t2-web 0.1.3 → 0.1.4

data/CHANGES

@@ -1,7 +1,9 @@
 = Changes log for the Taverna via the Web Gem
 
-== Version 0.1.3
-* Added /t2web in route to check status.. /runs/...
+== Version 0.1.4
+* Workflow results are now stored in the public_folder
+* We now support image results (not list of images in one taverna output yet)
+* Added /t2web in route to check the workflow execution status in taverna (was /runs/...)
 
 == Version 0.1.2
 * Moved everything in /public into /public/t2web to be able to redirect from apache et al.

data/Gemfile

@@ -0,0 +1,16 @@
+source 'http://rubygems.org'
+
+gem 'sinatra', '~> 1.3.2'
+gem 'thin', '~> 1.2.11'
+gem 'haml', '~> 3.1.2'
+gem 'rest-client', '~> 1.6.3'
+gem 't2-server', '~> 0.6.1'
+gem 'myexperiment-rest', '~> 0.3.3'
+
+group :development do
+  gem 'rdoc'
+end
+
+group :test do
+  gem 'webrat'
+end

data/Gemfile.lock

@@ -0,0 +1,52 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    daemons (1.1.8)
+    eventmachine (0.12.10)
+    haml (3.1.4)
+    hirb (0.6.2)
+    json (1.6.6)
+    libxml-ruby (2.2.2)
+    mime-types (1.18)
+    myexperiment-rest (0.3.3)
+      libxml-ruby (~> 2.2.2)
+      rest-client (~> 1.6.3)
+    nokogiri (1.5.2)
+    rack (1.4.1)
+    rack-protection (1.2.0)
+      rack
+    rack-test (0.6.1)
+      rack (>= 1.0)
+    rdoc (3.12)
+      json (~> 1.4)
+    rest-client (1.6.3)
+      mime-types (>= 1.16)
+    sinatra (1.3.2)
+      rack (~> 1.3, >= 1.3.6)
+      rack-protection (~> 1.2)
+      tilt (~> 1.3, >= 1.3.3)
+    t2-server (0.6.1)
+      hirb (>= 0.4.0)
+      libxml-ruby (>= 1.1.4)
+    thin (1.2.11)
+      daemons (>= 1.0.9)
+      eventmachine (>= 0.12.6)
+      rack (>= 1.0.0)
+    tilt (1.3.3)
+    webrat (0.7.3)
+      nokogiri (>= 1.2.0)
+      rack (>= 1.0)
+      rack-test (>= 0.5.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  haml (~> 3.1.2)
+  myexperiment-rest (~> 0.3.3)
+  rdoc
+  rest-client (~> 1.6.3)
+  sinatra (~> 1.3.2)
+  t2-server (~> 0.6.1)
+  thin (~> 1.2.11)
+  webrat

data/README

@@ -2,7 +2,7 @@
 
 
 Authors::     Konstantinos Karasavvas
-Gem Version:: 0.1.3
+Gem Version:: 0.1.4
 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
@@ -12,7 +12,7 @@ Copyright::   (c) 2012 Netherlands Bioinformatics Centre, The Netherlands
 
 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
+browser with no other dependencies. The web form interface is as good as the
 description provided in the workflow itself in myExperiment.
 
 
@@ -23,7 +23,7 @@ description provided in the workflow itself in myExperiment.
 
 == Usage
 
-  rackup -p 9494
+  thin -p 9494 start
 
 Run the above from the webapp's root directory to start the web application at port 9494 and wait for incoming requests. Uses rack's config.ru file.
 

data/Rakefile

@@ -12,14 +12,14 @@ require 'rdoc/task'
 
 spec = Gem::Specification.new do |s|
   s.name = 't2-web'
-  s.version = '0.1.3'
+  s.version = '0.1.4'
   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.executables = ['t2_webapp.rb']
-  s.files = %w(LICENSE README CHANGES Rakefile) + Dir.glob("{bin,lib,doc,spec,public,views}/**/*")
+  s.files = %w(LICENSE README CHANGES Rakefile Gemfile Gemfile.lock) + Dir.glob("{bin,lib,doc,spec,public,views}/**/*")
   s.require_path = "lib"
   s.bindir = "bin"
   s.add_dependency 'sinatra', '~> 1.3.0'

data/bin/config.ru

@@ -1,8 +1,7 @@
 require 'sinatra'
 require './t2_webapp'
 
