t2-web 0.1.1 → 0.1.2

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Files changed (115) hide show
  1. data/CHANGES +3 -1
  2. data/README +3 -3
  3. data/Rakefile +1 -1
  4. data/bin/t2_webapp.rb +5 -5
  5. data/public/{css → t2web/css}/form.css +0 -0
  6. data/public/t2web/css/results.css +29 -0
  7. data/public/{css → t2web/css}/results_header.css +0 -0
  8. data/public/{css → t2web/css}/results_navigation.css +0 -0
  9. data/public/{css → t2web/css}/tipsy.css +0 -0
  10. data/public/{images → t2web/images}/bullet_go.png +0 -0
  11. data/public/{images → t2web/images}/lumc_logo2.png +0 -0
  12. data/public/{images → t2web/images}/nbic_logo.gif +0 -0
  13. data/public/{images → t2web/images}/snake_transparent.gif +0 -0
  14. data/public/{images → t2web/images}/tipsy.gif +0 -0
  15. data/public/{scripts → t2web/scripts}/form.js +0 -0
  16. data/public/{scripts → t2web/scripts}/jquery-1.6.1.js +0 -0
  17. data/public/{scripts → t2web/scripts}/jquery.tipsy.js +0 -0
  18. data/public/{scripts → t2web/scripts}/results.js +0 -0
  19. data/views/form.haml +9 -9
  20. data/views/results.haml +3 -3
  21. metadata +19 -112
  22. data/doc/classes/WebT2App.html +0 -1123
  23. data/doc/classes/WebT2App.src/M000001.html +0 -18
  24. data/doc/classes/WebT2App.src/M000002.html +0 -25
  25. data/doc/classes/WebT2App.src/M000003.html +0 -22
  26. data/doc/classes/WebT2App.src/M000004.html +0 -18
  27. data/doc/classes/WebT2App.src/M000005.html +0 -18
  28. data/doc/classes/WebT2App.src/M000006.html +0 -18
  29. data/doc/classes/WebT2App.src/M000007.html +0 -18
  30. data/doc/classes/WebT2App.src/M000008.html +0 -32
  31. data/doc/classes/WebT2App.src/M000009.html +0 -27
  32. data/doc/classes/WebT2App.src/M000010.html +0 -18
  33. data/doc/classes/WebT2App.src/M000011.html +0 -21
  34. data/doc/classes/WebT2App.src/M000012.html +0 -25
  35. data/doc/classes/WebT2App.src/M000013.html +0 -22
  36. data/doc/classes/WebT2App.src/M000014.html +0 -23
  37. data/doc/classes/WebT2App.src/M000015.html +0 -32
  38. data/doc/classes/WebT2App.src/M000016.html +0 -27
  39. data/doc/classes/WebT2App.src/M000017.html +0 -18
  40. data/doc/classes/WebT2App.src/M000018.html +0 -25
  41. data/doc/classes/WebT2App.src/M000019.html +0 -22
  42. data/doc/classes/WebT2App.src/M000020.html +0 -18
  43. data/doc/classes/WebT2App.src/M000021.html +0 -18
  44. data/doc/classes/WebT2App.src/M000022.html +0 -18
  45. data/doc/classes/WebT2App.src/M000023.html +0 -18
  46. data/doc/classes/WebT2App.src/M000024.html +0 -32
  47. data/doc/classes/WebT2App.src/M000025.html +0 -27
  48. data/doc/classes/WebT2App.src/M000026.html +0 -18
  49. data/doc/classes/WebT2App.src/M000027.html +0 -21
  50. data/doc/classes/WebT2App.src/M000028.html +0 -25
  51. data/doc/classes/WebT2App.src/M000029.html +0 -22
  52. data/doc/classes/WebT2App.src/M000030.html +0 -23
  53. data/doc/classes/WebT2App.src/M000031.html +0 -32
  54. data/doc/classes/WebT2App.src/M000032.html +0 -27
  55. data/doc/classes/WebT2App.src/M000033.html +0 -18
  56. data/doc/classes/WebT2App.src/M000034.html +0 -25
