Add flags option to request JSON

Adds a `flags` parameter to the request JSON, appearing under the `compile.options` key (alongside such stalwarts as `compiler`, `timeout`, etc.).

This is primarily to support `-file-line-error` as an option, but could have other uses as well.

`flags` should be an array of strings, or absent. If supplied, the listed arguments are added to the base latexmk command.

services/clsi/app/coffee/CompileManager.coffee

@@ -93,6 +93,7 @@ module.exports = CompileManager =
 					compiler:  request.compiler
 					timeout:   request.timeout
 					image:     request.imageName
+					flags:     request.flags
 					environment: env
 				}, (error, output, stats, timings) ->
 					# request was for validation only

services/clsi/app/coffee/LatexRunner.coffee

@@ -8,24 +8,24 @@ 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, environment} = options
+		{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, "starting compile"
+		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
+			command = LatexRunner._pdflatexCommand mainFile, flags
 		else if compiler == "latex"
-			command = LatexRunner._latexCommand mainFile
+			command = LatexRunner._latexCommand mainFile, flags
 		else if compiler == "xelatex"
-			command = LatexRunner._xelatexCommand mainFile
+			command = LatexRunner._xelatexCommand mainFile, flags
 		else if compiler == "lualatex"
-			command = LatexRunner._lualatexCommand mainFile
+			command = LatexRunner._lualatexCommand mainFile, flags
 		else
 			return callback new Error("unknown compiler: #{compiler}")
 
@@ -63,31 +63,32 @@ module.exports = LatexRunner =
 		else
 			CommandRunner.kill ProcessTable[id], callback
 
-	_latexmkBaseCommand: (Settings?.clsi?.latexmkCommandPrefix || []).concat([
-		"latexmk", "-cd", "-f", "-jobname=output", "-auxdir=$COMPILE_DIR", "-outdir=$COMPILE_DIR",
-		"-synctex=1","-interaction=batchmode"
-		])
+	_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) ->
-		LatexRunner._latexmkBaseCommand.concat [
+	_pdflatexCommand: (mainFile, flags) ->
+		LatexRunner._latexmkBaseCommand(flags).concat [
 			"-pdf",
 			Path.join("$COMPILE_DIR", mainFile)
 		]
 
-	_latexCommand: (mainFile) ->
-		LatexRunner._latexmkBaseCommand.concat [
+	_latexCommand: (mainFile, flags) ->
+		LatexRunner._latexmkBaseCommand(flags).concat [
 			"-pdfdvi",
 			Path.join("$COMPILE_DIR", mainFile)
 		]
 
-	_xelatexCommand: (mainFile) ->
-		LatexRunner._latexmkBaseCommand.concat [
+	_xelatexCommand: (mainFile, flags) ->
+		LatexRunner._latexmkBaseCommand(flags).concat [
 			"-xelatex",
 			Path.join("$COMPILE_DIR", mainFile)
 		]
 
-	_lualatexCommand: (mainFile) ->
-		LatexRunner._latexmkBaseCommand.concat [
+	_lualatexCommand: (mainFile, flags) ->
+		LatexRunner._latexmkBaseCommand(flags).concat [
 			"-lualatex",
 			Path.join("$COMPILE_DIR", mainFile)
 		]

services/clsi/app/coffee/RequestParser.coffee

@@ -33,6 +33,10 @@ module.exports = RequestParser =
 			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

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

@@ -108,6 +108,7 @@ describe "CompileManager", ->
 				compiler: @compiler = "pdflatex"
 				timeout: @timeout = 42000
 				imageName: @image = "example.com/image"
+				flags: @flags = ["-file-line-error"]
 			@env = {}
 			@Settings.compileDir = "compiles"
 			@compileDir = "#{@Settings.path.compilesDir}/#{@project_id}-#{@user_id}"
@@ -135,6 +136,7 @@ describe "CompileManager", ->
 						compiler:  @compiler
 						timeout:   @timeout
 						image:     @image
+						flags:     @flags
 						environment: @env
 					})
 					.should.equal true
@@ -173,6 +175,7 @@ describe "CompileManager", ->
 						compiler:  @compiler
 						timeout:   @timeout
 						image:     @image
+						flags:     @flags
 						environment: {'CHKTEX_OPTIONS': '-nall -e9 -e10 -w15 -w16', 'CHKTEX_EXIT_ON_ERROR':1, 'CHKTEX_ULIMIT_OPTIONS': '-t 5 -v 64000'}
 					})
 					.should.equal true
@@ -191,6 +194,7 @@ describe "CompileManager", ->
 						compiler:  @compiler
 						timeout:   @timeout
 						image:     @image
+						flags:     @flags
 						environment: @env
 					})
 					.should.equal true

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

@@ -59,3 +59,21 @@ describe "LatexRunner", ->
 				mainFile = command.slice(-1)[0]
 				mainFile.should.equal "$COMPILE_DIR/main-file.tex"
 
+		describe "with a flags option", ->
+			beforeEach ->
+				@LatexRunner.runLatex @project_id,
+					directory: @directory
+					mainFile:  @mainFile
+					compiler:  @compiler
+					image:     @image
+					timeout:   @timeout = 42000
+					flags:     ["-file-line-error", "-halt-on-error"]
+					@callback
+
+			it "should include the flags in the command", ->
+				command = @CommandRunner.run.args[0][1]
+				flags = command.filter (arg) ->
+					(arg == "-file-line-error") || (arg == "-halt-on-error")
+				flags.length.should.equal 2
+				flags[0].should.equal "-file-line-error"
+				flags[1].should.equal "-halt-on-error"

services/clsi/test/unit/coffee/RequestParserTests.coffee

@@ -1,6 +1,7 @@
 SandboxedModule = require('sandboxed-module')
 sinon = require('sinon')
 require('chai').should()
+expect = require('chai').expect
 modulePath = require('path').join __dirname, '../../../app/js/RequestParser'
 tk = require("timekeeper")
 
@@ -66,6 +67,21 @@ describe "RequestParser", ->
 		it "should set the imageName", ->
 			@data.imageName.should.equal "basicImageName/here:2017-1"
 
+	describe "with flags set", ->
+		beforeEach ->
+			@validRequest.compile.options.flags = ["-file-line-error"]
+			@RequestParser.parse @validRequest, (error, @data) =>
+
+		it "should set the flags attribute", ->
+			expect(@data.flags).to.deep.equal ["-file-line-error"]
+
+	describe "with flags not specified", ->
+		beforeEach ->
+			@RequestParser.parse @validRequest, (error, @data) =>
+
+		it "it should have an empty flags list", ->
+			expect(@data.flags).to.deep.equal []
+
 	describe "without a timeout specified", ->
 		beforeEach ->
 			delete @validRequest.compile.options.timeout