reinouts/gist:3749414

## gistfile1.rb
#!/usr/bin/env ruby

require 'rubygems' if RUBY_VERSION < '1.9'
require 'sinatra/base'
require 'haml'
require 'open-uri'
require 'rest-client'
require 't2-server'
require 'myexperiment-rest'
require 'cgi'
require 'stringio'
#require "t2-web"

# TODO: move whole of T2WebApp in lib
# TODO: add constants.rb file in lib for all constants (e.g. myExp user URL,
#       TMP_UPLOAD_PATH, other URLs -- consider adding those in rack config.ru

class T2WebApp < Sinatra::Base

  WEB_APP_NAME = "t2web"

  set :views, File.dirname(__FILE__) + '/../views'
  #set :public_folder, '/var/lib/gems/1.9.1/gems/t2-web-0.1.9'
  set :public_folder, File.dirname(__FILE__) + '/../public'
  # puts settings.public_folder
  ENV.each { |e| puts "#{e[0]} => #{e[1]}" }

  # Can be used from routes and views (haml) -- not public methods
  helpers do

    # Used before we sent the workflow inputs to the taverna server. Just converts
    # double quotations to single ones. That is because the t2-server library
    # is confused with double quotes and apparently it is not easy to fix.
    def t2_library_sanitize(string)
      ex = string.gsub('"', "'")
    end

    # Deletes last new line of file if it exists! It is needed for t2 workflows that
    # do not sanitize properly, i.e. via a user-provided beanshell script
    def chomp_last_newline(file)

      if File.file?(file) and File.size(file) > 1
        f = open(file, "rb+")
        f.seek(-1, File::SEEK_END)
        f.truncate(File.size(file) - 1) if f.read(1) == "\n"
        f.close
      end

    end

    # Construct the complete or partial URL as MyExperimentRest lib expects it
    # TODO: Maybe update myExperimentREST lib to accept only wid and wkf_version
    def get_url_from_wid(wid, wkf_version)
      if wkf_version == "default"
        "/workflows/#{wid}"
      else
        "/workflows/#{wid}?version=#{wkf_version}"
      end
    end


    # Generates the contents of the header frame
    def generate_header_frame(my_exp_wkf, my_exp_usr)
      <<END
<html>
  <head><link href='/t2web/css/form.css' rel='stylesheet'/></head>
  <body>
    #{generate_header_table(my_exp_wkf, my_exp_usr)}
  </body>
</html>
END
    end


    # Generates the contents of the header frame table
    def generate_header_table(my_exp_wkf, my_exp_usr)
      <<END
    <div id='header'>
      <table class='header'>
        <tr>
          <td class='left'>
            <img alt='NBIC logo' src='/t2web/images/nbic_logo.gif' />
          </td>
          <td>
            <table class='header-title'>
              <tr>
                <td class='header-title'>#{@my_exp_wkf.title}</td>
              </tr>
              <tr>
                <td class='right'>workflow by <a href='http://www.myexperiment.org/users/#{@my_exp_usr.id}.html' target='_blank'>#{@my_exp_usr.name}</a></td>
              </tr>
            </table>
          </td>
          <td>
            <img alt='LUMC logo' class='right' src='/t2web/images/lumc_logo2.png' />
          </td>
        </tr>
      </table>
    </div>
END
    end


    # Generates tooltip html text with type prefix
    def generate_tooltip(type, input)
      if type =~ /description/i
        type << CGI::unescapeHTML(input.descriptions[0])
      else
        type << CGI::unescapeHTML(input.examples[0])
      end
    end


    # Generates the contents of the data-navigation frame
    def generate_data_navigation_frame(my_exp_wkf, uuid, wid, wkf_version, t2_server, finished_execution)

      data_navigation_frame = "<html><head><link href='/t2web/css/results_navigation.css' rel='stylesheet'/></head><body><table>"
      if my_exp_wkf.outputs.size >=1
        my_exp_wkf.outputs.each do |output|
          data_navigation_frame << "<tr>"
          if finished_execution
            # TODO: currently t2_server, wid and wkf_version are not used
            data_navigation_frame << "<td><a href='javascript:void(0);' onclick='parent.readTmpOutput(\\\"#{t2_server}\\\", \\\"#{uuid}\\\", " <<
                                     "\\\"#{output.name}\\\", \\\"#{wid}\\\", \\\"#{wkf_version}\\\");'>#{output.name}</a></td><td></td>"
          else
            data_navigation_frame << "<td>#{output.name}</td><td><img src='/t2web/images/snake_transparent.gif' alt='Loading Content...'></td>"
          end
          data_navigation_frame << "</tr>"
        end
      end
      data_navigation_frame << "</table></body></html>"
    end


