From 638ac52e4053a8b8e5bedeb2726532643274f4ca Mon Sep 17 00:00:00 2001
From: Shane Kilkelly <shane@kilkelly.me>
Date: Fri, 17 Jun 2016 14:38:08 +0100
Subject: [PATCH 01/19] Move the latexmk timing command into a configurable
 `latexmkCommandPrefix`.

By default, no timing information will be taken.
On Linux with GNU user land, this value should be configured to `["/usr/bin/time", "-v"]`.
On Mac, gnu-time should be installed and configured to `["/usr/local/bin/gtime", "-v"]`.
---
 services/clsi/app/coffee/LatexRunner.coffee   | 4 +++-
 services/clsi/config/settings.defaults.coffee | 3 +++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/services/clsi/app/coffee/LatexRunner.coffee b/services/clsi/app/coffee/LatexRunner.coffee
index 65a30464ee..748c277ff4 100644
--- a/services/clsi/app/coffee/LatexRunner.coffee
+++ b/services/clsi/app/coffee/LatexRunner.coffee
@@ -49,7 +49,9 @@ 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"]
+	_latexmkBaseCommand: (Settings?.clsi?.latexmkCommandPrefix || []).concat(
+			["latexmk", "-cd", "-f", "-jobname=output", "-auxdir=$COMPILE_DIR", "-outdir=$COMPILE_DIR"]
+		)
 
 	_pdflatexCommand: (mainFile) ->
 		LatexRunner._latexmkBaseCommand.concat [
diff --git a/services/clsi/config/settings.defaults.coffee b/services/clsi/config/settings.defaults.coffee
index ae8e132346..f77df86b1a 100644
--- a/services/clsi/config/settings.defaults.coffee
+++ b/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:

From 03188d2a57070aa3f85e17c84d2ca137841b47a0 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Wed, 8 Jun 2016 16:58:08 +0100
Subject: [PATCH 02/19] only keep a single cached output directory in per-user
 containers

---
 services/clsi/app/coffee/OutputCacheManager.coffee | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/services/clsi/app/coffee/OutputCacheManager.coffee b/services/clsi/app/coffee/OutputCacheManager.coffee
index 7f11bc89b0..25c24b885a 100644
--- a/services/clsi/app/coffee/OutputCacheManager.coffee
+++ b/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 0 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

From dd4e1e17b588ab5bcb304d79ff8a40f560b0b0df Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Wed, 29 Jun 2016 16:31:08 +0100
Subject: [PATCH 03/19] keep one extra build until per-page pdf serving is
 enabled

---
 services/clsi/app/coffee/OutputCacheManager.coffee | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/services/clsi/app/coffee/OutputCacheManager.coffee b/services/clsi/app/coffee/OutputCacheManager.coffee
index 25c24b885a..76692b3b71 100644
--- a/services/clsi/app/coffee/OutputCacheManager.coffee
+++ b/services/clsi/app/coffee/OutputCacheManager.coffee
@@ -90,7 +90,7 @@ module.exports = OutputCacheManager =
 						# 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 0 else null}
+						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)

From 92461742d0cc305bbc4513495067261d50a53bbe Mon Sep 17 00:00:00 2001
From: WaeCo <aaqqws@googlemail.com>
Date: Wed, 13 Jul 2016 13:26:32 -0700
Subject: [PATCH 04/19] Set default project_cache_length_ms to 1 day

`project_cache_length_ms` was only `60*60*24 = 1.5 min` which is a little bit short. Default of one day seams more reasonable.
---
 services/clsi/config/settings.defaults.coffee | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/services/clsi/config/settings.defaults.coffee b/services/clsi/config/settings.defaults.coffee
index f77df86b1a..f1f7492a63 100644
--- a/services/clsi/config/settings.defaults.coffee
+++ b/services/clsi/config/settings.defaults.coffee
@@ -44,5 +44,5 @@ module.exports =
 			url: "http://localhost:3013"
 			
 	smokeTest: false
-	project_cache_length_ms: 60 * 60 * 24
-	parallelFileDownloads:1
\ No newline at end of file
+	project_cache_length_ms: 1000 * 60 * 60 * 24
+	parallelFileDownloads:1

