  "requires": true,
-  "dependencies": {
-    "@google-cloud/common": {
-      "version": "2.2.3",
-      "resolved": "https://registry.npmjs.org/@google-cloud/common/-/common-2.2.3.tgz",
-      "integrity": "sha512-lvw54mGKn8VqVIy2NzAk0l5fntBFX4UwQhHk6HaqkyCQ7WBl5oz4XhzKMtMilozF/3ObPcDogqwuyEWyZ6rnQQ==",
-      "requires": {
-        "@google-cloud/projectify": "^1.0.0",
-        "@google-cloud/promisify": "^1.0.0",
-        "arrify": "^2.0.0",
-        "duplexify": "^3.6.0",
-        "ent": "^2.2.0",
-        "extend": "^3.0.2",
-        "google-auth-library": "^5.5.0",
-        "retry-request": "^4.0.0",
-        "teeny-request": "^5.2.1"
-      }
-    },
-    "@google-cloud/debug-agent": {
-      "version": "3.2.0",
-      "resolved": "https://registry.npmjs.org/@google-cloud/debug-agent/-/debug-agent-3.2.0.tgz",
-      "integrity": "sha512-fP87kYbS6aeDna08BivwQ1J260mwJGchRi99XdWCgqbRwuFac8ul0OT5i2wEeDSc5QaDX8ZuWQQ0igZvh1rTyQ==",
-      "requires": {
-        "@google-cloud/common": "^0.32.0",
-        "@sindresorhus/is": "^0.15.0",
-        "acorn": "^6.0.0",
-        "coffeescript": "^2.0.0",
-        "console-log-level": "^1.4.0",
-        "extend": "^3.0.1",
-        "findit2": "^2.2.3",
-        "gcp-metadata": "^1.0.0",
-        "lodash.pickby": "^4.6.0",
-        "p-limit": "^2.2.0",
-        "pify": "^4.0.1",
-        "semver": "^6.0.0",
-        "source-map": "^0.6.1",
-        "split": "^1.0.0"
-      },
-      "dependencies": {
-        "@google-cloud/common": {
-          "version": "0.32.1",
-          "resolved": "https://registry.npmjs.org/@google-cloud/common/-/common-0.32.1.tgz",
-          "integrity": "sha512-bLdPzFvvBMtVkwsoBtygE9oUm3yrNmPa71gvOgucYI/GqvNP2tb6RYsDHPq98kvignhcgHGDI5wyNgxaCo8bKQ==",
-          "requires": {
-            "@google-cloud/projectify": "^0.3.3",
-            "@google-cloud/promisify": "^0.4.0",
-            "@types/request": "^2.48.1",
-            "arrify": "^2.0.0",
-            "duplexify": "^3.6.0",
-            "ent": "^2.2.0",
-            "extend": "^3.0.2",
-            "google-auth-library": "^3.1.1",
-            "pify": "^4.0.1",
-            "retry-request": "^4.0.0",
-            "teeny-request": "^3.11.3"
-          }
-        },
-        "@google-cloud/projectify": {
-          "version": "0.3.3",
-          "resolved": "https://registry.npmjs.org/@google-cloud/projectify/-/projectify-0.3.3.tgz",
-          "integrity": "sha512-7522YHQ4IhaafgSunsFF15nG0TGVmxgXidy9cITMe+256RgqfcrfWphiMufW+Ou4kqagW/u3yxwbzVEW3dk2Uw=="
-        },
-        "@google-cloud/promisify": {
-          "version": "0.4.0",
-          "resolved": "https://registry.npmjs.org/@google-cloud/promisify/-/promisify-0.4.0.tgz",
-          "integrity": "sha512-4yAHDC52TEMCNcMzVC8WlqnKKKq+Ssi2lXoUg9zWWkZ6U6tq9ZBRYLHHCRdfU+EU9YJsVmivwGcKYCjRGjnf4Q=="
-        },
-        "coffeescript": {
-          "version": "2.4.1",
-          "resolved": "https://registry.npmjs.org/coffeescript/-/coffeescript-2.4.1.tgz",
-          "integrity": "sha512-34GV1aHrsMpTaO3KfMJL40ZNuvKDR/g98THHnE9bQj8HjMaZvSrLik99WWqyMhRtbe8V5hpx5iLgdcSvM/S2wg=="
-        },
-        "debug": {
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+          "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-7.0.3.tgz",
+          "integrity": "sha512-CwBLREIQ7LvYFB0WyRvwhq5N5qPhc6PMjD6bYggFlI5YyDgl+0vxq5VHbMOFqLg7hfWzmu8T5Z1QofhmTIhItA==",
+          "dev": true
+        },
+        "is-fullwidth-code-point": {
+          "version": "2.0.0",
+          "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-2.0.0.tgz",
+          "integrity": "sha1-o7MKXE8ZkYMWeqq5O+764937ZU8=",
+          "dev": true
+        },
+        "string-width": {
+          "version": "3.1.0",
+          "resolved": "https://registry.npmjs.org/string-width/-/string-width-3.1.0.tgz",
+          "integrity": "sha512-vafcv6KjVZKSgz06oM/H6GDBrAtz8vdhQakGjFIvNrHA6y3HCF1CInLy+QLq8dTJPQ1b+KDUqDFctkdRW44e1w==",
+          "dev": true,
+          "requires": {
+            "emoji-regex": "^7.0.1",
+            "is-fullwidth-code-point": "^2.0.0",
+            "strip-ansi": "^5.1.0"
+          }
+        },
+        "strip-ansi": {
+          "version": "5.2.0",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz",
+          "integrity": "sha512-DuRs1gKbBqsMKIZlrffwlug8MHkcnpjs5VPmL1PAh+mA30U0DTotfDZ0d2UUsXpPmPmMMJ6W773MaA3J+lbiWA==",
+          "dev": true,
+          "requires": {
+            "ansi-regex": "^4.1.0"
+          }
+        }
+      }
+    },
+    "wrappy": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
+      "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
+    },
+    "wrench": {
+      "version": "1.5.9",
+      "resolved": "https://registry.npmjs.org/wrench/-/wrench-1.5.9.tgz",
+      "integrity": "sha1-QRaRxjqbJTGxcAJnJ5veyiOyFCo="
+    },
+    "write": {
+      "version": "1.0.3",
+      "resolved": "https://registry.npmjs.org/write/-/write-1.0.3.tgz",
+      "integrity": "sha512-/lg70HAjtkUgWPVZhZcm+T4hkL8Zbtp1nFNOn3lRrxnlv50SRBv7cR7RqR+GMsd3hUXy9hWBo4CHTbFTcOYwig==",
+      "dev": true,
+      "requires": {
+        "mkdirp": "^0.5.1"
+      },
+      "dependencies": {
+        "mkdirp": {
+          "version": "0.5.1",
+          "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-0.5.1.tgz",
+          "integrity": "sha1-MAV0OOrGz3+MR2fzhkjWaX11yQM=",
+          "dev": true,
+          "requires": {
+            "minimist": "0.0.8"
+          }
+        }
+      }
+    },
+    "xregexp": {
+      "version": "4.3.0",
+      "resolved": "https://registry.npmjs.org/xregexp/-/xregexp-4.3.0.tgz",
+      "integrity": "sha512-7jXDIFXh5yJ/orPn4SXjuVrWWoi4Cr8jfV1eHv9CixKSbU+jY4mxfrBwAuDvupPNKpMUY+FeIqsVw/JLT9+B8g==",
+      "dev": true,
+      "requires": {
+        "@babel/runtime-corejs3": "^7.8.3"
+      }
+    },
+    "y18n": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.0.tgz",
+      "integrity": "sha512-r9S/ZyXu/Xu9q1tYlpsLIsa3EeLXXk0VwlxqTcFRfg9EhMW+17kbt9G0NrgCmhGb5vT2hyhJZLfDGx+7+5Uj/w==",
+      "dev": true
+    },
+    "yallist": {
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.0.3.tgz",
+      "integrity": "sha1-tLBJ4xS+VF486AIjbWzSLNkcPek="
+    },
+    "yargs": {
+      "version": "13.3.0",
+      "resolved": "https://registry.npmjs.org/yargs/-/yargs-13.3.0.tgz",
+      "integrity": "sha512-2eehun/8ALW8TLoIl7MVaRUrg+yCnenu8B4kBlRxj3GJGDKU1Og7sMXPNm1BYyM1DOJmTZ4YeN/Nwxv+8XJsUA==",
+      "dev": true,
+      "requires": {
+        "cliui": "^5.0.0",
+        "find-up": "^3.0.0",
+        "get-caller-file": "^2.0.1",
+        "require-directory": "^2.1.1",
+        "require-main-filename": "^2.0.0",
+        "set-blocking": "^2.0.0",
+        "string-width": "^3.0.0",
+        "which-module": "^2.0.0",
+        "y18n": "^4.0.0",
+        "yargs-parser": "^13.1.1"
+      },
+      "dependencies": {
+        "ansi-regex": {
+          "version": "4.1.0",
+          "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.1.0.tgz",
+          "integrity": "sha512-1apePfXM1UOSqw0o9IiFAovVz9M5S1Dg+4TrDwfMewQ6p/rmMueb7tWZjQ1rx4Loy1ArBggoqGpfqqdI4rondg==",
+          "dev": true
+        },
+        "emoji-regex": {
+          "version": "7.0.3",
+          "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-7.0.3.tgz",
+          "integrity": "sha512-CwBLREIQ7LvYFB0WyRvwhq5N5qPhc6PMjD6bYggFlI5YyDgl+0vxq5VHbMOFqLg7hfWzmu8T5Z1QofhmTIhItA==",
+          "dev": true
+        },
+        "find-up": {
+          "version": "3.0.0",
+          "resolved": "https://registry.npmjs.org/find-up/-/find-up-3.0.0.tgz",
+          "integrity": "sha512-1yD6RmLI1XBfxugvORwlck6f75tYL+iR0jqwsOrOxMZyGYqUuDhJ0l4AXdO1iX/FTs9cBAMEk1gWSEx1kSbylg==",
+          "dev": true,
+          "requires": {
+            "locate-path": "^3.0.0"
+          }
+        },
+        "is-fullwidth-code-point": {
+          "version": "2.0.0",
+          "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-2.0.0.tgz",
+          "integrity": "sha1-o7MKXE8ZkYMWeqq5O+764937ZU8=",
+          "dev": true
+        },
+        "locate-path": {
+          "version": "3.0.0",
+          "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-3.0.0.tgz",
+          "integrity": "sha512-7AO748wWnIhNqAuaty2ZWHkQHRSNfPVIsPIfwEOWO22AmaoVrWavlOcMR5nzTLNYvp36X220/maaRsrec1G65A==",
+          "dev": true,
+          "requires": {
+            "p-locate": "^3.0.0",
+            "path-exists": "^3.0.0"
+          }
+        },
+        "p-locate": {
+          "version": "3.0.0",
+          "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-3.0.0.tgz",
+          "integrity": "sha512-x+12w/To+4GFfgJhBEpiDcLozRJGegY+Ei7/z0tSLkMmxGZNybVMSfWj9aJn8Z5Fc7dBUNJOOVgPv2H7IwulSQ==",
+          "dev": true,
+          "requires": {
+            "p-limit": "^2.0.0"
+          }
+        },
+        "string-width": {
+          "version": "3.1.0",
+          "resolved": "https://registry.npmjs.org/string-width/-/string-width-3.1.0.tgz",
+          "integrity": "sha512-vafcv6KjVZKSgz06oM/H6GDBrAtz8vdhQakGjFIvNrHA6y3HCF1CInLy+QLq8dTJPQ1b+KDUqDFctkdRW44e1w==",
+          "dev": true,
+          "requires": {
+            "emoji-regex": "^7.0.1",
+            "is-fullwidth-code-point": "^2.0.0",
+            "strip-ansi": "^5.1.0"
+          }
+        },
+        "strip-ansi": {
+          "version": "5.2.0",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz",
+          "integrity": "sha512-DuRs1gKbBqsMKIZlrffwlug8MHkcnpjs5VPmL1PAh+mA30U0DTotfDZ0d2UUsXpPmPmMMJ6W773MaA3J+lbiWA==",
+          "dev": true,
+          "requires": {
+            "ansi-regex": "^4.1.0"
+          }
+        }
+      }
+    },
+    "yargs-parser": {
+      "version": "13.1.1",
+      "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.1.tgz",
+      "integrity": "sha512-oVAVsHz6uFrg3XQheFII8ESO2ssAf9luWuAd6Wexsu4F3OtIW0o8IribPXYrD4WC24LWtPrJlGy87y5udK+dxQ==",
+      "dev": true,
+      "requires": {
+        "camelcase": "^5.0.0",
+        "decamelize": "^1.2.0"
+      }
+    },
+    "yargs-unparser": {
+      "version": "1.6.0",
+      "resolved": "https://registry.npmjs.org/yargs-unparser/-/yargs-unparser-1.6.0.tgz",
+      "integrity": "sha512-W9tKgmSn0DpSatfri0nx52Joq5hVXgeLiqR/5G0sZNDoLZFOr/xjBUDcShCOGNsBnEMNo1KAMBkTej1Hm62HTw==",
+      "dev": true,
+      "requires": {
+        "flat": "^4.1.0",
+        "lodash": "^4.17.15",
+        "yargs": "^13.3.0"
+      }
+    },
+    "yn": {
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz",
+      "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q=="
+    }
+  }
+}

