t2-web 0.1.6 → 0.1.7

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Files changed (17) hide show
  1. data/CHANGES +4 -0
  2. data/README +1 -1
  3. data/Rakefile +1 -1
  4. data/bin/t2_webapp.rb +2 -2
  5. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/Pathway +1 -0
  6. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/clean_image +0 -0
  7. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/geneList +184 -0
  8. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/image +0 -0
  9. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/url +1 -0
  10. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/Pathway +1 -0
  11. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/clean_image +0 -0
  12. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/geneList +184 -0
  13. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/image +0 -0
  14. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/url +1 -0
  15. data/public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/UniProtID +185 -0
  16. data/public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/ValidatedProtein +10 -0
  17. metadata +15 -3
data/CHANGES CHANGED
@@ -1,5 +1,9 @@
1
1
  = Changes log for the Taverna via the Web App
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2
 
3
+ == Version 0.1.7
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+ * The clean image is truncated/copied only once now -- needed to remove the bold tabs from the image
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+ * Fixed minor bug with displaying images -- incorrect truncation since there is an extra \n
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+
3
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  == Version 0.1.6
4
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  * Now, for some list disambiguation, the first element of top level lists are in bold
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  * Increased side frames slightly
data/README CHANGED
@@ -2,7 +2,7 @@
2
2
 
3
3
 
4
4
  Authors:: Konstantinos Karasavvas
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- Gem Version:: 0.1.6
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+ Gem Version:: 0.1.7
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6
  Contact:: mailto:kostas.karasavvas@nbic.nl
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  Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
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  Copyright:: (c) 2012 Netherlands Bioinformatics Centre, The Netherlands
data/Rakefile CHANGED
@@ -12,7 +12,7 @@ require 'rdoc/task'
12
12
 
