RubyGems - t2-web - Versions diffs - 0.1.9 → 0.2.0 - Mend

t2-web 0.1.9 → 0.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (88) hide show

data/Gemfile CHANGED

@@ -1,5 +1,7 @@
 source 'http://rubygems.org'
+config.serve_static_assets = true
 gem 'sinatra', '~> 1.3.2'
 gem 'thin', '~> 1.2.11'
 gem 'haml', '~> 3.1.2'
@@ -14,3 +16,4 @@ end
 group :test do
   gem 'webrat'
 end

data/Rakefile CHANGED

@@ -12,12 +12,12 @@ require 'rdoc/task'
 spec = Gem::Specification.new do |s|
   s.name = 't2-web'
-  s.version = '0.1.9'
+  s.version = '0.2.0'
   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
-  s.author = 'Kostas Karasavvas'
-  s.email = 'kostas.karasavvas@nbic.nl'
+  s.authors = ['Kostas Karasavvas','Mark Thompson', 'Reinout van Schouwen']
+  s.email = 'mark9630@gmail.com'
   s.executables = ['t2-web']
   s.files = %w(LICENSE README CHANGES Rakefile Gemfile Gemfile.lock) + Dir.glob("{bin,lib,doc,spec,public,views}/**/*")
   s.require_path = "lib"
@@ -28,6 +28,7 @@ spec = Gem::Specification.new do |s|
   s.add_dependency 'rest-client', '~> 1.6.3'
   s.add_dependency 't2-server', '~> 0.6.1'
   s.add_dependency 'myexperiment-rest', '~> 0.3.3'
+  s.add_dependency 'nokogiri', '~> 1.5.9'
 end
 Gem::PackageTask.new(spec) do |p|

data/bin/t2-web CHANGED

File without changes

data/bin/t2_webapp.rb CHANGED

@@ -9,6 +9,7 @@ require 't2-server'
 require 'myexperiment-rest'
 require 'cgi'
 require 'stringio'
+require 'nokogiri'
 #require "t2-web"
 # TODO: move whole of T2WebApp in lib
@@ -20,7 +21,12 @@ class T2WebApp < Sinatra::Base
   WEB_APP_NAME = "t2web"
   set :views, File.dirname(__FILE__) + '/../views'
-  set :public_folder, File.dirname(__FILE__) + '/../public'
+  #set :public_folder, '/var/lib/gems/1.9.1/gems/t2-web-0.1.9'
+  #set :public_folder, File.dirname(__FILE__) + '/../public'
+  set :public_folder, File.expand_path(File.join('/', 'var', 'www', 't2web'))
+  #puts File.dirname(__FILE__) + '/../public'
+  #puts public_folder
+  #ENV.each { |e| puts "#{e[0]} => #{e[1]}" }
   # Can be used from routes and views (haml) -- not public methods
   helpers do
@@ -60,7 +66,7 @@ class T2WebApp < Sinatra::Base
     def generate_header_frame(my_exp_wkf, my_exp_usr)
       <<END
 <html>
-  <head><link href='/t2web/css/form.css' rel='stylesheet'/></head>
+  <head><link href='/css/form.css' rel='stylesheet'/></head>
   <body>
     #{generate_header_table(my_exp_wkf, my_exp_usr)}
   </body>
@@ -76,7 +82,7 @@ END
       <table class='header'>
         <tr>
           <td class='left'>
-            <img alt='NBIC logo' src='/t2web/images/nbic_logo.gif' />
+            <img alt='NBIC logo' src='/images/nbic_logo.gif' />
           </td>
           <td>
             <table class='header-title'>
@@ -89,7 +95,7 @@ END
             </table>
           </td>
           <td>
-            <img alt='LUMC logo' class='right' src='/t2web/images/lumc_logo2.png' />
+            <img alt='LUMC logo' class='right' src='/images/lumc_logo2.png' />
           </td>
         </tr>
       </table>
@@ -110,8 +116,9 @@ 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)
+      puts "generate data navigation frame function called"
-      data_navigation_frame = "<html><head><link href='/t2web/css/results_navigation.css' rel='stylesheet'/></head><body><table>"
+      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>"
@@ -120,7 +127,7 @@ END
             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>"
+            data_navigation_frame << "<td>#{output.name}</td><td><img src='/images/snake_transparent.gif' alt='Loading Content...'></td>"
           end
           data_navigation_frame << "</tr>"
         end
@@ -144,7 +151,12 @@ END
     # 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)
+      #puts data_lists.to_yaml # mark
       data = ""
+      if data_lists.instance_of? String
+          #puts ">>>>>>>>>>> changing type of data_lists"
+          data_lists = [ data_lists ]
+      end
       data_lists.each do |list|
         if list.instance_of? Array
           tmp_data = list.flatten.compact.map {|e| e.chomp}
@@ -200,11 +212,13 @@ END
     # 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"
+    #@t2_server = params[:server] || "http://test.mybiobank.org/taverna-server"
+    @t2_server = params[:server] || "http://localhost:8080/taverna-server"
     # Get myExperiment workflow object
     # TODO: catch exception
     @my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)
+    #puts @my_exp_wkf.to_yaml
     # Get myExperiment user object
     # TODO: catch exception
@@ -224,7 +238,8 @@ END
     # TODO: consider adding the following to a session
     @wid = params[:wid]
     @wkf_version = params[:wkf_version]
-    @t2_server = params[:server]
+    #@t2_server = params[:server]
+    @t2_server = "http://workflow.biosemantics.org/taverna-server" # hacked by mark
     @my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)
@@ -235,10 +250,23 @@ END
     #wkf_file = URI.parse(@my_exp_wkf.content_uri)
     wkf = open(@my_exp_wkf.content_uri).read
+    # Parse wkf XML to add username/password for RSHELL if applicable
+    wkf_xml = Nokogiri::XML(wkf)
+    rshellConfig = wkf_xml.xpath("//net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean").first
+    if (!(rshellConfig.nil?) and rshellConfig.xpath("//connectionSettings/username").first.nil?)
+     newNode = Nokogiri::XML::Node.new("username", wkf_xml)
+     wkf_xml.xpath("//net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean/connectionSettings").first.add_child(newNode)
+    end
+    #puts wkf_xml.xpath("//connectionSettings")
+    wkf = wkf_xml.to_s
     # create run
     begin
-      run = T2Server::Run.create(@t2_server, wkf)
+      run = T2Server::Run.create(@t2_server, wkf.sub(/<\?xml(.*)?>/,""))
+      #puts ">>> wkf from t2-web #{@my_exp_wkf.content_uri}:\n"
     rescue T2Server::T2ServerError => e
+      #mark: puts e.to_s
+      #mark: puts e.to_yaml
       return "404 Not Found: run could not be instantiated!"
     end
@@ -250,6 +278,7 @@ END
       if params[:"upload-checkbox-#{input.name}"] == "yes"
         filename = params[:"#{input.name}-file"]
         tmp_filename = "#{settings.public_folder}/#{WEB_APP_NAME}/tmp/#{filename}"
+        puts "tmp_filename: #{tmp_filename}"
         # make sure that the file is uploaded completely, i.e. all it's
         # connections are closed
@@ -265,8 +294,10 @@ END
     end
     # start run and wait until it is finished
+    puts "run started"
     run.start
+    puts "webapp name: #{WEB_APP_NAME}"
     haml :results
   end
@@ -277,8 +308,12 @@ END
     uuid = params[:uuid]
     t2_server = params[:server]
-    response = RestClient.get t2_server + "/rest/runs/" + uuid + "/status", :content_type => "text/plain"
+    forceNoCache = (0...8).map{65.+(rand(25)).chr}.join
+    statusUrl = t2_server + "/rest/runs/" + uuid + "/status" + "?random=" + forceNoCache
+    #puts "Getting status from: " + statusUrl
+    response = RestClient.get statusUrl, :content_type => "text/plain"
+    #puts response.to_str
     response.to_str
   end