services/clsi/package.json

@@ -7,48 +7,62 @@
     "url": "https://github.com/sharelatex/clsi-sharelatex.git"
   },
   "scripts": {
-    "compile:app": "([ -e app/coffee ] && coffee -m $COFFEE_OPTIONS -o app/js -c app/coffee || echo 'No CoffeeScript folder to compile') && ( [ -e app.coffee ] && coffee -m $COFFEE_OPTIONS -c app.coffee || echo 'No CoffeeScript app to compile')",
-    "start": "npm run compile:app && node $NODE_APP_OPTIONS app.js",
-    "test:acceptance:_run": "mocha --recursive --reporter spec --timeout 30000 --exit $@ test/acceptance/js",
-    "test:acceptance": "npm run compile:app && npm run compile:acceptance_tests && npm run test:acceptance:_run -- --grep=$MOCHA_GREP",
-    "test:unit:_run": "mocha --recursive --reporter spec --exit $@ test/unit/js",
-    "test:unit": "npm run compile:app && npm run compile:unit_tests && npm run test:unit:_run -- --grep=$MOCHA_GREP",
-    "compile:unit_tests": "[ ! -e test/unit/coffee ] &&  echo 'No unit tests to compile' || coffee -o test/unit/js -c test/unit/coffee",
-    "compile:acceptance_tests": "[ ! -e test/acceptance/coffee ] && echo 'No acceptance tests to compile' || coffee -o test/acceptance/js -c test/acceptance/coffee",
-    "compile:all": "npm run compile:app && npm run compile:unit_tests && npm run compile:acceptance_tests && npm run compile:smoke_tests",
+    "start": "node $NODE_APP_OPTIONS app.js",
+    "test:acceptance:_run": "mocha --recursive --reporter spec --timeout 15000 --exit $@ test/acceptance/js",
+    "test:acceptance": "npm run test:acceptance:_run -- --grep=$MOCHA_GREP",
+    "test:unit:_run": "mocha --recursive --reporter spec $@ test/unit/js",
+    "test:unit": "npm run test:unit:_run -- --grep=$MOCHA_GREP",
     "nodemon": "nodemon --config nodemon.json",
-    "compile:smoke_tests": "[ ! -e test/smoke/coffee ] &&  echo 'No smoke tests to compile' || coffee -o test/smoke/js -c test/smoke/coffee"
+    "lint": "node_modules/.bin/eslint .",
+    "format": "node_modules/.bin/prettier-eslint $PWD'/**/*.js' --list-different",
+    "format:fix": "node_modules/.bin/prettier-eslint $PWD'/**/*.js' --write"
   },
   "author": "James Allen <james@sharelatex.com>",
   "dependencies": {
-    "async": "0.2.9",
-    "body-parser": "^1.2.0",
-    "dockerode": "^2.5.3",
-    "express": "^4.2.0",
-    "fs-extra": "^0.16.3",
-    "heapdump": "^0.3.5",
-    "lockfile": "^1.0.3",
-    "logger-sharelatex": "^1.9.0",
-    "lynx": "0.0.11",
-    "metrics-sharelatex": "^2.3.0",
-    "mkdirp": "0.3.5",
-    "mysql": "2.6.2",
-    "request": "^2.21.0",
-    "sequelize": "^4.38.0",
+    "async": "3.2.0",
+    "body-parser": "^1.19.0",
+    "dockerode": "^3.1.0",
+    "express": "^4.17.1",
+    "fs-extra": "^8.1.0",
+    "heapdump": "^0.3.15",
+    "lockfile": "^1.0.4",
+    "logger-sharelatex": "^1.9.1",
+    "lynx": "0.2.0",
+    "metrics-sharelatex": "^2.6.0",
+    "mysql": "^2.18.1",
+    "request": "^2.88.2",
+    "sequelize": "^5.21.5",
     "settings-sharelatex": "git+https://github.com/sharelatex/settings-sharelatex.git#v1.1.0",
     "smoke-test-sharelatex": "git+https://github.com/sharelatex/smoke-test-sharelatex.git#v0.2.0",
-    "sqlite3": "^4.0.6",
-    "underscore": "^1.8.2",
-    "v8-profiler-node8": "^6.0.1",
-    "wrench": "~1.5.4"
+    "sqlite3": "^4.1.1",
+    "underscore": "^1.9.2",
+    "v8-profiler-node8": "^6.1.1",
+    "wrench": "~1.5.9"
   },
   "devDependencies": {
-    "bunyan": "^0.22.1",
-    "chai": "~1.8.1",
-    "coffeescript": "1.6.0",
-    "mocha": "^4.0.1",
-    "sandboxed-module": "~0.3.0",
-    "sinon": "~1.7.3",
-    "timekeeper": "0.0.4"
+    "babel-eslint": "^10.1.0",
+    "bunyan": "^1.8.12",
+    "chai": "~4.2.0",
+    "eslint": "^6.8.0",
+    "eslint-config-prettier": "^6.10.0",
+    "eslint-config-standard": "^14.1.0",
+    "eslint-config-standard-jsx": "^8.1.0",
+    "eslint-config-standard-react": "^9.2.0",
+    "eslint-plugin-chai-expect": "^2.1.0",
+    "eslint-plugin-chai-friendly": "^0.5.0",
+    "eslint-plugin-import": "^2.20.1",
+    "eslint-plugin-jsx-a11y": "^6.2.3",
+    "eslint-plugin-mocha": "^6.3.0",
+    "eslint-plugin-node": "^11.0.0",
+    "eslint-plugin-prettier": "^3.1.2",
+    "eslint-plugin-promise": "^4.2.1",
+    "eslint-plugin-react": "^7.19.0",
+    "eslint-plugin-standard": "^4.0.1",
+    "mocha": "^7.1.0",
+    "prettier": "^1.19.1",
+    "prettier-eslint-cli": "^5.0.0",
+    "sandboxed-module": "^2.0.3",
+    "sinon": "~9.0.1",
+    "timekeeper": "2.2.0"
   }
 }

services/clsi/test/acceptance/coffee/BrokenLatexFileTests.coffee

@@ -1,48 +0,0 @@
-Client = require "./helpers/Client"
-request = require "request"
-require("chai").should()
-ClsiApp = require "./helpers/ClsiApp"
-
-describe "Broken LaTeX file", ->
-	before (done)->
-		@broken_request =
-			resources: [
-				path: "main.tex"
-				content: '''
-					\\documentclass{articl % :(
-					\\begin{documen % :(
-					Broken
-					\\end{documen % :(
-				'''
-			]
-		@correct_request =
-			resources: [
-				path: "main.tex"
-				content: '''
-					\\documentclass{article}
-					\\begin{document}
-					Hello world
-					\\end{document}
-				'''
-			]
-		ClsiApp.ensureRunning done
-		
-	describe "on first run", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			Client.compile @project_id, @broken_request, (@error, @res, @body) => done()
-
-		it "should return a failure status", ->
-			@body.compile.status.should.equal "failure"
-
-	describe "on second run", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			Client.compile @project_id, @correct_request, () =>
-				Client.compile @project_id, @broken_request, (@error, @res, @body) =>
-					done()
-
-		it "should return a failure status", ->
-			@body.compile.status.should.equal "failure"
-		
-		

