initialize options,

removing unused routes which dont map to real functions
fixing indenting issues
prepare module includes comment structure
super -> super()
fixing winston
memory store
jquery file upload #TODO: fixing unlink async aguidrevitch/jquery-file-upload-middleware#85

app_api_template.coffee

@@ -54,8 +54,7 @@ startApp = ->
 		console.error 'Caught api exception: ' + err.stack
 		return
 
-	###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES###
-
+	#TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES
 
 	http.createServer(app).listen(app.get('port'), ->
 		console.log("ACAS API server listening on port " + app.get('port'))

app_template.coffee

@@ -15,6 +15,7 @@ startApp = ->
 	logger = require('morgan')
 	methodOverride = require('method-override')
 	session = require('express-session')
+	MemoryStore = require('memorystore')(session)
 	bodyParser = require('body-parser')
 	# multer = require('multer')
 	errorHandler = require('errorhandler')
@@ -71,7 +72,7 @@ startApp = ->
 #			next()
 
 	loginRoutes = require './routes/loginRoutes'
-
+	sessionStore = new MemoryStore();
 	global.app = express()
 	app.set 'port', config.all.client.port
 	app.set 'views', __dirname + '/views'
@@ -85,10 +86,12 @@ startApp = ->
 	app.use session
 		secret: 'acas needs login'
 		cookie: maxAge: 365 * 24 * 60 * 60 * 1000
+		store: sessionStore # MemoryStore is used automatically if no "store" field is set, but we need a handle on the sessionStore object for Socket.IO, so we'll manually create the store so we have a handle on the object
+
 	app.use flash()
 	app.use passport.initialize()
 	app.use passport.session pauseStream:  true
-#		app.use express.bodyParser()
+	# app.use express.bodyParser()
 	app.use(bodyParser.json({limit: '100mb'}))
 	app.use(bodyParser.urlencoded({limit: '100mb', extended: true,parameterLimit: 1000000}))
 	# app.use(multer())
@@ -102,8 +105,8 @@ startApp = ->
 
 
 	if not config.all.client.use.ssl
-		http.createServer(app).listen(app.get('port'), ->
-			console.log("Express server listening on port " + app.get('port'))
+		httpServer = http.createServer(app).listen(app.get('port'), ->
+			console.log("ACAS server listening on port " + app.get('port'))
 		)
 	else
 		console.log "------ Starting in SSL Mode"
@@ -115,12 +118,23 @@ startApp = ->
 			ca: fs.readFileSync config.all.server.ssl.cert.authority.file.path
 			passphrase: config.all.server.ssl.cert.passphrase
 		https.createServer(sslOptions, app).listen(app.get('port'), ->
-			console.log("Express server listening on port " + app.get('port'))
+			console.log("ACAS server listening on port " + app.get('port'))
 		)
 		#TODO hack to prevent bug: https://github.com/mikeal/request/issues/418
 		process.env.NODE_TLS_REJECT_UNAUTHORIZED = "0"
 
-	###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES###
+	io = require('socket.io')(httpServer)
+	passportSocketIo = require('passport.socketio')
+	cookieParser = require('cookie-parser')
+
+	io.use(passportSocketIo.authorize({
+		key: 'connect.sid',
+		secret: 'acas needs login',
+		store: sessionStore,
+		passport: passport,
+		cookieParser: cookieParser
+	}))
+	#TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES
 
 	options = if stubsMode then ["stubsMode"] else []
 	options.push ['--color']

modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee

@@ -210,7 +210,8 @@ class window.ACASLabelSequenceController extends AbstractFormController
 		"click .bv_save": "handleSaveClicked"
 		"click .bv_cancel": "handleCancelClicked"
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		if @model?
 			@completeInitialization()
 		else

modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee

@@ -1,6 +1,5 @@
 exports.setupAPIRoutes = (app) ->
 	app.get '/api/labelSequences', exports.getAllLabelSequences
-	app.get '/api/labelSequences/reagents/codename', exports.getReagentByCodename
 	app.post '/api/labelSequences/jsonArray', exports.saveLabelSequenceArray
 