-set :timeout, 600
-#not picked up!  ...  set :port, 9494
+set :timeout, 1800
 
-run WebT2App
+run T2WebApp
 

data/bin/log/thin.log

@@ -0,0 +1,36 @@
+>> Writing PID to tmp/pids/thin.pid
+>> Using rack adapter
+>> Thin web server (v1.2.11 codename Bat-Shit Crazy)
+>> Maximum connections set to 1024
+>> Listening on 0.0.0.0:3000, CTRL+C to stop
+>> Exiting!
+/home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/eventmachine-0.12.10/lib/eventmachine.rb:572:in `start_tcp_server': no acceptor (RuntimeError)
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/eventmachine-0.12.10/lib/eventmachine.rb:572:in `start_server'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/lib/thin/backends/tcp_server.rb:16:in `connect'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/lib/thin/backends/base.rb:53:in `start'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/eventmachine-0.12.10/lib/eventmachine.rb:256:in `call'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/eventmachine-0.12.10/lib/eventmachine.rb:256:in `run_machine'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/eventmachine-0.12.10/lib/eventmachine.rb:256:in `run'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/lib/thin/backends/base.rb:61:in `start'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/lib/thin/server.rb:159:in `start'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/lib/thin/controllers/controller.rb:86:in `start'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/lib/thin/runner.rb:185:in `send'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/lib/thin/runner.rb:185:in `run_command'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/lib/thin/runner.rb:151:in `run!'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/gems/thin-1.2.11/bin/thin:6
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/bin/thin:19:in `load'
+	from /home/kostas/.rvm/gems/ruby-1.8.7-p358@t2web/bin/thin:19
+>> Writing PID to tmp/pids/thin.pid
+>> Using rack adapter
+>> Thin web server (v1.2.11 codename Bat-Shit Crazy)
+>> Maximum connections set to 1024
+>> Listening on 0.0.0.0:9494, CTRL+C to stop
+>> Waiting for 6 connection(s) to finish, can take up to 30 sec, CTRL+C to stop now
+>> Exiting!
+>> Writing PID to tmp/pids/thin.pid
+>> Using rack adapter
+>> Thin web server (v1.2.11 codename Bat-Shit Crazy)
+>> Maximum connections set to 1024
+>> Listening on 0.0.0.0:9494, CTRL+C to stop
+>> Waiting for 1 connection(s) to finish, can take up to 30 sec, CTRL+C to stop now
+>> Exiting!

data/bin/t2_webapp.rb

@@ -9,20 +9,20 @@ require 't2-server'
 require 'myexperiment-rest'
 require 'cgi'
 require 'stringio'
-#require "t2-web" TODO: move whole of WebT2App in lib
+#require "t2-web" 
 
-# TODO: add constants.rb file in lib for all constants (e.g. myExp user URL, other URLs
+# 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 WebT2App < Sinatra::Base
+class T2WebApp < Sinatra::Base
 
   WEB_APP_NAME = "t2web"
-  # TODO: const for TMP_UPLOAD_PATH ? - need to read from config file?
 
-  #set :port, 9494     set from: rackup -p 9494
   set :views, File.dirname(__FILE__) + '/../views'
   set :public_folder, File.dirname(__FILE__) + '/../public'
 
-  # can be used from routes and views (haml)
+  # 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
@@ -32,10 +32,8 @@ class WebT2App < Sinatra::Base
       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
@@ -49,7 +47,6 @@ class WebT2App < Sinatra::Base
     
     # 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}"
@@ -110,12 +107,6 @@ END
       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
-
 
     # Generates the contents of the data-navigation frame
     def generate_data_navigation_frame(my_exp_wkf, uuid, wid, wkf_version, t2_server, finished_execution)
@@ -138,15 +129,19 @@ END
     end
 
 
-    # Check type of data and generate appropriate html for that result!
-    # Takes list as input -- TODO: rdoc methods properly!
+    # 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
+
 
-    # Check type of data and generate appropriate html for that result!
-    # Takes list as input, returns as file stream -- TODO: rdoc methods properly!
+    # Takes list as input (or single element), returns as file stream 
+    # TODO: for images it works when not a list!
     def flatten_list_results(list)
       data = ""
       #p list
@@ -163,11 +158,16 @@ END
 