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  spec = Gem::Specification.new do |s|
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  s.name = 't2-web'
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- s.version = '0.1.6'
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+ s.version = '0.1.7'
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  s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
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  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.'
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  s.description = s.summary
data/bin/t2_webapp.rb CHANGED
@@ -345,8 +345,8 @@ END
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  if mime_type =~ /image\/png|image\/jpg|image\/gif|image\/bmp|application\/octet-stream/
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  # clean image from <b></b> --- will not be needed after we deal with 'typing' properly t2-server-0.9.x
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  if mime_type =~ /octet-stream/
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- unless File.file?("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
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- new_length = File.size?(display_file) - 3 - 4 # for <b> and </b> respectively
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+ unless File.file?("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
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+ new_length = File.size?(display_file) - 3 - 5 # for <b> and </b>\n respectively
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  %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}" )
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  end
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  generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/Pathway ADDED
@@ -0,0 +1 @@
1
+ <b>path:hsa05016 Huntington's disease - Homo sapiens (human)</b>
data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/geneList ADDED
@@ -0,0 +1,184 @@
1
+ <b>100532726</b>
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data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/url ADDED
@@ -0,0 +1 @@
1
+ <b>http://soap.genome.jp/tmp/mark_pathway_www_api.133491304616025/hsa05016.png</b>
data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/Pathway ADDED
@@ -0,0 +1 @@
1
+ <b>path:hsa05016 Huntington's disease - Homo sapiens (human)</b>
data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/geneList ADDED
@@ -0,0 +1,184 @@
1
+ <b>100532726</b>
2
+ 10105
3
+ 10126
4
+ 10476
5
+ 10488
6
+ 10540
7
+ 10891
8
+ 10975
9
+ 1173
10
+ 1175
11
+ 1211
12
+ 1212
13
+ 1213
14
+ 125965
15
+ 126328
16
+ 1327
17
+ 1329
18
+ 1337
19
+ 1339
20
+ 1340
21
+ 1345
22
+ 1346
23
+ 1347
24
+ 1349
25
+ 1350
26
+ 1351
27
+ 1385
28
+ 1387
29
+ 146754
30
+ 148327
31
+ 1537
32
+ 160
33
+ 161
34
+ 163
35
+ 1639
36
+ 170712
37
+ 1742
38
+ 2033
39
+ 23186
40
+ 23236
41
+ 246721
42
+ 25942
43
+ 25981
44
+ 27019
45
+ 27089
46
+ 27113
47
+ 2776
48
+ 2876
49
+ 2902
50
+ 2904
51
+ 291
52
+ 2911
53
+ 2915
54
+ 292
55
+ 293
56
+ 29796
57
+ 3064
58
+ 3065
59
+ 3066
60
+ 3092
61
+ 317
62
+ 341947
63
+ 3708
64
+ 374291
65
+ 387332
66
+ 440567
67
+ 4508
68
+ 4509
69
+ 4512
70
+ 4513
71
+ 4514
72
+ 4519
73
+ 4694
74
+ 4695
75
+ 4696
76
+ 4697
77
+ 4698
78
+ 4700
79
+ 4701
80
+ 4702
81
+ 4704
82
+ 4705
83
+ 4706
84
+ 4707
85
+ 4708
86
+ 4709
87
+ 4710
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+ 4711
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+ 4712
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+ 4713
91
+ 4714
92
+ 4715
93
+ 4716
94
+ 4717
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+ 4718
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+ 4719
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+ 4720
98
+ 4722
99
+ 4723
100
+ 4724
101
+ 4725
102
+ 4726
103
+ 4728
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+ 4729
105
+ 4731
106
+ 4899
107
+ 498
108
+ 506
109
+ 509
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+ 51079
111
+ 51164
112
+ 513
113
+ 514
114
+ 515
115
+ 516
116
+ 517
117
+ 518
118
+ 522
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+ 5330
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+ 5331
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+ 5332
122
+ 539
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+ 54205
124
+ 5430
125
+ 5431
126
+ 5432
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+ 5433
128
+ 5434
129
+ 5435
130
+ 5436
131
+ 5437
132
+ 5438
133
+ 5439
134
+ 5440
135
+ 5441
136
+ 54539
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+ 5468
138
+ 548644
139
+ 55081
140
+ 55567
141
+ 55967
142
+ 56901
143
+ 581
144
+ 5978
145
+ 627
146
+ 6389
147
+ 6390
148
+ 6391
149
+ 6392
150
+ 64446
151
+ 64764
152
+ 6647
153
+ 6648
154
+ 6667
155
+ 6874
156
+ 6875
157
+ 6908
158
+ 7019
159
+ 7052
160
+ 7157
161
+ 7350
162
+ 7381
163
+ 7384
164
+ 7385
165
+ 7386
166
+ 7388
167
+ 7416
168
+ 7417
169
+ 7419
170
+ 7802
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+ 8218
172
+ 83447
173
+ 83544
174
+ 836
175
+ 841
176
+ 842
177
+ 84699
178
+ 84701
179
+ 9001
180
+ 90993
181
+ 9167
182
+ 9377
183
+ 9519
184
+ 9586
data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/url ADDED
@@ -0,0 +1 @@
1
+ <b>http://soap.genome.jp/tmp/mark_pathway_www_api.133491773910665/hsa05016.png</b>
data/public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/UniProtID ADDED
@@ -0,0 +1,185 @@
1
+ <b>P70386</b>
2
+ Q02527
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+ Q09327
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+ Q10470
5
+ Q14CK5
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+ Q6IC49
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+ Q9UH32
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+ P70386
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+ Q02527
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+ Q09327
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+ Q10470
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+ Q14CK5
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+ Q6IC49
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+ Q9UH32
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+ P70386
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+ Q02527
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+ Q09327
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+ Q10470
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+ Q14CK5
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+ Q6IC49
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+ Q9UH32
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+ P70386
23
+ Q02527
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+ Q09327
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+ Q10470
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+ Q14CK5
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+ Q6IC49
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+ Q9UH32
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+ <b>A8K7C2</b>
30
+ O73815
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+ P02571
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+ P02579
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+ P12714
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+ P14104
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+ P53478
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+ P60010
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+ P63259
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+ P63260
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+ P63261
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+ P99022
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+ Q5U032
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+ Q6P3K9
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+ Q7ZVI7
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+ Q96E67
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+ Q9P3X6
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+ Q9P3X7
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+ <b>P15943</b>
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+ Q06335
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+ Q06481
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+ Q13861
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+ Q14594
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+ Q14662
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+ Q71U10
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+ Q7M4L3
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+ Q9BT36
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+ Q9TVV0
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+ Q9U4H3
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+ Q9W5F1
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+ P05067
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+ P08592
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+ P09000
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+ P12023
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+ P78438
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+ P97487