    # Takes string list as input and prepares for HTML
    def generate_html_result(data)
      data.gsub(/[\n]/, '<br>')
    end

    # Takes image url and prepares for HTML
    def generate_image_result(img)
      "<img src=\"#{img}\" />"
    end


    # Takes list as input (or single element), returns as multi-line string
    # TODO: when 'typing' issues are resolved think of using system_flatten_list_results method
    # TODO: <b></b> is added to single images -- remember to clean after 'typing' work
    def flatten_list_results(data_lists)
      data = ""
      data_lists.each do |list|
        if list.instance_of? Array
          tmp_data = list.flatten.compact.map {|e| e.chomp}
          tmp_data[0] = "<b>" + tmp_data[0] + "</b>"
          data += tmp_data.join("\n") + "\n"
        else
          data += list.chomp + "\n"
        end
      end
      data
    end


    # Takes list as input (or single element), returns as file stream
    # TODO: for images it works when not a list!
    #def system_flatten_list_results(list)
    #  data = ""
    #  if list.instance_of? Array
    #    # flatten (sub-)list and remove nils and if present, newlines
    #    # then join list as a multi-line string
    #    data = list.flatten.compact.map {|e| e.chomp}.join("\n")
    #  else
    #    data = list.chomp
    #  end
    #  StringIO.new data
    #end


    # Copies output stream to a tmp file in the specified subdir
    def copy_to_tmp(subdir, filename, out)

      # used to copy them at tmp
      #FileUtils.mkdir_p("/tmp/#{WEB_APP_NAME}/#{subdir}") unless File.exist?("/tmp/#{WEB_APP_NAME}/#{subdir}")
      #tmp_file = File.open("/tmp/#{WEB_APP_NAME}/#{subdir}/#{filename}", "w")

      # copy at our tmp dir below public folder
      FileUtils.mkdir_p("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{subdir}") unless File.exist?("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{subdir}")
      tmp_file = File.open("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{subdir}/#{filename}", "w")
      FileUtils.copy_stream(out, tmp_file)
      tmp_file.close
      "Successfully copied #{filename}!!"
    end

  end


  # Create the Web UI for that workflow
  get "/#{WEB_APP_NAME}/workflow/:wid" do

    # Get http request's parameters
    # TODO: consider adding the following to a session
    @wid = params[:wid]
    @wkf_version = params[:wkf_version] || nil
    @t2_server = params[:server] || "http://test.mybiobank.org/taverna-server"

    # Get myExperiment workflow object
    # TODO: catch exception
    @my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)

    # Get myExperiment user object
    # TODO: catch exception
    @my_exp_usr = MyExperimentREST::User.from_uri(@my_exp_wkf.uploader_uri)

    haml :form

  end


  # Enact the workflow with the submitted parameters and returns
  # result display (involves checking run's status and getting results)
  post "/#{WEB_APP_NAME}/enact" do
    #p params

    # Get http POST request's parameters
    # TODO: consider adding the following to a session
    @wid = params[:wid]
    @wkf_version = params[:wkf_version]
    @t2_server = params[:server]

    @my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)

    # Get myExperiment user object (TODO: session!, exceptions)
    @my_exp_usr = MyExperimentREST::User.from_uri(@my_exp_wkf.uploader_uri)

    # use the uri reference to download the workflow locally
    #wkf_file = URI.parse(@my_exp_wkf.content_uri)
    wkf = open(@my_exp_wkf.content_uri).read

    # create run
    begin
      run = T2Server::Run.create(@t2_server, wkf)
    rescue T2Server::T2ServerError => e
      return "404 Not Found: run could not be instantiated!"
    end

    # Get the run as instance member to make visible in views
    @run_uuid = run.uuid

    # Set workflow inputs
    @my_exp_wkf.inputs.each do |input|
      if params[:"upload-checkbox-#{input.name}"] == "yes"
        filename = params[:"#{input.name}-file"]
        tmp_filename = "#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{filename}"

