lazar-gui 1.3.1 → 1.4.0.pre.0

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Files changed (130) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +3 -0
  3. data/FAQ.md +9 -6
  4. data/Gemfile +2 -2
  5. data/README.md +19 -8
  6. data/VERSION +1 -1
  7. data/api/api.json +1000 -0
  8. data/application.rb +269 -206
  9. data/config.ru +7 -2
  10. data/docker/Dockerfile +73 -0
  11. data/docker/start.sh +12 -0
  12. data/docker/swagger.html +107 -0
  13. data/helper.rb +46 -1
  14. data/lazar-gui.gemspec +6 -6
  15. data/lib/api.rb +29 -0
  16. data/lib/compound.rb +68 -0
  17. data/lib/dataset.rb +33 -0
  18. data/lib/endpoint.rb +23 -0
  19. data/lib/feature.rb +29 -0
  20. data/lib/model.rb +152 -0
  21. data/lib/report.rb +29 -0
  22. data/lib/substance.rb +34 -0
  23. data/lib/swagger.rb +3 -0
  24. data/lib/validation.rb +67 -0
  25. data/public/fonts/FontAwesome.otf +0 -0
  26. data/public/fonts/fontawesome-webfont.eot +0 -0
  27. data/public/fonts/fontawesome-webfont.svg +2671 -0
  28. data/public/fonts/fontawesome-webfont.ttf +0 -0
  29. data/public/fonts/fontawesome-webfont.woff +0 -0
  30. data/public/fonts/fontawesome-webfont.woff2 +0 -0
  31. data/public/images/orn-logo.jpg +0 -0
  32. data/public/javascripts/bootstrap.js +3944 -0
  33. data/public/javascripts/google_analytics_lazar.js +2 -2
  34. data/public/javascripts/jquery.min.js +2 -0
  35. data/public/javascripts/lazar-gui.js +313 -0
  36. data/public/javascripts/pagination.min.js +11 -0
  37. data/public/javascripts/popper.min.js +5 -0
  38. data/public/stylesheets/bootstrap.min.css +7 -0
  39. data/public/stylesheets/bootstrap.min.css.map +1 -0
  40. data/public/stylesheets/font-awesome.min.css +4 -0
  41. data/public/stylesheets/pagination.css +1 -0
  42. data/qmrf_report.rb +64 -14
  43. data/task.rb +68 -0
  44. data/unicorn.rb +0 -1
  45. data/views/batch.haml +48 -107
  46. data/views/details.haml +10 -2
  47. data/views/error.haml +4 -5
  48. data/views/faq.haml +6 -2
  49. data/views/help.haml +68 -0
  50. data/views/info.haml +3 -2
  51. data/views/layout.haml +68 -78
  52. data/views/model_details.haml +179 -144
  53. data/views/neighbors.haml +98 -80
  54. data/views/predict.haml +43 -178
  55. data/views/prediction.haml +109 -102
  56. data/views/style.scss +44 -37
  57. data/views/upload.haml +28 -0
  58. metadata +51 -105
  59. data/public/css/bootstrap-theme.min.css +0 -5
  60. data/public/css/bootstrap.min.css +0 -5
  61. data/public/css/bootstrap.vertical-tabs.min.css +0 -1
  62. data/public/css/images/black-asc.gif +0 -0
  63. data/public/css/images/black-desc.gif +0 -0
  64. data/public/css/images/black-unsorted.gif +0 -0
  65. data/public/css/images/bootstrap-black-unsorted.png +0 -0
  66. data/public/css/images/bootstrap-white-unsorted.png +0 -0
  67. data/public/css/images/dragtable-handle.png +0 -0
  68. data/public/css/images/dragtable-handle.svg +0 -7
  69. data/public/css/images/dropbox-asc-hovered.png +0 -0
  70. data/public/css/images/dropbox-asc.png +0 -0
  71. data/public/css/images/dropbox-desc-hovered.png +0 -0
  72. data/public/css/images/dropbox-desc.png +0 -0
  73. data/public/css/images/first.png +0 -0
  74. data/public/css/images/green-asc.gif +0 -0
  75. data/public/css/images/green-desc.gif +0 -0
  76. data/public/css/images/green-header.gif +0 -0
  77. data/public/css/images/green-unsorted.gif +0 -0
  78. data/public/css/images/ice-asc.gif +0 -0