From 9b58621fa8b0dadb124c4236186999c7919ed6ac Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Thu, 14 Jul 2016 14:47:36 +0100
Subject: [PATCH 05/19] add support for stopping compile

---
 services/clsi/app.coffee                      |  2 ++
 services/clsi/app/coffee/CommandRunner.coffee | 24 ++++++++++++++++---
 .../clsi/app/coffee/CompileController.coffee  | 12 ++++++++--
 .../clsi/app/coffee/CompileManager.coffee     | 11 +++++++++
 services/clsi/app/coffee/LatexRunner.coffee   | 15 +++++++++++-
 5 files changed, 58 insertions(+), 6 deletions(-)

diff --git a/services/clsi/app.coffee b/services/clsi/app.coffee
index fb3224e59d..d13798c4ea 100644
--- a/services/clsi/app.coffee
+++ b/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
diff --git a/services/clsi/app/coffee/CommandRunner.coffee b/services/clsi/app/coffee/CommandRunner.coffee
index 5ea6765c08..1d0b9e418b 100644
--- a/services/clsi/app/coffee/CommandRunner.coffee
+++ b/services/clsi/app/coffee/CommandRunner.coffee
@@ -9,9 +9,27 @@ module.exports = CommandRunner =
 		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
+		# 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
+
 		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()
\ No newline at end of file
+
+		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
+				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()
diff --git a/services/clsi/app/coffee/CompileController.coffee b/services/clsi/app/coffee/CompileController.coffee
index d4dddd4d82..610baac22e 100644
--- a/services/clsi/app/coffee/CompileController.coffee
+++ b/services/clsi/app/coffee/CompileController.coffee
@@ -15,7 +15,9 @@ 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?
 						logger.error err: error, project_id: request.project_id, "error running compile"
 						if error.timedout
 							status = "timedout"
@@ -43,7 +45,13 @@ module.exports = CompileController =
 								type: file.type
 								build: file.build
 					}
-		
+
+	stopCompile: (req, res, next) ->
+		{project_id, user_id, session_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?
diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index bb93dbdb9b..87e8734549 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -58,6 +58,13 @@ module.exports = CompileManager =
 					timeout:   request.timeout
 					image:     request.imageName
 				}, (error, output, stats, timings) ->
+					# compile was killed by user
+					if error?.terminated
+						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 +85,10 @@ 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)
diff --git a/services/clsi/app/coffee/LatexRunner.coffee b/services/clsi/app/coffee/LatexRunner.coffee
index 748c277ff4..8619e9baca 100644
--- a/services/clsi/app/coffee/LatexRunner.coffee
+++ b/services/clsi/app/coffee/LatexRunner.coffee
@@ -4,6 +4,8 @@ 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
@@ -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, (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
@@ -49,6 +54,14 @@ module.exports = LatexRunner =
 			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]?
+			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"]
 		)

From bd1e1de504ce06572f4069eaa54a245849a8f2cf Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Mon, 18 Jul 2016 11:05:45 +0100
Subject: [PATCH 06/19] remove dead code

---
 services/clsi/app/coffee/CompileController.coffee | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/services/clsi/app/coffee/CompileController.coffee b/services/clsi/app/coffee/CompileController.coffee
index 610baac22e..38d53f934b 100644
--- a/services/clsi/app/coffee/CompileController.coffee
+++ b/services/clsi/app/coffee/CompileController.coffee
@@ -47,7 +47,7 @@ module.exports = CompileController =
 					}
 
 	stopCompile: (req, res, next) ->
-		{project_id, user_id, session_id} = req.params
+		{project_id, user_id} = req.params
 		CompileManager.stopCompile project_id, user_id, (error) ->
 			return next(error) if error?
 			res.sendStatus(204)