services/clsi/test/acceptance/coffee/DeleteOldFilesTest.coffee

@@ -1,36 +0,0 @@
-Client = require "./helpers/Client"
-request = require "request"
-require("chai").should()
-ClsiApp = require "./helpers/ClsiApp"
-
-describe "Deleting Old Files", ->
-	before (done)->
-		@request =
-			resources: [
-				path: "main.tex"
-				content: '''
-					\\documentclass{article}
-					\\begin{document}
-					Hello world
-					\\end{document}
-				'''
-			]
-		ClsiApp.ensureRunning done
-
-	describe "on first run", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			Client.compile @project_id, @request, (@error, @res, @body) => done()
-
-		it "should return a success status", ->
-			@body.compile.status.should.equal "success"
-
-		describe "after file has been deleted", ->
-			before (done) ->
-				@request.resources = []
-				Client.compile @project_id, @request, (@error, @res, @body) =>
-					done()
-
-			it "should return a failure status", ->
-				@body.compile.status.should.equal "failure"
-

services/clsi/test/acceptance/coffee/ExampleDocumentTests.coffee

@@ -1,129 +0,0 @@
-Client = require "./helpers/Client"
-request = require "request"
-require("chai").should()
-fs = require "fs"
-ChildProcess = require "child_process"
-ClsiApp = require "./helpers/ClsiApp"
-logger = require("logger-sharelatex")
-Path = require("path")
-fixturePath = (path) -> Path.normalize(__dirname + "/../fixtures/" + path)
-process = require "process"
-console.log process.pid, process.ppid, process.getuid(),process.getgroups(), "PID"
-try
-	console.log "creating tmp directory", fixturePath("tmp")
-	fs.mkdirSync(fixturePath("tmp"))
-catch err
-	console.log err, fixturePath("tmp"), "unable to create fixture tmp path"
-
-MOCHA_LATEX_TIMEOUT = 60 * 1000
-
-convertToPng = (pdfPath, pngPath, callback = (error) ->) ->
-	command = "convert #{fixturePath(pdfPath)} #{fixturePath(pngPath)}"
-	console.log "COMMAND"
-	console.log command
-	convert = ChildProcess.exec command
-	stdout = ""
-	convert.stdout.on "data", (chunk) -> console.log "STDOUT", chunk.toString()
-	convert.stderr.on "data", (chunk) -> console.log "STDERR", chunk.toString()
-	convert.on "exit", () ->
-		callback()
-
-compare = (originalPath, generatedPath, callback = (error, same) ->) ->
-	diff_file = "#{fixturePath(generatedPath)}-diff.png"
-	proc = ChildProcess.exec "compare -metric mae #{fixturePath(originalPath)} #{fixturePath(generatedPath)} #{diff_file}"
-	stderr = ""
-	proc.stderr.on "data", (chunk) -> stderr += chunk
-	proc.on "exit", () ->
-		if stderr.trim() == "0 (0)"
-			# remove output diff if test matches expected image
-			fs.unlink diff_file, (err) ->
-				if err
-					throw err
-			callback null, true
-		else
-			console.log "compare result", stderr
-			callback null, false
-
-checkPdfInfo = (pdfPath, callback = (error, output) ->) ->
-	proc = ChildProcess.exec "pdfinfo #{fixturePath(pdfPath)}"
-	stdout = ""
-	proc.stdout.on "data", (chunk) -> stdout += chunk
-	proc.stderr.on "data", (chunk) -> console.log "STDERR", chunk.toString()
-	proc.on "exit", () ->
-		if stdout.match(/Optimized:\s+yes/)
-			callback null, true
-		else
-			callback null, false
-
-compareMultiplePages = (project_id, callback = (error) ->) ->
-	compareNext = (page_no, callback) ->
-		path = "tmp/#{project_id}-source-#{page_no}.png"
-		fs.stat fixturePath(path), (error, stat) ->
-			if error?
-				callback()
-			else
-				compare  "tmp/#{project_id}-source-#{page_no}.png", "tmp/#{project_id}-generated-#{page_no}.png", (error, same) =>
-					throw error if error?
-					same.should.equal true
-					compareNext page_no + 1, callback
-	compareNext 0, callback
-
-comparePdf = (project_id, example_dir, callback = (error) ->) ->
-	console.log "CONVERT"
-	console.log "tmp/#{project_id}.pdf", "tmp/#{project_id}-generated.png"
-	convertToPng "tmp/#{project_id}.pdf", "tmp/#{project_id}-generated.png", (error) =>
-		throw error if error?
-		convertToPng "examples/#{example_dir}/output.pdf", "tmp/#{project_id}-source.png", (error) =>
-			throw error if error?
-			fs.stat fixturePath("tmp/#{project_id}-source-0.png"), (error, stat) =>
-				if error?
-					compare  "tmp/#{project_id}-source.png", "tmp/#{project_id}-generated.png", (error, same) =>
-						throw error if error?
-						same.should.equal true
-						callback()
-				else
-					compareMultiplePages project_id, (error) ->
-						throw error if error?
-						callback()
-
-downloadAndComparePdf = (project_id, example_dir, url, callback = (error) ->) ->
-	writeStream = fs.createWriteStream(fixturePath("tmp/#{project_id}.pdf"))
-	request.get(url).pipe(writeStream)
-	console.log("writing file out", fixturePath("tmp/#{project_id}.pdf"))
-	writeStream.on "close", () =>
-		checkPdfInfo "tmp/#{project_id}.pdf", (error, optimised) =>
-			throw error if error?
-			optimised.should.equal true
-			comparePdf project_id, example_dir, callback
-
-Client.runServer(4242, fixturePath("examples"))
-
-describe "Example Documents", ->
-	before (done) ->
-		ChildProcess.exec("rm test/acceptance/fixtures/tmp/*").on "exit", () -> 
-			ClsiApp.ensureRunning done
-
-
-	for example_dir in fs.readdirSync fixturePath("examples")
-		do (example_dir) ->
-			describe example_dir, ->
-				before ->
-					@project_id = Client.randomId() + "_" + example_dir
-
-				it "should generate the correct pdf", (done) ->
-					this.timeout(MOCHA_LATEX_TIMEOUT)
-					Client.compileDirectory @project_id, fixturePath("examples"), example_dir, 4242, (error, res, body) =>
-						if error || body?.compile?.status is "failure"
-							console.log "DEBUG: error", error, "body", JSON.stringify(body)
-						pdf = Client.getOutputFile body, "pdf"
-						downloadAndComparePdf(@project_id, example_dir, pdf.url, done)
-
-				it "should generate the correct pdf on the second run as well", (done) ->
-					this.timeout(MOCHA_LATEX_TIMEOUT)
-					Client.compileDirectory @project_id, fixturePath("examples"), example_dir, 4242, (error, res, body) =>
-						if error || body?.compile?.status is "failure"
-							console.log "DEBUG: error", error, "body", JSON.stringify(body)
-						pdf = Client.getOutputFile body, "pdf"
-						downloadAndComparePdf(@project_id, example_dir, pdf.url, done)
-
-

services/clsi/test/acceptance/coffee/SimpleLatexFileTests.coffee

@@ -1,41 +0,0 @@
-Client = require "./helpers/Client"
-request = require "request"
-require("chai").should()
-ClsiApp = require "./helpers/ClsiApp"
-
-describe "Simple LaTeX file", ->
-	before (done) ->
-		@project_id = Client.randomId()
-		@request =
-			resources: [
-				path: "main.tex"
-				content: '''
-					\\documentclass{article}
-					\\begin{document}
-					Hello world
-					\\end{document}
-				'''
-			]
-		ClsiApp.ensureRunning =>
-			Client.compile @project_id, @request, (@error, @res, @body) => done()
-
-	it "should return the PDF", ->
-		pdf = Client.getOutputFile(@body, "pdf")
-		pdf.type.should.equal "pdf"
-		
-	it "should return the log", ->
-		log = Client.getOutputFile(@body, "log")
-		log.type.should.equal "log"
-
-	it "should provide the pdf for download", (done) ->
-		pdf = Client.getOutputFile(@body, "pdf")
-		request.get pdf.url, (error, res, body) ->
-			res.statusCode.should.equal 200
-			done()
-		
-	it "should provide the log for download", (done) ->
-		log = Client.getOutputFile(@body, "pdf")
-		request.get log.url, (error, res, body) ->
-			res.statusCode.should.equal 200
-			done()
-	

services/clsi/test/acceptance/coffee/SynctexTests.coffee

@@ -1,41 +0,0 @@
-Client = require "./helpers/Client"
-request = require "request"
-require("chai").should()
-expect = require("chai").expect
-ClsiApp = require "./helpers/ClsiApp"
-crypto = require("crypto")
-
-describe "Syncing", ->
-	before (done) ->
-		content = '''
-					\\documentclass{article}
-					\\begin{document}
-					Hello world
-					\\end{document}
-				'''
-		@request =
-			resources: [
-				path: "main.tex"
-				content: content
-			]
-		@project_id = Client.randomId()
-		ClsiApp.ensureRunning =>
-			Client.compile @project_id, @request, (@error, @res, @body) => done()
-
-	describe "from code to pdf", ->
-		it "should return the correct location", (done) ->
-			Client.syncFromCode @project_id, "main.tex", 3, 5, (error, pdfPositions) ->
-				throw error if error?
-				expect(pdfPositions).to.deep.equal(
-					pdf: [ { page: 1, h: 133.77, v: 134.76, height: 6.92, width: 343.71 } ]
-				)
-				done()
-
-	describe "from pdf to code", ->
-		it "should return the correct location", (done) ->
-			Client.syncFromPdf @project_id, 1, 100, 200, (error, codePositions) =>
-				throw error if error?
-				expect(codePositions).to.deep.equal(
-					code: [ { file: 'main.tex', line: 3, column: -1 } ]
-				)
-				done()

services/clsi/test/acceptance/coffee/TimeoutTests.coffee

@@ -1,34 +0,0 @@
-Client = require "./helpers/Client"
-request = require "request"
-require("chai").should()
-ClsiApp = require "./helpers/ClsiApp"
-
-
-describe "Timed out compile", ->
-	before (done) ->
-		@request =
-			options:
-				timeout: 10 #seconds
-			resources: [
-				path: "main.tex"
-				content: '''
-					\\documentclass{article}
-					\\begin{document}
-					\\def\\x{Hello!\\par\\x}
-					\\x
-					\\end{document}
-				'''
-			]
-		@project_id = Client.randomId()
-		ClsiApp.ensureRunning =>
-			Client.compile @project_id, @request, (@error, @res, @body) => done()
-
-	it "should return a timeout error", ->
-		@body.compile.error.should.equal "container timed out"
-
-	it "should return a timedout status", ->
-		@body.compile.status.should.equal "timedout"
-
-	it "should return the log output file name", ->
-		outputFilePaths = @body.compile.outputFiles.map((x) => x.path)
-		outputFilePaths.should.include('output.log')

