Release version 0.1.4

callback was previously async but is now synchronous, so high stack
usage.

app.coffee

@@ -12,6 +12,7 @@ Metrics.initialize("clsi")
 Metrics.open_sockets.monitor(logger)
 
 ProjectPersistenceManager = require "./app/js/ProjectPersistenceManager"
+OutputCacheManager = require "./app/js/OutputCacheManager"
 
 require("./app/js/db").sync()
 
@@ -36,7 +37,12 @@ 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
 
-staticServer = express.static Settings.path.compilesDir, setHeaders: (res, path, stat) ->
+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"
 		res.set("Content-Type", "application/pdf")
 		# Calculate an etag in the same way as nginx
@@ -50,7 +56,11 @@ staticServer = express.static Settings.path.compilesDir, setHeaders: (res, path,
 		# that could be used in same-origin/XSS attacks.
 		res.set("Content-Type", "text/plain")
 
-app.get "/project/:project_id/output/*", require("./app/js/SymlinkCheckerMiddlewear"), (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)
 
@@ -76,6 +86,15 @@ app.get "/health_check", (req, res)->
 	res.contentType(resCacher?.setContentType)
 	res.send resCacher?.code, resCacher?.body
 
+profiler = require "v8-profiler"
+app.get "/profile", (req, res) ->
+	time = parseInt(req.query.time || "1000")
+	profiler.startProfiling("test")
+	setTimeout () ->
+		profile = profiler.stopProfiling("test")
+		res.json(profile)
+	, time
+
 app.use (error, req, res, next) ->
 	logger.error err: error, "server error"
 	res.send error?.statusCode || 500

app/coffee/CompileController.coffee

@@ -35,6 +35,7 @@ module.exports = CompileController =
 							outputFiles: outputFiles.map (file) ->
 								url: "#{Settings.apis.clsi.url}/project/#{request.project_id}/output/#{file.path}"
 								type: file.type
+								build: file.build
 					}
 		
 	clearCache: (req, res, next = (error) ->) ->

app/coffee/CompileManager.coffee

@@ -1,6 +1,7 @@
 ResourceWriter = require "./ResourceWriter"
 LatexRunner = require "./LatexRunner"
 OutputFileFinder = require "./OutputFileFinder"
+OutputCacheManager = require "./OutputCacheManager"
 Settings = require("settings-sharelatex")
 Path = require "path"
 logger = require "logger-sharelatex"
@@ -32,7 +33,8 @@ module.exports = CompileManager =
 
 				OutputFileFinder.findOutputFiles request.resources, compileDir, (error, outputFiles) ->
 					return callback(error) if error?
-					callback null, outputFiles
+					OutputCacheManager.saveOutputFiles outputFiles, compileDir,  (error, newOutputFiles) ->
+						callback null, newOutputFiles
 	
