t2-web 0.0.9 → 0.1.0

data/CHANGES

@@ -1,5 +1,11 @@
 = Changes log for the Taverna via the Web Gem
 
+== Version 0.1.0
+* Results are downloaded directly and stored in tmp files - progress cycle works once
+* Added rackup configuration file: config.ru
+* webapp is run using rackup now to enable configuration of web server timeout
+* Increased tooltip size and anchored them to the 'west'
+* Port is set via: rackup -p 9494
 
 == Version 0.0.9
 * Changed " to ' in generate_header_table (header HTML block used in JS .write("") method)

data/README

@@ -2,7 +2,7 @@
 
 
 Authors::     Konstantinos Karasavvas
-Gem Version:: 0.0.9
+Gem Version:: 0.1.0
 Contact::     mailto:kostas.karasavvas@nbic.nl
 Licence::     MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
 Copyright::   (c) 2012 Netherlands Bioinformatics Centre, The Netherlands

data/Rakefile

@@ -12,7 +12,7 @@ require 'rdoc/task'
 
 spec = Gem::Specification.new do |s|
   s.name = 't2-web'
-  s.version = '0.0.9'
+  s.version = '0.1.0'
   s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
   s.summary = 'Web application that generates a Web UI form for a Taverna2 workflow, given its myExperiment id, for ease of execution. The only requirement for the user is a web browser.'
   s.description = s.summary

data/bin/config.ru

@@ -0,0 +1,8 @@
+require 'sinatra'
+require './t2_webapp'
+
+set :timeout, 600
+#not picked up!  ...  set :port, 9494
+
+run WebT2App
+

data/bin/t2_webapp.rb

@@ -1,13 +1,14 @@
 #!/usr/bin/env ruby
 
 require 'rubygems' if RUBY_VERSION < '1.9'
-require 'sinatra'
+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 WebT2App in lib
 
 # TODO: add constants.rb file in lib for all constants (e.g. myExp user URL, other URLs
@@ -17,7 +18,7 @@ class WebT2App < Sinatra::Base
   WEB_APP_NAME = "t2web"
   # TODO: const for TMP_UPLOAD_PATH ? - need to read from config file?
 
-  set :port, 9494
+  #set :port, 9494     set from: rackup -p 9494
   set :views, File.dirname(__FILE__) + '/../views'
   set :public_folder, File.dirname(__FILE__) + '/../public'
 
@@ -71,7 +72,7 @@ END
     end
 
     
-    # Generates the contents of the header frame
+    # Generates the contents of the header frame table
     def generate_header_table(my_exp_wkf, my_exp_usr)
       <<END
     <div id='header'>
@@ -100,15 +101,20 @@ END
     end
 
 
-    # Generates tooltip html text for descriptions
-    def generate_label_tooltip(input)
-      "Description: " << CGI::unescapeHTML(input.descriptions[0])
+    # 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
 
+    # TODO: remove 02/04/2012
     # Generates tooltip html text for textarea example
-    def generate_textarea_tooltip(input)
-      "Example: " << CGI::unescapeHTML(input.examples[0])
-    end
+    #def generate_textarea_tooltip(input)
+    #  "Example: " << CGI::unescapeHTML(input.examples[0])
+    #end
 
 
     # Generates the contents of the data-navigation frame
@@ -119,7 +125,8 @@ END
         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}\\\", " <<
+            # 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='/images/snake_transparent.gif' alt='Loading Content...'></td>"
@@ -132,17 +139,38 @@ END
 
 
     # Check type of data and generate appropriate html for that result!
+    # Takes list as input -- TODO: rdoc methods properly!
     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>')
+      data.gsub(/[\n]/, '<br>')
+    end
+
+
+    # Check type of data and generate appropriate html for that result!
+    # Takes list as input, returns as file stream -- TODO: rdoc methods properly!
+    def flatten_list_results(list)
+      data = ""
+      #p list
+      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
-        html = data
+        data = list.chomp
       end
-      html
+
+      StringIO.new data
+    end
+
+
+
+    # copies output stream to a tmp file in the specified subdir
+    # TODO: make proper rdoc
+    def copy_to_tmp(subdir, filename, out)
+      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")
+      FileUtils.copy_stream(out, tmp_file)
+      tmp_file.close
+      "Successfully copied #{filename}!!"
     end
 
   end
@@ -240,46 +268,58 @@ END
   end
 
 
-
-  # Get results for specified run and output - display it in data-display div
+  # Get results from all outputs and store in tmp folder
   # 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)
+  get "/#{WEB_APP_NAME}/run/:uuid/outputs" do
 
