t2-web 0.0.5

data/CHANGES

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+= Changes log for the Taverna via the Web Gem
+
+== Version 0.0.5
+* Updated to new myexperiment-rest API
+
+== Version 0.0.4
+* Improved the UI (added logos, tooltips, changed colours).
+* Made some code abstractions
+
+== Version 0.0.3
+* Improved the UI (changed divs with frames).
+
+== Version 0.0.2
+* Added upload functionality option for each input.
+
+== Version 0.0.1
+* Works. Very basic functionality and UI.
+

data/LICENSE

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+== t2-web 
+
+The MIT License
+
+Copyright (c) 2010 - Netherlands Bioinformatics Centre
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README

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+= t2-web interface generator
+
+
+Authors::     Konstantinos Karasavvas
+Gem Version:: 0.0.5
+Contact::     mailto:kostas.karasavvas@nbic.nl
+Licence::     MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
+Copyright::   (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
+
+
+== Synopsis
+
+This web application accepts a myExperiment workflow identifier and constructs
+a web form to allow end-users to configure and execute that workflow via a web
+browser with no other dependencies.. The web form interface is as good as the
+description provided in the workflow itself in myExperiment.
+
+
+== Installation
+
+  [sudo] gem install t2-web
+
+
+== Usage
+
+t2_webapp
+
+Runs the web application at port 9494 and waits for incoming requests.
+
+
+
+== References
+
+Taverna to Web Form Generator:: https://trac.nbic.nl/elabfactory/wiki/t2web
+Taverna2::       http://www.taverna.org.uk
+myExperiment::   http://www.myexperiment.org
+
+
+== Semantic Versioning
+
+This module uses semantic versioning concepts from http://semver.org/.

data/Rakefile

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+# 
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+ 
+
+require 'rubygems'
+require 'rake'
+require 'rake/clean'
+require 'rake/testtask'
+require 'rubygems/package_task'
+require 'rdoc/task'
+
+spec = Gem::Specification.new do |s|
+  s.name = 't2-web'
+  s.version = '0.0.5'
+  s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
+  s.summary = 'WS (with libs) that generates a Web UI form for a Taverna2 workflow and then enacts it to a T2 server.'
+  s.description = s.summary
+  s.author = 'Kostas Karasavvas'
+  s.email = 'kostas.karasavvas@nbic.nl'
+  s.executables = ['t2_webapp.rb']
+  s.files = %w(LICENSE README CHANGES Rakefile) + Dir.glob("{bin,lib,spec,public,views}/**/*")
+  s.require_path = "lib"
+  s.bindir = "bin"
+  s.add_dependency 'sinatra', '~> 1.2.6'
+  s.add_dependency 'haml', '~> 3.1.2'
+  s.add_dependency 'rest-client', '~> 1.6.3'
+  s.add_dependency 't2-server', '~> 0.6.1'
+  s.add_dependency 'myexperiment-rest', '~> 0.3.0'
+end
+
+Gem::PackageTask.new(spec) do |p|
+  p.gem_spec = spec
+  p.need_tar = true
+  p.need_zip = true
+end
+
+RDoc::Task.new do |rdoc|
+  files =['README', 'LICENSE', 'CHANGES', 'lib/**/*.rb']
+  rdoc.rdoc_files.add(files)
+  rdoc.main = "README" # page to start on
+  rdoc.title = "web-t2 Docs"
+  rdoc.rdoc_dir = 'doc/rdoc' # rdoc output folder
+  rdoc.options << '--line-numbers'
+end
+
+Rake::TestTask.new do |t|
+  t.test_files = FileList['test/**/*.rb']
+end
+
+# make gem and copy to test deployment server
+task :copy_to_server => :gem do
+  `scp pkg/#{spec.name}-#{spec.version}.gem  kostas@mybiobank.org:/home/kostas`
+end