  57. data/doc/classes/WebT2App.src/M000035.html +0 -22
  58. data/doc/classes/WebT2App.src/M000036.html +0 -18
  59. data/doc/classes/WebT2App.src/M000037.html +0 -18
  60. data/doc/classes/WebT2App.src/M000038.html +0 -18
  61. data/doc/classes/WebT2App.src/M000039.html +0 -18
  62. data/doc/classes/WebT2App.src/M000040.html +0 -32
  63. data/doc/classes/WebT2App.src/M000041.html +0 -27
  64. data/doc/classes/WebT2App.src/M000042.html +0 -18
  65. data/doc/classes/WebT2App.src/M000043.html +0 -25
  66. data/doc/classes/WebT2App.src/M000044.html +0 -22
  67. data/doc/classes/WebT2App.src/M000045.html +0 -18
  68. data/doc/classes/WebT2App.src/M000046.html +0 -18
  69. data/doc/classes/WebT2App.src/M000047.html +0 -18
  70. data/doc/classes/WebT2App.src/M000048.html +0 -18
  71. data/doc/classes/WebT2App.src/M000049.html +0 -32
  72. data/doc/classes/WebT2App.src/M000050.html +0 -27
  73. data/doc/created.rid +0 -1
  74. data/doc/files/bin/t2_webapp_rb.html +0 -115
  75. data/doc/files/pkg/t2-web-0_0_2/bin/web_t2_service_rb.html +0 -114
  76. data/doc/files/pkg/t2-web-0_0_3/bin/t2_webapp_rb.html +0 -115
  77. data/doc/files/pkg/t2-web-0_0_3/bin/web_t2_service_rb.html +0 -114
  78. data/doc/files/pkg/t2-web-0_0_4/bin/t2_webapp_rb.html +0 -115
  79. data/doc/files/pkg/t2-web-0_0_5/bin/t2_webapp_rb.html +0 -115
  80. data/doc/fr_class_index.html +0 -27
  81. data/doc/fr_file_index.html +0 -32
  82. data/doc/fr_method_index.html +0 -76
  83. data/doc/index.html +0 -24
  84. data/doc/rdoc/CHANGES.html +0 -170
  85. data/doc/rdoc/LICENSE.html +0 -111
  86. data/doc/rdoc/README.html +0 -142
  87. data/doc/rdoc/created.rid +0 -4
  88. data/doc/rdoc/images/brick.png +0 -0
  89. data/doc/rdoc/images/brick_link.png +0 -0
  90. data/doc/rdoc/images/bug.png +0 -0
  91. data/doc/rdoc/images/bullet_black.png +0 -0
  92. data/doc/rdoc/images/bullet_toggle_minus.png +0 -0
  93. data/doc/rdoc/images/bullet_toggle_plus.png +0 -0
  94. data/doc/rdoc/images/date.png +0 -0
  95. data/doc/rdoc/images/find.png +0 -0
  96. data/doc/rdoc/images/loadingAnimation.gif +0 -0
  97. data/doc/rdoc/images/macFFBgHack.png +0 -0
  98. data/doc/rdoc/images/package.png +0 -0
  99. data/doc/rdoc/images/page_green.png +0 -0
  100. data/doc/rdoc/images/page_white_text.png +0 -0
  101. data/doc/rdoc/images/page_white_width.png +0 -0
  102. data/doc/rdoc/images/plugin.png +0 -0
  103. data/doc/rdoc/images/ruby.png +0 -0
  104. data/doc/rdoc/images/tag_green.png +0 -0
  105. data/doc/rdoc/images/wrench.png +0 -0
  106. data/doc/rdoc/images/wrench_orange.png +0 -0
  107. data/doc/rdoc/images/zoom.png +0 -0
  108. data/doc/rdoc/index.html +0 -115
  109. data/doc/rdoc/js/darkfish.js +0 -116
  110. data/doc/rdoc/js/jquery.js +0 -32
  111. data/doc/rdoc/js/quicksearch.js +0 -114
  112. data/doc/rdoc/js/thickbox-compressed.js +0 -10
  113. data/doc/rdoc/rdoc.css +0 -763
  114. data/doc/rdoc-style.css +0 -208
  115. data/public/images/info.png +0 -0
data/CHANGES CHANGED
@@ -1,7 +1,9 @@
1
1
  = Changes log for the Taverna via the Web Gem
2
2
 