     @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
+    # 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! -- 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)
+    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 tmp
+      copy_to_tmp("outputs/#{@run_uuid}", t2_output, data_stream)
     end
-    
-    # that should be a sample of the results -- not the complete results!
-    data = generate_html_result(data_lists)
 
-    data
+    # return success!
+    "Successful download!"
+  end
+
+
+  # Get results for specified run and output (stored locally from tmp)
+  # display it in data-display div
+  # Cross-domain AJAX to get result from T2
+  get "/#{WEB_APP_NAME}/run/:uuid/output/:out" do
+
+    run_uuid = params[:uuid]
+    t2_output = params[:out]
+
+    # add HTML tags to display properly
+    data = File.open("/tmp/#{WEB_APP_NAME}/outputs/#{run_uuid}/#{t2_output}", "r").read
+
+    generate_html_result(data)
   end
 
 
   # Used from input's upload-form to upload files without refresh (actually
   # a hidden iframe is refreshed).
+  # TODO: use copy_to_tmp method!!
   post "/#{WEB_APP_NAME}/upload" do
     filename = params[:file][:filename]
     tempfile = params[:file][:tempfile]
@@ -288,8 +328,10 @@ END
     "Successfully copied #{filename}!!"
   end
 
+  # start the server if ruby file executed directly
+  run! if app_file == $0
 end
 
 
 # Start Web App
-WebT2App.run!
+# $ rackup -p 9494

data/doc/rdoc/CHANGES.html

@@ -76,6 +76,21 @@
     
 <h1>Changes log for the Taverna via the Web Gem</h1>
 
+<h2>Version 0.1.0</h2>
+<ul><li>
+<p>Results are downloaded directly and stored in tmp files - progress cycle
+works once</p>
+</li><li>
+<p>Added rackup configuration file: config.ru</p>
+</li><li>
+<p>webapp is run using rackup now to enable configuration of web server
+timeout</p>
+</li><li>
+<p>Increased tooltip size and anchored them to the ‘west’</p>
+</li><li>
+<p>Port is set via: rackup -p 9494</p>
+</li></ul>
+
 <h2>Version 0.0.9</h2>
 <ul><li>
 <p>Changed “ to ‘ in generate_header_table (header HTML block used in JS

data/doc/rdoc/README.html

@@ -80,7 +80,7 @@
 <p>Konstantinos Karasavvas</p>
 </td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
 <td>
-<p>0.0.9</p>
+<p>0.1.0</p>
 </td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
 <td>
 <p><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a></p>

data/doc/rdoc/created.rid

@@ -1,4 +1,4 @@
-Wed, 21 Mar 2012 16:46:27 +0100
+Wed, 04 Apr 2012 14:30:43 +0200
 LICENSE	Fri, 22 Jul 2011 16:33:48 +0200
-README	Tue, 20 Mar 2012 17:41:35 +0100
-CHANGES	Wed, 21 Mar 2012 15:19:25 +0100
+README	Fri, 23 Mar 2012 10:39:17 +0100
+CHANGES	Mon, 02 Apr 2012 17:10:11 +0200

data/doc/rdoc/index.html

@@ -29,7 +29,7 @@
 <p>Konstantinos Karasavvas</p>
 </td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
 <td>
-<p>0.0.9</p>
+<p>0.1.0</p>
 </td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
 <td>
 <p><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a></p>

data/public/css/form.css

@@ -19,6 +19,7 @@ td.header-title {
   padding: 12px;
   border-bottom: 4px solid #909090;
   border-top: 4px solid #909090;
+  text-align: center;
 }
 
 #inputs {

data/public/css/tipsy.css

@@ -1,5 +1,5 @@
 .tipsy { padding: 5px; font-size: 13px; opacity: 0.8; filter: alpha(opacity=80); background-repeat: no-repeat;  background-image: url(../images/tipsy.gif); }
-  .tipsy-inner { padding: 5px 8px 4px 8px; background-color: #161616; color: white; max-width: 240px; text-align: left; }
+  .tipsy-inner { padding: 5px 8px 4px 8px; background-color: #161616; color: white; max-width: 300px; text-align: left; }
   .tipsy-inner { -moz-border-radius:3px; -webkit-border-radius:3px; }
   .tipsy-north { background-position: top center; }
   .tipsy-south { background-position: bottom center; }

data/public/scripts/form.js

@@ -41,23 +41,9 @@ function uploadFile(input) { //, files) {
   // TODO: what if it exists already!? - currently replaces it
   $('#workflow-form').append("<input name='" + input + "-file' type='hidden' value='" + filename +"' />");
 