services/clsi/test/acceptance/coffee/UrlCachingTests.coffee

@@ -1,222 +0,0 @@
-Client = require "./helpers/Client"
-request = require "request"
-require("chai").should()
-sinon = require "sinon"
-ClsiApp = require "./helpers/ClsiApp"
-
-host = "localhost"
-
-Server =
-	run: () ->
-		express = require "express"
-		app = express()
-
-		staticServer = express.static __dirname + "/../fixtures/"
-		app.get "/:random_id/*", (req, res, next) =>
-			@getFile(req.url)
-			req.url = "/" + req.params[0]
-			staticServer(req, res, next)
-
-		app.listen 31415, host
-
-	getFile: () ->
-
-	randomId: () ->
-		Math.random().toString(16).slice(2)
-
-Server.run()
-
-describe "Url Caching", ->
-	describe "Downloading an image for the first time", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			@file = "#{Server.randomId()}/lion.png"
-			@request =
-				resources: [{
-					path: "main.tex"
-					content: '''
-						\\documentclass{article}
-						\\usepackage{graphicx}
-						\\begin{document}
-						\\includegraphics{lion.png}
-						\\end{document}
-					'''
-				}, {
-					path: "lion.png"
-					url: "http://#{host}:31415/#{@file}"
-				}]
-
-			sinon.spy Server, "getFile"
-			ClsiApp.ensureRunning =>
-				Client.compile @project_id, @request, (@error, @res, @body) => done()
-
-		afterEach ->
-			Server.getFile.restore()
-
-		it "should download the image", ->
-			Server.getFile
-				.calledWith("/" + @file)
-				.should.equal true
-				
-	describe "When an image is in the cache and the last modified date is unchanged", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			@file = "#{Server.randomId()}/lion.png"
-			@request =
-				resources: [{
-					path: "main.tex"
-					content: '''
-						\\documentclass{article}
-						\\usepackage{graphicx}
-						\\begin{document}
-						\\includegraphics{lion.png}
-						\\end{document}
-					'''
-				}, @image_resource = {
-					path: "lion.png"
-					url: "http://#{host}:31415/#{@file}"
-					modified: Date.now()
-				}]
-
-			Client.compile @project_id, @request, (@error, @res, @body) =>
-				sinon.spy Server, "getFile"
-				Client.compile @project_id, @request, (@error, @res, @body) =>
-					done()
-
-		after ->
-			Server.getFile.restore()
-
-		it "should not download the image again", ->
-			Server.getFile.called.should.equal false
-
-	describe "When an image is in the cache and the last modified date is advanced", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			@file = "#{Server.randomId()}/lion.png"
-			@request =
-				resources: [{
-					path: "main.tex"
-					content: '''
-						\\documentclass{article}
-						\\usepackage{graphicx}
-						\\begin{document}
-						\\includegraphics{lion.png}
-						\\end{document}
-					'''
-				}, @image_resource = {
-					path: "lion.png"
-					url: "http://#{host}:31415/#{@file}"
-					modified: @last_modified = Date.now()
-				}]
-
-			Client.compile @project_id, @request, (@error, @res, @body) =>
-				sinon.spy Server, "getFile"
-				@image_resource.modified = new Date(@last_modified + 3000)
-				Client.compile @project_id, @request, (@error, @res, @body) =>
-					done()
-
-		afterEach ->
-			Server.getFile.restore()
-
-		it "should download the image again", ->
-			Server.getFile.called.should.equal true
-
-	describe "When an image is in the cache and the last modified date is further in the past", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			@file = "#{Server.randomId()}/lion.png"
-			@request =
-				resources: [{
-					path: "main.tex"
-					content: '''
-						\\documentclass{article}
-						\\usepackage{graphicx}
-						\\begin{document}
-						\\includegraphics{lion.png}
-						\\end{document}
-					'''
-				}, @image_resource = {
-					path: "lion.png"
-					url: "http://#{host}:31415/#{@file}"
-					modified: @last_modified = Date.now()
-				}]
-
-			Client.compile @project_id, @request, (@error, @res, @body) =>
-				sinon.spy Server, "getFile"
-				@image_resource.modified = new Date(@last_modified - 3000)
-				Client.compile @project_id, @request, (@error, @res, @body) =>
-					done()
-
-		afterEach ->
-			Server.getFile.restore()
-
-		it "should not download the image again", ->
-			Server.getFile.called.should.equal false
-
-	describe "When an image is in the cache and the last modified date is not specified", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			@file = "#{Server.randomId()}/lion.png"
-			@request =
-				resources: [{
-					path: "main.tex"
-					content: '''
-						\\documentclass{article}
-						\\usepackage{graphicx}
-						\\begin{document}
-						\\includegraphics{lion.png}
-						\\end{document}
-					'''
-				}, @image_resource = {
-					path: "lion.png"
-					url: "http://#{host}:31415/#{@file}"
-					modified: @last_modified = Date.now()
-				}]
-
-			Client.compile @project_id, @request, (@error, @res, @body) =>
-				sinon.spy Server, "getFile"
-				delete @image_resource.modified
-				Client.compile @project_id, @request, (@error, @res, @body) =>
-					done()
-
-		afterEach ->
-			Server.getFile.restore()
-
-		it "should download the image again", ->
-			Server.getFile.called.should.equal true
-		
-	describe "After clearing the cache", ->
-		before (done) ->
-			@project_id = Client.randomId()
-			@file = "#{Server.randomId()}/lion.png"
-			@request =
-				resources: [{
-					path: "main.tex"
-					content: '''
-						\\documentclass{article}
-						\\usepackage{graphicx}
-						\\begin{document}
-						\\includegraphics{lion.png}
-						\\end{document}
-					'''
-				}, @image_resource = {
-					path: "lion.png"
-					url: "http://#{host}:31415/#{@file}"
-					modified: @last_modified = Date.now()
-				}]
-
-			Client.compile @project_id, @request, (error) =>
-				throw error if error?
-				Client.clearCache @project_id, (error, res, body) =>
-					throw error if error?
-					sinon.spy Server, "getFile"
-					Client.compile @project_id, @request, (@error, @res, @body) =>
-						done()
-
-		afterEach ->
-			Server.getFile.restore()
-
-		it "should download the image again", ->
-			Server.getFile.called.should.equal true
-		
-				

services/clsi/test/acceptance/coffee/WordcountTests.coffee

@@ -1,38 +0,0 @@
-Client = require "./helpers/Client"
-request = require "request"
-require("chai").should()
-expect = require("chai").expect
-path = require("path")
-fs = require("fs")
-ClsiApp = require "./helpers/ClsiApp"
-
-describe "Syncing", ->
-	before (done) ->
-		@request =
-			resources: [
-				path: "main.tex"
-				content: fs.readFileSync(path.join(__dirname,"../fixtures/naugty_strings.txt"),"utf-8")
-			]
-		@project_id = Client.randomId()
-		ClsiApp.ensureRunning =>
-			Client.compile @project_id, @request, (@error, @res, @body) => done()
-
-	describe "wordcount file", ->
-		it "should return wordcount info", (done) ->
-			Client.wordcount @project_id, "main.tex", (error, result) ->
-				throw error if error?
-				expect(result).to.deep.equal(
-					texcount: { 
-						encode: "utf8"
-						textWords: 2281
-						headWords: 2
-						outside: 0
-						headers: 2
-						elements: 0
-						mathInline: 6
-						mathDisplay: 0
-						errors: 0
-						messages: ""
-					}
-				)
-				done()

services/clsi/test/acceptance/coffee/helpers/Client.coffee

@@ -1,105 +0,0 @@
-request = require "request"
-fs = require "fs"
-Settings = require "settings-sharelatex"
-
-host = "localhost"
-
-module.exports = Client =
-	host: Settings.apis.clsi.url
-
-	randomId: () ->
-		Math.random().toString(16).slice(2)
-
-	compile: (project_id, data, callback = (error, res, body) ->) ->
-		request.post {
-			url: "#{@host}/project/#{project_id}/compile"
-			json:
-				compile: data
-		}, callback
-
-	clearCache: (project_id, callback = (error, res, body) ->) ->
-		request.del "#{@host}/project/#{project_id}", callback
-
-	getOutputFile: (response, type) ->
-		for file in response.compile.outputFiles
-			if file.type == type and file.url.match("output.#{type}")
-				return file
-		return null
-
-	runServer: (port, directory) ->
-		express = require("express")
-		app = express()
-		app.use express.static(directory)
-		console.log("starting test server on", port, host)
-		app.listen(port, host).on "error", (error) ->
-			console.error "error starting server:", error.message
-			process.exit(1)
-
-
-	syncFromCode: (project_id, file, line, column, callback = (error, pdfPositions) ->) ->
-		request.get {
-			url: "#{@host}/project/#{project_id}/sync/code"
-			qs: {
-				file: file
-				line: line
-				column: column
-			}
-		}, (error, response, body) ->
-			return callback(error) if error?
-			callback null, JSON.parse(body)
-
-	syncFromPdf: (project_id, page, h, v, callback = (error, pdfPositions) ->) ->
-		request.get {
-			url: "#{@host}/project/#{project_id}/sync/pdf"
-			qs: {
-				page: page,
-				h: h, v: v
-			}
-		}, (error, response, body) ->
-			return callback(error) if error?
-			callback null, JSON.parse(body)
-
-	compileDirectory: (project_id, baseDirectory, directory, serverPort, callback = (error, res, body) ->) ->
-		resources = []
-		entities = fs.readdirSync("#{baseDirectory}/#{directory}")
-		rootResourcePath = "main.tex"
-		while (entities.length > 0)
-			entity = entities.pop()
-			stat = fs.statSync("#{baseDirectory}/#{directory}/#{entity}")
-			if stat.isDirectory()
-				entities = entities.concat fs.readdirSync("#{baseDirectory}/#{directory}/#{entity}").map (subEntity) ->
-					if subEntity == "main.tex"
-						rootResourcePath = "#{entity}/#{subEntity}"
-					return "#{entity}/#{subEntity}"
-			else if stat.isFile() and entity != "output.pdf"
-				extension = entity.split(".").pop()
-				if ["tex", "bib", "cls", "sty", "pdf_tex", "Rtex", "ist", "md", "Rmd"].indexOf(extension) > -1
-					resources.push
-						path: entity
-						content: fs.readFileSync("#{baseDirectory}/#{directory}/#{entity}").toString()
-				else if ["eps", "ttf", "png", "jpg", "pdf", "jpeg"].indexOf(extension) > -1
-					resources.push
-						path: entity
-						url: "http://#{host}:#{serverPort}/#{directory}/#{entity}"
-						modified: stat.mtime
-
-		fs.readFile "#{baseDirectory}/#{directory}/options.json", (error, body) =>
-			req =
-				resources: resources
-				rootResourcePath: rootResourcePath
-
-			if !error?
-				body = JSON.parse body
-				req.options = body
-
-			@compile project_id, req, callback
-
-	wordcount: (project_id, file, callback = (error, pdfPositions) ->) ->
-		request.get {
-			url: "#{@host}/project/#{project_id}/wordcount"
-			qs: {
-				file: file
-			}
-		}, (error, response, body) ->
-			return callback(error) if error?
-			callback null, JSON.parse(body)