data/bin/t2_webapp.rb

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+#!/usr/bin/env ruby
+
+require 'rubygems' if RUBY_VERSION < '1.9'
+require 'sinatra'
+require 'haml'
+require 'open-uri'
+require 'rest-client'
+require 't2-server'
+require 'myexperiment-rest'
+require 'cgi'
+#require "web-t2" TODO: move whole of WebT2App in lib
+
+
+class WebT2App < Sinatra::Base
+
+  WEB_APP_NAME = "t2web"
+  # TODO: const for TMP_UPLOAD_PATH ? - need to read from config file?
+
+  set :port, 9494
+  set :views, File.dirname(__FILE__) + '/../views'
+  set :public, File.dirname(__FILE__) + '/../public'
+
+  # can be used from routes and views (haml)
+  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
+    # Minor for now
+    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='/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
+    def generate_header_table(my_exp_wkf, my_exp_usr)
+      <<END
+    <div id='header'>
+      <table class='header'>
+        <tr>
+          <td>
+            <img alt='NBIC logo' src='/images/nbic_logo.gif' />
+          </td>
+          <td>
+            <table class='header-title'>
+              <tr>
+                <td class='header-title'>Workflow: #{@my_exp_wkf.title}</td>
+              </tr>
+              <tr>
+                <td class='right'>workflow by #{@my_exp_usr.name}</td>
+
+              </tr>
+            </table>
+          </td>
+          <td>
+            <img alt='LUMC logo' class='right' src='/images/lumc_logo2.png' />
+          </td>
+        </tr>
+      </table>
+    </div>
+END
+    end
+
+
+    # Generates tooltip html text for descriptions
+    def generate_label_tooltip(input)
+      "Description: " << CGI::unescapeHTML(input.descriptions[0])
+    end
+
+    # Generates tooltip html text for textarea example
+    def generate_textarea_tooltip(input)
+      "Example: " << CGI::unescapeHTML(input.examples[0])
+    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='/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
+            data_navigation_frame << "<td><a href='javascript:void(0);' onclick='parent.getSampleOutput(\\\"#{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='/images/snake_transparent.gif' alt='Loading Content...'></td>"
+          end
+          data_navigation_frame << "</tr>"
+        end
+      end
+      data_navigation_frame << "</table></body></html>"
+    end
+
+
+    # Check type of data and generate appropriate html for that result!
+    def generate_html_result(data)
+      html = ""
+      #p data
+      if data.instance_of? Array
+        html = data.flatten.join('<br>')
+      elsif data.instance_of? String
+        html = data.gsub(/[\n]/, '<br>')
+      else
+        html = data
+      end
+      html
+    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 -- make custom exceptions?
+    @my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)
+
+    # Get myExperiment user object
+    # TODO: catch exception -- make custom exceptions?
+    @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 = "/tmp/#{WEB_APP_NAME}/#{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 '/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 for specified run and output - display it in data-display div
+  # Cross-domain AJAX to get result from T2
+  get "/#{WEB_APP_NAME}/run/:uuid/output/:out" do
+
+    # Get http request's parameters
+    # TODO: consider adding the following to a session
+    @wid = params[:wid]
+    @wkf_version = params[:wkf_version]
+
+    # Get myExperiment workflow object
+    # TODO: with sessions that would be remembered
+    @my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)
+
+    @run_uuid = params[:uuid]
+    @t2_server = params[:server]
+    t2_output = params[:out]
+
+    # Get t2 server and then the run using uuid
+    server = T2Server::Server.connect(@t2_server)
+    run = server.run(@run_uuid)
+
+    # Get output from t2 server
+    # TODO: that gets the whole output.. request client lib to support partial
+    # download! -- refs could then be used to download the full results!
+    begin
+      data_lists = run.get_output(t2_output, false)
+    rescue Exception => e
+      data_lists = run.get_output("#{t2_output}.error", false)
+    end
+    
+    # that should be a sample of the results -- not the complete results!
+    data = generate_html_result(data_lists)
+
+    data
+  end
+
+
+  # Used from input's upload-form to upload files without refresh (actually
+  # a hidden iframe is refreshed).
+  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
+
+end
+
+
+# Start Web App
+WebT2App.run!

data/public/css/form.css

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+body{
+    background-color: #fdfdfd;
+}
+
+table.header {
+  width: 100%;
+}
+
+table.header-title {
+  border-collapse: collapse;
+  /* With equal left-right margins table will be aligned in the centre */
+  margin-left: auto;
+  margin-right: auto;
+}
+
+td.header-title {
+  font-size: 200%;
+  background-color: #f0f0f0;
+  padding: 12px;
+  border-bottom: 4px solid #909090;
+  border-top: 4px solid #909090;
+}
+
+#inputs {
+}
+
+table.inputs {
+  width: 800px;
+  border-collapse: collapse;
+  /* With equal left-right margins table will be aligned in the centre */
+  margin-left: auto;
+  margin-right: auto;
+}
+
+th.inputs {
+  font-size: 120%;
+  background-color: #f0f0f0;
+  padding: 10px;
+  border-bottom: 1px solid #909090;
+  border-top: 4px solid #909090;
+}
+
+td.inputs {
+  padding: 5px;
+  vertical-align: top;
+}
+
+td.right {
+  text-align: right;
+}
+
+img.right {
+  float: right;
+}
+
+#description {
+}
+
+#inputs {
+}
+
+#outputs {
+}
+
+#note {
+}
+
+label {
+  text-decoration: underline;
+}