-
-  //var file = files[0];
-
-  // create form to send to server-side upload handler
-  //var formdata = new FormData();
-
-  // include file to form
-  //formdata.append("file", file);
-
-
   // get the form from the document (jQuery selector wasn't working inside function!)
   var formdata = new FormData(document.getElementById(input + '-upload-form'));
 
-  //$.ajax({
-  //  type: "POST",
-  //  url: "http://" + document.location.host + "/t2web/upload",
-
   var xhr = new XMLHttpRequest();
   //xhr.file = file; // not necessary if you create scopes like this
   xhr.upload.addEventListener('progress', function(e) {
@@ -65,7 +51,6 @@ function uploadFile(input) { //, files) {
       console.log('xhr progress: ' + (Math.floor(done/total*1000)/10) + '%');
   }, false);
   if ( xhr.upload ) {
-      console.log("AAAAAAAAAAAAAAAA");
       xhr.upload.onprogress = function(e) {
           var done = e.position || e.loaded, total = e.totalSize || e.total;
           console.log('xhr.upload progress: ' + done + ' / ' + total + ' = ' + (Math.floor(done/total*1000)/10) + '%');
@@ -79,20 +64,11 @@ function uploadFile(input) { //, files) {
 
   xhr.open('post', "http://" + document.location.host + "/t2web/upload", false);
   xhr.send(formdata);
-  
-
-
-  // submit the form to upload the file
-  // we would like to do that via XHR to include client-side progress bar!
-  //$('#' + input + '-upload-form').submit();
-
 }
 
 // initilises certain html elements to employ tipsy for their tooltips
 function initialiseTipsys() {
-  $('[name$="-input"]').tipsy({gravity: 'e', fade: true, html: true, fallback: "No available example"});
-  $('[for$="-label"]').tipsy({gravity: 'e', fade: true, html: true, fallback: "No available description"});
-  //$('[name$="-input"]').tooltip();
-
+  $('[name$="-input"]').tipsy({gravity: 'w', fade: true, html: true, fallback: "No available example"});
+  $('[for$="-label"]').tipsy({gravity: 'w', fade: true, html: true, fallback: "No available description"});
 }
 

data/public/scripts/results.js

@@ -1,30 +1,81 @@
+// TODO: remove soon! (not used anymore! files are stored locally in tmp!!
 function getSampleOutput(t2_server, uuid, output, wid, wkf_version) {
   // t2 server REST call to sample output
+  // the following RESt is used for displaying tmp local files to the screen
   var httpcall = "http://" + document.location.host + "/t2web/run/" + uuid + "/output/" + output +
                  "?server=" + t2_server + "&wid=" + wid + "&wkf_version=" + wkf_version;
 
-  // display progress cycle icon in output during fetching
-
   // ajax request
   $.get(httpcall, function (result) {
     window.frames['data-display'].document.documentElement.innerHTML = result;
   });
 
-  // remove progress cycle icon in output
+}
+
+function readTmpOutput(t2_server, uuid, output, wid, wkf_version) {
+  // TODO: currently t2_server, wid and wkf_version are not used
+
+  // t2web server call to get wkf results from tmp file
+  var httpcall = "http://" + document.location.host + "/t2web/run/" + uuid + "/output/" + output;
+
+  $.get(httpcall, function (result) {
+    window.frames['data-display'].document.documentElement.innerHTML = result;
+  });
 
 }
 
-function checkRunStatus(t2_server, uuid) {
+function checkRunStatus(t2_server, uuid, wid, wkf_version) {
   // t2 server REST call to uuid's status
   var httpcall = "http://" + document.location.host + "/runs/" + uuid + "/status?server=" + t2_server;
 
-  // ajax request
-  $.get(httpcall, function (result) {
-    if (result == 'Finished') {
-      window.frames['data-navigation'].document.documentElement.innerHTML = results_navigation;
-      clearInterval(runStatusIntervalId);
-    }
-  });
+  // ajax request to confirm finished execution
+  //$.get(httpcall, function (result) {
+  //  if (result == 'Finished') {
+
+      // TODO: that probably causes the browser status to show that it's still working!!
+  //    clearInterval(runStatusIntervalId);
+
+  //    getOutputs(t2_server, uuid);
+      //getOutputs("http://test.mybiobank.org/taverna-server", "f3dca934-a6d7-44e3-acc3-f8c1f30e0973");
+  //  }
+  //});
 