 
 
-    # copies output stream to a tmp file in the specified subdir
-    # TODO: make proper rdoc
+    # Copies output stream to a tmp file in the specified subdir
     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")
+
+      # 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}!!"
@@ -187,11 +187,11 @@ END
     @t2_server = params[:server] || "http://test.mybiobank.org/taverna-server"
 
     # Get myExperiment workflow object
-    # TODO: catch exception -- make custom exceptions?
+    # TODO: catch exception
     @my_exp_wkf = MyExperimentREST::Workflow.from_id_and_version(@wid, @wkf_version)
 
     # Get myExperiment user object
-    # TODO: catch exception -- make custom exceptions?
+    # TODO: catch exception
     @my_exp_usr = MyExperimentREST::User.from_uri(@my_exp_wkf.uploader_uri)
 
     haml :form
@@ -215,7 +215,6 @@ END
     # 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
@@ -234,7 +233,7 @@ END
     @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}"
+        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
@@ -282,7 +281,7 @@ END
     # 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!
+    #       download if result too large! 
     run.get_output_ports.each do |t2_output|
       begin
         data_lists = run.get_output(t2_output, false)
@@ -293,7 +292,7 @@ END
       # flatten the results 
       data_stream = flatten_list_results(data_lists)
 
-      # copy results to tmp
+      # copy results to our app's tmp
       copy_to_tmp("outputs/#{@run_uuid}", t2_output, data_stream)
     end
 
@@ -303,23 +302,37 @@ END
 
 
   # Get results for specified run and output (stored locally from tmp)
-  # display it in data-display div
+  # 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]
 
-    # add HTML tags to display properly
-    data = File.open("/tmp/#{WEB_APP_NAME}/outputs/#{run_uuid}/#{t2_output}", "r").read
+    data = File.open("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}", "r").read
+
+    # Add HTML tags to display properly
 
-    generate_html_result(data)
+    # 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 #{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output} )
+    if mime_type.include?("image/")
+      generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}")
+    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!!
+  # 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]
@@ -333,5 +346,6 @@ END
 end
 
 
-# Start Web App
-# $ rackup -p 9494
+# Start Web App from the ./bin directory in deamon mode at port 9494
+# $ thin -d -p 9494
+

data/public/t2web/tmp/outputs/08620310-4804-4f85-9d49-692504c29efd/SummedSimilarity

@@ -0,0 +1,2 @@
+1.7257954402415606E-4
+2.982841744031976E-7

data/public/t2web/tmp/outputs/08620310-4804-4f85-9d49-692504c29efd/TopContributingConcepts

@@ -0,0 +1,20 @@
+EZH2
+HDAC1
+histone
+Hdac1l
+Deacetylase
+Transcriptional Repression
+epigene
+chromatin immunoprecipitation
+Repression
+histone deacetylase inhibitor
+candidate disease gene
+all nervous tissue
+Nerve Tissue
+Genes
+Aggressive behavior
+Cell membrane
+carrier of disorder
+lysine
+Lysine
+Methylation

data/public/t2web/tmp/outputs/08620310-4804-4f85-9d49-692504c29efd/TopMatchingConcepts

@@ -0,0 +1,2 @@
+<http://rdf.biosemantics.org/owl/concept#3092985/>
+<http://rdf.biosemantics.org/owl/concept#3099696/>

data/public/t2web/tmp/outputs/08620310-4804-4f85-9d49-692504c29efd/contributionTable_xml