  79. data/public/css/images/ice-desc.gif +0 -0
  80. data/public/css/images/ice-unsorted.gif +0 -0
  81. data/public/css/images/last.png +0 -0
  82. data/public/css/images/loading.gif +0 -0
  83. data/public/css/images/metro-black-asc.png +0 -0
  84. data/public/css/images/metro-black-desc.png +0 -0
  85. data/public/css/images/metro-loading.gif +0 -0
  86. data/public/css/images/metro-unsorted.png +0 -0
  87. data/public/css/images/metro-white-asc.png +0 -0
  88. data/public/css/images/metro-white-desc.png +0 -0
  89. data/public/css/images/next.png +0 -0
  90. data/public/css/images/prev.png +0 -0
  91. data/public/css/images/white-asc.gif +0 -0
  92. data/public/css/images/white-desc.gif +0 -0
  93. data/public/css/images/white-unsorted.gif +0 -0
  94. data/public/css/jquery-ui.css +0 -1225
  95. data/public/css/jquery-ui.theme.min.css +0 -5
  96. data/public/css/theme.bootstrap.css +0 -158
  97. data/public/css/theme.bootstrap.min.css +0 -1
  98. data/public/css/theme.default.min.css +0 -1
  99. data/public/fonts/glyphicons-halflings-regular.eot +0 -0
  100. data/public/fonts/glyphicons-halflings-regular.svg +0 -288
  101. data/public/fonts/glyphicons-halflings-regular.ttf +0 -0
  102. data/public/fonts/glyphicons-halflings-regular.woff +0 -0
  103. data/public/fonts/glyphicons-halflings-regular.woff2 +0 -0
  104. data/public/images/Email.png +0 -0
  105. data/public/images/Facebook.png +0 -0
  106. data/public/images/Google+.png +0 -0
  107. data/public/images/LinkedIn.png +0 -0
  108. data/public/images/OpenToxEuro2013_small.png +0 -0
  109. data/public/images/Twitter.png +0 -0
  110. data/public/images/arrow_down_float.png +0 -0
  111. data/public/images/arrow_left_float.png +0 -0
  112. data/public/images/arrow_right_float.png +0 -0
  113. data/public/images/arrow_up_float.png +0 -0
  114. data/public/images/asc.gif +0 -0
  115. data/public/images/bg.gif +0 -0
  116. data/public/images/desc.gif +0 -0
  117. data/public/images/gray_jean.png +0 -0
  118. data/public/images/info_white.png +0 -0
  119. data/public/javascripts/bootstrap.min.js +0 -7
  120. data/public/javascripts/jquery-1.11.2.min.js +0 -4
  121. data/public/javascripts/jquery-1.8.3.min.js +0 -2
  122. data/public/javascripts/jquery-ui-1.10.3.custom.min.js +0 -6
  123. data/public/javascripts/jquery.bpopup.min.js +0 -7
  124. data/public/javascripts/jquery.tablesorter.min.js +0 -2
  125. data/public/javascripts/jquery.tablesorter.widgets.js +0 -2678
  126. data/public/javascripts/jquery.tools.min.js +0 -5
  127. data/public/rect.png +0 -0
  128. data/test/lazarweb.rb +0 -193
  129. data/test/setup.rb +0 -7
  130. data/views/significant_fragments.haml +0 -66
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data/public/rect.png DELETED
Binary file
data/test/lazarweb.rb DELETED
@@ -1,193 +0,0 @@
1
- require 'minitest/autorun'
2
- require 'capybara'
3
- require 'capybara-webkit'
4
-
5
- ENV['DISPLAY'] ="localhost:1.0"
6
-
7
- Capybara.register_driver :webkit do |app|
8
- Capybara::Webkit::Driver.new(app).tap{|d| d.browser.ignore_ssl_errors}
9
- end
10
- Capybara.default_driver = :webkit
11
- Capybara.default_max_wait_time = 20
12
- Capybara.javascript_driver = :webkit
13
- Capybara.run_server = false
14
- Capybara.app_host = "http://localhost:8088"
15
-
16
- begin
17
- puts "Service URI is: http://localhost:8088"
18
- rescue
19
- puts "Unable to start service."