services/clsi/test/acceptance/coffee/helpers/ClsiApp.coffee

@@ -1,24 +0,0 @@
-app = require('../../../../app')
-require("logger-sharelatex").logger.level("info")
-logger = require("logger-sharelatex")
-Settings = require("settings-sharelatex")
-
-module.exports =
-	running: false
-	initing: false
-	callbacks: []
-	ensureRunning: (callback = (error) ->) ->
-		if @running
-			return callback()
-		else if @initing
-			@callbacks.push callback
-		else
-			@initing = true
-			@callbacks.push callback
-			app.listen Settings.internal?.clsi?.port, "localhost", (error) => 
-				throw error if error?
-				@running = true
-				logger.log("clsi running in dev mode")
-
-				for callback in @callbacks
-					callback()

services/clsi/test/acceptance/js/BrokenLatexFileTests.js

@@ -0,0 +1,88 @@
+/* eslint-disable
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Client = require('./helpers/Client')
+const request = require('request')
+require('chai').should()
+const ClsiApp = require('./helpers/ClsiApp')
+
+describe('Broken LaTeX file', function() {
+  before(function(done) {
+    this.broken_request = {
+      resources: [
+        {
+          path: 'main.tex',
+          content: `\
+\\documentclass{articl % :(
+\\begin{documen % :(
+Broken
+\\end{documen % :(\
+`
+        }
+      ]
+    }
+    this.correct_request = {
+      resources: [
+        {
+          path: 'main.tex',
+          content: `\
+\\documentclass{article}
+\\begin{document}
+Hello world
+\\end{document}\
+`
+        }
+      ]
+    }
+    return ClsiApp.ensureRunning(done)
+  })
+
+  describe('on first run', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      return Client.compile(
+        this.project_id,
+        this.broken_request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          return done()
+        }
+      )
+    })
+
+    return it('should return a failure status', function() {
+      return this.body.compile.status.should.equal('failure')
+    })
+  })
+
+  return describe('on second run', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      return Client.compile(this.project_id, this.correct_request, () => {
+        return Client.compile(
+          this.project_id,
+          this.broken_request,
+          (error, res, body) => {
+            this.error = error
+            this.res = res
+            this.body = body
+            return done()
+          }
+        )
+      })
+    })
+
+    return it('should return a failure status', function() {
+      return this.body.compile.status.should.equal('failure')
+    })
+  })
+})

services/clsi/test/acceptance/js/DeleteOldFilesTest.js

@@ -0,0 +1,73 @@
+/* eslint-disable
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Client = require('./helpers/Client')
+const request = require('request')
+require('chai').should()
+const ClsiApp = require('./helpers/ClsiApp')
+
+describe('Deleting Old Files', function() {
+  before(function(done) {
+    this.request = {
+      resources: [
+        {
+          path: 'main.tex',
+          content: `\
+\\documentclass{article}
+\\begin{document}
+Hello world
+\\end{document}\
+`
+        }
+      ]
+    }
+    return ClsiApp.ensureRunning(done)
+  })
+
+  return describe('on first run', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          return done()
+        }
+      )
+    })
+
+    it('should return a success status', function() {
+      return this.body.compile.status.should.equal('success')
+    })
+
+    return describe('after file has been deleted', function() {
+      before(function(done) {
+        this.request.resources = []
+        return Client.compile(
+          this.project_id,
+          this.request,
+          (error, res, body) => {
+            this.error = error
+            this.res = res
+            this.body = body
+            return done()
+          }
+        )
+      })
+
+      return it('should return a failure status', function() {
+        return this.body.compile.status.should.equal('failure')
+      })
+    })
+  })
+})

services/clsi/test/acceptance/js/ExampleDocumentTests.js

@@ -0,0 +1,285 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-path-concat,
+    no-return-assign,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Client = require('./helpers/Client')
+const request = require('request')
+require('chai').should()
+const fs = require('fs')
+const fsExtra = require('fs-extra')
+const ChildProcess = require('child_process')
+const ClsiApp = require('./helpers/ClsiApp')
+const logger = require('logger-sharelatex')
+const Path = require('path')
+const fixturePath = path => {
+  if (path.slice(0, 3) === 'tmp') {
+    return '/tmp/clsi_acceptance_tests' + path.slice(3)
+  }
+  return Path.normalize(__dirname + '/../fixtures/' + path)
+}
+const process = require('process')
+console.log(
+  process.pid,
+  process.ppid,
+  process.getuid(),
+  process.getgroups(),
+  'PID'
+)
+
+const MOCHA_LATEX_TIMEOUT = 60 * 1000
+
+const convertToPng = function(pdfPath, pngPath, callback) {
+  if (callback == null) {
+    callback = function(error) {}
+  }
+  const command = `convert ${fixturePath(pdfPath)} ${fixturePath(pngPath)}`
+  console.log('COMMAND')
+  console.log(command)
+  const convert = ChildProcess.exec(command)
+  const stdout = ''
+  convert.stdout.on('data', chunk => console.log('STDOUT', chunk.toString()))
+  convert.stderr.on('data', chunk => console.log('STDERR', chunk.toString()))
+  return convert.on('exit', () => callback())
+}
+
+const compare = function(originalPath, generatedPath, callback) {
+  if (callback == null) {
+    callback = function(error, same) {}
+  }
+  const diff_file = `${fixturePath(generatedPath)}-diff.png`
+  const proc = ChildProcess.exec(
+    `compare -metric mae ${fixturePath(originalPath)} ${fixturePath(
+      generatedPath
+    )} ${diff_file}`
+  )
+  let stderr = ''
+  proc.stderr.on('data', chunk => (stderr += chunk))
+  return proc.on('exit', () => {
+    if (stderr.trim() === '0 (0)') {
+      // remove output diff if test matches expected image
+      fs.unlink(diff_file, err => {
+        if (err) {
+          throw err
+        }
+      })
+      return callback(null, true)
+    } else {
+      console.log('compare result', stderr)
+      return callback(null, false)
+    }
+  })
+}
+
+const checkPdfInfo = function(pdfPath, callback) {
+  if (callback == null) {
+    callback = function(error, output) {}
+  }
+  const proc = ChildProcess.exec(`pdfinfo ${fixturePath(pdfPath)}`)
+  let stdout = ''
+  proc.stdout.on('data', chunk => (stdout += chunk))
+  proc.stderr.on('data', chunk => console.log('STDERR', chunk.toString()))
+  return proc.on('exit', () => {
+    if (stdout.match(/Optimized:\s+yes/)) {
+      return callback(null, true)
+    } else {
+      return callback(null, false)
+    }
+  })
+}
+
+const compareMultiplePages = function(project_id, callback) {
+  if (callback == null) {
+    callback = function(error) {}
+  }
+  var compareNext = function(page_no, callback) {
+    const path = `tmp/${project_id}-source-${page_no}.png`
+    return fs.stat(fixturePath(path), (error, stat) => {
+      if (error != null) {
+        return callback()
+      } else {
+        return compare(
+          `tmp/${project_id}-source-${page_no}.png`,
+          `tmp/${project_id}-generated-${page_no}.png`,
+          (error, same) => {
+            if (error != null) {
+              throw error
+            }
+            same.should.equal(true)
+            return compareNext(page_no + 1, callback)
+          }
+        )
+      }
+    })
+  }
+  return compareNext(0, callback)
+}
+
+const comparePdf = function(project_id, example_dir, callback) {
+  if (callback == null) {
+    callback = function(error) {}
+  }
+  console.log('CONVERT')
+  console.log(`tmp/${project_id}.pdf`, `tmp/${project_id}-generated.png`)
+  return convertToPng(
+    `tmp/${project_id}.pdf`,
+    `tmp/${project_id}-generated.png`,
+    error => {
+      if (error != null) {
+        throw error
+      }
+      return convertToPng(
+        `examples/${example_dir}/output.pdf`,
+        `tmp/${project_id}-source.png`,
+        error => {
+          if (error != null) {
+            throw error
+          }
+          return fs.stat(
+            fixturePath(`tmp/${project_id}-source-0.png`),
+            (error, stat) => {
+              if (error != null) {
+                return compare(
+                  `tmp/${project_id}-source.png`,
+                  `tmp/${project_id}-generated.png`,
+                  (error, same) => {
+                    if (error != null) {
+                      throw error
+                    }
+                    same.should.equal(true)
+                    return callback()
+                  }
+                )
+              } else {
+                return compareMultiplePages(project_id, error => {
+                  if (error != null) {
+                    throw error
+                  }
+                  return callback()
+                })
+              }
+            }
+          )
+        }
+      )
+    }
+  )
+}
+
+const downloadAndComparePdf = function(project_id, example_dir, url, callback) {
+  if (callback == null) {
+    callback = function(error) {}
+  }
+  const writeStream = fs.createWriteStream(fixturePath(`tmp/${project_id}.pdf`))
+  request.get(url).pipe(writeStream)
+  console.log('writing file out', fixturePath(`tmp/${project_id}.pdf`))
+  return writeStream.on('close', () => {
+    return checkPdfInfo(`tmp/${project_id}.pdf`, (error, optimised) => {
+      if (error != null) {
+        throw error
+      }
+      optimised.should.equal(true)
+      return comparePdf(project_id, example_dir, callback)
+    })
+  })
+}
+
+Client.runServer(4242, fixturePath('examples'))
+
+describe('Example Documents', function() {
+  before(function(done) {
+    ClsiApp.ensureRunning(done)
+  })
+  before(function(done) {
+    fsExtra.remove(fixturePath('tmp'), done)
+  })
+  before(function(done) {
+    fs.mkdir(fixturePath('tmp'), done)
+  })
+  after(function(done) {
+    fsExtra.remove(fixturePath('tmp'), done)
+  })
+
+  return Array.from(fs.readdirSync(fixturePath('examples'))).map(example_dir =>
+    (example_dir =>
+      describe(example_dir, function() {
+        before(function() {
+          return (this.project_id = Client.randomId() + '_' + example_dir)
+        })
+
+        it('should generate the correct pdf', function(done) {
+          this.timeout(MOCHA_LATEX_TIMEOUT)
+          return Client.compileDirectory(
+            this.project_id,
+            fixturePath('examples'),
+            example_dir,
+            4242,
+            (error, res, body) => {
+              if (
+                error ||
+                __guard__(
+                  body != null ? body.compile : undefined,
+                  x => x.status
+                ) === 'failure'
+              ) {
+                console.log('DEBUG: error', error, 'body', JSON.stringify(body))
+              }
+              const pdf = Client.getOutputFile(body, 'pdf')
+              return downloadAndComparePdf(
+                this.project_id,
+                example_dir,
+                pdf.url,
+                done
+              )
+            }
+          )
+        })
+
+        return it('should generate the correct pdf on the second run as well', function(done) {
+          this.timeout(MOCHA_LATEX_TIMEOUT)
+          return Client.compileDirectory(
+            this.project_id,
+            fixturePath('examples'),
+            example_dir,
+            4242,
+            (error, res, body) => {
+              if (
+                error ||
+                __guard__(
+                  body != null ? body.compile : undefined,
+                  x => x.status
+                ) === 'failure'
+              ) {
+                console.log('DEBUG: error', error, 'body', JSON.stringify(body))
+              }
+              const pdf = Client.getOutputFile(body, 'pdf')
+              return downloadAndComparePdf(
+                this.project_id,
+                example_dir,
+                pdf.url,
+                done
+              )
+            }
+          )
+        })
+      }))(example_dir)
+  )
+})
+
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/test/acceptance/js/SimpleLatexFileTests.js