@@ -0,0 +1,2 @@
+<ConceptContributionTable><ConceptContribution><conceptName>EZH2</conceptName><contribution>31.88125789165497</contribution><conceptId>3091515</conceptId></ConceptContribution><ConceptContribution><conceptName>HDAC1</conceptName><contribution>22.398044168949127</contribution><conceptId>3092985</conceptId></ConceptContribution><ConceptContribution><conceptName>histone</conceptName><contribution>15.102960169315338</contribution><conceptId>4278518</conceptId></ConceptContribution><ConceptContribution><conceptName>Hdac1l</conceptName><contribution>13.64096999168396</contribution><conceptId>3070448</conceptId></ConceptContribution><ConceptContribution><conceptName>Deacetylase</conceptName><contribution>3.7955906242132187</contribution><conceptId>1333261</conceptId></ConceptContribution><ConceptContribution><conceptName>Transcriptional Repression</conceptName><contribution>1.364685595035553</contribution><conceptId>920533</conceptId></ConceptContribution><ConceptContribution><conceptName>epigene</conceptName><contribution>1.0359483771026134</contribution><conceptId>2900273</conceptId></ConceptContribution><ConceptContribution><conceptName>chromatin immunoprecipitation</conceptName><contribution>0.7878270000219345</contribution><conceptId>1328856</conceptId></ConceptContribution><ConceptContribution><conceptName>Repression</conceptName><contribution>0.7402509450912476</contribution><conceptId>35143</conceptId></ConceptContribution><ConceptContribution><conceptName>histone deacetylase inhibitor</conceptName><contribution>0.6155987735837698</contribution><conceptId>1512474</conceptId></ConceptContribution></ConceptContributionTable>
+<ConceptContributionTable><ConceptContribution><conceptName>candidate disease gene</conceptName><contribution>36.36130690574646</contribution><conceptId>1332838</conceptId></ConceptContribution><ConceptContribution><conceptName>all nervous tissue</conceptName><contribution>5.341833457350731</contribution><conceptId>1762608</conceptId></ConceptContribution><ConceptContribution><conceptName>Nerve Tissue</conceptName><contribution>5.339629203081131</contribution><conceptId>27757</conceptId></ConceptContribution><ConceptContribution><conceptName>Genes</conceptName><contribution>5.2357688546180725</contribution><conceptId>17337</conceptId></ConceptContribution><ConceptContribution><conceptName>Aggressive behavior</conceptName><contribution>3.674016520380974</contribution><conceptId>1807</conceptId></ConceptContribution><ConceptContribution><conceptName>Cell membrane</conceptName><contribution>2.3985113948583603</contribution><conceptId>7603</conceptId></ConceptContribution><ConceptContribution><conceptName>carrier of disorder</conceptName><contribution>2.014324814081192</contribution><conceptId>560175</conceptId></ConceptContribution><ConceptContribution><conceptName>lysine</conceptName><contribution>1.8032535910606384</contribution><conceptId>4275268</conceptId></ConceptContribution><ConceptContribution><conceptName>Lysine</conceptName><contribution>1.8017882481217384</contribution><conceptId>4005689</conceptId></ConceptContribution><ConceptContribution><conceptName>Methylation</conceptName><contribution>1.6273731365799904</contribution><conceptId>25723</conceptId></ConceptContribution></ConceptContributionTable>

data/public/t2web/tmp/outputs/12b9a7b5-1023-47e2-a83d-78b3c6ca32b1/Pathway

@@ -0,0 +1 @@
+path:hsa05016 Huntington's disease - Homo sapiens (human)

data/public/t2web/tmp/outputs/12b9a7b5-1023-47e2-a83d-78b3c6ca32b1/geneList

@@ -0,0 +1,184 @@
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data/public/t2web/tmp/outputs/12b9a7b5-1023-47e2-a83d-78b3c6ca32b1/url

@@ -0,0 +1 @@
+http://soap.genome.jp/tmp/mark_pathway_www_api.133459237222169/hsa05016.png

data/public/t2web/tmp/outputs/5ed0a0a3-ea27-4cdc-854a-37ae23a1022a/SummedSimilarity

@@ -0,0 +1,2 @@
+0.005384722088064496
+8.28447701454222E-7

data/public/t2web/tmp/outputs/5ed0a0a3-ea27-4cdc-854a-37ae23a1022a/TopContributingConcepts