 exports.setupRoutes = (app, loginRoutes) ->

modules/AdminPanel/src/client/AdminPanel.coffee

@@ -45,11 +45,11 @@ class window.AdminPanelController extends AbstractFormController
 recursivelyIterateAndDisplayValues = (dict) ->
 	keys = Object.keys dict
 	_.each(keys, (key) ->
-  	if isObject dict[key]
-  		recursivelyIterateAndDisplayValues dict[key]
-  	else
-			unless typeof dict[key] is "object"
-				@$('.bv_configProperties').append("<b>" + key + ":</b> " + dict[key] + "<br />")
+	if isObject dict[key]
+		recursivelyIterateAndDisplayValues dict[key]
+	else
+		unless typeof dict[key] is "object"
+			@$('.bv_configProperties').append("<b>" + key + ":</b> " + dict[key] + "<br />")
 	)
 	#TODO add full paths - Matt
 

modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee

@@ -121,6 +121,6 @@ prepRouteIncludes = (apiMode) ->
 	routeLines
 
 routeLines = prepRouteIncludes(false)
-insertToLayoutTemplate "  /*TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES */", routeLines, "#{ACAS_HOME}/app_template.js", "#{ACAS_HOME}/app.js"
+insertToLayoutTemplate "//TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES", routeLines, "#{ACAS_HOME}/app_template.js", "#{ACAS_HOME}/app.js"
 routeLines = prepRouteIncludes(true)
-insertToLayoutTemplate "  /*TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES */", routeLines, "#{ACAS_HOME}/app_api_template.js", "#{ACAS_HOME}/app_api.js"
+insertToLayoutTemplate "//TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES", routeLines, "#{ACAS_HOME}/app_api_template.js", "#{ACAS_HOME}/app_api.js"

modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee

@@ -1,5 +1,4 @@
 exports.setupAPIRoutes = (app) ->
-	app.post '/api/cmpdReg', exports.postAssignedProperties
 	app.get '/cmpdReg/scientists', exports.getScientists
 	app.get '/cmpdReg/metalots/corpName/[\\S]*', exports.getMetaLot
 	app.post '/cmpdReg/metalots', exports.metaLots

modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee

@@ -18,7 +18,8 @@ class window.AbstractCmpdRegAdminController extends AbstractFormController
 		"click .bv_cancelClear": "handleCancelClearClicked"
 		"click .bv_confirmClear": "handleConfirmClearClicked"
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		console.log "initializing Abstract Controller"
 		if @model?
 			@completeInitialization()

modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee

@@ -19,7 +19,8 @@ class window.CmpdRegAdminSimpleSearchController extends AbstractFormController
   	Instantiating controller must provide urlRoot and toDisplay in options
 	###
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		@searchUrl = ""
 		@searchUrl = @options.urlRoot + '/search/'
 

modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee

@@ -1,7 +1,6 @@
 path = require 'path'
 
-exports.setupAPIRoutes = (app) ->
-	app.post '/api/cmpdRegBulkLoader', exports.postAssignedProperties
+exports.setupAPIRoutes = (app, loginRoutes) ->
 	app.post '/api/cmpdRegBulkLoader/registerCmpds', exports.registerCmpds
 	app.post '/api/cmpdRegBulkLoader/validateCmpds', exports.validateCmpds
 	app.post '/api/cmpdRegBulkLoader/validationProperties', exports.validationProperties
@@ -17,7 +16,6 @@ exports.setupRoutes = (app, loginRoutes) ->
 	app.post '/api/cmpdRegBulkLoader/saveTemplate', loginRoutes.ensureAuthenticated, exports.saveTemplate
 	app.post '/api/cmpdRegBulkLoader/registerCmpds', loginRoutes.ensureAuthenticated, exports.registerCmpds
 	app.post '/api/cmpdRegBulkLoader/validateCmpds', loginRoutes.ensureAuthenticated, exports.validateCmpds
-	app.post '/api/cmpdRegBulkLoader', loginRoutes.ensureAuthenticated, exports.postAssignedProperties
 	app.post '/api/cmpdRegBulkLoader/checkFileDependencies', loginRoutes.ensureAuthenticated, exports.checkFileDependencies
 	app.post '/api/cmpdRegBulkLoader/purgeFile', loginRoutes.ensureAuthenticated, exports.purgeFile
 

modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee

@@ -25,7 +25,8 @@ class window.AbstractCodeTablesAdminController extends AbstractFormController
 		"click .bv_cancelClear": "handleCancelClearClicked"
 		"click .bv_confirmClear": "handleConfirmClearClicked"
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		console.log "initializing Abstract Controller"
 		if @model?
 			@completeInitialization()

modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee

@@ -21,7 +21,8 @@ class window.CodeTablesAdminSimpleSearchController extends AbstractFormControlle
   	Instantiating controller must provide urlRoot and toDisplay in options
 	###
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		@searchUrl = ""
 		@searchUrl = @options.urlRoot + '/search/'
 
@@ -111,7 +112,8 @@ class window.CodeTablesAdminRowSummaryController extends Backbone.View
 
 ############################################################################
 class window.CodeTablesAdminSummaryTableController extends Backbone.View
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		if @options.showIgnore?
 			@showIgnore = @options.showIgnore
 		else

modules/Components/src/client/ACASFormChemicalStructure.coffee

@@ -68,6 +68,9 @@ class window.ACASFormChemicalStructureController extends Backbone.View
 	tagName: "DIV"
 	template: _.template($("#ACASFormChemicalStructureControllerView").html())
 
+	initialize: (options) ->
+		@options = options
+
 	render: =>
 		$(@el).empty()
 		$(@el).html @template()

modules/Components/src/client/ACASFormFields.coffee

@@ -28,7 +28,8 @@ class window.ACASFormAbstractFieldController extends Backbone.View
 		"mouseover .label-tooltip": "handleToolTipMouseover"
 		"mouseoff .label-tooltip": "handleToolTipMouseoff"
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		@modelKey = @options.modelKey
 		@thingRef = @options.thingRef
 		@errorSet = false
@@ -331,7 +332,7 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon
     Do whatever else is required or optional in ACASFormAbstractFieldController
 	###
 	events: ->
-		_.extend {}, super,
+		_.extend {}, super(),
 		"change select": "handleInputChanged"
 
 	template: _.template($("#ACASFormLSCodeValueFieldView").html())
@@ -437,9 +438,11 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF
     Do whatever else is required or optional in ACASFormAbstractFieldController
 	###
 	events: ->
-		_.extend {}, super,
+		_.extend {}, super(),
 		"change select": "handleInputChanged"
 
+	initialize: (options) ->
+		@options = options
 	template: _.template($("#ACASFormLSThingInteractionFieldView").html())
 
 	applyOptions: ->
@@ -642,7 +645,7 @@ class window.ACASFormLSDateValueFieldController extends ACASFormAbstractFieldCon
 
 	template: _.template($("#ACASFormLSDateValueFieldView").html())
 	events: ->
-		_.extend {}, super,
+		_.extend {}, super(),
 		"change input": "handleInputChanged"
 		"click .bv_dateIcon": "handleDateIconClicked"
 
@@ -693,7 +696,7 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon
 
 	template: _.template($("#ACASFormLSFileValueFieldView").html())
 	events: ->
-		_.extend {}, super,
+		_.extend {}, super(),
 		"click .bv_deleteSavedFile": "handleDeleteSavedFile"
 
 	applyOptions: ->

modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee

@@ -8,7 +8,8 @@ class window.ACASFormCodeValueCheckboxController extends ACASFormAbstractFieldCo
     events: ->
         "change input": "handleInputChanged"
 
-    initialize: ->
+    initialize: (options) ->
+        @options = options
         @stateRef = @options.stateRef
         @thingRef = @options.thingRef
         @keyBase = @options.keyBase

modules/Components/src/client/ACASFormStateDisplayUpdate.coffee

@@ -7,6 +7,9 @@
 class window.ACASFormStateDisplayUpdateHeaderRowController extends Backbone.View
 	tagName: 'tr'
 