From 3135ff2842643cf631cfc1b27fc8304e9641baa7 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Tue, 26 Jul 2016 12:30:29 +0100
Subject: [PATCH 07/19] add support for passing additional environment
 parameters to command runner

includes an example of passing environment variables to chktex
---
 services/clsi/app/coffee/CommandRunner.coffee          |  9 +++++++--
 services/clsi/app/coffee/CompileManager.coffee         | 10 +++++++++-
 services/clsi/app/coffee/LatexRunner.coffee            |  6 +++---
 .../clsi/test/unit/coffee/CompileManagerTests.coffee   |  2 ++
 services/clsi/test/unit/coffee/LatexRunnerTests.coffee |  6 ++++--
 5 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/services/clsi/app/coffee/CommandRunner.coffee b/services/clsi/app/coffee/CommandRunner.coffee
index 1d0b9e418b..298a495051 100644
--- a/services/clsi/app/coffee/CommandRunner.coffee
+++ b/services/clsi/app/coffee/CommandRunner.coffee
@@ -4,13 +4,18 @@ 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"
 
+		# 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
+		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"
diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 87e8734549..81c2c03975 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -41,7 +41,14 @@ module.exports = CompileManager =
 					DraftModeManager.injectDraftMode Path.join(compileDir, request.rootResourcePath), callback
 				else
 					callback()
-			
+
+			# set up environment variables for chktex
+			env = {}
+			if request.chktex?
+				env['CHKTEX_OPTIONS'] =  '-nall -e9 -e10 -e15 -e16 -e27'
+				if request.chktex is 'error'
+					env['CHKTEX_EXIT_ON_ERROR'] =  1
+
 			injectDraftModeIfRequired (error) ->
 				return callback(error) if error?
 				timer = new Metrics.Timer("run-compile")
@@ -57,6 +64,7 @@ module.exports = CompileManager =
 					compiler:  request.compiler
 					timeout:   request.timeout
 					image:     request.imageName
+					environment: env
 				}, (error, output, stats, timings) ->
 					# compile was killed by user
 					if error?.terminated
diff --git a/services/clsi/app/coffee/LatexRunner.coffee b/services/clsi/app/coffee/LatexRunner.coffee
index 8619e9baca..e743cf0174 100644
--- a/services/clsi/app/coffee/LatexRunner.coffee
+++ b/services/clsi/app/coffee/LatexRunner.coffee
@@ -8,11 +8,11 @@ ProcessTable = {}  # table of currently running jobs (pids or docker container n
 
 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.
@@ -34,7 +34,7 @@ module.exports = LatexRunner =
 
 		id = "#{project_id}" # record running project under this id
 
-		ProcessTable[id] = CommandRunner.run project_id, command, directory, image, timeout, (error, output) ->
+		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
diff --git a/services/clsi/test/unit/coffee/CompileManagerTests.coffee b/services/clsi/test/unit/coffee/CompileManagerTests.coffee
index 611ed11b01..62132f89e4 100644
--- a/services/clsi/test/unit/coffee/CompileManagerTests.coffee
+++ b/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
 
diff --git a/services/clsi/test/unit/coffee/LatexRunnerTests.coffee b/services/clsi/test/unit/coffee/LatexRunnerTests.coffee
index ace3d18ab7..c26fa642b2 100644
--- a/services/clsi/test/unit/coffee/LatexRunnerTests.coffee
+++ b/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", ->

From d6d6e18b895b88285959b0fc723fe383d10307b2 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Tue, 26 Jul 2016 16:22:38 +0100
Subject: [PATCH 08/19] run chktex when request has check:true