@@ -0,0 +1,49 @@
+Set of ErrorDocumentS to follow.
+ErrorDocument 1
+Set of ErrorDocumentS to follow.
+ErrorDocument 1
+Set of ErrorDocumentS to follow.
+ErrorDocument 1
+Set of ErrorDocumentS to follow.
+ErrorDocument 1
+java.lang.NullPointerException
+org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:222)
+org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:129)
+org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
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+org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(unknown file)
+org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(unknown file)
+org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(unknown file)
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+org.apache.xerces.parsers.AbstractSAXParser.parse(unknown file)
+org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(unknown file)
+javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
+org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227)
+org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
+org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
+org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62)
+org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
+org.apache.axis.client.Call.invokeEngine(Call.java:2784)
+org.apache.axis.client.Call.invoke(Call.java:2767)
+org.apache.axis.client.Call.invoke(Call.java:1910)
+net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
+net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
+net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:265)
+net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
+java.lang.Thread.run(Thread.java:636)
+
+
+
+
+serotonin
+candidate disease gene
+Genetic Polymorphism
+Genotype
+Genes
+Cell membrane
+Mental Depression
+BDNF
+all nervous tissue
+Nerve Tissue

data/public/t2web/tmp/outputs/5ed0a0a3-ea27-4cdc-854a-37ae23a1022a/TopMatchingConcepts

@@ -0,0 +1,2 @@
+<http://rdf.biosemantics.org/owl/concept#3092985/>
+<http://rdf.biosemantics.org/owl/concept#3099696/>

data/public/t2web/tmp/outputs/5ed0a0a3-ea27-4cdc-854a-37ae23a1022a/contributionTable_xml

@@ -0,0 +1,34 @@
+Set of ErrorDocumentS to follow.
+ErrorDocument 1
+Set of ErrorDocumentS to follow.
+ErrorDocument 1
+java.lang.NullPointerException
+org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:222)
+org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:129)
+org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
+org.apache.xerces.parsers.AbstractSAXParser.endElement(unknown file)
+org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(unknown file)
+org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(unknown file)
+org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(unknown file)
+org.apache.xerces.parsers.XML11Configuration.parse(unknown file)
+org.apache.xerces.parsers.XML11Configuration.parse(unknown file)
+org.apache.xerces.parsers.XMLParser.parse(unknown file)
+org.apache.xerces.parsers.AbstractSAXParser.parse(unknown file)
+org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(unknown file)
+javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
+org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227)
+org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
+org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
+org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62)
+org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
+org.apache.axis.client.Call.invokeEngine(Call.java:2784)
+org.apache.axis.client.Call.invoke(Call.java:2767)
+org.apache.axis.client.Call.invoke(Call.java:1910)
+net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
+net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
+net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:265)
+net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
+java.lang.Thread.run(Thread.java:636)
+
+
+<ConceptContributionTable><ConceptContribution><conceptName>serotonin</conceptName><contribution>27.518025040626526</contribution><conceptId>4274509</conceptId></ConceptContribution><ConceptContribution><conceptName>candidate disease gene</conceptName><contribution>12.319853156805038</contribution><conceptId>1332838</conceptId></ConceptContribution><ConceptContribution><conceptName>Genetic Polymorphism</conceptName><contribution>5.391879379749298</contribution><conceptId>32529</conceptId></ConceptContribution><ConceptContribution><conceptName>Genotype</conceptName><contribution>4.17584702372551</contribution><conceptId>17431</conceptId></ConceptContribution><ConceptContribution><conceptName>Genes</conceptName><contribution>3.701891750097275</contribution><conceptId>17337</conceptId></ConceptContribution><ConceptContribution><conceptName>Cell membrane</conceptName><contribution>2.4947386234998703</contribution><conceptId>7603</conceptId></ConceptContribution><ConceptContribution><conceptName>Mental Depression</conceptName><contribution>1.722344383597374</contribution><conceptId>11570</conceptId></ConceptContribution><ConceptContribution><conceptName>BDNF</conceptName><contribution>1.4445194974541664</contribution><conceptId>3105912</conceptId></ConceptContribution><ConceptContribution><conceptName>all nervous tissue</conceptName><contribution>1.235499046742916</contribution><conceptId>1762608</conceptId></ConceptContribution><ConceptContribution><conceptName>Nerve Tissue</conceptName><contribution>1.2348570860922337</contribution><conceptId>27757</conceptId></ConceptContribution></ConceptContributionTable>

data/public/t2web/tmp/outputs/9f15e720-87d0-439d-96c3-09f433435699/Pathway

@@ -0,0 +1 @@
+path:hsa05016 Huntington's disease - Homo sapiens (human)

data/public/t2web/tmp/outputs/9f15e720-87d0-439d-96c3-09f433435699/geneList

@@ -0,0 +1,184 @@
+100532726
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+9586

data/public/t2web/tmp/outputs/9f15e720-87d0-439d-96c3-09f433435699/url

@@ -0,0 +1 @@
+http://soap.genome.jp/tmp/mark_pathway_www_api.133465606115487/hsa05016.png

data/public/t2web/tmp/outputs/edf6bf6a-a530-49b9-acdf-52c490ba57c7/SummedSimilarity