 	clearProject: (project_id, _callback = (error) ->) ->
 		callback = (error) ->

app/coffee/OutputCacheManager.coffee

@@ -0,0 +1,113 @@
+async = require "async"
+fs = require "fs"
+fse = require "fs-extra"
+Path = require "path"
+logger = require "logger-sharelatex"
+_ = require "underscore"
+
+OutputFileOptimiser = require "./OutputFileOptimiser"
+
+module.exports = OutputCacheManager =
+	CACHE_SUBDIR: '.cache/clsi'
+	BUILD_REGEX: /^[0-9a-f]+$/  # build id is Date.now() converted to hex
+	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
+
+	saveOutputFiles: (outputFiles, compileDir, 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
+		buildId = Date.now().toString(16)
+		cacheDir = Path.join(compileDir, OutputCacheManager.CACHE_SUBDIR, buildId)
+		# let file expiry run in the background
+		OutputCacheManager.expireOutputFiles cacheRoot, {keep: buildId}
+
+		checkFile = (src, callback) ->
+			# check if we have a valid file to copy into the cache
+			fs.stat src, (err, stats) ->
+				if err?
+					# some problem reading the file
+					logger.error err: err, file: src, "stat error for file in cache"
+					callback(err)
+				else if not stats.isFile()
+					# other filetype - reject it
+					logger.error err: err, src: src, dst: dst, stat: stats, "nonfile output - refusing to copy to cache"
+					callback(new Error("output file is not a file"), file)
+				else
+					# it's a plain file, ok to copy
+					callback(null)
+
+		copyFile = (src, dst, callback) ->
+			# copy output file into the cache
+			fse.copy src, dst, (err) ->
+				if err?
+					logger.error err: err, src: src, dst: dst, "copy error for file in cache"
+					callback(err)
+				else
+					# call the optimiser for the file too
+					OutputFileOptimiser.optimiseFile src, dst, callback
+
+		# 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
+				async.mapSeries outputFiles, (file, cb) ->
+					newFile = _.clone(file)
+					[src, dst] = [Path.join(compileDir, file.path), Path.join(cacheDir, file.path)]
+					checkFile src, (err) ->
+						copyFile src, dst, (err) ->
+							if not err?
+								newFile.build = buildId  # attach a build id if we cached the file
+							cb(err, newFile)
+				, (err, results) ->
+					if err?
+						# pass back the original files if we encountered *any* error
+						callback(err, outputFiles)
+					else
+						# pass back the list of new files in the cache
+						callback(err, results)
+
+	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 hard limit
+				return true if index > OutputCacheManager.CACHE_LIMIT
+				# we can get the build time from the directory name
+				dirTime = parseInt(dir, 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

app/coffee/OutputFileFinder.coffee

@@ -17,19 +17,11 @@ module.exports = OutputFileFinder =
 			jobs = []
 			outputFiles = []
 			for file in allFiles
-				do (file) ->
+				if !incomingResources[file]
-					jobs.push (callback) ->
-						if incomingResources[file]
-							return callback()
-						else
 					outputFiles.push {
 						path: file
 						type: file.match(/\.([^\.]+)$/)?[1]
 					}
-							callback()
-
-			async.series jobs, (error) ->
-				return callback(error) if error?
 			callback null, outputFiles
 
 	_getAllFiles: (directory, _callback = (error, fileList) ->) ->
@@ -37,7 +29,7 @@ module.exports = OutputFileFinder =
 			_callback(error, fileList)
 			_callback = () ->
 				
-		args = [directory, "-type", "f"]
+		args = [directory, "-name", ".cache", "-prune", "-o", "-type", "f", "-print"]
 		logger.log args: args, "running find command"
 
 		proc = spawn("find", args)

app/coffee/OutputFileOptimiser.coffee

@@ -0,0 +1,37 @@
+fs = require "fs"
+Path = require "path"
+spawn = require("child_process").spawn
+logger = require "logger-sharelatex"
+_ = 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(/\.pdf$/)
+			OutputFileOptimiser.optimisePDF src, dst, callback
+		else
+			callback (null)
+
+	optimisePDF: (src, dst, callback = (error) ->) ->
+		tmpOutput = dst + '.opt'
+		args = ["--linearize", src, tmpOutput]
+		logger.log args: args, "running qpdf command"
+
+		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) ->
+			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

app/coffee/StaticServerForbidSymlinks.coffee

@@ -0,0 +1,24 @@
+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
+		requestedFsPath = Path.normalize("#{basePath}/#{path}")
+		fs.realpath requestedFsPath, (err, realFsPath)->
+			if err?
+				logger.warn err:err, requestedFsPath:requestedFsPath, realFsPath:realFsPath, path: req.params[0], project_id: req.params.project_id, "error checking file access"
+				if err.code == 'ENOENT'
+					return res.sendStatus(404)
+				else
+					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)

app/coffee/SymlinkCheckerMiddlewear.coffee

@@ -1,17 +0,0 @@
-Path = require("path")
-fs = require("fs")
-Settings = require("settings-sharelatex")
-logger = require("logger-sharelatex")
-
-
-module.exports = (req, res, next)->
-	basePath = Path.resolve("#{Settings.path.compilesDir}/#{req.params.project_id}")
-	requestedFsPath = Path.normalize("#{basePath}/#{req.params[0]}")
-	fs.realpath requestedFsPath, (err, realFsPath)->
-		if err?
-			return res.send(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.send(404)
-		else
-			return next()