3
+ == Version 0.1.2
4
+ * Moved everything in /public into /public/t2web to be able to redirect from apache et al.
5
+
3
6
  == Version 0.1.1
4
- * Added config.ru to gem
5
7
  * Removed t2_webap from executables
6
8
 
7
9
  == Version 0.1.0
data/README CHANGED
@@ -2,7 +2,7 @@
2
2
 
3
3
 
4
4
  Authors:: Konstantinos Karasavvas
5
- Gem Version:: 0.1.1
5
+ Gem Version:: 0.1.2
6
6
  Contact:: mailto:kostas.karasavvas@nbic.nl
7
7
  Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
8
8
  Copyright:: (c) 2012 Netherlands Bioinformatics Centre, The Netherlands
@@ -23,9 +23,9 @@ description provided in the workflow itself in myExperiment.
23
23
 
24
24
  == Usage
25
25
 
26
- rackup -p 9494
26
+ rackup -p 9494
27
27
 
28
- Runs the web application at port 9494 and waits for incoming requests. Uses rack's config.ru file.
28
+ 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.
29
29
 
30
30
 
31
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data/Rakefile CHANGED
@@ -12,7 +12,7 @@ require 'rdoc/task'
12
12
 
13
13
  spec = Gem::Specification.new do |s|
14
14
  s.name = 't2-web'
15
- s.version = '0.1.1'
15
+ s.version = '0.1.2'
16
16
  s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
17
17
  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.'
18
18
  s.description = s.summary
data/bin/t2_webapp.rb CHANGED
@@ -63,7 +63,7 @@ class WebT2App < Sinatra::Base
63
63
  def generate_header_frame(my_exp_wkf, my_exp_usr)
64
64
  <<END
65
65
  <html>
66
- <head><link href='/css/form.css' rel='stylesheet'/></head>
66
+ <head><link href='/t2web/css/form.css' rel='stylesheet'/></head>
67
67
  <body>
68
68
  #{generate_header_table(my_exp_wkf, my_exp_usr)}
69
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  </body>
@@ -79,7 +79,7 @@ END
79
79
  <table class='header'>
80
80
  <tr>
81
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  <td class='left'>
82
- <img alt='NBIC logo' src='/images/nbic_logo.gif' />
82
+ <img alt='NBIC logo' src='/t2web/images/nbic_logo.gif' />
83
83
  </td>
84
84
  <td>
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85
  <table class='header-title'>
@@ -92,7 +92,7 @@ END
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92
  </table>
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  </td>
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  <td>
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- <img alt='LUMC logo' class='right' src='/images/lumc_logo2.png' />
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+ <img alt='LUMC logo' class='right' src='/t2web/images/lumc_logo2.png' />
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96
  </td>
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  </tr>
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  </table>
@@ -120,7 +120,7 @@ END
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  # Generates the contents of the data-navigation frame
121
121
  def generate_data_navigation_frame(my_exp_wkf, uuid, wid, wkf_version, t2_server, finished_execution)
122
122
 