@@ -0,0 +1,2 @@
+1.7257954402415606E-4
+2.982841744031976E-7

data/public/t2web/tmp/outputs/edf6bf6a-a530-49b9-acdf-52c490ba57c7/TopContributingConcepts

@@ -0,0 +1,20 @@
+EZH2
+HDAC1
+histone
+Hdac1l
+Deacetylase
+Transcriptional Repression
+epigene
+chromatin immunoprecipitation
+Repression
+histone deacetylase inhibitor
+candidate disease gene
+all nervous tissue
+Nerve Tissue
+Genes
+Aggressive behavior
+Cell membrane
+carrier of disorder
+lysine
+Lysine
+Methylation

data/public/t2web/tmp/outputs/edf6bf6a-a530-49b9-acdf-52c490ba57c7/TopMatchingConcepts

@@ -0,0 +1,2 @@
+<http://rdf.biosemantics.org/owl/concept#3092985/>
+<http://rdf.biosemantics.org/owl/concept#3099696/>

data/public/t2web/tmp/outputs/edf6bf6a-a530-49b9-acdf-52c490ba57c7/contributionTable_xml

@@ -0,0 +1,2 @@
+<ConceptContributionTable><ConceptContribution><conceptName>EZH2</conceptName><contribution>31.88125789165497</contribution><conceptId>3091515</conceptId></ConceptContribution><ConceptContribution><conceptName>HDAC1</conceptName><contribution>22.398044168949127</contribution><conceptId>3092985</conceptId></ConceptContribution><ConceptContribution><conceptName>histone</conceptName><contribution>15.102960169315338</contribution><conceptId>4278518</conceptId></ConceptContribution><ConceptContribution><conceptName>Hdac1l</conceptName><contribution>13.64096999168396</contribution><conceptId>3070448</conceptId></ConceptContribution><ConceptContribution><conceptName>Deacetylase</conceptName><contribution>3.7955906242132187</contribution><conceptId>1333261</conceptId></ConceptContribution><ConceptContribution><conceptName>Transcriptional Repression</conceptName><contribution>1.364685595035553</contribution><conceptId>920533</conceptId></ConceptContribution><ConceptContribution><conceptName>epigene</conceptName><contribution>1.0359483771026134</contribution><conceptId>2900273</conceptId></ConceptContribution><ConceptContribution><conceptName>chromatin immunoprecipitation</conceptName><contribution>0.7878270000219345</contribution><conceptId>1328856</conceptId></ConceptContribution><ConceptContribution><conceptName>Repression</conceptName><contribution>0.7402509450912476</contribution><conceptId>35143</conceptId></ConceptContribution><ConceptContribution><conceptName>histone deacetylase inhibitor</conceptName><contribution>0.6155987735837698</contribution><conceptId>1512474</conceptId></ConceptContribution></ConceptContributionTable>
+<ConceptContributionTable><ConceptContribution><conceptName>candidate disease gene</conceptName><contribution>36.36130690574646</contribution><conceptId>1332838</conceptId></ConceptContribution><ConceptContribution><conceptName>all nervous tissue</conceptName><contribution>5.341833457350731</contribution><conceptId>1762608</conceptId></ConceptContribution><ConceptContribution><conceptName>Nerve Tissue</conceptName><contribution>5.339629203081131</contribution><conceptId>27757</conceptId></ConceptContribution><ConceptContribution><conceptName>Genes</conceptName><contribution>5.2357688546180725</contribution><conceptId>17337</conceptId></ConceptContribution><ConceptContribution><conceptName>Aggressive behavior</conceptName><contribution>3.674016520380974</contribution><conceptId>1807</conceptId></ConceptContribution><ConceptContribution><conceptName>Cell membrane</conceptName><contribution>2.3985113948583603</contribution><conceptId>7603</conceptId></ConceptContribution><ConceptContribution><conceptName>carrier of disorder</conceptName><contribution>2.014324814081192</contribution><conceptId>560175</conceptId></ConceptContribution><ConceptContribution><conceptName>lysine</conceptName><contribution>1.8032535910606384</contribution><conceptId>4275268</conceptId></ConceptContribution><ConceptContribution><conceptName>Lysine</conceptName><contribution>1.8017882481217384</contribution><conceptId>4005689</conceptId></ConceptContribution><ConceptContribution><conceptName>Methylation</conceptName><contribution>1.6273731365799904</contribution><conceptId>25723</conceptId></ConceptContribution></ConceptContributionTable>

