Merge branch 'master' into sk-node-upgrade

services/clsi/app.coffee

@@ -56,6 +56,7 @@ app.param 'build_id', (req, res, next, build_id) ->
 
 
 app.post   "/project/:project_id/compile", bodyParser.json(limit: "5mb"), 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
@@ -65,6 +66,7 @@ app.get  "/project/:project_id/status", CompileController.status
 
 # Per-user containers
 app.post   "/project/:project_id/user/:user_id/compile", bodyParser.json(limit: "5mb"), 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

services/clsi/app/coffee/CommandRunner.coffee

@@ -4,14 +4,41 @@ logger = require "logger-sharelatex"
 logger.info "using standard command runner"
 
 module.exports = CommandRunner =
-	run: (project_id, command, directory, image, timeout, callback = (error) ->) ->
+	run: (project_id, command, directory, image, timeout, environment, callback = (error) ->) ->
 		command = (arg.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"
 
-		proc = spawn command[0], command.slice(1), stdio: "inherit", cwd: directory
+		# 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), stdio: "inherit", cwd: directory, detached: true, env: env
+
 		proc.on "error", (err)->
 			logger.err err:err, project_id:project_id, command: command, directory: directory, "error running command"
 			callback(err)
-		proc.on "close", () ->
-			callback()
+
+		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()
+
+		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/CompileController.coffee

@@ -15,7 +15,11 @@ module.exports = CompileController =
 			ProjectPersistenceManager.markProjectAsJustAccessed request.project_id, (error) ->
 				return next(error) if error?
 				CompileManager.doCompile request, (error, outputFiles = []) ->
-					if error?
+					if error?.terminated
+						status = "terminated"
+					else if error?.validate
+						status = "validation-#{error.validate}"
+					else if error?
 						logger.error err: error, project_id: request.project_id, "error running compile"
 						if error.timedout
 							status = "timedout"
@@ -43,7 +47,13 @@ module.exports = CompileController =
 								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?

services/clsi/app/coffee/CompileManager.coffee

@@ -28,7 +28,7 @@ module.exports = CompileManager =
 		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, "starting compile"
+		logger.log project_id: request.project_id, user_id: request.user_id, "syncing resources to disk"
 		ResourceWriter.syncResourcesToDisk request.project_id, request.resources, compileDir, (error) ->
 			if error?
 				logger.err err:error, project_id: request.project_id, user_id: request.user_id, "error writing resources to disk"
@@ -41,7 +41,16 @@ module.exports = CompileManager =
 					DraftModeManager.injectDraftMode Path.join(compileDir, request.rootResourcePath), callback
 				else
 					callback()
-			
+
+			# set up environment variables for chktex
+			env = {}
+			if request.check?
+				env['CHKTEX_OPTIONS'] = '-nall -e9 -e10 -w15 -w16'
+				if request.check is 'error'
+					env['CHKTEX_EXIT_ON_ERROR'] =  1
+				if request.check is 'validate'
+					env['CHKTEX_VALIDATE'] =  1
+
 			injectDraftModeIfRequired (error) ->
 				return callback(error) if error?
 				timer = new Metrics.Timer("run-compile")
@@ -57,7 +66,24 @@ module.exports = CompileManager =
 					compiler:  request.compiler
 					timeout:   request.timeout
 					image:     request.imageName
+					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
+						OutputFileFinder.findOutputFiles request.resources, compileDir, (err, outputFiles) ->
+							return callback(err) if err?
+							callback(error, outputFiles) # return output files so user can check logs
+						return
+					# compile completed normally
 					return callback(error) if error?
 					Metrics.inc("compiles-succeeded")
 					for metric_key, metric_value of stats or {}
@@ -78,6 +104,10 @@ module.exports = CompileManager =
 						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)
@@ -163,6 +193,8 @@ module.exports = CompileManager =
 	_runSynctex: (args, callback = (error, stdout) ->) ->
 		bin_path = Path.resolve(__dirname + "/../../bin/synctex")
 		seconds = 1000
+		if Settings.clsi?.synctexCommandWrapper?
+			[bin_path, args] = Settings.clsi?.synctexCommandWrapper bin_path, args
 		child_process.execFile bin_path, args, timeout: 10 * seconds, (error, stdout, stderr) ->
 			if error?
 				logger.err err:error, args:args, "error running synctex"
@@ -199,19 +231,20 @@ module.exports = CompileManager =
 	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", '-inc', file_path, "-out=" + file_path + ".wc"]
+		command = [ "texcount", '-nocol', '-inc', file_path, "-out=" + file_path + ".wc"]
 		directory = getCompileDir(project_id, user_id)
 		timeout = 10 * 1000
 		compileName = getCompileName(project_id, user_id)
 