@@ -0,0 +1,71 @@
+/* eslint-disable
+    handle-callback-err,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Client = require('./helpers/Client')
+const request = require('request')
+require('chai').should()
+const ClsiApp = require('./helpers/ClsiApp')
+
+describe('Simple LaTeX file', function() {
+  before(function(done) {
+    this.project_id = Client.randomId()
+    this.request = {
+      resources: [
+        {
+          path: 'main.tex',
+          content: `\
+\\documentclass{article}
+\\begin{document}
+Hello world
+\\end{document}\
+`
+        }
+      ]
+    }
+    return ClsiApp.ensureRunning(() => {
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          return done()
+        }
+      )
+    })
+  })
+
+  it('should return the PDF', function() {
+    const pdf = Client.getOutputFile(this.body, 'pdf')
+    return pdf.type.should.equal('pdf')
+  })
+
+  it('should return the log', function() {
+    const log = Client.getOutputFile(this.body, 'log')
+    return log.type.should.equal('log')
+  })
+
+  it('should provide the pdf for download', function(done) {
+    const pdf = Client.getOutputFile(this.body, 'pdf')
+    return request.get(pdf.url, (error, res, body) => {
+      res.statusCode.should.equal(200)
+      return done()
+    })
+  })
+
+  return it('should provide the log for download', function(done) {
+    const log = Client.getOutputFile(this.body, 'pdf')
+    return request.get(log.url, (error, res, body) => {
+      res.statusCode.should.equal(200)
+      return done()
+    })
+  })
+})

services/clsi/test/acceptance/js/SynctexTests.js

@@ -0,0 +1,91 @@
+/* eslint-disable
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Client = require('./helpers/Client')
+const request = require('request')
+require('chai').should()
+const { expect } = require('chai')
+const ClsiApp = require('./helpers/ClsiApp')
+const crypto = require('crypto')
+
+describe('Syncing', function() {
+  before(function(done) {
+    const content = `\
+\\documentclass{article}
+\\begin{document}
+Hello world
+\\end{document}\
+`
+    this.request = {
+      resources: [
+        {
+          path: 'main.tex',
+          content
+        }
+      ]
+    }
+    this.project_id = Client.randomId()
+    return ClsiApp.ensureRunning(() => {
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          return done()
+        }
+      )
+    })
+  })
+
+  describe('from code to pdf', function() {
+    return it('should return the correct location', function(done) {
+      return Client.syncFromCode(
+        this.project_id,
+        'main.tex',
+        3,
+        5,
+        (error, pdfPositions) => {
+          if (error != null) {
+            throw error
+          }
+          expect(pdfPositions).to.deep.equal({
+            pdf: [
+              { page: 1, h: 133.77, v: 134.76, height: 6.92, width: 343.71 }
+            ]
+          })
+          return done()
+        }
+      )
+    })
+  })
+
+  return describe('from pdf to code', function() {
+    return it('should return the correct location', function(done) {
+      return Client.syncFromPdf(
+        this.project_id,
+        1,
+        100,
+        200,
+        (error, codePositions) => {
+          if (error != null) {
+            throw error
+          }
+          expect(codePositions).to.deep.equal({
+            code: [{ file: 'main.tex', line: 3, column: -1 }]
+          })
+          return done()
+        }
+      )
+    })
+  })
+})

services/clsi/test/acceptance/js/TimeoutTests.js

@@ -0,0 +1,62 @@
+/* eslint-disable
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Client = require('./helpers/Client')
+const request = require('request')
+require('chai').should()
+const ClsiApp = require('./helpers/ClsiApp')
+
+describe('Timed out compile', function() {
+  before(function(done) {
+    this.request = {
+      options: {
+        timeout: 10
+      }, // seconds
+      resources: [
+        {
+          path: 'main.tex',
+          content: `\
+\\documentclass{article}
+\\begin{document}
+\\def\\x{Hello!\\par\\x}
+\\x
+\\end{document}\
+`
+        }
+      ]
+    }
+    this.project_id = Client.randomId()
+    return ClsiApp.ensureRunning(() => {
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          return done()
+        }
+      )
+    })
+  })
+
+  it('should return a timeout error', function() {
+    return this.body.compile.error.should.equal('container timed out')
+  })
+
+  it('should return a timedout status', function() {
+    return this.body.compile.status.should.equal('timedout')
+  })
+
+  return it('should return the log output file name', function() {
+    const outputFilePaths = this.body.compile.outputFiles.map(x => x.path)
+    return outputFilePaths.should.include('output.log')
+  })
+})