        # make sure that the file is uploaded completely, i.e. all it's
        # connections are closed
        #while `lsof -c cp | grep /tmp/#{WEB_APP_NAME}/#{filename}` != ""
        #  sleep 1
        #end

        chomp_last_newline(tmp_filename)
        run.upload_input_file(input.name, tmp_filename)
      else
        run.set_input(input.name, t2_library_sanitize(params["#{input.name}-input".to_sym]) )
      end
    end

    # start run and wait until it is finished
    run.start

    haml :results
  end


  # Proxy operation (to bypass cross-domain AJAX) to get T2 run's status
  get "/#{WEB_APP_NAME}/runs/:uuid/status" do
    uuid = params[:uuid]
    t2_server = params[:server]

    response = RestClient.get t2_server + "/rest/runs/" + uuid + "/status", :content_type => "text/plain"

    response.to_str
  end


  # Get results from all outputs and store in tmp folder
  # Cross-domain AJAX to get result from T2
  get "/#{WEB_APP_NAME}/run/:uuid/outputs" do

    @run_uuid = params[:uuid]
    @t2_server = params[:server]

    # Get t2 server and then the run using uuid
    server = T2Server::Server.connect(@t2_server)
    run = server.run(@run_uuid)

    # Get output ports from t2 server and store in tmp folder
    # TODO: TMP folder constant from config!
    # TODO: that gets the whole output.. request client lib to support partial
    #       download if result too large!
    run.get_output_ports.each do |t2_output|
      begin
        data_lists = run.get_output(t2_output, false)
      rescue Exception => e
        data_lists = run.get_output("#{t2_output}.error", false)
      end

      # flatten the results
      data_stream = flatten_list_results(data_lists)

      # copy results to our app's tmp
      copy_to_tmp("outputs/#{@run_uuid}", t2_output, (StringIO.new data_stream))
    end

    # return success!
    "Successful download!"
  end


  # Get results for specified run and output (stored locally from tmp)
  # and display it in data-display div
  # Cross-domain AJAX to get result from T2
  get "/#{WEB_APP_NAME}/run/:uuid/output/:out" do

    # change public only for this route so that /tmp/t2web can be accessed
    # unfortunately contrary to an article the following does not work
    #set :public_folder, "./tmp/#{WEB_APP_NAME}"

    run_uuid = params[:uuid]
    t2_output = params[:out]

    display_file = "#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}"

    data = File.open(display_file, "r").read

    # Add HTML tags to display properly

    # Check what kind of file it is. for now use system 'file' -- note that it will only
    # work with one image since flatten_list_results only deals with multi-line strings
    # and single strings or single images (indirectly!)
    mime_type = %x( file --mime-type #{display_file} )

    # TODO: image types can go to array and regex auto-generated
    # TODO: application/octet-stream is a temporary hack until we deal with 'typing' properly
    if mime_type =~ /image\/png|image\/jpg|image\/gif|image\/bmp|application\/octet-stream/
      # clean image from <b></b> --- will not be needed after we deal with 'typing' properly t2-server-0.9.x
      if mime_type =~ /octet-stream/
        unless File.file?("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
          new_length = File.size?(display_file) - 3 - 5   # for <b> and </b>\n respectively
          %x( dd if="#{display_file}" of="#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}" bs=1 skip=3 count="#{new_length}" )
        end
        generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
      else
        generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}")
      end
    else
      generate_html_result(data)
    end
  end


  # Used from input's upload-form to upload files without refresh (actually
  # a hidden iframe is refreshed).
  # TODO: use copy_to_tmp method!! Uploads still go to system's tmp and not
  #       to our webapp's public tmp
  post "/#{WEB_APP_NAME}/upload" do
    filename = params[:file][:filename]
    tempfile = params[:file][:tempfile]
    FileUtils.mkdir("/tmp/#{WEB_APP_NAME}") unless File.exist?("/tmp/#{WEB_APP_NAME}")
    FileUtils.copy(tempfile.path, "/tmp/#{WEB_APP_NAME}/#{filename}")
    "Successfully copied #{filename}!!"
  end