package.json

@@ -1,7 +1,7 @@
 {
   "name": "node-clsi",
   "description": "A Node.js implementation of the CLSI LaTeX web-API",
-  "version": "0.1.3",
+  "version": "0.1.4",
   "repository": {
     "type": "git",
     "url": "https://github.com/sharelatex/clsi-sharelatex.git"
@@ -21,7 +21,10 @@
     "smoke-test-sharelatex": "git+https://github.com/sharelatex/smoke-test-sharelatex.git#v1.0.0",
     "sqlite3": "~2.2.0",
     "express": "^4.2.0",
-    "body-parser": "^1.2.0"
+    "body-parser": "^1.2.0",
+    "fs-extra": "^0.16.3",
+    "underscore": "^1.8.2",
+    "v8-profiler": "^5.2.4"
   },
   "devDependencies": {
     "mocha": "1.10.0",

test/unit/coffee/CompileControllerTests.coffee

@@ -36,9 +36,11 @@ describe "CompileController", ->
 			@output_files = [{
 				path: "output.pdf"
 				type: "pdf"
+				build: 1234
 			}, {
 				path: "output.log"
 				type: "log"
+				build: 1234
 			}]
 			@RequestParser.parse = sinon.stub().callsArgWith(1, null, @request)
 			@ProjectPersistenceManager.markProjectAsJustAccessed = sinon.stub().callsArg(1)
@@ -73,6 +75,7 @@ describe "CompileController", ->
 							outputFiles: @output_files.map (file) =>
 								url: "#{@Settings.apis.clsi.url}/project/#{@project_id}/output/#{file.path}"
 								type: file.type
+								build: file.build
 					)
 					.should.equal true
 			

test/unit/coffee/CompileManagerTests.coffee

@@ -12,6 +12,7 @@ describe "CompileManager", ->
 			"./LatexRunner": @LatexRunner = {}
 			"./ResourceWriter": @ResourceWriter = {}
 			"./OutputFileFinder": @OutputFileFinder = {}
+			"./OutputCacheManager": @OutputCacheManager = {}
 			"settings-sharelatex": @Settings = { path: compilesDir: "/compiles/dir" }
 			"logger-sharelatex": @logger = { log: sinon.stub() }
 			"child_process": @child_process = {}
@@ -26,6 +27,15 @@ describe "CompileManager", ->
 				path: "output.pdf"
 				type: "pdf"
 			}]
+			@build_files = [{
+				path: "output.log"
+				type: "log"
+				build: 1234
+			}, {
+				path: "output.pdf"
+				type: "pdf"
+				build: 1234
+			}]
 			@request =
 				resources: @resources = "mock-resources"
 				rootResourcePath: @rootResourcePath = "main.tex"
@@ -37,6 +47,7 @@ describe "CompileManager", ->
 			@ResourceWriter.syncResourcesToDisk = sinon.stub().callsArg(3)
 			@LatexRunner.runLatex = sinon.stub().callsArg(2)
 			@OutputFileFinder.findOutputFiles = sinon.stub().callsArgWith(2, null, @output_files)
+			@OutputCacheManager.saveOutputFiles = sinon.stub().callsArgWith(2, null, @build_files)
 			@CompileManager.doCompile @request, @callback
 
 		it "should write the resources to disk", ->
@@ -60,7 +71,8 @@ describe "CompileManager", ->
 				.should.equal true
 
 		it "should return the output files", ->
-			@callback.calledWith(null, @output_files).should.equal true
+			console.log 'output_files', @build_files
+			@callback.calledWith(null, @build_files).should.equal true
 