---
 services/clsi/app/coffee/CommandRunner.coffee     | 4 ++++
 services/clsi/app/coffee/CompileController.coffee | 2 ++
 services/clsi/app/coffee/CompileManager.coffee    | 8 ++++----
 services/clsi/app/coffee/RequestParser.coffee     | 3 +++
 4 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/services/clsi/app/coffee/CommandRunner.coffee b/services/clsi/app/coffee/CommandRunner.coffee
index 298a495051..11bbff82d3 100644
--- a/services/clsi/app/coffee/CommandRunner.coffee
+++ b/services/clsi/app/coffee/CommandRunner.coffee
@@ -27,6 +27,10 @@ module.exports = CommandRunner =
 				err = new Error("terminated")
 				err.terminated = true
 				return callback(err)
+			else if code
+				err = new Error("exit")
+				err.code = code
+				return callback(err)
 			else
 				callback()
 
diff --git a/services/clsi/app/coffee/CompileController.coffee b/services/clsi/app/coffee/CompileController.coffee
index 38d53f934b..3c9af677ae 100644
--- a/services/clsi/app/coffee/CompileController.coffee
+++ b/services/clsi/app/coffee/CompileController.coffee
@@ -17,6 +17,8 @@ module.exports = CompileController =
 				CompileManager.doCompile request, (error, outputFiles = []) ->
 					if error?.terminated
 						status = "terminated"
+					else if error?.code is 1
+						status = "exited"
 					else if error?
 						logger.error err: error, project_id: request.project_id, "error running compile"
 						if error.timedout
diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 81c2c03975..3b19cecaba 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -44,9 +44,9 @@ module.exports = CompileManager =
 
 			# set up environment variables for chktex
 			env = {}
-			if request.chktex?
-				env['CHKTEX_OPTIONS'] =  '-nall -e9 -e10 -e15 -e16 -e27'
-				if request.chktex is 'error'
+			if request.check?
+				env['CHKTEX_OPTIONS'] =  '-nall -e9 -e10 -w15 -w16 -w27'
+				if request.check is 'error'
 					env['CHKTEX_EXIT_ON_ERROR'] =  1
 
 			injectDraftModeIfRequired (error) ->
@@ -67,7 +67,7 @@ module.exports = CompileManager =
 					environment: env
 				}, (error, output, stats, timings) ->
 					# compile was killed by user
-					if error?.terminated
+					if error?.terminated or error?.code is 1
 						OutputFileFinder.findOutputFiles request.resources, compileDir, (err, outputFiles) ->
 							return callback(err) if err?
 							callback(error, outputFiles) # return output files so user can check logs
diff --git a/services/clsi/app/coffee/RequestParser.coffee b/services/clsi/app/coffee/RequestParser.coffee
index bd081fd011..5979c75c20 100644
--- a/services/clsi/app/coffee/RequestParser.coffee
+++ b/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

From ffea361d12a3af97cd830ac35bf7fa5a1e415ac5 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Wed, 27 Jul 2016 16:54:27 +0100
Subject: [PATCH 09/19] provide validation mode where compilation always exits
 after chktex

---
 services/clsi/app/coffee/CompileController.coffee | 4 ++--
 services/clsi/app/coffee/CompileManager.coffee    | 8 +++++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/services/clsi/app/coffee/CompileController.coffee b/services/clsi/app/coffee/CompileController.coffee
index 3c9af677ae..56237bf205 100644
--- a/services/clsi/app/coffee/CompileController.coffee
+++ b/services/clsi/app/coffee/CompileController.coffee
@@ -17,8 +17,8 @@ module.exports = CompileController =
 				CompileManager.doCompile request, (error, outputFiles = []) ->
 					if error?.terminated
 						status = "terminated"
-					else if error?.code is 1
-						status = "exited"
+					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
diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 3b19cecaba..4c89a0ba3d 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -48,6 +48,8 @@ module.exports = CompileManager =
 				env['CHKTEX_OPTIONS'] =  '-nall -e9 -e10 -w15 -w16 -w27'
 				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?
@@ -66,8 +68,12 @@ module.exports = CompileManager =
 					image:     request.imageName
 					environment: env
 				}, (error, output, stats, timings) ->
+					if request.check is "validate"
+						result = if error?.code then "fail" else "pass"
+						error = new Error("validation")
+						error.validate = result
 					# compile was killed by user
-					if error?.terminated or error?.code is 1
+					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