data/public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/SummedSimilarity

@@ -0,0 +1,2 @@
+1.7257954402415606E-4
+2.982841744031976E-7

data/public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/TopContributingConcepts

@@ -0,0 +1,20 @@
+EZH2
+HDAC1
+histone
+Hdac1l
+Deacetylase
+Transcriptional Repression
+epigene
+chromatin immunoprecipitation
+Repression
+histone deacetylase inhibitor
+candidate disease gene
+all nervous tissue
+Nerve Tissue
+Genes
+Aggressive behavior
+Cell membrane
+carrier of disorder
+lysine
+Lysine
+Methylation

data/public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/TopMatchingConcepts

@@ -0,0 +1,2 @@
+<http://rdf.biosemantics.org/owl/concept#3092985/>
+<http://rdf.biosemantics.org/owl/concept#3099696/>

data/public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/contributionTable_xml

@@ -0,0 +1,2 @@
+<ConceptContributionTable><ConceptContribution><conceptName>EZH2</conceptName><contribution>31.88125789165497</contribution><conceptId>3091515</conceptId></ConceptContribution><ConceptContribution><conceptName>HDAC1</conceptName><contribution>22.398044168949127</contribution><conceptId>3092985</conceptId></ConceptContribution><ConceptContribution><conceptName>histone</conceptName><contribution>15.102960169315338</contribution><conceptId>4278518</conceptId></ConceptContribution><ConceptContribution><conceptName>Hdac1l</conceptName><contribution>13.64096999168396</contribution><conceptId>3070448</conceptId></ConceptContribution><ConceptContribution><conceptName>Deacetylase</conceptName><contribution>3.7955906242132187</contribution><conceptId>1333261</conceptId></ConceptContribution><ConceptContribution><conceptName>Transcriptional Repression</conceptName><contribution>1.364685595035553</contribution><conceptId>920533</conceptId></ConceptContribution><ConceptContribution><conceptName>epigene</conceptName><contribution>1.0359483771026134</contribution><conceptId>2900273</conceptId></ConceptContribution><ConceptContribution><conceptName>chromatin immunoprecipitation</conceptName><contribution>0.7878270000219345</contribution><conceptId>1328856</conceptId></ConceptContribution><ConceptContribution><conceptName>Repression</conceptName><contribution>0.7402509450912476</contribution><conceptId>35143</conceptId></ConceptContribution><ConceptContribution><conceptName>histone deacetylase inhibitor</conceptName><contribution>0.6155987735837698</contribution><conceptId>1512474</conceptId></ConceptContribution></ConceptContributionTable>
+<ConceptContributionTable><ConceptContribution><conceptName>candidate disease gene</conceptName><contribution>36.36130690574646</contribution><conceptId>1332838</conceptId></ConceptContribution><ConceptContribution><conceptName>all nervous tissue</conceptName><contribution>5.341833457350731</contribution><conceptId>1762608</conceptId></ConceptContribution><ConceptContribution><conceptName>Nerve Tissue</conceptName><contribution>5.339629203081131</contribution><conceptId>27757</conceptId></ConceptContribution><ConceptContribution><conceptName>Genes</conceptName><contribution>5.2357688546180725</contribution><conceptId>17337</conceptId></ConceptContribution><ConceptContribution><conceptName>Aggressive behavior</conceptName><contribution>3.674016520380974</contribution><conceptId>1807</conceptId></ConceptContribution><ConceptContribution><conceptName>Cell membrane</conceptName><contribution>2.3985113948583603</contribution><conceptId>7603</conceptId></ConceptContribution><ConceptContribution><conceptName>carrier of disorder</conceptName><contribution>2.014324814081192</contribution><conceptId>560175</conceptId></ConceptContribution><ConceptContribution><conceptName>lysine</conceptName><contribution>1.8032535910606384</contribution><conceptId>4275268</conceptId></ConceptContribution><ConceptContribution><conceptName>Lysine</conceptName><contribution>1.8017882481217384</contribution><conceptId>4005689</conceptId></ConceptContribution><ConceptContribution><conceptName>Methylation</conceptName><contribution>1.6273731365799904</contribution><conceptId>25723</conceptId></ConceptContribution></ConceptContributionTable>

