t2-web 0.1.5 → 0.1.6

data/CHANGES

@@ -1,4 +1,8 @@
-= Changes log for the Taverna via the Web Gem
+= Changes log for the Taverna via the Web App
+
+== Version 0.1.6
+* Now, for some list disambiguation, the first element of top level lists are in bold
+* Increased side frames slightly
 
 == Version 0.1.5
 * Improved checking of mime-type for outputs for specific image types!

data/README

@@ -2,7 +2,7 @@
 
 
 Authors::     Konstantinos Karasavvas
-Gem Version:: 0.1.5
+Gem Version:: 0.1.6
 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 = '0.1.5'
+  s.version = '0.1.6'
   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/t2_webapp.rb

@@ -140,23 +140,39 @@ END
     end
 
 
-    # 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)
+    # Takes list as input (or single element), returns as multi-line string
+    # 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)
       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
-        data = list.chomp
+      data_lists.each do |list|
+        if list.instance_of? Array
+          tmp_data = list.flatten.compact.map {|e| e.chomp}
+          tmp_data[0] = "<b>" + tmp_data[0] + "</b>" 
+          data += tmp_data.join("\n") + "\n"
+        else
+          data += list.chomp + "\n"
+        end
       end
-
-      StringIO.new data
+      data
     end
 
 
+    # Takes list as input (or single element), returns as file stream 
+    # TODO: for images it works when not a list!
+    #def system_flatten_list_results(list)
+    #  data = ""
+    #  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
+    #    data = list.chomp
+    #  end
+    #  StringIO.new data
+    #end
+
+
 
     # Copies output stream to a tmp file in the specified subdir
     def copy_to_tmp(subdir, filename, out)
@@ -293,7 +309,7 @@ END
       data_stream = flatten_list_results(data_lists)
 
       # copy results to our app's tmp
-      copy_to_tmp("outputs/#{@run_uuid}", t2_output, data_stream)
+      copy_to_tmp("outputs/#{@run_uuid}", t2_output, (StringIO.new data_stream))
     end
 
     # return success!
@@ -313,16 +329,30 @@ END
     run_uuid = params[:uuid]
     t2_output = params[:out]
 
-    data = File.open("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}", "r").read
+    display_file = "#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}"
+
+    data = File.open(display_file, "r").read
 
     # Add HTML tags to display properly
 
     # 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 =~ /image\/png|image\/jpg|image\/gif|image\/bmp/
-      generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}")
+    mime_type = %x( file --mime-type #{display_file} )
+    
+    # TODO: image types can go to array and regex auto-generated
+    # TODO: application/octet-stream is a temporary hack until we deal with 'typing' properly
+    if mime_type =~ /image\/png|image\/jpg|image\/gif|image\/bmp|application\/octet-stream/
+      # clean image from <b></b> --- will not be needed after we deal with 'typing' properly t2-server-0.9.x
+      if mime_type =~ /octet-stream/
+        unless File.file?("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
+          new_length = File.size?(display_file) - 3 - 4   # for <b> and </b> respectively
+          %x( dd if="#{display_file}" of="#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}" bs=1 skip=3 count="#{new_length}" )
+        end
+        generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
+      else
+        generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/#{t2_output}")
+      end
     else
       generate_html_result(data)
     end

data/public/t2web/tmp/outputs/043341ee-a7ac-451d-9cb0-f8cd9ac67bb2/UniProtID

@@ -0,0 +1,185 @@
+<b>P70386</b>
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+<b>A8K7C2</b>
+O73815
+P02571
+P02579
+P12714
+P14104
+P53478
+P60010
+P63259
+P63260
+P63261
+P99022
+Q5U032
+Q6P3K9
+Q7ZVI7
+Q96E67
+Q9P3X6
+Q9P3X7
+<b>P15943</b>
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+P15943
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+P15943
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+<b>P08396</b>
+P08397
+P19356
+P22907
+P28789
+Q16012
+Q2VQW9
+<b>Q08AP2</b>
+Q08AP3
+Q15439
+Q15440
+Q15441
+Q60721
+Q60722
+Q62211
+Q62655
+Q64072
+Q80UE8
+Q99N33

data/public/t2web/tmp/outputs/043341ee-a7ac-451d-9cb0-f8cd9ac67bb2/ValidatedProtein

@@ -0,0 +1,10 @@
+<b>GnT-III</b>
+GnT-III
+GnT-III
+GnT-III
+gamma-actin
+<b>APP</b>
+APP
+APP
+UPS
+TFE

data/public/t2web/tmp/outputs/17a9e3a7-01e8-4906-bb4e-17afc495c3f2/UniProtID

@@ -0,0 +1,185 @@
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+A8K7C2
+O73815
+P02571
+P02579
+P12714
+P14104
+P53478
+P60010
+P63259
+P63260
+P63261
+P99022
+Q5U032
+Q6P3K9
+Q7ZVI7
+Q96E67
+Q9P3X6
+Q9P3X7
+P15943
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+P15943
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+P15943
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+P08396
+P08397
+P19356
+P22907
+P28789
+Q16012
+Q2VQW9
+Q08AP2
+Q08AP3
+Q15439
+Q15440
+Q15441
+Q60721
+Q60722
+Q62211
+Q62655
+Q64072
+Q80UE8
+Q99N33