20
- exit
21
- end
22
-
23
- class LazarWebTest < MiniTest::Test
24
-
25
- def self.test_order
26
- :sorted
27
- end
28
-
29
- include Capybara::DSL
30
-
31
- def test_00_xsetup
32
- `Xvfb :1 -screen 0 1024x768x16 2>/dev/null &`
33
- sleep 2
34
- end
35
-
36
- def test_01_visit
37
- visit('/predict')
38
- assert page.has_content?('Lazar Toxicity Predictions')
39
- assert page.has_content?("Draw a chemical structure")
40
- assert page.has_content?("enter")
41
- assert page.has_content?("upload")
42
- assert page.has_content?("Select one or more endpoints")
43
- assert page.has_content?("Acute toxicity")
44
- assert page.has_content?("Fathead minnow")
45
- assert page.has_content?("Carcinogenicity")
46
- assert page.has_content?("Rat")
47
- assert page.has_content?("Rodents (multiple species/sites)")
48
- assert page.has_content?("Mouse")
49
- assert page.has_content?("Maximum Recommended Daily Dose")
50
- assert page.has_content?("Human")
51
- assert page.has_content?("Predict")
52
- end
53
-
54
- def test_02_insert_wrong_smiles
55
- visit('/')
56
- page.fill_in 'identifier', :with => "blahblah"
57
- check('selection[Rat]')
58
- first(:button, '>>').click
59
- assert page.has_content?('Attention')
60
- end
61
-
62
- def test_03_check_all_links_exists
63
- visit('/')
64
- links = ["Details | Validation", "SMILES", "toxicology gmbh 2004 - #{Time.now.year.to_s}"]
65
- links.each{|l| assert page.has_link?(l), "true"}
66
- end
67
-
68
- def test_04_model_details
69
- visit("/")
70
- details = page.all('a', :text => 'Details | Validation')
71
- details[0].click
72
- assert page.has_content?('Model:')
73
- assert page.has_content?('Source: http://www.epa.gov/comptox/dsstox/sdf_epafhm.html')
74
- assert page.has_content?('Algorithm: LAZAR')
75
- assert page.has_content?('Type: regression')
76
- assert page.has_content?('Training dataset: EPAFHM.csv')
77
- assert page.has_content?('Training compounds: 617')
78
- assert page.has_content?('Validation:')
79
- assert page.has_content?('Num folds: 10')
80
- details[0].click
81
- #
82
- details[1].click
83
- assert page.has_content?('Model:')
84
- assert page.has_content?('Source: http://www.epa.gov/ncct/dsstox/sdf_cpdbas.html')
85
- assert page.has_content?('Algorithm: LAZAR')
86
- assert page.has_content?('Type: classification')
87
- assert page.has_content?('Training dataset: DSSTox_Carcinogenic_Potency_DBS_Rat.csv')
88
- assert page.has_content?('Training compounds: 1195')
89
- assert page.has_content?('Validation:')
90
- assert page.has_content?('Num folds: 10')
91
- details[1].click
92
- #
93
- details[2].click
94
- assert page.has_content?('Model:')
95
- assert page.has_content?('Source: http://www.epa.gov/ncct/dsstox/sdf_cpdbas.html')
96
- assert page.has_content?('Algorithm: LAZAR')
97
- assert page.has_content?('Type: classification')
98
- assert page.has_content?('Training dataset: DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv')
99
- assert page.has_content?('Training compounds: 1116')
100
- assert page.has_content?('Validation:')
101
- assert page.has_content?('Num folds: 10')
102
- details[2].click
103
- #
104
- details[3].click
105
- assert page.has_content?('Model:')
106
- assert page.has_content?('Source: http://www.epa.gov/ncct/dsstox/sdf_cpdbas.html')
