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

t2-web 0.1.9 → 0.2.0

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 @@
+<b>P70386</b>
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