+	initialize: (options) ->
+		@options = options
+
 	render: =>
 		for val in @options.tableDef.values
 			displayName = val.fieldSettings.formLabel
@@ -23,6 +26,9 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View
 	events: ->
 		"click": "handleCellClicked"
 
+	initialize: (options) ->
+		@options = options
+
 	render: =>
 		$(@el).empty()
 		if @collection.length == 0
@@ -52,6 +58,9 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View
 class window.ACASFormStateDisplayUpdateRowController extends Backbone.View
 	tagName: 'tr'
 
+	initialize: (options) ->
+		@options = options
+
 	render: =>
 		for valDef in @options.tableDef.values
 			vals = @collection.where lsKind: valDef.modelDefaults.kind
@@ -69,7 +78,8 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View
 	rowNumberKind: 'row number'
 	template: _.template($("#ACASFormStateDisplayUpdateView").html())
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		@thingRef = @options.thingRef
 		@tableDef = @options.tableDef
 		@tableSetupComplete = false
@@ -218,6 +228,9 @@ class window.ACASFormStateDisplayOldValueController extends Backbone.View
 	tagName: 'tr'
 	template: _.template($("#ACASFormStateDisplayOldValueView").html())
 
+	initialize: (options) ->
+		@options = options
+
 	render: =>
 		value = @model.get(@model.get('lsType'))
 		if @options.valueDef.displayOverride?
@@ -258,7 +271,8 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View
 		"click .bv_cancelBtn": "handleCancelClicked"
 		"click .bv_saveBtn": "handleSaveClicked"
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		@tableDef = @options.tableDef
 		for valDef in @tableDef.values
 			if valDef.modelDefaults.kind == @collection.at(0).get('lsKind')

modules/Components/src/client/ACASFormStateTable.coffee

@@ -223,7 +223,7 @@ class window.ACASFormStateTableController extends Backbone.View
 			columns: @colDefs
 			search: @tableDef.search
 			currentRowClassName: 'bv_stateDisplayCurrentRow',
-  			currentColClassName: 'bv_stateDisplayCurrentColumn'
+			currentColClassName: 'bv_stateDisplayCurrentColumn'
 			cells: (row, col, prop) =>
 				cellProperties = {}
 				if @tableReadOnly

modules/Components/src/client/LSErrorNotification.coffee

@@ -15,7 +15,8 @@ class window.LSAbstractNotificationCounterController extends Backbone.View
 	container: null
 	notificationsList: null
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		_.bindAll(@,
 			'render')
 		@notificationsList = @.options.notificationsList
@@ -66,7 +67,8 @@ class window.LSErrorController extends Backbone.View
 	notificationsList: null
 	badgeEl: null
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		_.bindAll(@,
 			'render')
 		@notificationsList = @.options.notificationsList
@@ -88,7 +90,8 @@ class window.LSWarningController extends Backbone.View
 	notificationsList: null
 	badgeEl: null
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		_.bindAll(@,
 			'render')
 		@notificationsList = @.options.notificationsList
@@ -110,7 +113,8 @@ class window.LSInfoController extends Backbone.View
 	notificationsList: null
 	badgeEl: null
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		_.bindAll(@,
 			'render')
 		@notificationsList = @.options.notificationsList
@@ -139,7 +143,8 @@ class window.LSNotificationController extends Backbone.View
 	events:
 		'click .bv_notificationCountContainer': 'toggleShowNotificationMessages'
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		_.bindAll(@, 
 			'render',
 			'addError',

modules/Components/src/client/LSFileChooser.coffee

@@ -28,7 +28,8 @@ class window.LSFileChooserController extends Backbone.View
 	requiresValidation: true
 	hideDelete: false #for hiding delete button after successful file upload
 
-	initialize: ->
+	initialize: (options) ->
+		@options = options
 		_.bindAll(@,
 			'render',
 			'handleDragOverDocument',