 	describe "clearProject", ->
 		describe "succesfully", ->

test/unit/coffee/StaticServerForbidSymlinksTests.coffee

@@ -0,0 +1,82 @@
+should = require('chai').should()
+SandboxedModule = require('sandboxed-module')
+assert = require('assert')
+path = require('path')
+sinon = require('sinon')
+modulePath = path.join __dirname, "../../../app/js/StaticServerForbidSymlinks"
+expect = require("chai").expect
+
+describe "StaticServerForbidSymlinks", ->
+
+	beforeEach ->
+
+		@settings = 
+			path:
+				compilesDir: "/compiles/here"
+
+		@fs = {}
+		@ForbidSymlinks = SandboxedModule.require modulePath, requires:
+			"settings-sharelatex":@settings
+			"logger-sharelatex": 
+				log:->
+				warn:->
+			"fs":@fs
+
+		@dummyStatic = (rootDir, options) ->
+			return (req, res, next) ->
+				# console.log "dummyStatic serving file", rootDir, "called with", req.url
+				# serve it
+				next()
+
+		@StaticServerForbidSymlinks = @ForbidSymlinks @dummyStatic, @settings.path.compilesDir
+		@req = 
+			params:
+				project_id:"12345"
+
+		@res = {}
+		@req.url = "/12345/output.pdf"
+
+
+	describe "sending a normal file through", ->
+		beforeEach ->
+			@fs.realpath = sinon.stub().callsArgWith(1, null, "#{@settings.path.compilesDir}/#{@req.params.project_id}/output.pdf")
+
+		it "should call next", (done)->
+			@res.sendStatus = (resCode)->
+				resCode.should.equal 200
+				done()
+			@StaticServerForbidSymlinks @req, @res, done
+
+
+	describe "with a missing file", ->
+		beforeEach ->
+			@fs.realpath = sinon.stub().callsArgWith(1, {code: 'ENOENT'}, "#{@settings.path.compilesDir}/#{@req.params.project_id}/unknown.pdf")
+
+		it "should send a 404", (done)->
+			@res.sendStatus = (resCode)->
+				resCode.should.equal 404
+				done()
+			@StaticServerForbidSymlinks @req, @res
+
+
+	describe "with a symlink file", ->
+		beforeEach ->
+			@fs.realpath = sinon.stub().callsArgWith(1, null, "/etc/#{@req.params.project_id}/output.pdf")
+
+		it "should send a 404", (done)->
+			@res.sendStatus = (resCode)->
+				resCode.should.equal 404
+				done()
+			@StaticServerForbidSymlinks @req, @res
+
+	describe "with an error from fs.realpath", ->
+
+		beforeEach ->
+			@fs.realpath = sinon.stub().callsArgWith(1, "error")
+
+		it "should send a 500", (done)->
+			@res.sendStatus = (resCode)->
+				resCode.should.equal 500
+				done()
+			@StaticServerForbidSymlinks @req, @res
+

test/unit/coffee/SymlinkCheckerMiddlewearTests.coffee

@@ -1,60 +0,0 @@
-should = require('chai').should()
-SandboxedModule = require('sandboxed-module')
-assert = require('assert')
-path = require('path')
-sinon = require('sinon')
-modulePath = path.join __dirname, "../../../app/js/SymlinkCheckerMiddlewear"
-expect = require("chai").expect
-
-describe "SymlinkCheckerMiddlewear", ->
-
-	beforeEach ->
-
-		@settings = 
-			path:
-				compilesDir: "/compiles/here"
-
-		@fs = {}
-		@SymlinkCheckerMiddlewear = SandboxedModule.require modulePath, requires:
-			"settings-sharelatex":@settings
-			"logger-sharelatex": 
-				log:->
-				warn:->
-			"fs":@fs
-		@req = 
-			params:
-				project_id:"12345"
-
-		@res = {}
-		@req.params[0]= "output.pdf"
-
-
-	describe "sending a normal file through", ->
-		beforeEach ->
-			@fs.realpath = sinon.stub().callsArgWith(1, null, "#{@settings.path.compilesDir}/#{@req.params.project_id}/output.pdf")
-
-		it "should call next", (done)->
-			@SymlinkCheckerMiddlewear @req, @res, done
-
-
-	describe "with a symlink file", ->
-		beforeEach ->
-			@fs.realpath = sinon.stub().callsArgWith(1, null, "/etc/#{@req.params.project_id}/output.pdf")
-
-		it "should send a 404", (done)->
-			@res.send = (resCode)->
-				resCode.should.equal 404
-				done()
-			@SymlinkCheckerMiddlewear @req, @res
-
-	describe "with an error from fs.realpath", ->
-
-		beforeEach ->
-			@fs.realpath = sinon.stub().callsArgWith(1, "error")
-
-		it "should send a 500", (done)->
-			@res.send = (resCode)->
-				resCode.should.equal 500
-				done()
-			@SymlinkCheckerMiddlewear @req, @res
-