107
- assert page.has_content?('Algorithm: LAZAR')
108
- assert page.has_content?('Type: classification')
109
- assert page.has_content?('Training dataset: DSSTox_Carcinogenic_Potency_DBS_Mouse.csv')
110
- assert page.has_content?('Training compounds: 973')
111
- assert page.has_content?('Validation:')
112
- assert page.has_content?('Num folds: 10')
113
- details[3].click
114
- #
115
- details[4].click
116
- assert page.has_content?('Model:')
117
- assert page.has_content?('Source: http://www.epa.gov/comptox/dsstox/sdf_fdamdd.html')
118
- assert page.has_content?('Algorithm: LAZAR')
119
- assert page.has_content?('Type: regression')
120
- assert page.has_content?('Training dataset: FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv')
121
- assert page.has_content?('Training compounds: 1216')
122
- assert page.has_content?('Validation:')
123
- assert page.has_content?('Num folds: 10')
124
- details[4].click
125
- end
126
-
127
- def test_05_predict
128
- visit('/')
129
- page.fill_in('identifier', :with => "NNc1ccccc1")
130
- check('selection[Rat]')
131
- first(:button, '>>').click
132
- assert page.has_content?('Carcinogenicity (Rat)'), "true"
133
- assert page.has_content?('Type: Classification'), "true"
134
- assert page.has_content?('Prediction: active'), "true"
135
- assert page.has_content?('Confidence: 0.019'), "true"
136
- assert page.has_content?('Neighbors'), "true"
137
- assert page.has_content?('Compound'), "true"
138
- assert page.has_content?('Measured Activity'), "true"
139
- assert page.has_content?('Similarity'), "true"
140
- =begin
141
- assert page.has_link?('Significant fragments'), "true"
142
- assert page.has_link?('v'), "true"
143
- open 'significant fragments' view
144
- find_link('linkPredictionSf').click
145
- sleep 5
146
- within_frame('details_overview') do
147
- assert page.has_content?('Predominantly in compounds with activity "inactive"'), "true"
148
- assert page.has_content?('Predominantly in compounds with activity "active"'), "true"
149
- assert page.has_content?('p value'), "true"
150
- # inactive
151
- assert page.has_content?('[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]-[#7&A]'), "true"
152
- assert page.has_content?('0.98674'), "true"
153
- assert page.has_content?('[#6&a]:[#6&a](-[#7&A])(:[#6&a]:[#6&a]:[#6&a])'), "true"
154
- assert page.has_content?('0.97699'), "true"
155
- assert page.has_content?('[#6&a]:[#6&a](-[#7&A])(:[#6&a]:[#6&a])'), "true"
156
- assert page.has_content?('0.97699'), "true"
157
- assert page.has_content?('[#6&a]:[#6&a](-[#7&A])(:[#6&a])'), "true"
158
- assert page.has_content?('0.97699'), "true"
159
- assert page.has_content?('[#6&a]:[#6&a]'), "true"
160
- assert page.has_content?('0.99605'), "true"
161
- assert page.has_content?('[#6&a]:[#6&a]:[#6&a]:[#6&a]'), "true"
162
- assert page.has_content?('0.99791'), "true"
163
- assert page.has_content?('[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]'), "true"
164
- assert page.has_content?('0.99985'), "true"
165
- # active
166
- assert page.has_content?('[#7&A]-[#7&A]'), "true"
167
- assert page.has_content?('0.99993'), "true"
168
- # close 'significant fragments' view
169
- find_button('closebutton').click
170
- end
171
- find_link('link0').click
172
- sleep 2
173