-		CommandRunner.run compileName, command, directory, image, timeout, (error) ->
+		CommandRunner.run compileName, command, directory, image, timeout, {}, (error) ->
 			return callback(error) if error?
-			try
-				stdout = fs.readFileSync(directory + "/" + file_name + ".wc", "utf-8")
-			catch err
-				logger.err err:err, command:command, directory:directory, project_id:project_id, user_id:user_id, "error reading word count output"
-				return callback(err)
-			callback null, CompileManager._parseWordcountFromOutput(stdout)
+			fs.readFile directory + "/" + file_name + ".wc", "utf-8", (err, stdout) ->
+				if err?
+					logger.err err:err, command:command, directory:directory, 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 = {
@@ -223,6 +256,8 @@ module.exports = CompileManager =
 			elements: 0
 			mathInline: 0
 			mathDisplay: 0
+			errors: 0
+			messages: ""
 		}
 		for line in output.split("\n")
 			[data, info] = line.split(":")
@@ -242,4 +277,8 @@ module.exports = CompileManager =
 				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/LatexRunner.coffee

@@ -4,13 +4,15 @@ logger = require "logger-sharelatex"
 Metrics = require "./Metrics"
 CommandRunner = require(Settings.clsi?.commandRunner or "./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} = options
+		{directory, mainFile, compiler, timeout, image, environment} = options
 		compiler ||= "pdflatex"
 		timeout  ||= 60000 # milliseconds
 
-		logger.log directory: directory, compiler: compiler, timeout: timeout, mainFile: mainFile, "starting compile"
+		logger.log directory: directory, compiler: compiler, timeout: timeout, mainFile: mainFile, environment: environment, "starting compile"
 
 		# We want to run latexmk on the tex file which we will automatically
 		# generate from the Rtex/Rmd/md file.
@@ -30,7 +32,10 @@ module.exports = LatexRunner =
 		if Settings.clsi?.strace
 			command = ["strace", "-o", "strace", "-ff"].concat(command)
 
-		CommandRunner.run project_id, command, directory, image, timeout, (error, output) ->
+		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
@@ -49,7 +54,17 @@ module.exports = LatexRunner =
 			timings["sys-time"] = stderr?.match(/System time.*: (\d+.\d+)/m)?[1] or 0
 			callback error, output, stats, timings
 
-	_latexmkBaseCommand: ["/usr/bin/time", "-v", "latexmk", "-cd", "-f", "-jobname=output", "-auxdir=$COMPILE_DIR", "-outdir=$COMPILE_DIR"]
+	killLatex: (project_id, callback = (error) ->) ->
+		id = "#{project_id}"
+		logger.log {id:id}, "killing running compile"
+		if not ProcessTable[id]?
+			return callback new Error("no such project to kill")
+		else
+			CommandRunner.kill ProcessTable[id], callback
+
+	_latexmkBaseCommand: (Settings?.clsi?.latexmkCommandPrefix || []).concat(
+			["latexmk", "-cd", "-f", "-jobname=output", "-auxdir=$COMPILE_DIR", "-outdir=$COMPILE_DIR"]
+		)
 
 	_pdflatexCommand: (mainFile) ->
 		LatexRunner._latexmkBaseCommand.concat [

services/clsi/app/coffee/OutputCacheManager.coffee

@@ -45,9 +45,8 @@ module.exports = OutputCacheManager =
 		cacheRoot = Path.join(compileDir, OutputCacheManager.CACHE_SUBDIR)
 		# Put the files into a new cache subdirectory
 		cacheDir = Path.join(compileDir, OutputCacheManager.CACHE_SUBDIR, buildId)
-
-		# let file expiry run in the background
-		OutputCacheManager.expireOutputFiles cacheRoot, {keep: 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
@@ -83,9 +82,15 @@ module.exports = OutputCacheManager =
 					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: dir, "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)
@@ -116,6 +121,8 @@ module.exports = OutputCacheManager =
 