data/public/t2web/scripts/results.js CHANGED

@@ -26,7 +26,8 @@ function readTmpOutput(t2_server, uuid, output, wid, wkf_version) {
 function checkRunStatus(t2_server, uuid, wid, wkf_version) {
   // t2 server REST call to uuid's status
-  var httpcall = "http://" + document.location.host + "/t2web/runs/" + uuid + "/status?server=" + t2_server;
+  var httpcall = "http://" + document.location.host + "/t2web/runs/" + uuid + "/status?server=" + t2_server + "&random=" + Math.random();
+  console.log("httpcall: " + httpcall);
   // ajax request to confirm finished execution
   //$.get(httpcall, function (result) {
@@ -44,19 +45,22 @@ function checkRunStatus(t2_server, uuid, wid, wkf_version) {
             type: "GET",
             url: httpcall,
             success: function (result) {
+              console.log("Result: " + result);
               if (result == 'Finished') {
+                console.log("Finished!");
                 clearInterval(runStatusIntervalId);
                 getOutputs(t2_server, uuid);
               }
             }
           });
+ console.log("after ajax call");
 }
 function getOutputs(t2_server, uuid) {
      // prepare get outputs call (to local ruby, cross-domain ajax call)
       var httpoutputs = "http://" + document.location.host + "/t2web/run/" + uuid + "/outputs" +
                         "?server=" + t2_server;
-      console.log("in new function!!!!");
+      console.log("in new function!!!!" + httpoutputs);
       // ajax request to get outputs
       //$.get(httpoutputs, function (reply) {

data/public/t2web/tmp/outputs/049c41c6-77ed-457b-a342-1a779055156a/UniProtID ADDED

@@ -0,0 +1,166 @@
+<b>P70386</b>
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data/public/t2web/tmp/outputs/049c41c6-77ed-457b-a342-1a779055156a/ValidatedProtein ADDED

@@ -0,0 +1,8 @@
+<b>GnT-III</b>
+GnT-III
+GnT-III
+GnT-III
+<b>gamma-actin</b>
+<b>APP</b>
+APP
+APP

data/public/t2web/tmp/outputs/146d17ee-9418-4b59-89db-d9d0b9b8986d/Document_ID ADDED

	@@ -0,0 +1 @@
1	+ <b>19614980</b>

data/public/t2web/tmp/outputs/146d17ee-9418-4b59-89db-d9d0b9b8986d/Document_title ADDED

	@@ -0,0 +1 @@
1	+ <b>L-Glutamine-induced apoptosis in microglia is mediated by mitochondrial dysfunction.</b>

data/public/t2web/tmp/outputs/2dbcdad5-5344-42c6-b75d-0786bb64ab21/UniProtID ADDED

@@ -0,0 +1,185 @@
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