  # start the server if ruby file executed directly
  run! if app_file == $0
end


# Start Web App from the ./bin directory in deamon mode at port 9494
# $ thin -d -p 9494
	#!/usr/bin/env ruby

	require 'rubygems' if RUBY_VERSION < '1.9'
	require 'sinatra/base'
	require 'haml'
	require 'open-uri'
	require 'rest-client'
	require 't2-server'
	require 'myexperiment-rest'
	require 'cgi'
	require 'stringio'
	#require "t2-web"

	# TODO: move whole of T2WebApp in lib
	# TODO: add constants.rb file in lib for all constants (e.g. myExp user URL,
	# TMP_UPLOAD_PATH, other URLs -- consider adding those in rack config.ru

	class T2WebApp < Sinatra::Base

	WEB_APP_NAME = "t2web"

	set :views, File.dirname(__FILE__) + '/../views'
	#set :public_folder, '/var/lib/gems/1.9.1/gems/t2-web-0.1.9'
	set :public_folder, File.dirname(__FILE__) + '/../public'
	# puts settings.public_folder
	ENV.each { \|e\| puts "#{e[0]} => #{e[1]}" }

	# Can be used from routes and views (haml) -- not public methods
	helpers do

	# Used before we sent the workflow inputs to the taverna server. Just converts
	# double quotations to single ones. That is because the t2-server library
	# is confused with double quotes and apparently it is not easy to fix.
	def t2_library_sanitize(string)
	ex = string.gsub('"', "'")
	end

	# Deletes last new line of file if it exists! It is needed for t2 workflows that
	# do not sanitize properly, i.e. via a user-provided beanshell script
	def chomp_last_newline(file)

	if File.file?(file) and File.size(file) > 1
	f = open(file, "rb+")
	f.seek(-1, File::SEEK_END)
	f.truncate(File.size(file) - 1) if f.read(1) == "\n"
	f.close
	end

	end

	# Construct the complete or partial URL as MyExperimentRest lib expects it
	# TODO: Maybe update myExperimentREST lib to accept only wid and wkf_version
	def get_url_from_wid(wid, wkf_version)
	if wkf_version == "default"
	"/workflows/#{wid}"
	else
	"/workflows/#{wid}?version=#{wkf_version}"
	end
	end


	# Generates the contents of the header frame
	def generate_header_frame(my_exp_wkf, my_exp_usr)
	<<END
	<html>
	<head><link href='/t2web/css/form.css' rel='stylesheet'/></head>
	<body>
	#{generate_header_table(my_exp_wkf, my_exp_usr)}
	</body>
	</html>
	END
	end


	# Generates the contents of the header frame table
	def generate_header_table(my_exp_wkf, my_exp_usr)
	<<END
	<div id='header'>
	<table class='header'>
	<tr>
	<td class='left'>
	<img alt='NBIC logo' src='/t2web/images/nbic_logo.gif' />
	</td>
	<td>
	<table class='header-title'>
	<tr>
	<td class='header-title'>#{@my_exp_wkf.title}</td>
	</tr>
	<tr>
	<td class='right'>workflow by <a href='http://www.myexperiment.org/users/#{@my_exp_usr.id}.html' target='_blank'>#{@my_exp_usr.name}</a></td>
	</tr>
	</table>
	</td>
	<td>
	<img alt='LUMC logo' class='right' src='/t2web/images/lumc_logo2.png' />
	</td>
	</tr>
	</table>
	</div>
	END
	end


	# Generates tooltip html text with type prefix
	def generate_tooltip(type, input)
	if type =~ /description/i
	type << CGI::unescapeHTML(input.descriptions[0])
	else
	type << CGI::unescapeHTML(input.examples[0])
	end
	end


	# Generates the contents of the data-navigation frame
	def generate_data_navigation_frame(my_exp_wkf, uuid, wid, wkf_version, t2_server, finished_execution)

	data_navigation_frame = "<html><head><link href='/t2web/css/results_navigation.css' rel='stylesheet'/></head><body><table>"
	if my_exp_wkf.outputs.size >=1
	my_exp_wkf.outputs.each do \|output\|
	data_navigation_frame << "<tr>"
	if finished_execution
	# TODO: currently t2_server, wid and wkf_version are not used
	data_navigation_frame << "<td><a href='javascript:void(0);' onclick='parent.readTmpOutput(\\\"#{t2_server}\\\", \\\"#{uuid}\\\", " <<
	"\\\"#{output.name}\\\", \\\"#{wid}\\\", \\\"#{wkf_version}\\\");'>#{output.name}</a></td><td></td>"
	else
	data_navigation_frame << "<td>#{output.name}</td><td><img src='/t2web/images/snake_transparent.gif' alt='Loading Content...'></td>"
	end
	data_navigation_frame << "</tr>"
	end
	end
	data_navigation_frame << "</table></body></html>"
	end