services/clsi/test/acceptance/js/UrlCachingTests.js

@@ -0,0 +1,373 @@
+/* eslint-disable
+    no-path-concat,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Client = require('./helpers/Client')
+const request = require('request')
+require('chai').should()
+const sinon = require('sinon')
+const ClsiApp = require('./helpers/ClsiApp')
+
+const host = 'localhost'
+
+const Server = {
+  run() {
+    const express = require('express')
+    const app = express()
+
+    const staticServer = express.static(__dirname + '/../fixtures/')
+    app.get('/:random_id/*', (req, res, next) => {
+      this.getFile(req.url)
+      req.url = `/${req.params[0]}`
+      return staticServer(req, res, next)
+    })
+
+    return app.listen(31415, host)
+  },
+
+  getFile() {},
+
+  randomId() {
+    return Math.random()
+      .toString(16)
+      .slice(2)
+  }
+}
+
+Server.run()
+
+describe('Url Caching', function() {
+  describe('Downloading an image for the first time', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      this.file = `${Server.randomId()}/lion.png`
+      this.request = {
+        resources: [
+          {
+            path: 'main.tex',
+            content: `\
+\\documentclass{article}
+\\usepackage{graphicx}
+\\begin{document}
+\\includegraphics{lion.png}
+\\end{document}\
+`
+          },
+          {
+            path: 'lion.png',
+            url: `http://${host}:31415/${this.file}`
+          }
+        ]
+      }
+
+      sinon.spy(Server, 'getFile')
+      return ClsiApp.ensureRunning(() => {
+        return Client.compile(
+          this.project_id,
+          this.request,
+          (error, res, body) => {
+            this.error = error
+            this.res = res
+            this.body = body
+            return done()
+          }
+        )
+      })
+    })
+
+    afterEach(function() {
+      return Server.getFile.restore()
+    })
+
+    return it('should download the image', function() {
+      return Server.getFile.calledWith(`/${this.file}`).should.equal(true)
+    })
+  })
+
+  describe('When an image is in the cache and the last modified date is unchanged', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      this.file = `${Server.randomId()}/lion.png`
+      this.request = {
+        resources: [
+          {
+            path: 'main.tex',
+            content: `\
+\\documentclass{article}
+\\usepackage{graphicx}
+\\begin{document}
+\\includegraphics{lion.png}
+\\end{document}\
+`
+          },
+          (this.image_resource = {
+            path: 'lion.png',
+            url: `http://${host}:31415/${this.file}`,
+            modified: Date.now()
+          })
+        ]
+      }
+
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          sinon.spy(Server, 'getFile')
+          return Client.compile(
+            this.project_id,
+            this.request,
+            (error1, res1, body1) => {
+              this.error = error1
+              this.res = res1
+              this.body = body1
+              return done()
+            }
+          )
+        }
+      )
+    })
+
+    after(function() {
+      return Server.getFile.restore()
+    })
+
+    return it('should not download the image again', function() {
+      return Server.getFile.called.should.equal(false)
+    })
+  })
+
+  describe('When an image is in the cache and the last modified date is advanced', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      this.file = `${Server.randomId()}/lion.png`
+      this.request = {
+        resources: [
+          {
+            path: 'main.tex',
+            content: `\
+\\documentclass{article}
+\\usepackage{graphicx}
+\\begin{document}
+\\includegraphics{lion.png}
+\\end{document}\
+`
+          },
+          (this.image_resource = {
+            path: 'lion.png',
+            url: `http://${host}:31415/${this.file}`,
+            modified: (this.last_modified = Date.now())
+          })
+        ]
+      }
+
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          sinon.spy(Server, 'getFile')
+          this.image_resource.modified = new Date(this.last_modified + 3000)
+          return Client.compile(
+            this.project_id,
+            this.request,
+            (error1, res1, body1) => {
+              this.error = error1
+              this.res = res1
+              this.body = body1
+              return done()
+            }
+          )
+        }
+      )
+    })
+
+    afterEach(function() {
+      return Server.getFile.restore()
+    })
+
+    return it('should download the image again', function() {
+      return Server.getFile.called.should.equal(true)
+    })
+  })
+
+  describe('When an image is in the cache and the last modified date is further in the past', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      this.file = `${Server.randomId()}/lion.png`
+      this.request = {
+        resources: [
+          {
+            path: 'main.tex',
+            content: `\
+\\documentclass{article}
+\\usepackage{graphicx}
+\\begin{document}
+\\includegraphics{lion.png}
+\\end{document}\
+`
+          },
+          (this.image_resource = {
+            path: 'lion.png',
+            url: `http://${host}:31415/${this.file}`,
+            modified: (this.last_modified = Date.now())
+          })
+        ]
+      }
+
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          sinon.spy(Server, 'getFile')
+          this.image_resource.modified = new Date(this.last_modified - 3000)
+          return Client.compile(
+            this.project_id,
+            this.request,
+            (error1, res1, body1) => {
+              this.error = error1
+              this.res = res1
+              this.body = body1
+              return done()
+            }
+          )
+        }
+      )
+    })
+
+    afterEach(function() {
+      return Server.getFile.restore()
+    })
+
+    return it('should not download the image again', function() {
+      return Server.getFile.called.should.equal(false)
+    })
+  })
+
+  describe('When an image is in the cache and the last modified date is not specified', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      this.file = `${Server.randomId()}/lion.png`
+      this.request = {
+        resources: [
+          {
+            path: 'main.tex',
+            content: `\
+\\documentclass{article}
+\\usepackage{graphicx}
+\\begin{document}
+\\includegraphics{lion.png}
+\\end{document}\
+`
+          },
+          (this.image_resource = {
+            path: 'lion.png',
+            url: `http://${host}:31415/${this.file}`,
+            modified: (this.last_modified = Date.now())
+          })
+        ]
+      }
+
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          sinon.spy(Server, 'getFile')
+          delete this.image_resource.modified
+          return Client.compile(
+            this.project_id,
+            this.request,
+            (error1, res1, body1) => {
+              this.error = error1
+              this.res = res1
+              this.body = body1
+              return done()
+            }
+          )
+        }
+      )
+    })
+
+    afterEach(function() {
+      return Server.getFile.restore()
+    })
+
+    return it('should download the image again', function() {
+      return Server.getFile.called.should.equal(true)
+    })
+  })
+
+  return describe('After clearing the cache', function() {
+    before(function(done) {
+      this.project_id = Client.randomId()
+      this.file = `${Server.randomId()}/lion.png`
+      this.request = {
+        resources: [
+          {
+            path: 'main.tex',
+            content: `\
+\\documentclass{article}
+\\usepackage{graphicx}
+\\begin{document}
+\\includegraphics{lion.png}
+\\end{document}\
+`
+          },
+          (this.image_resource = {
+            path: 'lion.png',
+            url: `http://${host}:31415/${this.file}`,
+            modified: (this.last_modified = Date.now())
+          })
+        ]
+      }
+
+      return Client.compile(this.project_id, this.request, error => {
+        if (error != null) {
+          throw error
+        }
+        return Client.clearCache(this.project_id, (error, res, body) => {
+          if (error != null) {
+            throw error
+          }
+          sinon.spy(Server, 'getFile')
+          return Client.compile(
+            this.project_id,
+            this.request,
+            (error1, res1, body1) => {
+              this.error = error1
+              this.res = res1
+              this.body = body1
+              return done()
+            }
+          )
+        })
+      })
+    })
+
+    afterEach(function() {
+      return Server.getFile.restore()
+    })
+
+    return it('should download the image again', function() {
+      return Server.getFile.called.should.equal(true)
+    })
+  })
+})

services/clsi/test/acceptance/js/WordcountTests.js

@@ -0,0 +1,72 @@
+/* eslint-disable
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const Client = require('./helpers/Client')
+const request = require('request')
+require('chai').should()
+const { expect } = require('chai')
+const path = require('path')
+const fs = require('fs')
+const ClsiApp = require('./helpers/ClsiApp')
+
+describe('Syncing', function() {
+  before(function(done) {
+    this.request = {
+      resources: [
+        {
+          path: 'main.tex',
+          content: fs.readFileSync(
+            path.join(__dirname, '../fixtures/naugty_strings.txt'),
+            'utf-8'
+          )
+        }
+      ]
+    }
+    this.project_id = Client.randomId()
+    return ClsiApp.ensureRunning(() => {
+      return Client.compile(
+        this.project_id,
+        this.request,
+        (error, res, body) => {
+          this.error = error
+          this.res = res
+          this.body = body
+          return done()
+        }
+      )
+    })
+  })
+
+  return describe('wordcount file', function() {
+    return it('should return wordcount info', function(done) {
+      return Client.wordcount(this.project_id, 'main.tex', (error, result) => {
+        if (error != null) {
+          throw error
+        }
+        expect(result).to.deep.equal({
+          texcount: {
+            encode: 'utf8',
+            textWords: 2281,
+            headWords: 2,
+            outside: 0,
+            headers: 2,
+            elements: 0,
+            mathInline: 6,
+            mathDisplay: 0,
+            errors: 0,
+            messages: ''
+          }
+        })
+        return done()
+      })
+    })
+  })
+})

services/clsi/test/acceptance/js/helpers/Client.js

@@ -0,0 +1,208 @@
+/* eslint-disable
+    camelcase,
+    handle-callback-err,
+    no-unused-vars,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+let Client
+const request = require('request')
+const fs = require('fs')
+const Settings = require('settings-sharelatex')
+
+const host = 'localhost'
+
+module.exports = Client = {
+  host: Settings.apis.clsi.url,
+
+  randomId() {
+    return Math.random()
+      .toString(16)
+      .slice(2)
+  },
+
+  compile(project_id, data, callback) {
+    if (callback == null) {
+      callback = function(error, res, body) {}
+    }
+    return request.post(
+      {
+        url: `${this.host}/project/${project_id}/compile`,
+        json: {
+          compile: data
+        }
+      },
+      callback
+    )
+  },
+
+  clearCache(project_id, callback) {
+    if (callback == null) {
+      callback = function(error, res, body) {}
+    }
+    return request.del(`${this.host}/project/${project_id}`, callback)
+  },
+
+  getOutputFile(response, type) {
+    for (const file of Array.from(response.compile.outputFiles)) {
+      if (file.type === type && file.url.match(`output.${type}`)) {
+        return file
+      }
+    }
+    return null
+  },
+
+  runServer(port, directory) {
+    const express = require('express')
+    const app = express()
+    app.use(express.static(directory))
+    console.log('starting test server on', port, host)
+    return app.listen(port, host).on('error', error => {
+      console.error('error starting server:', error.message)
+      return process.exit(1)
+    })
+  },
+
+  syncFromCode(project_id, file, line, column, callback) {
+    if (callback == null) {
+      callback = function(error, pdfPositions) {}
+    }
+    return request.get(
+      {
+        url: `${this.host}/project/${project_id}/sync/code`,
+        qs: {
+          file,
+          line,
+          column
+        }
+      },
+      (error, response, body) => {
+        if (error != null) {
+          return callback(error)
+        }
+        return callback(null, JSON.parse(body))
+      }
+    )
+  },
+
+  syncFromPdf(project_id, page, h, v, callback) {
+    if (callback == null) {
+      callback = function(error, pdfPositions) {}
+    }
+    return request.get(
+      {
+        url: `${this.host}/project/${project_id}/sync/pdf`,
+        qs: {
+          page,
+          h,
+          v
+        }
+      },
+      (error, response, body) => {
+        if (error != null) {
+          return callback(error)
+        }
+        return callback(null, JSON.parse(body))
+      }
+    )
+  },
+
+  compileDirectory(project_id, baseDirectory, directory, serverPort, callback) {
+    if (callback == null) {
+      callback = function(error, res, body) {}
+    }
+    const resources = []
+    let entities = fs.readdirSync(`${baseDirectory}/${directory}`)
+    let rootResourcePath = 'main.tex'
+    while (entities.length > 0) {
+      var entity = entities.pop()
+      const stat = fs.statSync(`${baseDirectory}/${directory}/${entity}`)
+      if (stat.isDirectory()) {
+        entities = entities.concat(
+          fs
+            .readdirSync(`${baseDirectory}/${directory}/${entity}`)
+            .map(subEntity => {
+              if (subEntity === 'main.tex') {
+                rootResourcePath = `${entity}/${subEntity}`
+              }
+              return `${entity}/${subEntity}`
+            })
+        )
+      } else if (stat.isFile() && entity !== 'output.pdf') {
+        const extension = entity.split('.').pop()
+        if (
+          [
+            'tex',
+            'bib',
+            'cls',
+            'sty',
+            'pdf_tex',
+            'Rtex',
+            'ist',
+            'md',
+            'Rmd'
+          ].indexOf(extension) > -1
+        ) {
+          resources.push({
+            path: entity,
+            content: fs
+              .readFileSync(`${baseDirectory}/${directory}/${entity}`)
+              .toString()
+          })
+        } else if (
+          ['eps', 'ttf', 'png', 'jpg', 'pdf', 'jpeg'].indexOf(extension) > -1
+        ) {
+          resources.push({
+            path: entity,
+            url: `http://${host}:${serverPort}/${directory}/${entity}`,
+            modified: stat.mtime
+          })
+        }
+      }
+    }
+
+    return fs.readFile(
+      `${baseDirectory}/${directory}/options.json`,
+      (error, body) => {
+        const req = {
+          resources,
+          rootResourcePath
+        }
+
+        if (error == null) {
+          body = JSON.parse(body)
+          req.options = body
+        }
+
+        return this.compile(project_id, req, callback)
+      }
+    )
+  },
+
+  wordcount(project_id, file, callback) {
+    if (callback == null) {
+      callback = function(error, pdfPositions) {}
+    }
+    return request.get(
+      {
+        url: `${this.host}/project/${project_id}/wordcount`,
+        qs: {
+          file
+        }
+      },
+      (error, response, body) => {
+        if (error != null) {
+          return callback(error)
+        }
+        return callback(null, JSON.parse(body))
+      }
+    )
+  }
+}