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+ P97942
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+ Q10651
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+ Q13764
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+ Q13778
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+ Q13793
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+ Q16011
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+ Q16020
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+ Q18583
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+ Q547B7
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+ Q6GSC0
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+ Q8WZ99
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+ Q95ZX1
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+ Q99K32
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+ Q9BT38
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+ Q9UC33
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+ Q9UCA9
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+ Q9UCB6
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+ Q9UCC8
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+ Q9UCD1
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+ P15943
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+ Q06335
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+ Q06481
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+ Q13861
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+ Q14594
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+ Q14662
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+ Q71U10
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+ Q7M4L3
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+ Q9BT36
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+ Q9U4H3
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+ Q9W5F1
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+ P05067
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+ P08592
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+ P09000
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+ P12023
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+ Q99K32
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+ Q9BT38
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+ Q9UC33
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+ Q9UCA9
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+ Q9UCB6
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+ Q9UCC8
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+ Q9UCD1
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+ Q9UQ58
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+ P15943
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+ Q06335
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+ Q06481
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+ Q13861
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+ Q14594
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+ Q14662
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+ Q9BT36
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+ Q9TVV0
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+ Q9U4H3
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+ Q9W5F1
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+ P05067
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+ P08592
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+ P09000
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+ P12023
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+ P78438
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+ P97487
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+ P97942
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+ Q10651
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+ Q13764
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+ Q13778
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+ Q13793
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+ Q16011
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+ Q16014
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+ Q16019
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+ Q16020
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+ Q18583
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+ Q547B7
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+ Q6GSC0
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+ Q8WZ99
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+ Q95ZX1
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+ Q99K32
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+ Q9BT38
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+ Q9UC33
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+ Q9UCC8
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+ Q9UCD1
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+ Q9UQ58
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+ <b>P08396</b>
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+ P08397
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+ P19356
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+ P22907
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+ P28789
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+ Q16012
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+ Q2VQW9
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+ <b>Q08AP2</b>
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+ Q08AP3
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+ Q15439
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+ Q15440
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+ Q60721
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+ Q62211
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+ Q64072
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+ Q80UE8
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+ Q99N33
data/public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/ValidatedProtein ADDED
@@ -0,0 +1,10 @@
1
+ <b>GnT-III</b>
2
+ GnT-III
3
+ GnT-III
4
+ GnT-III
5
+ <b>gamma-actin</b>
6
+ <b>APP</b>
7
+ APP
8
+ APP
9
+ <b>UPS</b>
10
+ <b>TFE</b>
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: 23
4
+ hash: 21
5
5
  prerelease:
6
6
  segments:
7
7
  - 0
8
8
  - 1
9
- - 6
10
- version: 0.1.6
9
+ - 7
10
+ version: 0.1.7
11
11
  platform: ruby
12
12
  authors:
13
13
  - Kostas Karasavvas
@@ -146,6 +146,11 @@ files:
146
146
  - public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/TopContributingConcepts
147
147
  - public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/TopMatchingConcepts
148
148
  - public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/SummedSimilarity
149
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/image
150
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/url
151
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/Pathway
152
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/clean_image
153
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/geneList
149
154
  - public/t2web/tmp/outputs/1dbfe89e-527b-4bbd-9aff-e2acb0250480/image
150
155
  - public/t2web/tmp/outputs/1dbfe89e-527b-4bbd-9aff-e2acb0250480/url
151
156
  - public/t2web/tmp/outputs/1dbfe89e-527b-4bbd-9aff-e2acb0250480/Pathway
@@ -190,6 +195,11 @@ files:
190
195
  - public/t2web/tmp/outputs/17a9e3a7-01e8-4906-bb4e-17afc495c3f2/UniProtID
191
196
  - public/t2web/tmp/outputs/dc51d833-8d87-4e89-8343-46bca8898345/ValidatedProtein
192
197
  - public/t2web/tmp/outputs/dc51d833-8d87-4e89-8343-46bca8898345/UniProtID
198
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/image
199
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/url
200
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/Pathway
201
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/clean_image
202
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/geneList
193
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  - public/t2web/tmp/outputs/98992f59-65d0-4f07-a35d-c9cdc5a8ce82/image
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  - public/t2web/tmp/outputs/98992f59-65d0-4f07-a35d-c9cdc5a8ce82/url
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  - public/t2web/tmp/outputs/98992f59-65d0-4f07-a35d-c9cdc5a8ce82/Pathway
@@ -256,6 +266,8 @@ files:
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  - public/t2web/tmp/outputs/d1461a45-200f-4f48-84a8-d01ca3e79b0b/UniProtID
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  - public/t2web/tmp/outputs/dcbec202-78b9-4a0f-ad2e-b1373190e21a/ValidatedProtein
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  - public/t2web/tmp/outputs/dcbec202-78b9-4a0f-ad2e-b1373190e21a/UniProtID
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+ - public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/ValidatedProtein
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+ - public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/UniProtID
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  - public/t2web/tmp/outputs/ecc62b90-7989-4165-addd-0b53581a9627/image
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  - public/t2web/tmp/outputs/ecc62b90-7989-4165-addd-0b53581a9627/url
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  - public/t2web/tmp/outputs/ecc62b90-7989-4165-addd-0b53581a9627/Pathway