	# Takes string list as input and prepares for HTML
	def generate_html_result(data)
	data.gsub(/[\n]/, '<br>')
	end

	# Takes image url and prepares for HTML
	def generate_image_result(img)
	"<img src=\"#{img}\" />"
	end


	# Takes list as input (or single element), returns as multi-line string
	# TODO: when 'typing' issues are resolved think of using system_flatten_list_results method
	# TODO: <b></b> is added to single images -- remember to clean after 'typing' work
	def flatten_list_results(data_lists)
	data = ""
	data_lists.each do \|list\|
	if list.instance_of? Array
	tmp_data = list.flatten.compact.map {\|e\| e.chomp}
	tmp_data[0] = "<b>" + tmp_data[0] + "</b>"
	data += tmp_data.join("\n") + "\n"
	else
	data += list.chomp + "\n"
	end
	end
	data
	end


	# Takes list as input (or single element), returns as file stream
	# TODO: for images it works when not a list!
	#def system_flatten_list_results(list)
	# data = ""
	# if list.instance_of? Array
	# # flatten (sub-)list and remove nils and if present, newlines
	# # then join list as a multi-line string
	# data = list.flatten.compact.map {\|e\| e.chomp}.join("\n")
	# else
	# data = list.chomp
	# end
	# StringIO.new data
	#end



	# Copies output stream to a tmp file in the specified subdir
	def copy_to_tmp(subdir, filename, out)

	# used to copy them at tmp
	#FileUtils.mkdir_p("/tmp/#{WEB_APP_NAME}/#{subdir}") unless File.exist?("/tmp/#{WEB_APP_NAME}/#{subdir}")
	#tmp_file = File.open("/tmp/#{WEB_APP_NAME}/#{subdir}/#{filename}", "w")

	# copy at our tmp dir below public folder
	FileUtils.mkdir_p("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{subdir}") unless File.exist?("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{subdir}")
	tmp_file = File.open("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{subdir}/#{filename}", "w")
	FileUtils.copy_stream(out, tmp_file)
	tmp_file.close
	"Successfully copied #{filename}!!"
	end

	end



	# Create the Web UI for that workflow
	get "/#{WEB_APP_NAME}/workflow/:wid" do

	# Get http request's parameters
	# TODO: consider adding the following to a session
	@wid = params[:wid]
	@wkf_version = params[:wkf_version] \|\| nil
	@t2_server = params[:server] \|\| "http://test.mybiobank.org/taverna-server"

	# Get myExperiment workflow object
	# TODO: catch exception
	@my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)

	# Get myExperiment user object
	# TODO: catch exception
	@my_exp_usr = MyExperimentREST::User.from_uri(@my_exp_wkf.uploader_uri)

	haml :form

	end


	# Enact the workflow with the submitted parameters and returns
	# result display (involves checking run's status and getting results)
	post "/#{WEB_APP_NAME}/enact" do
	#p params

	# Get http POST request's parameters
	# TODO: consider adding the following to a session
	@wid = params[:wid]
	@wkf_version = params[:wkf_version]
	@t2_server = params[:server]

	@my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)

	# Get myExperiment user object (TODO: session!, exceptions)
	@my_exp_usr = MyExperimentREST::User.from_uri(@my_exp_wkf.uploader_uri)

	# use the uri reference to download the workflow locally
	#wkf_file = URI.parse(@my_exp_wkf.content_uri)
	wkf = open(@my_exp_wkf.content_uri).read

	# create run
	begin
	run = T2Server::Run.create(@t2_server, wkf)
	rescue T2Server::T2ServerError => e
	return "404 Not Found: run could not be instantiated!"
	end

	# Get the run as instance member to make visible in views
	@run_uuid = run.uuid

	# Set workflow inputs
	@my_exp_wkf.inputs.each do \|input\|
	if params[:"upload-checkbox-#{input.name}"] == "yes"
	filename = params[:"#{input.name}-file"]
	tmp_filename = "#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{filename}"