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: t2-web
 version: !ruby/object:Gem::Version 
-  hash: 29
+  hash: 19
   prerelease: 
   segments: 
   - 0
   - 1
-  - 3
-  version: 0.1.3
+  - 4
+  version: 0.1.4
 platform: ruby
 authors: 
 - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-04-12 00:00:00 Z
+date: 2012-04-17 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: sinatra
@@ -112,12 +112,39 @@ files:
 - README
 - CHANGES
 - Rakefile
+- Gemfile
+- Gemfile.lock
 - bin/config.ru
+- bin/log/thin.log
 - bin/t2_webapp.rb
 - public/t2web/scripts/results.js
 - public/t2web/scripts/form.js
 - public/t2web/scripts/jquery-1.6.1.js
 - public/t2web/scripts/jquery.tipsy.js
+- public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/contributionTable_xml
+- public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/TopContributingConcepts
+- public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/TopMatchingConcepts
+- public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/SummedSimilarity
+- public/t2web/tmp/outputs/12b9a7b5-1023-47e2-a83d-78b3c6ca32b1/image
+- public/t2web/tmp/outputs/12b9a7b5-1023-47e2-a83d-78b3c6ca32b1/url
+- public/t2web/tmp/outputs/12b9a7b5-1023-47e2-a83d-78b3c6ca32b1/Pathway
+- public/t2web/tmp/outputs/12b9a7b5-1023-47e2-a83d-78b3c6ca32b1/geneList
+- public/t2web/tmp/outputs/9f15e720-87d0-439d-96c3-09f433435699/image
+- public/t2web/tmp/outputs/9f15e720-87d0-439d-96c3-09f433435699/url
+- public/t2web/tmp/outputs/9f15e720-87d0-439d-96c3-09f433435699/Pathway
+- public/t2web/tmp/outputs/9f15e720-87d0-439d-96c3-09f433435699/geneList
+- public/t2web/tmp/outputs/5ed0a0a3-ea27-4cdc-854a-37ae23a1022a/contributionTable_xml
+- public/t2web/tmp/outputs/5ed0a0a3-ea27-4cdc-854a-37ae23a1022a/TopContributingConcepts
+- public/t2web/tmp/outputs/5ed0a0a3-ea27-4cdc-854a-37ae23a1022a/TopMatchingConcepts
+- public/t2web/tmp/outputs/5ed0a0a3-ea27-4cdc-854a-37ae23a1022a/SummedSimilarity
+- public/t2web/tmp/outputs/08620310-4804-4f85-9d49-692504c29efd/contributionTable_xml
+- public/t2web/tmp/outputs/08620310-4804-4f85-9d49-692504c29efd/TopContributingConcepts
+- public/t2web/tmp/outputs/08620310-4804-4f85-9d49-692504c29efd/TopMatchingConcepts
+- public/t2web/tmp/outputs/08620310-4804-4f85-9d49-692504c29efd/SummedSimilarity
+- public/t2web/tmp/outputs/edf6bf6a-a530-49b9-acdf-52c490ba57c7/contributionTable_xml
+- public/t2web/tmp/outputs/edf6bf6a-a530-49b9-acdf-52c490ba57c7/TopContributingConcepts
+- public/t2web/tmp/outputs/edf6bf6a-a530-49b9-acdf-52c490ba57c7/TopMatchingConcepts
+- public/t2web/tmp/outputs/edf6bf6a-a530-49b9-acdf-52c490ba57c7/SummedSimilarity
 - public/t2web/css/results.css
 - public/t2web/css/results_header.css
 - public/t2web/css/tipsy.css