123
- data_navigation_frame = "<html><head><link href='/css/results_navigation.css' rel='stylesheet'/></head><body><table>"
123
+ data_navigation_frame = "<html><head><link href='/t2web/css/results_navigation.css' rel='stylesheet'/></head><body><table>"
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  if my_exp_wkf.outputs.size >=1
125
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  my_exp_wkf.outputs.each do |output|
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  data_navigation_frame << "<tr>"
@@ -129,7 +129,7 @@ END
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  data_navigation_frame << "<td><a href='javascript:void(0);' onclick='parent.readTmpOutput(\\\"#{t2_server}\\\", \\\"#{uuid}\\\", " <<
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  "\\\"#{output.name}\\\", \\\"#{wid}\\\", \\\"#{wkf_version}\\\");'>#{output.name}</a></td><td></td>"
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  else
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- data_navigation_frame << "<td>#{output.name}</td><td><img src='/images/snake_transparent.gif' alt='Loading Content...'></td>"
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+ data_navigation_frame << "<td>#{output.name}</td><td><img src='/t2web/images/snake_transparent.gif' alt='Loading Content...'></td>"
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  end
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  data_navigation_frame << "</tr>"
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  end
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@@ -0,0 +1,29 @@
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+ body{
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+ background-color: mintcream;
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+ }
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+
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+ #header{
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+ text-align: center;
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+ margin: 0px;
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+ height: 50px;
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+ border-bottom: blue 2px solid;
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+ }
11
+
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+ #results{
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+ position: relative;
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+ height: 100%;
15
+ }
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+
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+ #data-navigation{
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+ float: left;
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+ padding-left: 1em;
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+ padding-top: 1em;
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+ width: 10em;
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+ height: 100%;
23
+ }
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+
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+ #data-display{
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+ margin-left: 11em;
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+ padding-top: 1em;
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+ text-align: left;
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+ }
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data/views/form.haml CHANGED
@@ -2,11 +2,11 @@
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  %html
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  %head
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  %title Workflow: #{@my_exp_wkf.title}
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- %link(rel="stylesheet" href="/css/form.css")
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- %link(rel="stylesheet" href="/css/tipsy.css")
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- %script{:type => "text/javascript", :src => "/scripts/jquery-1.6.1.js"}
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- %script{:type => "text/javascript", :src => "/scripts/jquery.tipsy.js"}
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- %script{:type => "text/javascript", :src => "/scripts/form.js"}
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+ %link(rel="stylesheet" href="/t2web/css/form.css")
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+ %link(rel="stylesheet" href="/t2web/css/tipsy.css")
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+ %script{:type => "text/javascript", :src => "/t2web/scripts/jquery-1.6.1.js"}
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+ %script{:type => "text/javascript", :src => "/t2web/scripts/jquery.tipsy.js"}
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+ %script{:type => "text/javascript", :src => "/t2web/scripts/form.js"}
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  %body
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@@ -106,24 +106,24 @@
106
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  %th.inputs
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  %tr
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  %td.inputs
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- %img{:src => "/images/bullet_go.png", :alt => "Important!" }
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+ %img{:src => "/t2web/images/bullet_go.png", :alt => "Important!" }
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  %td.inputs
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111
  Some workflows are not up-to-date or have dependencies that cannot be met by the specific Taverna server that you specified during generation of this tool. You can make sure that the workflow is valid by running it in the Taverna Workbench first to confirm that it works before running it via the Web.
112
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  %tr
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  %td.inputs
114
- %img{:src => "/images/bullet_go.png", :alt => "Important!" }
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+ %img{:src => "/t2web/images/bullet_go.png", :alt => "Important!" }
115
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  %td.inputs
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116
  There might be some repetitions in the workflow description in some of the generated workflows. This is due to a backwards compatibility issue on the myExperiment repository which keeps the old descriptions to make sure that no information is lost.
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  %tr
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  %td.inputs
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- %img{:src => "/images/bullet_go.png", :alt => "Important!" }
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+ %img{:src => "/t2web/images/bullet_go.png", :alt => "Important!" }
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  %td.inputs
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  For more information on this workflow please visit the
122
122
  %a{ :href => "http://www.myExperiment.org/workflows/#{@wid}", :target => "_blank" } myExperiment website
123
123
  -# if #{@my_exp_wkf.user.email}
124
124
  %tr
125
125
  %td.inputs
126
- %img{:src => "/images/bullet_go.png", :alt => "Important!" }
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+ %img{:src => "/t2web/images/bullet_go.png", :alt => "Important!" }
127
127
  %td.inputs
128
128
  For questions/comments you can also contact the workflow creator at:
129
129
  %a{ :href => "mailto:#{@my_exp_usr.email}" } #{@my_exp_usr.email}
data/views/results.haml CHANGED
@@ -2,8 +2,8 @@
2
2
  %html
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  %head
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4
  %title Results:
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- %link(rel="stylesheet" href="/css/results.css")
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- %script{:type => "text/javascript", :src => "/scripts/jquery-1.6.1.js"}
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+ %link(rel="stylesheet" href="/t2web/css/results.css")
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+ %script{:type => "text/javascript", :src => "/t2web/scripts/jquery-1.6.1.js"}
7
7
  %script{:type => "text/javascript"}
8
8
  :plain
9
9
  var runStatusIntervalId = 0;
@@ -16,7 +16,7 @@
16
16
  runStatusIntervalId = window.setInterval( "checkRunStatus('#{@t2_server}', '#{@run_uuid}')", 5000);
17
17
  //checkRunStatus("#{@t2_server}", "#{@run_uuid}");
18
18
  });
19
- %script{:type => "text/javascript", :src => "/scripts/results.js"}
19
+ %script{:type => "text/javascript", :src => "/t2web/scripts/results.js"}
20
20
 