 			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

services/clsi/app/coffee/RequestParser.coffee

@@ -28,6 +28,9 @@ module.exports = RequestParser =
 				compile.options.draft,
 				default: false,
 				type: "boolean"
+			response.check = @_parseAttribute "check",
+				compile.options.check,
+				type: "string"
 
 			if response.timeout > RequestParser.MAX_TIMEOUT
 				response.timeout = RequestParser.MAX_TIMEOUT

services/clsi/config/settings.defaults.coffee

@@ -28,6 +28,9 @@ module.exports =
 	# 		modem:
 	# 			socketPath: false
 	# 		user: "tex"
+	# 		latexmkCommandPrefix: []
+	# 		# latexmkCommandPrefix: ["/usr/bin/time", "-v"]         # on Linux
+	# 		# latexmkCommandPrefix: ["/usr/local/bin/gtime", "-v"]  # on Mac OSX, installed with `brew install gnu-time`
 
 	internal:
 		clsi:
@@ -41,5 +44,5 @@ module.exports =
 			url: "http://localhost:3013"
 			
 	smokeTest: false
-	project_cache_length_ms: 60 * 60 * 24
-	parallelFileDownloads:1
+	project_cache_length_ms: 1000 * 60 * 60 * 24
+	parallelFileDownloads:1

services/clsi/test/unit/coffee/CompileManagerTests.coffee

@@ -47,6 +47,7 @@ describe "CompileManager", ->
 				compiler: @compiler = "pdflatex"
 				timeout: @timeout = 42000
 				imageName: @image = "example.com/image"
+			@env = {}
 			@Settings.compileDir = "compiles"
 			@compileDir = "#{@Settings.path.compilesDir}/#{@project_id}-#{@user_id}"
 			@ResourceWriter.syncResourcesToDisk = sinon.stub().callsArg(3)
@@ -72,6 +73,7 @@ describe "CompileManager", ->
 						compiler:  @compiler
 						timeout:   @timeout
 						image:     @image
+						environment: @env
 					})
 					.should.equal true
 
@@ -200,8 +202,8 @@ describe "CompileManager", ->
 
 	describe "wordcount", ->
 		beforeEach ->
-			@CommandRunner.run = sinon.stub().callsArg(5)
-			@fs.readFileSync = sinon.stub().returns @stdout = "Encoding: ascii\nWords in text: 2"
+			@CommandRunner.run = sinon.stub().callsArg(6)
+			@fs.readFile = sinon.stub().callsArgWith(2, null, @stdout = "Encoding: ascii\nWords in text: 2")
 			@callback  = sinon.stub()
 
 			@project_id = "project-id-123"
@@ -215,10 +217,10 @@ describe "CompileManager", ->
 		it "should run the texcount command", ->
 			@directory = "#{@Settings.path.compilesDir}/#{@project_id}-#{@user_id}"
 			@file_path = "$COMPILE_DIR/#{@file_name}"
-			@command =[ "texcount", "-inc", @file_path, "-out=" + @file_path + ".wc"]
+			@command =[ "texcount", "-nocol", "-inc", @file_path, "-out=" + @file_path + ".wc"]
 			
 			@CommandRunner.run
-				.calledWith("#{@project_id}-#{@user_id}", @command, @directory, @image, @timeout)
+				.calledWith("#{@project_id}-#{@user_id}", @command, @directory, @image, @timeout, {})
 				.should.equal true
 
 		it "should call the callback with the parsed output", ->
@@ -232,5 +234,7 @@ describe "CompileManager", ->
 					elements: 0
 					mathInline: 0
 					mathDisplay: 0
+					errors: 0
+					messages: ""
 				})
 				.should.equal true

services/clsi/test/unit/coffee/LatexRunnerTests.coffee

@@ -22,10 +22,11 @@ describe "LatexRunner", ->
 		@image     = "example.com/image"
 		@callback  = sinon.stub()
 		@project_id = "project-id-123"
+		@env       = {'foo': '123'}
 
 	describe "runLatex", ->
 		beforeEach ->
-			@CommandRunner.run = sinon.stub().callsArg(5)
+			@CommandRunner.run = sinon.stub().callsArg(6)
 
 		describe "normally", ->
 			beforeEach ->
@@ -35,11 +36,12 @@ describe "LatexRunner", ->
 					compiler:  @compiler
 					timeout:   @timeout = 42000
 					image:     @image
+					environment: @env
 					@callback
 
 			it "should run the latex command", ->
 				@CommandRunner.run
-					.calledWith(@project_id, sinon.match.any, @directory, @image, @timeout)
+					.calledWith(@project_id, sinon.match.any, @directory, @image, @timeout, @env)
 					.should.equal true
 
 		describe "with an .Rtex main file", ->