	# make sure that the file is uploaded completely, i.e. all it's
	# connections are closed
	#while `lsof -c cp \| grep /tmp/#{WEB_APP_NAME}/#{filename}` != ""
	# sleep 1
	#end

	chomp_last_newline(tmp_filename)
	run.upload_input_file(input.name, tmp_filename)
	else
	run.set_input(input.name, t2_library_sanitize(params["#{input.name}-input".to_sym]) )
	end
	end

	# start run and wait until it is finished
	run.start

	haml :results
	end



	# Proxy operation (to bypass cross-domain AJAX) to get T2 run's status
	get "/#{WEB_APP_NAME}/runs/:uuid/status" do
	uuid = params[:uuid]
	t2_server = params[:server]

	response = RestClient.get t2_server + "/rest/runs/" + uuid + "/status", :content_type => "text/plain"

	response.to_str
	end


	# Get results from all outputs and store in tmp folder
	# Cross-domain AJAX to get result from T2
	get "/#{WEB_APP_NAME}/run/:uuid/outputs" do

	@run_uuid = params[:uuid]
	@t2_server = params[:server]

	# Get t2 server and then the run using uuid
	server = T2Server::Server.connect(@t2_server)
	run = server.run(@run_uuid)

	# Get output ports from t2 server and store in tmp folder
	# TODO: TMP folder constant from config!
	# TODO: that gets the whole output.. request client lib to support partial
	# download if result too large!
	run.get_output_ports.each do \|t2_output\|
	begin
	data_lists = run.get_output(t2_output, false)
	rescue Exception => e
	data_lists = run.get_output("#{t2_output}.error", false)
	end

	# flatten the results
	data_stream = flatten_list_results(data_lists)

	# copy results to our app's tmp
	copy_to_tmp("outputs/#{@run_uuid}", t2_output, (StringIO.new data_stream))
	end

	# return success!
	"Successful download!"
	end


	# Get results for specified run and output (stored locally from tmp)
	# and display it in data-display div
	# Cross-domain AJAX to get result from T2
	get "/#{WEB_APP_NAME}/run/:uuid/output/:out" do

	# change public only for this route so that /tmp/t2web can be accessed
	# unfortunately contrary to an article the following does not work
	#set :public_folder, "./tmp/#{WEB_APP_NAME}"

	run_uuid = params[:uuid]
	t2_output = params[:out]

	display_file = "#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}"

	data = File.open(display_file, "r").read

	# Add HTML tags to display properly

	# Check what kind of file it is. for now use system 'file' -- note that it will only
	# work with one image since flatten_list_results only deals with multi-line strings
	# and single strings or single images (indirectly!)
	mime_type = %x( file --mime-type #{display_file} )

	# TODO: image types can go to array and regex auto-generated
	# TODO: application/octet-stream is a temporary hack until we deal with 'typing' properly
	if mime_type =~ /image\/png\|image\/jpg\|image\/gif\|image\/bmp\|application\/octet-stream/
	# clean image from <b></b> --- will not be needed after we deal with 'typing' properly t2-server-0.9.x
	if mime_type =~ /octet-stream/
	unless File.file?("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
	new_length = File.size?(display_file) - 3 - 5 # for <b> and </b>\n respectively
	%x( dd if="#{display_file}" of="#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}" bs=1 skip=3 count="#{new_length}" )
	end
	generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
	else
	generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}")
	end
	else
	generate_html_result(data)
	end
	end


	# Used from input's upload-form to upload files without refresh (actually
	# a hidden iframe is refreshed).
	# TODO: use copy_to_tmp method!! Uploads still go to system's tmp and not
	# to our webapp's public tmp
	post "/#{WEB_APP_NAME}/upload" do
	filename = params[:file][:filename]
	tempfile = params[:file][:tempfile]
	FileUtils.mkdir("/tmp/#{WEB_APP_NAME}") unless File.exist?("/tmp/#{WEB_APP_NAME}")
	FileUtils.copy(tempfile.path, "/tmp/#{WEB_APP_NAME}/#{filename}")
	"Successfully copied #{filename}!!"
	end

	# start the server if ruby file executed directly
	run! if app_file == $0
	end


	# Start Web App from the ./bin directory in deamon mode at port 9494
	# $ thin -d -p 9494