+  $.ajax({
+            type: "GET",
+            url: httpcall,
+            success: function (result) {
+              if (result == 'Finished') {
+                clearInterval(runStatusIntervalId);
+                getOutputs(t2_server, uuid);
+              }
+            }
+          });
 }
 
+function getOutputs(t2_server, uuid) {
+     // prepare get outputs call (to local ruby, cross-domain ajax call)
+      var httpoutputs = "http://" + document.location.host + "/t2web/run/" + uuid + "/outputs" +
+                        "?server=" + t2_server;
+      console.log("in new function!!!!");
+
+      // ajax request to get outputs
+      //$.get(httpoutputs, function (reply) {
+      //  if (reply == 'Successful download!') {
+      //    window.frames['data-navigation'].document.documentElement.innerHTML = results_navigation;
+      //  }
+      //});
+
+      $.ajax({
+                type: "GET",
+                url: httpoutputs,
+                success: function(reply) {
+                  if (reply == 'Successful download!') {
+                    window.frames['data-navigation'].document.documentElement.innerHTML = results_navigation;
+                  }
+                }//,
+                //error: function(reply) {
+                //    window.frames['data-navigation'].document.documentElement.innerHTML = results_navigation;
+                //}
+              });
+
+}

data/views/form.haml

@@ -38,12 +38,11 @@
               %input{:type => "submit", :value => "Execute", :class => "button"}
       - if @my_exp_wkf.inputs.size >=1
         - @my_exp_wkf.inputs.each do |input|
-          -# TODO: make helper create_input_tooltip(input) to return proper tooltip html string!!!
           - if input.descriptions.size >=1
-            - input_label_tooltip = generate_label_tooltip(input)
+            - input_label_tooltip = generate_tooltip("Description: ", input)
           - input_textarea_tooltip = ""
           - if input.examples.size >=1
-            - input_textarea_tooltip = generate_textarea_tooltip(input)
+            - input_textarea_tooltip = generate_tooltip("Example: ", input)
           %div{:id => "#{input.name}-upload-form-div"}
             -#%form{:id => "#{input.name}-upload-form", :enctype => "multipart/form-data", :target => "hidden-iframe", :action => "/t2web/upload", :method => "post"}
             %form{:id => "#{input.name}-upload-form", :enctype => "multipart/form-data"}
@@ -120,7 +119,7 @@
             %img{:src => "/images/bullet_go.png", :alt => "Important!" }
           %td.inputs
             For more information on this workflow please visit the
-            %a{ :href => "http://www.myExperiment.org/workflows/#{@wid}" } myExperiment website
+            %a{ :href => "http://www.myExperiment.org/workflows/#{@wid}", :target => "_blank" } myExperiment website
         -# if #{@my_exp_wkf.user.email}
           %tr
             %td.inputs

data/views/results.haml

@@ -14,6 +14,7 @@
           window.frames['header'].document.write("#{generate_header_frame(@my_exp_wkf, @my_exp_usr).gsub!(/\n/, "")}");
           window.frames['data-navigation'].document.write("#{generate_data_navigation_frame(@my_exp_wkf, @run_uuid, @wid, @wkf_version, @t2_server, false)}");
           runStatusIntervalId = window.setInterval( "checkRunStatus('#{@t2_server}', '#{@run_uuid}')", 5000);
+          //checkRunStatus("#{@t2_server}", "#{@run_uuid}");
         });
     %script{:type => "text/javascript", :src => "/scripts/results.js"}
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: t2-web
 version: !ruby/object:Gem::Version 
-  hash: 13
+  hash: 27
   prerelease: 
   segments: 
   - 0
+  - 1
   - 0
-  - 9
-  version: 0.0.9
+  version: 0.1.0
 platform: ruby
 authors: 
 - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-03-21 00:00:00 Z
+date: 2012-04-04 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: sinatra
@@ -112,6 +112,7 @@ files:
 - README
 - CHANGES
 - Rakefile
+- bin/config.ru
 - bin/t2_webapp.rb
 - doc/rdoc-style.css
 - doc/fr_file_index.html