- assert page.has_content?('Supporting information'), "true"
174
- first(:link, 'linkCompound').click
175
- sleep 5
176
- within_frame('details_overview') do
177
- assert page.has_content?('SMILES:'), "true"
178
- assert page.has_content?('c1ccc(cc1)NN'), "true"
179
- assert page.has_content?('InChI:'), "true"
180
- assert page.has_content?('1S/C6H8N2/c7-8-6-4-2-1-3-5-6/h1-5,8H,7H2'), "true"
181
- assert page.has_content?('Names:'), "true"
182
- assert page.has_content?('Phenylhydrazine'), "true"
183
- assert page.has_link?('PubChem read across'), "true"
184
- end
185
- =end
186
- end
187
-
188
- def test_99_kill
189
- `pidof Xvfb|xargs kill`
190
- end
191
-
192
- end
193
-
data/test/setup.rb DELETED
@@ -1,7 +0,0 @@
1
- require 'minitest/autorun'
2
- require_relative '../lib/lazar.rb'
3
- include OpenTox
4
- TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
5
- DATA_DIR ||= File.join(TEST_DIR,"data")
6
- #$mongo.database.drop
7
- #$gridfs = $mongo.database.fs # recreate GridFS indexes
@@ -1,66 +0,0 @@
1
- %div.modal-body{:style=>"padding:10px;"}
2
- %button.close{ :type=>" button", data: { dismiss:"modal"}} &times;
3
- - if @type =~ /classification/i
4
- %div.row
5
- %div.col-md-4
6
- %h3{:style=>"margin-left:8px;"}
7
- Significant fragments:
8
- %img{:src=>"#{@compound.uri}/image", :alt=>"#{@compound.smiles}", :title=>"#{@compound.smiles}", :width=>"300px", :heigth=>"300px"}
9
- - if !@significant_fragments.empty?
10
- %div.col-md-8
11
- %table{:id => "sf"}
12
- %tr
13
- / @value_map => hash; interpret the effect
14
- %th{:style=>"border:2px solid #E6E6E6;"}
15
- Predominantly in compounds with activity "inactive"
16
- %th{:style=>"border:2px solid #E6E6E6;"}
17
- p value
18
- - @significant_fragments.each do |fragments|
19
- / fragments == [effect, smarts, pValue]
20
- / fragments[0] = effect
21
- /- $logger.debug "effect:\t#{fragments[0]}\n"
22
- - if fragments[0] == @value_map.index("inactive")
23
- %tr
24
- %td
25
- / fragments[1] = smarts
26
- = fragments[1]
27
- -#%img{:src => "http://smartsview.de/smartsview/auto/png/1/both/#{CGI.escape(fragments[1])}", :class => "smarts"}
28
- %td
29
- /fragments[2] = pValue
30
- = fragments[2]
31
- %tr
32
- %th{:style=>"border:2px solid #E6E6E6;"}
33
- Predominantly in compounds with activity "active"
34
- %th{:style=>"border:2px solid #E6E6E6;"}
35
- p value
36
- - @significant_fragments.each do |fragments|
37
- / fragments == [effect, smarts, pValue]
38
- - if fragments[0] == @value_map.index("active")
39
- %tr
40
- %td
41
- -#%img{:src => "http://smartsview.de/smartsview/auto/png/1/both/#{CGI.escape(fragments[1])}", :class => "smarts"}
42
- = fragments[1]
43
- %td
44
- = fragments[2]
45
- %br
46
- - if @type =~ /regression/i
47
- %div.row
48
- %div.col-md-4
49
- %h3
50
- Descriptors:
51
- %img{:src=>"#{@compound.uri}/image", :alt=>"#{@compound.smiles}", :title=>"#{@compound.smiles}", :width=>"300px", :heigth=>"300px"}
52
- - if !@significant_fragments.empty?
53
- %div.col-md-8
54
- %table{:id =>"de"}
55
- %tr
56
- %th{:style=>"border:2px solid #E6E6E6;"}
57
- Descriptor
58
- %th{:style=>"border:2px solid #E6E6E6;"}
59
- value
60
- - @significant_fragments.each do |fragments|
61
- %tr
62
- %td
63
- = fragments[0]
64
- %td
65
- = fragments[1][0].round(3)
66
- %br