services/clsi/test/acceptance/js/helpers/ClsiApp.js

@@ -0,0 +1,64 @@
+/* eslint-disable
+    handle-callback-err,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS101: Remove unnecessary use of Array.from
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS103: Rewrite code to no longer use __guard__
+ * DS205: Consider reworking code to avoid use of IIFEs
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const app = require('../../../../app')
+require('logger-sharelatex').logger.level('info')
+const logger = require('logger-sharelatex')
+const Settings = require('settings-sharelatex')
+
+module.exports = {
+  running: false,
+  initing: false,
+  callbacks: [],
+  ensureRunning(callback) {
+    if (callback == null) {
+      callback = function(error) {}
+    }
+    if (this.running) {
+      return callback()
+    } else if (this.initing) {
+      return this.callbacks.push(callback)
+    } else {
+      this.initing = true
+      this.callbacks.push(callback)
+      return app.listen(
+        __guard__(
+          Settings.internal != null ? Settings.internal.clsi : undefined,
+          x => x.port
+        ),
+        'localhost',
+        error => {
+          if (error != null) {
+            throw error
+          }
+          this.running = true
+          logger.log('clsi running in dev mode')
+
+          return (() => {
+            const result = []
+            for (callback of Array.from(this.callbacks)) {
+              result.push(callback())
+            }
+            return result
+          })()
+        }
+      )
+    }
+  }
+}
+function __guard__(value, transform) {
+  return typeof value !== 'undefined' && value !== null
+    ? transform(value)
+    : undefined
+}

services/clsi/test/load/coffee/loadTest.coffee

@@ -1,71 +0,0 @@
-request = require "request"
-Settings = require "settings-sharelatex"
-async = require("async")
-fs = require("fs")
-_ = require("underscore")
-concurentCompiles = 5
-totalCompiles = 50
-
-buildUrl = (path) -> "http://#{Settings.internal.clsi.host}:#{Settings.internal.clsi.port}/#{path}"
-
-mainTexContent = fs.readFileSync("./bulk.tex", "utf-8")
-
-compileTimes = []
-failedCount = 0
-
-getAverageCompileTime = ->
-	totalTime = _.reduce compileTimes, (sum, time)->
-		sum + time
-	, 0
-	return totalTime / compileTimes.length
-
-makeRequest = (compileNumber, callback)->
-	bulkBodyCount = 7
-	bodyContent = ""
-	while --bulkBodyCount
-		bodyContent = bodyContent+=mainTexContent
-
-
-	startTime = new Date()
-	request.post {
-		url: buildUrl("project/loadcompile-#{compileNumber}/compile")
-		json:
-			compile:
-				resources: [
-					path: "main.tex"
-					content: """
-						\\documentclass{article}
-						\\begin{document}
-						#{bodyContent}
-						\\end{document}
-					"""
-				]
-		}, (err, response, body)->
-			if response.statusCode != 200
-				failedCount++
-				return callback("compile #{compileNumber} failed")
-			if err?
-				failedCount++
-				return callback("failed")
-			totalTime = new Date() - startTime
-			console.log totalTime+"ms"
-			compileTimes.push(totalTime)
-			callback(err)
-
-
-jobs = _.map [1..totalCompiles], (i)->
-	return (cb)->
-		makeRequest(i, cb)
-
-startTime = new Date()
-async.parallelLimit jobs, concurentCompiles, (err)->
-	if err?
-		console.error err
-	console.log("total time taken = #{(new Date() - startTime)/1000}s")
-	console.log("total compiles = #{totalCompiles}")
-	console.log("concurent compiles = #{concurentCompiles}")
-	console.log("average time = #{getAverageCompileTime()/1000}s")
-	console.log("max time = #{_.max(compileTimes)/1000}s")
-	console.log("min time = #{_.min(compileTimes)/1000}s")
-	console.log("total failures = #{failedCount}")
-

services/clsi/test/load/js/loadTest.js

@@ -0,0 +1,103 @@
+/* eslint-disable
+    standard/no-callback-literal,
+*/
+// TODO: This file was created by bulk-decaffeinate.
+// Fix any style issues and re-enable lint.
+/*
+ * decaffeinate suggestions:
+ * DS102: Remove unnecessary code created because of implicit returns
+ * DS207: Consider shorter variations of null checks
+ * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
+ */
+const request = require('request')
+const Settings = require('settings-sharelatex')
+const async = require('async')
+const fs = require('fs')
+const _ = require('underscore')
+const concurentCompiles = 5
+const totalCompiles = 50
+
+const buildUrl = path =>
+  `http://${Settings.internal.clsi.host}:${Settings.internal.clsi.port}/${path}`
+
+const mainTexContent = fs.readFileSync('./bulk.tex', 'utf-8')
+
+const compileTimes = []
+let failedCount = 0
+
+const getAverageCompileTime = function() {
+  const totalTime = _.reduce(compileTimes, (sum, time) => sum + time, 0)
+  return totalTime / compileTimes.length
+}
+
+const makeRequest = function(compileNumber, callback) {
+  let bulkBodyCount = 7
+  let bodyContent = ''
+  while (--bulkBodyCount) {
+    bodyContent = bodyContent += mainTexContent
+  }
+
+  const startTime = new Date()
+  return request.post(
+    {
+      url: buildUrl(`project/loadcompile-${compileNumber}/compile`),
+      json: {
+        compile: {
+          resources: [
+            {
+              path: 'main.tex',
+              content: `\
+\\documentclass{article}
+\\begin{document}
+${bodyContent}
+\\end{document}\
+`
+            }
+          ]
+        }
+      }
+    },
+    (err, response, body) => {
+      if (response.statusCode !== 200) {
+        failedCount++
+        return callback(`compile ${compileNumber} failed`)
+      }
+      if (err != null) {
+        failedCount++
+        return callback('failed')
+      }
+      const totalTime = new Date() - startTime
+      console.log(totalTime + 'ms')
+      compileTimes.push(totalTime)
+      return callback(err)
+    }
+  )
+}
+
+const jobs = _.map(__range__(1, totalCompiles, true), i => cb =>
+  makeRequest(i, cb)
+)
+
+const startTime = new Date()
+async.parallelLimit(jobs, concurentCompiles, err => {
+  if (err != null) {
+    console.error(err)
+  }
+  console.log(`total time taken = ${(new Date() - startTime) / 1000}s`)
+  console.log(`total compiles = ${totalCompiles}`)
+  console.log(`concurent compiles = ${concurentCompiles}`)
+  console.log(`average time = ${getAverageCompileTime() / 1000}s`)
+  console.log(`max time = ${_.max(compileTimes) / 1000}s`)
+  console.log(`min time = ${_.min(compileTimes) / 1000}s`)
+  return console.log(`total failures = ${failedCount}`)
+})
+
+function __range__(left, right, inclusive) {
+  const range = []
+  const ascending = left < right
+  const end = !inclusive ? right : ascending ? right + 1 : right - 1
+  for (let i = left; ascending ? i < end : i > end; ascending ? i++ : i--) {
+    range.push(i)
+  }
+  return range
+}

services/clsi/test/smoke/coffee/SmokeTests.coffee

@@ -1,64 +0,0 @@
-chai = require("chai")
-chai.should() unless Object.prototype.should?
-expect = chai.expect
-request = require "request"
-Settings = require "settings-sharelatex"
-
-buildUrl = (path) -> "http://#{Settings.internal.clsi.host}:#{Settings.internal.clsi.port}/#{path}"
-
-url = buildUrl("project/smoketest-#{process.pid}/compile")
-
-describe "Running a compile", ->
-	before (done) ->
-		request.post {
-			url: url
-			json:
-				compile:
-					resources: [
-						path: "main.tex"
-						content: """
-% Membrane-like surface
-% Author: Yotam Avital
-\\documentclass{article}
-\\usepackage{tikz}
-\\usetikzlibrary{calc,fadings,decorations.pathreplacing}
-\\begin{document}
-\\begin{tikzpicture}
-  \\def\\nuPi{3.1459265}
-  \\foreach \\i in {5,4,...,2}{% This one doesn't matter
-    \\foreach \\j in {3,2,...,0}{% This will crate a membrane
-                               % with the front lipids visible
-      % top layer
-      \\pgfmathsetmacro{\\dx}{rand*0.1}% A random variance in the x coordinate
-      \\pgfmathsetmacro{\\dy}{rand*0.1}% A random variance in the y coordinate,
-                                     % gives a hight fill to the lipid
-      \\pgfmathsetmacro{\\rot}{rand*0.1}% A random variance in the
-                                      % molecule orientation      
-      \\shade[ball color=red] ({\\i+\\dx+\\rot},{0.5*\\j+\\dy+0.4*sin(\\i*\\nuPi*10)}) circle(0.45);
-      \\shade[ball color=gray] (\\i+\\dx,{0.5*\\j+\\dy+0.4*sin(\\i*\\nuPi*10)-0.9}) circle(0.45);
-      \\shade[ball color=gray] (\\i+\\dx-\\rot,{0.5*\\j+\\dy+0.4*sin(\\i*\\nuPi*10)-1.8}) circle(0.45);
-      % bottom layer
-      \\pgfmathsetmacro{\\dx}{rand*0.1}
-      \\pgfmathsetmacro{\\dy}{rand*0.1}
-      \\pgfmathsetmacro{\\rot}{rand*0.1}
-      \\shade[ball color=gray] (\\i+\\dx+\\rot,{0.5*\\j+\\dy+0.4*sin(\\i*\\nuPi*10)-2.8}) circle(0.45);
-      \\shade[ball color=gray] (\\i+\\dx,{0.5*\\j+\\dy+0.4*sin(\\i*\\nuPi*10)-3.7}) circle(0.45);
-      \\shade[ball color=red] (\\i+\\dx-\\rot,{0.5*\\j+\\dy+0.4*sin(\\i*\\nuPi*10)-4.6}) circle(0.45);
-    }
-  }
-\\end{tikzpicture}
-\\end{document}
-						"""
-					]
-		}, (@error, @response, @body) =>
-			done()
-
-	it "should return the pdf", ->
-		for file in @body.compile.outputFiles
-			return if file.type == "pdf"
-		throw new Error("no pdf returned")
-	
-	it "should return the log", ->
-		for file in @body.compile.outputFiles
-			return if file.type == "log"
-		throw new Error("no log returned")