21
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  -# we use border for FF and framespacing for IE
22
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  %frameset{ :rows => "113px, *", :border => "1", :framespacing => "1" }
metadata CHANGED
@@ -1,13 +1,13 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: t2-web
3
3
  version: !ruby/object:Gem::Version
4
- hash: 25
4
+ hash: 31
5
5
  prerelease:
6
6
  segments:
7
7
  - 0
8
8
  - 1
9
- - 1
10
- version: 0.1.1
9
+ - 2
10
+ version: 0.1.2
11
11
  platform: ruby
12
12
  authors:
13
13
  - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
15
15
  bindir: bin
16
16
  cert_chain: []
17
17
 
18
- date: 2012-04-04 00:00:00 Z
18
+ date: 2012-04-12 00:00:00 Z
19
19
  dependencies:
20
20
  - !ruby/object:Gem::Dependency
21
21
  name: sinatra
@@ -114,113 +114,20 @@ files:
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  - Rakefile
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  - bin/config.ru
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  - bin/t2_webapp.rb
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- - doc/rdoc-style.css
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- - doc/fr_file_index.html
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- - doc/classes/WebT2App.src/M000048.html
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- - doc/classes/WebT2App.src/M000036.html
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- - doc/classes/WebT2App.src/M000034.html
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- - doc/classes/WebT2App.src/M000047.html
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- - doc/classes/WebT2App.src/M000045.html
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- - doc/classes/WebT2App.src/M000006.html
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- - doc/classes/WebT2App.src/M000049.html
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- - doc/classes/WebT2App.src/M000042.html
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- - doc/classes/WebT2App.src/M000043.html
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- - doc/classes/WebT2App.src/M000035.html
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- - doc/classes/WebT2App.src/M000015.html
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- - doc/classes/WebT2App.src/M000039.html
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- - doc/classes/WebT2App.src/M000014.html
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- - doc/classes/WebT2App.src/M000016.html
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- - doc/classes/WebT2App.src/M000027.html
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- - doc/classes/WebT2App.src/M000044.html
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- - doc/classes/WebT2App.src/M000031.html
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- - doc/classes/WebT2App.src/M000007.html
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- - doc/classes/WebT2App.src/M000012.html
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- - doc/classes/WebT2App.src/M000010.html
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- - doc/classes/WebT2App.src/M000028.html
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- - doc/classes/WebT2App.src/M000020.html
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- - doc/classes/WebT2App.src/M000046.html
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- - doc/classes/WebT2App.src/M000033.html
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- - doc/classes/WebT2App.src/M000011.html
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- - doc/classes/WebT2App.src/M000022.html
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- - doc/classes/WebT2App.src/M000038.html
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- - doc/classes/WebT2App.src/M000013.html
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- - doc/classes/WebT2App.src/M000002.html
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- - doc/classes/WebT2App.src/M000001.html
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- - doc/classes/WebT2App.src/M000024.html
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- - doc/classes/WebT2App.src/M000026.html
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- - doc/classes/WebT2App.src/M000018.html
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- - doc/classes/WebT2App.src/M000050.html
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- - doc/classes/WebT2App.src/M000032.html
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- - doc/classes/WebT2App.src/M000023.html