From f0c7b455a59605183c9bd08b8027851be5208111 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Fri, 29 Jul 2016 14:54:24 +0100
Subject: [PATCH 10/19] provide setting to override child_process.execFile for
 synctex

---
 services/clsi/app/coffee/CompileManager.coffee | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 87e8734549..16c36471e3 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -174,7 +174,8 @@ module.exports = CompileManager =
 	_runSynctex: (args, callback = (error, stdout) ->) ->
 		bin_path = Path.resolve(__dirname + "/../../bin/synctex")
 		seconds = 1000
-		child_process.execFile bin_path, args, timeout: 10 * seconds, (error, stdout, stderr) ->
+		synctex = Settings.clsi?.synctex?.command?(__dirname, child_process) || child_process
+		synctex.execFile bin_path, args, timeout: 10 * seconds, (error, stdout, stderr) ->
 			if error?
 				logger.err err:error, args:args, "error running synctex"
 				return callback(error)

From 08a446f03d974d5e794ffbc3e8d9058b09579220 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Thu, 4 Aug 2016 16:07:36 +0100
Subject: [PATCH 11/19] change logging message to be different from LatexRunner

---
 services/clsi/app/coffee/CompileManager.coffee | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index bf71477c0f..5d14bdf01d 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/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"

From c5917d4a757d1a74d508e5bd3eae62ec9a2dc44c Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Thu, 4 Aug 2016 16:08:14 +0100
Subject: [PATCH 12/19] use a command wrapper for synctex

instead of an alternative child_process object
---
 services/clsi/app/coffee/CompileManager.coffee | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 5d14bdf01d..34a3a57b89 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -188,8 +188,9 @@ module.exports = CompileManager =
 	_runSynctex: (args, callback = (error, stdout) ->) ->
 		bin_path = Path.resolve(__dirname + "/../../bin/synctex")
 		seconds = 1000
-		synctex = Settings.clsi?.synctex?.command?(__dirname, child_process) || child_process
-		synctex.execFile bin_path, args, timeout: 10 * seconds, (error, stdout, stderr) ->
+		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"
 				return callback(error)

From 872dbc5215a3c2043e96967dbb6d4b623316bef2 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Thu, 11 Aug 2016 09:29:03 +0100
Subject: [PATCH 13/19] add missing argument parameter to wordcount call

---
 services/clsi/app/coffee/CompileManager.coffee | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 34a3a57b89..39cff29d40 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -231,7 +231,7 @@ module.exports = CompileManager =
 		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")

From 400590b3ad353b50b846b849ef54ee9b8942b469 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Thu, 11 Aug 2016 09:32:47 +0100
Subject: [PATCH 14/19] read wordcount output asynchronously

---
 services/clsi/app/coffee/CompileManager.coffee | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 39cff29d40..e3a218be6f 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -233,12 +233,11 @@ module.exports = CompileManager =
 
 		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)
+				callback null, CompileManager._parseWordcountFromOutput(stdout)
 
 	_parseWordcountFromOutput: (output) ->
 		results = {

From ed5acc9f93bd28cf711fccc445881196ba1398c6 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Thu, 11 Aug 2016 09:40:08 +0100
Subject: [PATCH 15/19] capture texcount error output