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- - doc/classes/WebT2App.src/M000009.html
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- - doc/classes/WebT2App.src/M000040.html
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- - doc/classes/WebT2App.src/M000008.html
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- - doc/classes/WebT2App.src/M000005.html
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- - doc/classes/WebT2App.src/M000041.html
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- - doc/classes/WebT2App.src/M000025.html
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- - doc/classes/WebT2App.src/M000037.html
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- - doc/classes/WebT2App.src/M000003.html
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- - doc/classes/WebT2App.src/M000004.html
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- - doc/classes/WebT2App.src/M000029.html
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- - doc/classes/WebT2App.src/M000019.html
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- - doc/classes/WebT2App.src/M000021.html
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- - doc/classes/WebT2App.src/M000017.html
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- - doc/classes/WebT2App.src/M000030.html
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- - doc/classes/WebT2App.html
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- - doc/fr_class_index.html
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- - doc/index.html
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- - doc/files/bin/t2_webapp_rb.html
173
- - doc/files/pkg/t2-web-0_0_4/bin/t2_webapp_rb.html
174
- - doc/files/pkg/t2-web-0_0_2/bin/web_t2_service_rb.html
175
- - doc/files/pkg/t2-web-0_0_5/bin/t2_webapp_rb.html
176
- - doc/files/pkg/t2-web-0_0_3/bin/web_t2_service_rb.html
177
- - doc/files/pkg/t2-web-0_0_3/bin/t2_webapp_rb.html
178
- - doc/fr_method_index.html
179
- - doc/rdoc/rdoc.css
180
- - doc/rdoc/LICENSE.html
181
- - doc/rdoc/index.html
182
- - doc/rdoc/js/jquery.js
183
- - doc/rdoc/js/thickbox-compressed.js
184
- - doc/rdoc/js/darkfish.js
185
- - doc/rdoc/js/quicksearch.js
186
- - doc/rdoc/README.html
187
- - doc/rdoc/created.rid
188
- - doc/rdoc/CHANGES.html
189
- - doc/rdoc/images/find.png
190
- - doc/rdoc/images/bug.png
191
- - doc/rdoc/images/bullet_toggle_minus.png
192
- - doc/rdoc/images/wrench.png
193
- - doc/rdoc/images/bullet_black.png
194
- - doc/rdoc/images/macFFBgHack.png
195
- - doc/rdoc/images/page_white_text.png
196
- - doc/rdoc/images/ruby.png
197
- - doc/rdoc/images/bullet_toggle_plus.png
198
- - doc/rdoc/images/loadingAnimation.gif
199
- - doc/rdoc/images/brick.png
200
- - doc/rdoc/images/zoom.png
201
- - doc/rdoc/images/tag_green.png
202
- - doc/rdoc/images/page_green.png
203
- - doc/rdoc/images/brick_link.png
204
- - doc/rdoc/images/wrench_orange.png
205
- - doc/rdoc/images/date.png
206
- - doc/rdoc/images/page_white_width.png
207
- - doc/rdoc/images/package.png
208
- - doc/rdoc/images/plugin.png
209
- - doc/created.rid
210
- - public/scripts/results.js
211
- - public/scripts/form.js
212
- - public/scripts/jquery-1.6.1.js
213
- - public/scripts/jquery.tipsy.js
214
- - public/css/results_header.css
215
- - public/css/tipsy.css
216
- - public/css/form.css
217
- - public/css/results_navigation.css
218
- - public/images/nbic_logo.gif
219
- - public/images/snake_transparent.gif
220
- - public/images/bullet_go.png
221
- - public/images/tipsy.gif
222
- - public/images/info.png
223
- - public/images/lumc_logo2.png
117
+ - public/t2web/scripts/results.js
118
+ - public/t2web/scripts/form.js
119
+ - public/t2web/scripts/jquery-1.6.1.js
120
+ - public/t2web/scripts/jquery.tipsy.js
121
+ - public/t2web/css/results.css
122
+ - public/t2web/css/results_header.css
123
+ - public/t2web/css/tipsy.css
124
+ - public/t2web/css/form.css
125
+ - public/t2web/css/results_navigation.css
126
+ - public/t2web/images/nbic_logo.gif
127
+ - public/t2web/images/snake_transparent.gif
128
+ - public/t2web/images/bullet_go.png
129
+ - public/t2web/images/tipsy.gif
130
+ - public/t2web/images/lumc_logo2.png
224
131
  - views/results.haml
225
132
  - views/form.haml
226
133
  homepage:
@@ -252,7 +159,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
252
159
  requirements: []
253
160
 
254
161
  rubyforge_project:
255
- rubygems_version: 1.8.19
162
+ rubygems_version: 1.8.21
256
163
  signing_key:
257
164
  specification_version: 3
258
165
  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.