---
 services/clsi/app/coffee/CompileManager.coffee | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index e3a218be6f..5192b7fab7 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -226,7 +226,7 @@ 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)
@@ -237,7 +237,9 @@ module.exports = CompileManager =
 				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)
-				callback null, CompileManager._parseWordcountFromOutput(stdout)
+				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 = {
@@ -249,6 +251,8 @@ module.exports = CompileManager =
 			elements: 0
 			mathInline: 0
 			mathDisplay: 0
+			errors: 0
+			messages: ""
 		}
 		for line in output.split("\n")
 			[data, info] = line.split(":")
@@ -268,4 +272,8 @@ 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

From a26971ba2e7c36adabaf21d6a52119af58813602 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Thu, 11 Aug 2016 10:31:37 +0100
Subject: [PATCH 16/19] update tests

---
 .../clsi/test/unit/coffee/CompileManagerTests.coffee   | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/services/clsi/test/unit/coffee/CompileManagerTests.coffee b/services/clsi/test/unit/coffee/CompileManagerTests.coffee
index 62132f89e4..d2b6a100a8 100644
--- a/services/clsi/test/unit/coffee/CompileManagerTests.coffee
+++ b/services/clsi/test/unit/coffee/CompileManagerTests.coffee
@@ -202,8 +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"
@@ -217,10 +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", ->
@@ -234,5 +234,7 @@ describe "CompileManager", ->
 					elements: 0
 					mathInline: 0
 					mathDisplay: 0
+					errors: 0
+					messages: ""
 				})
 				.should.equal true

From 1af44b32b33bd1b4269094ecf726fc085e95e864 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Mon, 22 Aug 2016 15:11:39 +0100
Subject: [PATCH 17/19] remove chktex error

too many false positives from 'unable to execute latex command'
---
 services/clsi/app/coffee/CompileManager.coffee | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 5192b7fab7..356346d308 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -45,7 +45,7 @@ module.exports = CompileManager =
 			# set up environment variables for chktex
 			env = {}
 			if request.check?
-				env['CHKTEX_OPTIONS'] =  '-nall -e9 -e10 -w15 -w16 -w27'
+				env['CHKTEX_OPTIONS'] = '-nall -e9 -e10 -w15 -w16'
 				if request.check is 'error'
 					env['CHKTEX_EXIT_ON_ERROR'] =  1
 				if request.check is 'validate'

From 481e842f3325c16cf16fd29ce51658ae697ba9f5 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Wed, 24 Aug 2016 15:45:26 +0100
Subject: [PATCH 18/19] fix commandRunner error to match dockerRunner

---
 services/clsi/app/coffee/CommandRunner.coffee | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/services/clsi/app/coffee/CommandRunner.coffee b/services/clsi/app/coffee/CommandRunner.coffee
index 11bbff82d3..f47af00177 100644
--- a/services/clsi/app/coffee/CommandRunner.coffee
+++ b/services/clsi/app/coffee/CommandRunner.coffee
@@ -27,8 +27,8 @@ module.exports = CommandRunner =
 				err = new Error("terminated")
 				err.terminated = true
 				return callback(err)
-			else if code
-				err = new Error("exit")
+			else if code is 1 # exit status from chktex
+				err = new Error("exited")
 				err.code = code
 				return callback(err)
 			else

From e23512f0e0d90c5a5f3642c8dbb894420f2e0f21 Mon Sep 17 00:00:00 2001
From: Brian Gough <bjg@network-theory.co.uk>
Date: Wed, 24 Aug 2016 15:46:47 +0100
Subject: [PATCH 19/19] handle failed compile due to validation error

---
 services/clsi/app/coffee/CompileManager.coffee | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/services/clsi/app/coffee/CompileManager.coffee b/services/clsi/app/coffee/CompileManager.coffee
index 356346d308..5d2bebb3bc 100644
--- a/services/clsi/app/coffee/CompileManager.coffee
+++ b/services/clsi/app/coffee/CompileManager.coffee
@@ -68,11 +68,16 @@ module.exports = CompileManager =
 					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
-					# compile was killed by user
+					# 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?